pmid:31676851

Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci.

Salvatore Pisanu · Carla Cacciotto · Daniela Pagnozzi · Giulia Maria Grazia Puggioni · Sergio Uzzau · Paolo Ciaramella · Jacopo Guccione · Martina Penati · Claudia Pollera · Paolo Moroni · Valerio Bronzo · Maria Filippa Addis

Scientific reports · 2019 doi:10.1038/s41598-019-52063-2

Paper

complete

Experiment

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Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.

In this file

The fields below come from the published .science file. Expand a section to inspect its evidence.

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title

Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci.

doi

10.1038/s41598-019-52063-2

pmid

31676851

authors array · 12 items

[0]

Salvatore Pisanu

[1]

Carla Cacciotto

[2]

Daniela Pagnozzi

[3]

Giulia Maria Grazia Puggioni

[4]

Sergio Uzzau

[5]

Paolo Ciaramella

[6]

Jacopo Guccione

[7]

Martina Penati

[8]

Claudia Pollera

[9]

Paolo Moroni

[10]

Valerio Bronzo

[11]

Maria Filippa Addis

journal

Scientific reports

year

2019

abstract

Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355).

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The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018).

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sections[24] "Data availability" paragraph 2

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The data have been deposited to the ProteomeXchange with identifier PXD012355.

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title

Proteomic changes in the milk of water buffalo (Bubalus bubalis) with intramammary infection by Staphylococcus aureus and by non-aureus staphylococciProteomic changes in the milk of water buffalo (Bubalus bubalis) with intramammary infection by Staphylococcus aureus and by non-aureus staphylococci

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Sample groups, milk samples, and their characteristics.

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Animals and milk samples

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Table 1

caption

Sample groups, milk samples, and their characteristics.

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SCCa (cells/mL × 103)

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Bacteriology

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[0]

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[2]

[2] array · 3 items

[0]

[1]

4091

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Staphylococcus aureus

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3782

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Staphylococcus aureus

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8440

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Staphylococcus aureus

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[1]

>10000

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Summary of differential proteomic results.

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PMC6825138

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section_title

Shotgun proteomics and differential analysis

row_count

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Table 2

caption

Summary of differential proteomic results.

rows array · 4 items

[0] array · 6 items

[0]

[1]

Eligible for comparison*

[2]

Changed**

[3]

Differential***1.5 ≤ RSC ≤ −1.5

[4]

Increased***RSC ≥ 1.5

[5]

Decreased***RSC ≤ −1.5

[1] array · 6 items

[0]

Posa/negb

[1]

1034

[2]

302

[3]

152

[4]

119

[5]

[2] array · 6 items

[0]

SAUc/neg

[1]

1025

[2]

268

[3]

162

[4]

128

[5]

[3] array · 6 items

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NASd/neg

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940

[2]

202

[3]

127

[4]

108

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Significantly differential proteins in Staphylococcus-positive milk with RSC ≥ 1.5 or RSC ≤ −1.5.

structure object · 5 fields

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PMC6825138

section_index

section_title

Shotgun proteomics and differential analysis

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182

column_count

table object · 8 fields

label

Table 3

caption

Significantly differential proteins in Staphylococcus-positive milk with RSC ≥ 1.5 or RSC ≤ −1.5.

rows array · 182 items

[0] array · 6 items

[0]

Accession

[1]

Description

[2]

RSCPos/Neg

[3]

RSCSAU/Neg

[4]

RSCNAS/Neg

[5]

Generalfunction

[1] array · 6 items

[0]

P48616

[1]

Vimentin*

[2]

4.78

[3]

4.96

[4]

4.58

[5]

[2] array · 6 items

[0]

A0A0A7NSG7

[1]

Cathelicidin 4*

[2]

4.75

[3]

4.72

[4]

4.78

[5]

[3] array · 6 items

[0]

Q1JPB0

[1]

Leukocyte elastase inhibitor*

[2]

4.09

[3]

4.17

[4]

[5]

[4] array · 6 items

[0]

X5I0G0

[1]

Cathelicidin 1*

[2]

4.04

[3]

4.1

[4]

3.98

[5]

[5] array · 6 items

[0]

C8CF42

[1]

Probactenecin 7*

[2]

3.91

[3]

4.02

[4]

3.78

[5]

[6] array · 6 items

[0]

P46193

[1]

Annexin A1

[2]

3.86

[3]

4.02

[4]

3.67

[5]

[7] array · 6 items

[0]

P52176

[1]

Matrix metalloproteinase-9*

[2]

3.8

[3]

3.93

[4]

3.66

[5]

[8] array · 6 items

[0]

P54228

[1]

Cathelicidin 6*

[2]

3.67

[3]

3.72

[4]

3.62

[5]

[9] array · 6 items

[0]

A0A0A7V3V9

[1]

Cathelicidin 2*

[2]

3.64

[3]

3.74

[4]

3.52

[5]

[10] array · 6 items

[0]

E1AHZ7

[1]

Protein S100A8*

[2]

3.52

[3]

3.54

[4]

3.51

[5]

[11] array · 6 items

[0]

Q92176

[1]

Coronin-1A*

[2]

3.51

[3]

3.51

[4]

3.51

[5]

[12] array · 6 items

[0]

A5D7D1

[1]

Alpha-actinin-4

[2]

3.48

[3]

3.63

[4]

3.31

[5]

[13] array · 6 items

[0]

P62803

[1]

Histone H4*

[2]

3.47

[3]

3.67

[4]

3.24

[5]

[14] array · 6 items

[0]

Q2KJD0

[1]

Tubulin beta-5 chain

[2]

3.45

[3]

3.63

[4]

3.25

[5]

[15] array · 6 items

[0]

Q0VCM4

[1]

Glycogen phosphorylase

[2]

3.42

[3]

3.43

[4]

3.42

[5]

[16] array · 6 items

[0]

Q3MHM5

[1]

Tubulin beta-4B chain

[2]

3.37

[3]

3.49

[4]

3.23

[5]

[17] array · 6 items

[0]

Q3T149

[1]

Heat shock protein beta-1*

[2]

3.33

[3]

3.39

[4]

3.26

[5]

[18] array · 6 items

[0]

Q27991

[1]

Myosin-10*

[2]

3.31

[3]

3.28

[4]

3.34

[5]

[19] array · 6 items

[0]

L0L830

[1]

Cathelicidin 7*

[2]

3.26

[3]

3.37

[4]

3.15

[5]

[20] array · 6 items

[0]

P40673

[1]

High mobility group protein B2*

[2]

3.25

[3]

3.43

[4]

3.04

[5]

[21] array · 6 items

[0]

Q5MAR3

[1]

Integrin beta*

[2]

3.22

[3]

3.48

[4]

2.9

[5]

[22] array · 6 items

[0]

Q0VCW4

[1]

L-serine dehydratase/L-threonine deaminase*

[2]

3.09

[3]

3.16

[4]

3.01

[5]

[23] array · 6 items

[0]

P55052

[1]

Fatty acid-binding protein, epidermal*

[2]

3.08

[3]

3.08

[4]

3.08

[5]

[24] array · 6 items

[0]

P02253

[1]

Histone H1.2*

[2]

3.08

[3]

3.06

[4]

3.11

[5]

[25] array · 6 items

[0]

F6MFD5

[1]

Peptidoglycan-recognition protein

[2]

3.08

[3]

3.26

[4]

2.86

[5]

[26] array · 6 items

[0]

P62808

[1]

Histone H2B type 1

[2]

3.04

[3]

3.04

[4]

3.04

[5]

[27] array · 6 items

[0]

Q9TU25

[1]

Ras-related C3 botulinum toxin substrate 2

[2]

2.97

[3]

2.99

[4]

2.95

[5]

[28] array · 6 items

[0]

Q9TU03

[1]

Rho GDP-dissociation inhibitor 2*

[2]

2.97

[3]

3.13

[4]

2.79

[5]

[29] array · 6 items

[0]

Q2TBL6

[1]

Transaldolase*

[2]

2.96

[3]

3.05

[4]

2.86

[5]

[30] array · 6 items

[0]

V9LY96

[1]

Cathelicidin 5*

[2]

2.95

[3]

3.05

[4]

2.84

[5]

[31] array · 6 items

[0]

Q2HJ86

[1]

Tubulin alpha-1D chain

[2]

2.95

[3]

3.11

[4]

2.76

[5]

[32] array · 6 items

[0]

Q3SWX7

[1]

Annexin A3*

[2]

2.86

[3]

3.04

[4]

2.65

[5]

[33] array · 6 items

[0]

Q3B7N2

[1]

Alpha-actinin-1

[2]

2.85

[3]

3.01

[4]

2.68

[5]

[34] array · 6 items

[0]

Q5E9F5

[1]

Transgelin-2*

[2]

2.85

[3]

2.83

[4]

2.86

[5]

[35] array · 6 items

[0]

Q3SYV4

[1]

Adenylyl cyclase-associated protein 1

[2]

2.84

[3]

2.78

[4]

2.9

[5]

[36] array · 6 items

[0]

Q2KJH4

[1]

WD repeat-containing protein 1*

[2]

2.81

[3]

2.63

[4]

2.97

[5]

[37] array · 6 items

[0]

P68432

[1]

Histone H3.1*

[2]

2.79

[3]

2.91

[4]

2.66

[5]

[38] array · 6 items

[0]

A7E3Q8

[1]

Plastin-3*

[2]

2.79

[3]

2.86

[4]

2.7

[5]

[39] array · 6 items

[0]

P81948

[1]

Tubulin alpha-4A chain

[2]

2.74

[3]

2.93

[4]

2.51

[5]

[40] array · 6 items

[0]

Q3MHR7

[1]

Actin-related protein 2/3 complex subunit 2*

[2]

2.68

[3]

2.61

[4]

2.75

[5]

[41] array · 6 items

[0]

A7MB62

[1]

Actin-related protein 2

[2]

2.62

[3]

2.6

[4]

2.64

[5]

[42] array · 6 items

[0]

Q5E9B1

[1]

L-lactate dehydrogenase B chain

[2]

2.61

[3]

2.69

[4]

2.52

[5]

[43] array · 6 items

[0]

M1JVB9

[1]

Haptoglobin

[2]

2.59

[3]

2.68

[4]

2.49

[5]

[44] array · 6 items

[0]

A0A0C5AGQ3

[1]

Lysozyme*

[2]

2.59

[3]

2.64

[4]

2.55

[5]

[45] array · 6 items

[0]

Q6B855

[1]

Transketolase

[2]

2.59

[3]

2.65

[4]

2.54

[5]

[46] array · 6 items

[0]

P02584

[1]

Profilin-1

[2]

2.58

[3]

2.6

[4]

2.56

[5]

[47] array · 6 items

[0]

Q5E956

[1]

Triosephosphate isomerase

[2]

2.53

[3]

2.56

[4]

2.49

[5]

[48] array · 6 items

[0]

P10103

[1]

High mobility group protein B1

[2]

2.52

[3]

2.73

[4]

2.28

[5]

[49] array · 6 items

[0]

A2I7N1

[1]

Serpin A3-5

[2]

2.52

[3]

2.67

[4]

2.35

[5]

[50] array · 6 items

[0]

Q3ZBD7

[1]

Glucose-6-phosphate isomerase

[2]

2.5

[3]

2.59

[4]

2.4

[5]

[51] array · 6 items

[0]

P0C0S9

[1]

Histone H2A type 1

[2]

2.5

[3]

2.54

[4]

2.45

[5]

[52] array · 6 items

[0]

Q3T0P6

[1]

Phosphoglycerate kinase 1

[2]

2.5

[3]

2.53

[4]

2.47

[5]

[53] array · 6 items

[0]

P19858

[1]

L-lactate dehydrogenase A chain

[2]

2.48

[3]

2.43

[4]

2.52

[5]

[54] array · 6 items

[0]

Q3T114

[1]

Ribonuclease UK114*

[2]

2.47

[3]

2.4

[4]

2.53

[5]

[55] array · 6 items

[0]

Q32LE5

[1]

Isoaspartyl peptidase/L-asparaginase*

[2]

2.46

[3]

2.34

[4]

2.58

[5]

[56] array · 6 items

[0]

P30922

[1]

Chitinase-3-like protein 1

[2]

2.45

[3]

2.32

[4]

2.57

[5]

[57] array · 6 items

[0]

Q2HJ60

[1]

Heterogeneous nuclear ribonucleoproteins A2/B1*

[2]

2.39

[3]

2.66

[4]

2.06

[5]

[58] array · 6 items

[0]

A5A4L2

[1]

Histone H2B*,a

[2]

2.38

[3]

2.59

[4]

[5]

[59] array · 6 items

[0]

P79136

[1]

F-actin-capping protein subunit beta

[2]

2.32

[3]

2.41

[4]

2.23

[5]

[60] array · 6 items

[0]

P61157

[1]

Actin-related protein 3

[2]

2.31

[3]

2.27

[4]

2.35

[5]

[61] array · 6 items

[0]

Q5KR47

[1]

Tropomyosin alpha-3 chain

[2]

2.31

[3]

2.37

[4]

2.24

[5]

[62] array · 6 items

[0]

P09867

[1]

Heterogeneous nuclear ribonucleoprotein A1*

[2]

2.3

[3]

2.45

[4]

2.14

[5]

[63] array · 6 items

[0]

A4IF97

[1]

Myosin regulatory light chain 12B*

[2]

2.27

[3]

2.39

[4]

2.14

[5]

[64] array · 6 items

[0]

A3KMV5

[1]

Ubiquitin-like modifier-activating enzyme 1*

[2]

2.26

[3]

2.57

[4]

1.87

[5]

[65] array · 6 items

[0]

Q2HJ57

[1]

Coactosin-like protein*

[2]

2.22

[3]

2.24

[4]

2.21

[5]

[66] array · 6 items

[0]

Q58CQ2

[1]

Actin-related protein 2/3 complex subunit 1B*

[2]

2.2

[3]

2.22

[4]

2.18

[5]

[67] array · 6 items

[0]

G3N131

[1]

Histone H1.1*

[2]

2.19

[3]

[4]

[5]

[68] array · 6 items

[0]

P49951

[1]

Clathrin heavy chain 1*

[2]

2.08

[3]

2.22

[4]

1.92

[5]

[69] array · 6 items

[0]

A5D7A0

[1]

EF-hand domain-containing protein D2*

[2]

2.08

[3]

2.2

[4]

1.95

[5]

[70] array · 6 items

[0]

Q2TA49

[1]

Vasodilator-stimulated phosphoprotein

[2]

2.06

[3]

2.42

[4]

1.58

[5]

[71] array · 6 items

[0]

Q3ZC84

[1]

Cytosolic non-specific dipeptidase

[2]

2.05

[3]

2.18

[4]

1.91

[5]

[72] array · 6 items

[0]

P10096

[1]

Glyceraldehyde-3-phosphate dehydrogenase

[2]

2.05

[3]

2.14

[4]

1.97

[5]

[73] array · 6 items

[0]

P60661

[1]

Myosin light polypeptide 6

[2]

2.02

[3]

2.15

[4]

1.87

[5]

[74] array · 6 items

[0]

Q3T0D0

[1]

Heterogeneous nuclear ribonucleoprotein K*

[2]

2.01

[3]

2.08

[4]

1.94

[5]

[75] array · 6 items

[0]

P33433

[1]

Histidine-rich glycoproteina

[2]

2.01

[3]

2.52

[4]

[5]

[76] array · 6 items

[0]

Q4U5R3

[1]

Proteasome activator complex subunit 1

[2]

2.01

[3]

2.07

[4]

1.96

[5]

[77] array · 6 items

[0]

Q32PI5

[1]

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

[2]

1.98

[3]

2.29

[4]

1.59

[5]

[78] array · 6 items

[0]

Q56JZ9

[1]

Glia maturation factor gamma*

[2]

1.97

[3]

2.02

[4]

1.92

[5]

[79] array · 6 items

[0]

Q0VCX1

[1]

Complement C1s subcomponent*

[2]

1.96

[3]

2.24

[4]

1.62

[5]

[80] array · 6 items

[0]

Q3SZH7

[1]

Leukotriene A-4 hydrolase*

[2]

1.96

[3]

1.91

[4]

2.02

[5]

[81] array · 6 items

[0]

P31081

[1]

60 kDa heat shock protein, mitochondrial*

[2]

1.95

[3]

2.12

[4]

1.76

[5]

[82] array · 6 items

[0]

Q32LP0

[1]

Fermitin family homolog 3*

[2]

1.94

[3]

2.15

[4]

1.69

[5]

[83] array · 6 items

[0]

D2U6Q0

[1]

Serum amyloid A protein*

[2]

1.93

[3]

1.86

[4]

[5]

[84] array · 6 items

[0]

P62326

[1]

Thymosin beta-4*

[2]

1.91

[3]

2.03

[4]

1.78

[5]

[85] array · 6 items

[0]

P13752

[1]

BOLA class I histocompatibility antigen, alpha chain BL3-6*

[2]

1.9

[3]

2.08

[4]

1.7

[5]

[86] array · 6 items

[0]

Q2KJI3

[1]

Protein FAM49B*

[2]

1.89

[3]

1.87

[4]

1.92

[5]

[87] array · 6 items

[0]

Q762I5

[1]

Resistin*

[2]

1.89

[3]

1.92

[4]

1.85

[5]

[88] array · 6 items

[0]

Q76LV2

[1]

Heat shock protein HSP 90-alpha

[2]

1.88

[3]

2.06

[4]

1.68

[5]

[89] array · 6 items

[0]

Q3SZ54

[1]

Eukaryotic initiation factor 4A-I

[2]

1.85

[3]

1.82

[4]

1.88

[5]

[90] array · 6 items

[0]

Q3MHL4

[1]

Adenosylhomocysteinase

[2]

1.83

[3]

1.82

[4]

1.84

[5]

[91] array · 6 items

[0]

P80724

[1]

Brain acid soluble protein 1*

[2]

1.82

[3]

1.61

[4]

[5]

[92] array · 6 items

[0]

P60712

[1]

Actin, cytoplasmic 1

[2]

1.8

[3]

2.01

[4]

1.57

[5]

[93] array · 6 items

[0]

J9Q6V1

[1]

Glutathione peroxidase*

[2]

1.8

[3]

2.05

[4]

1.5

[5]

[94] array · 6 items

[0]

P55859

[1]

Purine nucleoside phosphorylase*

[2]

1.78

[3]

1.51

[4]

[5]

[95] array · 6 items

[0]

Q9XSJ4

[1]

Alpha-enolase

[2]

1.77

[3]

1.8

[4]

1.75

[5]

[96] array · 6 items

[0]

Q27970

[1]

Calpain-1 catalytic subunita

[2]

1.77

[3]

2.13

[4]

[5]

[97] array · 6 items

[0]

Q865V6

[1]

Macrophage-capping protein*

[2]

1.76

[3]

1.65

[4]

1.86

[5]

[98] array · 6 items

[0]

Q9GMB8

[1]

Serine–tRNA ligase, cytoplasmica

[2]

1.74

[3]

2.02

[4]

[5]

[99] array · 6 items

[0]

Q9BGI1

[1]

Peroxiredoxin-5, mitochondrial

[2]

1.73

[3]

1.92

[4]

1.52

[5]

[100] array · 6 items

[0]

P51122

[1]

Acidic leucine-rich nuclear phosphoprotein 32 family member Aa

[2]

[3]

1.72

[4]

[5]

[101] array · 6 items

[0]

Q148J6

[1]

Actin-related protein 2/3 complex subunit 4*

[2]

1.7

[3]

1.71

[4]

1.69

[5]

[102] array · 6 items

[0]

A4FUA8

[1]

F-actin-capping protein subunit alpha-1*

[2]

1.68

[3]

1.63

[4]

1.73

[5]

[103] array · 6 items

[0]

P06868

[1]

Plasminogen

[2]

1.68

[3]

1.77

[4]

1.58

[5]

[104] array · 6 items

[0]

P07589

[1]

Fibronectin

[2]

1.67

[3]

[4]

[5]

[105] array · 6 items

[0]

P13753

[1]

BOLA class I histocompatibility antigen, alpha chain BL3-7*,a

[2]

1.65

[3]

1.96

[4]

[5]

[106] array · 6 items

[0]

O46522

[1]

Cytochrome b-245 heavy chaina

[2]

1.64

[3]

[4]

[5]

[107] array · 6 items

[0]

Q3SZI4

[1]

14-3-3 protein theta

[2]

1.62

[3]

1.69

[4]

1.55

[5]

[108] array · 6 items

[0]

A6H742

[1]

Plastin-1*

[2]

1.62

[3]

1.54

[4]

1.69

[5]

[109] array · 6 items

[0]

D2U6Z5

[1]

Ceruloplasminb

[2]

1.61

[3]

[4]

1.75

[5]

[110] array · 6 items

[0]

Q3T035

[1]

Actin-related protein 2/3 complex subunit 3*,a

[2]

1.57

[3]

1.71

[4]

[5]

[111] array · 6 items

[0]

P20000

[1]

Aldehyde dehydrogenase, mitochondrial*,a

[2]

1.57

[3]

1.71

[4]

[5]

[112] array · 6 items

[0]

P01030

[1]

Complement C4b

[2]

1.57

[3]

[4]

1.72

[5]

[113] array · 6 items

[0]

P0C0S4

[1]

Histone H2A.Za

[2]

1.56

[3]

1.66

[4]

[5]

[114] array · 6 items

[0]

Q27996

[1]

Lysozyme C, tracheal isozyme

[2]

1.56

[3]

1.51

[4]

1.61

[5]

[115] array · 6 items

[0]

Q5E9B7

[1]

Chloride intracellular channel protein 1

[2]

1.55

[3]

1.52

[4]

1.57

[5]

[116] array · 6 items

[0]

P68138

[1]

Actin, alpha skeletal musclea

[2]

1.54

[3]

1.72

[4]

[5]

[117] array · 6 items

[0]

X2IZ01

[1]

Signal transducer and activator of transcriptiona

[2]

1.54

[3]

1.59

[4]

[5]

[118] array · 6 items

[0]

Q3ZBT1

[1]

Transitional endoplasmic reticulum ATPasea

[2]

1.54

[3]

1.68

[4]

[5]

[119] array · 6 items

[0]

Q2HJG5

[1]

Vacuolar protein sorting-associated protein 35a

[2]

1.54

[3]

1.84

[4]

[5]

[120] array · 6 items

[0]

O97680

[1]

Thioredoxina

[2]

1.53

[3]

1.79

[4]

[5]

[121] array · 6 items

[0]

P19483

[1]

ATP synthase subunit alpha, mitochondrialb

[2]

[3]

[4]

1.52

[5]

[122] array · 6 items

[0]

P02676

[1]

Fibrinogen beta chaina

[2]

[3]

1.79

[4]

[5]

[123] array · 6 items

[0]

P02672

[1]

Fibrinogen alpha chaina

[2]

[3]

1.83

[4]

[5]

[124] array · 6 items

[0]

Q5E9R3

[1]

EH domain-containing protein 1a

[2]

[3]

1.78

[4]

[5]

CaM

[125] array · 6 items

[0]

P00829

[1]

ATP synthase subunit beta, mitochondriala

[2]

[3]

1.66

[4]

[5]

[126] array · 6 items

[0]

P81644

[1]

Apolipoprotein A-IIa

[2]

[3]

1.64

[4]

[5]

[127] array · 6 items

[0]

Q3B7M5

[1]

LIM and SH3 domain protein 1a

[2]

[3]

1.61

[4]

[5]

[128] array · 6 items

[0]

A6H7G2

[1]

Drebrin-like proteina

[2]

[3]

1.58

[4]

[5]

[129] array · 6 items

[0]

Q3ZBH0

[1]

T-complex protein 1 subunit betaa

[2]

[3]

1.57

[4]

[5]

[130] array · 6 items

[0]

Q3MHL7

[1]

T-complex protein 1 subunit zetaa

[2]

[3]

1.52

[4]

[5]

[131] array · 6 items

[0]

Q7SIH1

[1]

Alpha-2-macroglobulina

[2]

[3]

1.52

[4]

[5]

[132] array · 6 items

[0]

P27214

[1]

Annexin A11a

[2]

[3]

1.52

[4]

[5]

[133] array · 6 items

[0]

Q3SZV7

[1]

Hemopexina

[2]

[3]

1.5

[4]

[5]

[134] array · 6 items

[0]

P11116

[1]

Galectin-1b

[2]

[3]

[4]

1.61

[5]

[135] array · 6 items

[0]

P35466

[1]

Protein S100-A4b

[2]

[3]

[4]

1.6

[5]

[136] array · 6 items

[0]

O02675

[1]

Dihydropyrimidinase-related protein 2*,b

[2]

[3]

[4]

1.51

[5]

[137] array · 6 items

[0]

Q3T054

[1]

GTP-binding nuclear protein Ranb

[2]

[3]

[4]

1.61

[5]

[138] array · 6 items

[0]

Q3T0D7

[1]

GTP-binding protein SAR1a

[2]

−1.51

[3]

[4]

[5]

[139] array · 6 items

[0]

Q71SP7

[1]

Fatty acid synthasea

[2]

−1.52

[3]

−1.8

[4]

[5]

[140] array · 6 items

[0]

P02638

[1]

Protein S100-B

[2]

−1.53

[3]

[4]

[5]

[141] array · 6 items

[0]

P10790

[1]

Fatty acid-binding protein, hearta

[2]

[3]

−1.53

[4]

[5]

[142] array · 6 items

[0]

M9WP41

[1]

BTN1A1a

[2]

[3]

−1.57

[4]

[5]

[143] array · 6 items

[0]

Q17QE5

[1]

Calcium and integrin-binding protein 1a

[2]

−1.56

[3]

−1.85

[4]

[5]

[144] array · 6 items

[0]

Q9N0T1

[1]

Stanniocalcin-1a

[2]

−1.57

[3]

−1.9

[4]

[5]

CaM

[145] array · 6 items

[0]

A0A0C5GDU2

[1]

Myostatina

[2]

[3]

−1.59

[4]

[5]

[146] array · 6 items

[0]

Q6RUS0

[1]

Butyrophilinb

[2]

−1.6

[3]

[4]

−1.75

[5]

[147] array · 6 items

[0]

G1AQP3

[1]

Xanthine dehydrogenase/oxidasea

[2]

−1.61

[3]

−1.81

[4]

[5]

[148] array · 6 items

[0]

E9NV81

[1]

ATP-binding cassette sub-family G (WHITE) member 2a

[2]

−1.62

[3]

−1.95

[4]

[5]

[149] array · 6 items

[0]

Q05927

[1]

5′-nucleotidaseb

[2]

−1.65

[3]

[4]

−1.88

[5]

[150] array · 6 items

[0]

M4QG36

[1]

Insulin induced protein 1a

[2]

−1.65

[3]

−1.88

[4]

[5]

[151] array · 6 items

[0]

O77588

[1]

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1a

[2]

−1.68

[3]

−2.19

[4]

[5]

[152] array · 6 items

[0]

A5PK13

[1]

Volume-regulated anion channel subunit LRRC8C

[2]

−1.68

[3]

[4]

[5]

[153] array · 6 items

[0]

Q2KIY5

[1]

Putative phospholipase B-like 2a

[2]

−1.69

[3]

−2.24

[4]

[5]

[154] array · 6 items

[0]

P81127

[1]

Gamma-soluble NSF attachment protein

[2]

−1.71

[3]

[4]

[5]

[155] array · 6 items

[0]

Q58CY6

[1]

Prostamide/prostaglandin F synthaseb

[2]

−1.73

[3]

[4]

−1.83

[5]

[156] array · 6 items

[0]

Q06805

[1]

Tyrosine-protein kinase receptor Tie-1

[2]

−1.73

[3]

[4]

[5]

[157] array · 6 items

[0]

P37980

[1]

Inorganic pyrophosphatase

[2]

−1.74

[3]

−1.99

[4]

−1.53

[5]

[158] array · 6 items

[0]

Q3T0Q2

[1]

Transmembrane protein 59

[2]

−1.75

[3]

−1.87

[4]

−1.63

[5]

[159] array · 6 items

[0]

Q3SYV1

[1]

Transmembrane protein 263

[2]

−1.77

[3]

[4]

[5]

[160] array · 6 items

[0]

Q3SYS6

[1]

Calcineurin B homologous protein 1

[2]

−1.81

[3]

−1.87

[4]

−1.75

[5]

CaM

[161] array · 6 items

[0]

Q58DD4

[1]

Syndecan-2a

[2]

−1.81

[3]

−2.13

[4]

[5]

[162] array · 6 items

[0]

D3K0R6

[1]

Plasma membrane calcium-transporting ATPase 4

[2]

−1.93

[3]

−2.04

[4]

−1.82

[5]

CaM

[163] array · 6 items

[0]

C1KGU3

[1]

Solute carrier family 11 member 2

[2]

−1.93

[3]

−2.02

[4]

−1.85

[5]

[164] array · 6 items

[0]

Q5GJ77

[1]

Glycerol-3-phosphate acyltransferase 1, mitochondrial

[2]

−2.01

[3]

−2.13

[4]

−1.91

[5]

[165] array · 6 items

[0]

A0A088F8E5

[1]

Acyl-CoA synthetase short-chain family member 2

[2]

−2.08

[3]

−2.19

[4]

−1.97

[5]

[166] array · 6 items

[0]

P08239

[1]

Guanine nucleotide-binding protein G(o) subunit alpha

[2]

−2.14

[3]

−2.25

[4]

−2.03

[5]

[167] array · 6 items

[0]

P08169

[1]

Cation-independent mannose-6-phosphate receptor

[2]

−2.15

[3]

−2.47

[4]

−1.88

[5]

[168] array · 6 items

[0]

Q3ZBE9

[1]

Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating

[2]

−2.17

[3]

−2.65

[4]

−1.8

[5]

[169] array · 6 items

[0]

Q2YDI9

[1]

Ferritin, mitochondrial

[2]

−2.28

[3]

−2.4

[4]

−2.17

[5]

[170] array · 6 items

[0]

Q58DW6

[1]

Ras-related protein Rab-25

[2]

−2.28

[3]

−2.39

[4]

−2.17

[5]

[171] array · 6 items

[0]

Q3MHW6

[1]

Monocarboxylate transporter 1

[2]

−2.48

[3]

−2.55

[4]

−2.41

[5]

[172] array · 6 items

[0]

A0A097P9M4

[1]

Long-chain fatty acid-CoA ligase 1

[2]

−2.6

[3]

−3.2

[4]

−2.17

[5]

[173] array · 6 items

[0]

P84466

[1]

Lanosterol synthase

[2]

−2.71

[3]

−2.83

[4]

−2.61

[5]

[174] array · 6 items

[0]

Q3MHX6

[1]

Protein OS-9a

[2]

[3]

−1.57

[4]

[5]

[175] array · 6 items

[0]

Q2TBX4

[1]

Heat shock 70 kDa protein 13a

[2]

[3]

−1.59

[4]

[5]

[176] array · 6 items

[0]

Q0VD19

[1]

Sphingomyelin phosphodiesterasea

[2]

[3]

−1.72

[4]

[5]

[177] array · 6 items

[0]

Q1RMU3

[1]

Prolyl 4-hydroxylase subunit alpha-1a

[2]

[3]

−1.73

[4]

[5]

[178] array · 6 items

[0]

Q5EA88

[1]

Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmica

[2]

[3]

−1.8

[4]

[5]

[179] array · 6 items

[0]

Q0IIG7

[1]

Ras-related protein Rab-5Aa

[2]

[3]

−2.11

[4]

[5]

[180] array · 6 items

[0]

A6QR11

[1]

Protein kinase C-binding protein NELL2a

[2]

[3]

−2.37

[4]

[5]

CaM

[181] array · 6 items

[0]

Q5E9B5

[1]

Actin, gamma-enteric smooth muscleb

[2]

[3]

[4]

−3.76

[5]

row_count

182

column_count

numeric_cells

653

header_rows

locator

section[5]/table-wrap[2]#Tab3

[5] object · 16 fields

asset:table:pmid:31676851:4

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jats-table

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application/vnd.jats.table+json

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null

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sha256:4ee0cf8f71af1d337684ae52f021f6d3dd5743011e1042233e8fefb18104ea14

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717

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open

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verified

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read_table

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available

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section[3]/table-wrap[1]#Tab1

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null

note

Sample groups, milk samples, and their characteristics.

structure object · 5 fields

pmcid

PMC6825138

section_index

section_title

Animals and milk samples

row_count

column_count

table object · 8 fields

label

Table 1

caption

Sample groups, milk samples, and their characteristics.

rows array · 15 items

[0] array · 3 items

[0]

Sample group

[1]

SCCa (cells/mL × 103)

[2]

Bacteriology

[1] array · 3 items

[0]

Positive

[1]

Mean value 5545 (CMTb + 3)

[2]

[2] array · 3 items

[0]

[1]

4091

[2]

Staphylococcus aureus

[3] array · 3 items

[0]

[1]

3782

[2]

Staphylococcus aureus

[4] array · 3 items

[0]

[1]

8440

[2]

Staphylococcus aureus

[5] array · 3 items

[0]

[1]

>10000

[2]

Non-aureus staphylococci

[6] array · 3 items

[0]

[1]

4035

[2]

Non-aureus staphylococci

[7] array · 3 items

[0]

[1]

2924

[2]

Non-aureus staphylococci

[8] array · 3 items

[0]

Negative

[1]

Mean value 23.5 (CMT Neg)

[2]

[9] array · 3 items

[0]

[1]

[2]

Negative

[10] array · 3 items

[0]

[1]

[2]

Negative

[11] array · 3 items

[0]

[1]

[2]

Negative

[12] array · 3 items

[0]

[1]

[2]

Negative

[13] array · 3 items

[0]

[1]

[2]

Negative

[14] array · 3 items

[0]

[1]

[2]

Negative

row_count

column_count

numeric_cells

header_rows

locator

section[3]/table-wrap[1]#Tab1

gaps array · 2 items

[0]

asset:data:geo:PXD012355 not downloaded

[1]

asset:data:geo:PXD012355 licence not read

analysis object · 4 fields

state

partial

methods array · 1 item

[0] object · 10 fields

method-1

family

group_comparison

specific

wilcoxon

label

Group comparison

dsl_operations array · 0 items

missing_operations array · 1 item

[0]

group_comparison_wilcoxon

expressible

false

parameters object · 0 fields

data_shapes array · 1 item

[0]

two_or_more_groups_continuous

evidence object · 3 fields

score

band

verbatim

quote

targets array · 0 items

gaps array · 1 item

[0]

method.group_comparison_wilcoxon

capability object · 3 fields

state

complete

requirements array · 1 item

[0] object · 6 fields

capability_id

capability:computational_analysis

label

Computational analysis platform

assay_families array · 9 items

[0]

meta_analysis

[1]

machine_learning

[2]

survival_analysis

[3]

statistical_regression

[4]

pca

[5]

molecular_docking

[6]

network_analysis

[7]

differential_expression

[8]

gwas

availability_state

owned

tier_unlocked

candidate

Automated Assays Laravel application and simulated adapters

gaps array · 0 items

readiness object · 8 fields

state

complete

tier

blocking_axis

none

blocked_on

nothing:replicable_now

axes object · 3 fields

method object · 5 fields

tier

expressible

false

required_operations array · 0 items

missing_operations array · 1 item

[0]

group_comparison_wilcoxon

basis

The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon.

capability object · 4 fields

tier

capability_id

capability:computational_analysis

availability_state

owned

basis

The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.

data object · 6 fields

tier

reachable

true

accessions array · 1 item

[0]

PXD012355

resolved_accessions array · 1 item

[0]

PXD012355

statements array · 1 item

[0]

The data have been deposited to the ProteomeXchange with identifier PXD012355.

basis

The paper names PXD012355 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.

can_run object · 3 fields

dsl_operations array · 0 items

assets array · 6 items

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source:pmid:31676851

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data:geo:PXD012355

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must_build object · 5 fields

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group_comparison_wilcoxon

unlocks_papers

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data:geo:PXD012355

gaps array · 0 items

review object · 5 fields

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partial

machine_critique object · 5 fields

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extraction_review

reader object · 5 fields

model

MiniMax-M3.1-Flash

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minimax

provider_family

minimax

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single_reader

evidence_check object · 2 fields

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verbatim

availability

verbatim

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usage object · 3 fields

prompt_tokens

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completion_tokens

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null

stages array · 1 item

[0] object · 4 fields

extraction

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MiniMax-M3.1-Flash

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review.independent_reader

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review.human_critique

execution object · 5 fields

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absent

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not_run

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execution.not_run

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paper

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source:pmid:31676851

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manuscript

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PMID 31676851 full text

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data:geo:PXD012355

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dataset

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GEO PXD012355

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classification

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paper

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[1] object · 3 fields

source:pmid:31676851

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manuscript

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PMID 31676851 full text

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data:geo:PXD012355

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GEO PXD012355

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agent:corpus-assay-engine

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[0]

source:pmid:31676851

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agent:minimax-reader

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activity-resolve-PXD012355

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accession_resolution

used array · 1 item

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data:geo:PXD012355

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st increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis.

[1]

d haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buff

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Complete file

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31676851", "kind": "science-record", "revision": 7, "content_hash": "sha256:00a0aa759d4d8d3dc0a226b18ee30ab6e8d232babed74aac1c46e5e698e2d4aa", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:00:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci.", "doi": "10.1038/s41598-019-52063-2", "pmid": "31676851", "authors": ["Salvatore Pisanu", "Carla Cacciotto", "Daniela Pagnozzi", "Giulia Maria Grazia Puggioni", "Sergio Uzzau", "Paolo Ciaramella", "Jacopo Guccione", "Martina Penati", "Claudia Pollera", "Paolo Moroni", "Valerio Bronzo", "Maria Filippa Addis"], "journal": "Scientific reports", "year": 2019, "abstract": "Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355).", "claims": [{"id": "claim-method", "statement": "The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31676851", "locator": "sections[19] \"Proteomic data analysis\" paragraph 2", "quote": "The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data have been deposited to the ProteomeXchange with identifier PXD012355.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31676851", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "The data have been deposited to the ProteomeXchange with identifier PXD012355."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:31676851"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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"row_count": 182, "column_count": 6}, "table": {"label": "Table 3", "caption": "Significantly differential proteins in Staphylococcus-positive milk with RSC ≥ 1.5 or RSC ≤ −1.5.", "rows": [["Accession", "Description", "RSCPos/Neg", "RSCSAU/Neg", "RSCNAS/Neg", "Generalfunction"], ["P48616", "Vimentin*", "4.78", "4.96", "4.58", "S"], ["A0A0A7NSG7", "Cathelicidin 4*", "4.75", "4.72", "4.78", "I"], ["Q1JPB0", "Leukocyte elastase inhibitor*", "4.09", "4.17", "4", "I"], ["X5I0G0", "Cathelicidin 1*", "4.04", "4.1", "3.98", "I"], ["C8CF42", "Probactenecin 7*", "3.91", "4.02", "3.78", "I"], ["P46193", "Annexin A1", "3.86", "4.02", "3.67", "I"], ["P52176", "Matrix metalloproteinase-9*", "3.8", "3.93", "3.66", "I"], ["P54228", "Cathelicidin 6*", "3.67", "3.72", "3.62", "I"], ["A0A0A7V3V9", "Cathelicidin 2*", "3.64", "3.74", "3.52", "I"], ["E1AHZ7", "Protein S100A8*", "3.52", "3.54", "3.51", "I"], ["Q92176", "Coronin-1A*", "3.51", "3.51", "3.51", "I"], ["A5D7D1", "Alpha-actinin-4", "3.48", "3.63", "3.31", "S"], ["P62803", "Histone H4*", "3.47", "3.67", "3.24", "S"], ["Q2KJD0", "Tubulin beta-5 chain", "3.45", "3.63", "3.25", "S"], ["Q0VCM4", "Glycogen phosphorylase", "3.42", "3.43", "3.42", "CM"], ["Q3MHM5", "Tubulin beta-4B chain", "3.37", "3.49", "3.23", "S"], ["Q3T149", "Heat shock protein beta-1*", "3.33", "3.39", "3.26", "PD"], ["Q27991", "Myosin-10*", "3.31", "3.28", "3.34", "S"], ["L0L830", "Cathelicidin 7*", "3.26", "3.37", "3.15", "I"], ["P40673", "High mobility group protein B2*", "3.25", "3.43", "3.04", "I"], ["Q5MAR3", "Integrin beta*", "3.22", "3.48", "2.9", "I"], ["Q0VCW4", "L-serine dehydratase/L-threonine deaminase*", "3.09", "3.16", "3.01", "AM"], ["P55052", "Fatty acid-binding protein, epidermal*", "3.08", "3.08", "3.08", "LM"], ["P02253", "Histone H1.2*", "3.08", "3.06", "3.11", "S"], ["F6MFD5", "Peptidoglycan-recognition protein", "3.08", "3.26", "2.86", "I"], ["P62808", "Histone H2B type 1", "3.04", "3.04", "3.04", "S"], ["Q9TU25", "Ras-related C3 botulinum toxin substrate 2", "2.97", "2.99", "2.95", "I"], ["Q9TU03", "Rho GDP-dissociation inhibitor 2*", "2.97", "3.13", "2.79", "S"], ["Q2TBL6", "Transaldolase*", "2.96", "3.05", "2.86", "CM"], ["V9LY96", "Cathelicidin 5*", "2.95", "3.05", "2.84", "I"], ["Q2HJ86", "Tubulin alpha-1D chain", "2.95", "3.11", "2.76", "S"], ["Q3SWX7", "Annexin A3*", "2.86", "3.04", "2.65", "I"], ["Q3B7N2", "Alpha-actinin-1", "2.85", "3.01", "2.68", "S"], ["Q5E9F5", "Transgelin-2*", "2.85", "2.83", "2.86", "S"], ["Q3SYV4", "Adenylyl cyclase-associated protein 1", "2.84", "2.78", "2.9", "S"], ["Q2KJH4", "WD repeat-containing protein 1*", "2.81", "2.63", "2.97", "S"], ["P68432", "Histone H3.1*", "2.79", "2.91", "2.66", "S"], ["A7E3Q8", "Plastin-3*", "2.79", "2.86", "2.7", "S"], ["P81948", "Tubulin alpha-4A chain", "2.74", "2.93", "2.51", "S"], ["Q3MHR7", "Actin-related protein 2/3 complex subunit 2*", "2.68", "2.61", "2.75", "S"], ["A7MB62", "Actin-related protein 2", "2.62", "2.6", "2.64", "S"], ["Q5E9B1", "L-lactate dehydrogenase B chain", "2.61", "2.69", "2.52", "CM"], ["M1JVB9", "Haptoglobin", "2.59", "2.68", "2.49", "I"], ["A0A0C5AGQ3", "Lysozyme*", "2.59", "2.64", "2.55", "I"], ["Q6B855", "Transketolase", "2.59", "2.65", "2.54", "CM"], ["P02584", "Profilin-1", "2.58", "2.6", "2.56", "S"], ["Q5E956", "Triosephosphate isomerase", "2.53", "2.56", "2.49", "S"], ["P10103", "High mobility group protein B1", "2.52", "2.73", "2.28", "I"], ["A2I7N1", "Serpin A3-5", "2.52", "2.67", "2.35", "PD"], ["Q3ZBD7", "Glucose-6-phosphate isomerase", "2.5", "2.59", "2.4", "CM"], ["P0C0S9", "Histone H2A type 1", "2.5", "2.54", "2.45", "S"], ["Q3T0P6", "Phosphoglycerate kinase 1", "2.5", "2.53", "2.47", "CM"], ["P19858", "L-lactate dehydrogenase A chain", "2.48", "2.43", "2.52", "CM"], ["Q3T114", "Ribonuclease UK114*", "2.47", "2.4", "2.53", "CP"], ["Q32LE5", "Isoaspartyl peptidase/L-asparaginase*", "2.46", "2.34", "2.58", "CP"], ["P30922", "Chitinase-3-like protein 1", "2.45", "2.32", "2.57", "I"], ["Q2HJ60", "Heterogeneous nuclear ribonucleoproteins A2/B1*", "2.39", "2.66", "2.06", "NM"], ["A5A4L2", "Histone H2B*,a", "2.38", "2.59", "", "I"], ["P79136", "F-actin-capping protein subunit beta", "2.32", "2.41", "2.23", "S"], ["P61157", "Actin-related protein 3", "2.31", "2.27", "2.35", "S"], ["Q5KR47", "Tropomyosin alpha-3 chain", "2.31", "2.37", "2.24", "S"], ["P09867", "Heterogeneous nuclear ribonucleoprotein A1*", "2.3", "2.45", "2.14", "S"], ["A4IF97", "Myosin regulatory light chain 12B*", "2.27", "2.39", "2.14", "S"], ["A3KMV5", "Ubiquitin-like modifier-activating enzyme 1*", "2.26", "2.57", "1.87", "PD"], ["Q2HJ57", "Coactosin-like protein*", "2.22", "2.24", "2.21", "I"], ["Q58CQ2", "Actin-related protein 2/3 complex subunit 1B*", "2.2", "2.22", "2.18", "S"], ["G3N131", "Histone H1.1*", "2.19", "", "", "S"], ["P49951", "Clathrin heavy chain 1*", "2.08", "2.22", "1.92", "S"], ["A5D7A0", "EF-hand domain-containing protein D2*", "2.08", "2.2", "1.95", "S"], ["Q2TA49", "Vasodilator-stimulated phosphoprotein", "2.06", "2.42", "1.58", "S"], ["Q3ZC84", "Cytosolic non-specific dipeptidase", "2.05", "2.18", "1.91", "OM"], ["P10096", "Glyceraldehyde-3-phosphate dehydrogenase", "2.05", "2.14", "1.97", "CM"], ["P60661", "Myosin light polypeptide 6", "2.02", "2.15", "1.87", "S"], ["Q3T0D0", "Heterogeneous nuclear ribonucleoprotein K*", "2.01", "2.08", "1.94", "NM"], ["P33433", "Histidine-rich glycoproteina", "2.01", "2.52", "", "I"], ["Q4U5R3", "Proteasome activator complex subunit 1", "2.01", "2.07", "1.96", "PD"], ["Q32PI5", "Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform", "1.98", "2.29", "1.59", "S"], ["Q56JZ9", "Glia maturation factor gamma*", "1.97", "2.02", "1.92", "S"], ["Q0VCX1", "Complement C1s subcomponent*", "1.96", "2.24", "1.62", "I"], ["Q3SZH7", "Leukotriene A-4 hydrolase*", "1.96", "1.91", "2.02", "I"], ["P31081", "60 kDa heat shock protein, mitochondrial*", "1.95", "2.12", "1.76", "I"], ["Q32LP0", "Fermitin family homolog 3*", "1.94", "2.15", "1.69", "I"], ["D2U6Q0", "Serum amyloid A protein*", "1.93", "1.86", "2", "I"], ["P62326", "Thymosin beta-4*", "1.91", "2.03", "1.78", "I"], ["P13752", "BOLA class I histocompatibility antigen, alpha chain BL3-6*", "1.9", "2.08", "1.7", "I"], ["Q2KJI3", "Protein FAM49B*", "1.89", "1.87", "1.92", "I"], ["Q762I5", "Resistin*", "1.89", "1.92", "1.85", "LM"], ["Q76LV2", "Heat shock protein HSP 90-alpha", "1.88", "2.06", "1.68", "PD"], ["Q3SZ54", "Eukaryotic initiation factor 4A-I", "1.85", "1.82", "1.88", "GE"], ["Q3MHL4", "Adenosylhomocysteinase", "1.83", "1.82", "1.84", "AM"], ["P80724", "Brain acid soluble protein 1*", "1.82", "1.61", "2", "GE"], ["P60712", "Actin, cytoplasmic 1", "1.8", "2.01", "1.57", "S"], ["J9Q6V1", "Glutathione peroxidase*", "1.8", "2.05", "1.5", "OM"], ["P55859", "Purine nucleoside phosphorylase*", "1.78", "1.51", "2", "NM"], ["Q9XSJ4", "Alpha-enolase", "1.77", "1.8", "1.75", "CM"], ["Q27970", "Calpain-1 catalytic subunita", "1.77", "2.13", "", "PD"], ["Q865V6", "Macrophage-capping protein*", "1.76", "1.65", "1.86", "S"], ["Q9GMB8", "Serine–tRNA ligase, cytoplasmica", "1.74", "2.02", "", "AM"], ["Q9BGI1", "Peroxiredoxin-5, mitochondrial", "1.73", "1.92", "1.52", "OM"], ["P51122", "Acidic leucine-rich nuclear phosphoprotein 32 family member Aa", "", "1.72", "", "CT"], ["Q148J6", "Actin-related protein 2/3 complex subunit 4*", "1.7", "1.71", "1.69", "S"], ["A4FUA8", "F-actin-capping protein subunit alpha-1*", "1.68", "1.63", "1.73", "S"], ["P06868", "Plasminogen", "1.68", "1.77", "1.58", "C"], ["P07589", "Fibronectin", "1.67", "", "", "I"], ["P13753", "BOLA class I histocompatibility antigen, alpha chain BL3-7*,a", "1.65", "1.96", "", "I"], ["O46522", "Cytochrome b-245 heavy chaina", "1.64", "2", "", "I"], ["Q3SZI4", "14-3-3 protein theta", "1.62", "1.69", "1.55", "GE"], ["A6H742", "Plastin-1*", "1.62", "1.54", "1.69", "S"], ["D2U6Z5", "Ceruloplasminb", "1.61", "", "1.75", "IM"], ["Q3T035", "Actin-related protein 2/3 complex subunit 3*,a", "1.57", "1.71", "", "S"], ["P20000", "Aldehyde dehydrogenase, mitochondrial*,a", "1.57", "1.71", "", "CM"], ["P01030", "Complement C4b", "1.57", "", "1.72", "I"], ["P0C0S4", "Histone H2A.Za", "1.56", "1.66", "", "S"], ["Q27996", "Lysozyme C, tracheal isozyme", "1.56", "1.51", "1.61", "I"], ["Q5E9B7", "Chloride intracellular channel protein 1", "1.55", "1.52", "1.57", "C"], ["P68138", "Actin, alpha skeletal musclea", "1.54", "1.72", "", "S"], ["X2IZ01", "Signal transducer and activator of transcriptiona", "1.54", "1.59", "", "I"], ["Q3ZBT1", "Transitional endoplasmic reticulum ATPasea", "1.54", "1.68", "", "CT"], ["Q2HJG5", "Vacuolar protein sorting-associated protein 35a", "1.54", "1.84", "", "I"], ["O97680", "Thioredoxina", "1.53", "1.79", "", "OM"], ["P19483", "ATP synthase subunit alpha, mitochondrialb", "", "", "1.52", "CT"], ["P02676", "Fibrinogen beta chaina", "", "1.79", "", "C"], ["P02672", "Fibrinogen alpha chaina", "", "1.83", "", "I"], ["Q5E9R3", "EH domain-containing protein 1a", "", "1.78", "", "CaM"], ["P00829", "ATP synthase subunit beta, mitochondriala", "", "1.66", "", "OM"], ["P81644", "Apolipoprotein A-IIa", "", "1.64", "", "LM"], ["Q3B7M5", "LIM and SH3 domain protein 1a", "", "1.61", "", "S"], ["A6H7G2", "Drebrin-like proteina", "", "1.58", "", "I"], ["Q3ZBH0", "T-complex protein 1 subunit betaa", "", "1.57", "", "PD"], ["Q3MHL7", "T-complex protein 1 subunit zetaa", "", "1.52", "", "PD"], ["Q7SIH1", "Alpha-2-macroglobulina", "", "1.52", "", "I"], ["P27214", "Annexin A11a", "", "1.52", "", "S"], ["Q3SZV7", "Hemopexina", "", "1.5", "", "IM"], ["P11116", "Galectin-1b", "", "", "1.61", "I"], ["P35466", "Protein S100-A4b", "", "", "1.6", "I"], ["O02675", "Dihydropyrimidinase-related protein 2*,b", "", "", "1.51", "S"], ["Q3T054", "GTP-binding nuclear protein Ranb", "", "", "1.61", "CT"], ["Q3T0D7", "GTP-binding protein SAR1a", "−1.51", "", "", "CT"], ["Q71SP7", "Fatty acid synthasea", "−1.52", "−1.8", "", "LM"], ["P02638", "Protein S100-B", "−1.53", "", "", "I"], ["P10790", "Fatty acid-binding protein, hearta", "", "−1.53", "", "LM"], ["M9WP41", "BTN1A1a", "", "−1.57", "", "S"], ["Q17QE5", "Calcium and integrin-binding protein 1a", "−1.56", "−1.85", "", "I"], ["Q9N0T1", "Stanniocalcin-1a", "−1.57", "−1.9", "", "CaM"], ["A0A0C5GDU2", "Myostatina", "", "−1.59", "", "S"], ["Q6RUS0", "Butyrophilinb", "−1.6", "", "−1.75", "LM"], ["G1AQP3", "Xanthine dehydrogenase/oxidasea", "−1.61", "−1.81", "", "LM"], ["E9NV81", "ATP-binding cassette sub-family G (WHITE) member 2a", "−1.62", "−1.95", "", "LM"], ["Q05927", "5′-nucleotidaseb", "−1.65", "", "−1.88", "NM"], ["M4QG36", "Insulin induced protein 1a", "−1.65", "−1.88", "", "S"], ["O77588", "Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1a", "−1.68", "−2.19", "", "S"], ["A5PK13", "Volume-regulated anion channel subunit LRRC8C", "−1.68", "", "", "LM"], ["Q2KIY5", "Putative phospholipase B-like 2a", "−1.69", "−2.24", "", "LM"], ["P81127", "Gamma-soluble NSF attachment protein", "−1.71", "", "", "CT"], ["Q58CY6", "Prostamide/prostaglandin F synthaseb", "−1.73", "", "−1.83", "LM"], ["Q06805", "Tyrosine-protein kinase receptor Tie-1", "−1.73", "", "", "A"], ["P37980", "Inorganic pyrophosphatase", "−1.74", "−1.99", "−1.53", "LM"], ["Q3T0Q2", "Transmembrane protein 59", "−1.75", "−1.87", "−1.63", "CT"], ["Q3SYV1", "Transmembrane protein 263", "−1.77", "", "", "CT"], ["Q3SYS6", "Calcineurin B homologous protein 1", "−1.81", "−1.87", "−1.75", "CaM"], ["Q58DD4", "Syndecan-2a", "−1.81", "−2.13", "", "S"], ["D3K0R6", "Plasma membrane calcium-transporting ATPase 4", "−1.93", "−2.04", "−1.82", "CaM"], ["C1KGU3", "Solute carrier family 11 member 2", "−1.93", "−2.02", "−1.85", "CT"], ["Q5GJ77", "Glycerol-3-phosphate acyltransferase 1, mitochondrial", "−2.01", "−2.13", "−1.91", "LM"], ["A0A088F8E5", "Acyl-CoA synthetase short-chain family member 2", "−2.08", "−2.19", "−1.97", "LM"], ["P08239", "Guanine nucleotide-binding protein G(o) subunit alpha", "−2.14", "−2.25", "−2.03", "CT"], ["P08169", "Cation-independent mannose-6-phosphate receptor", "−2.15", "−2.47", "−1.88", "I"], ["Q3ZBE9", "Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating", "−2.17", "−2.65", "−1.8", "LM"], ["Q2YDI9", "Ferritin, mitochondrial", "−2.28", "−2.4", "−2.17", "IM"], ["Q58DW6", "Ras-related protein Rab-25", "−2.28", "−2.39", "−2.17", "CR"], ["Q3MHW6", "Monocarboxylate transporter 1", "−2.48", "−2.55", "−2.41", "CM"], ["A0A097P9M4", "Long-chain fatty acid-CoA ligase 1", "−2.6", "−3.2", "−2.17", "LM"], ["P84466", "Lanosterol synthase", "−2.71", "−2.83", "−2.61", "LM"], ["Q3MHX6", "Protein OS-9a", "", "−1.57", "", "S"], ["Q2TBX4", "Heat shock 70 kDa protein 13a", "", "−1.59", "", "PD"], ["Q0VD19", "Sphingomyelin phosphodiesterasea", "", "−1.72", "", "LM"], ["Q1RMU3", "Prolyl 4-hydroxylase subunit alpha-1a", "", "−1.73", "", "S"], ["Q5EA88", "Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmica", "", "−1.8", "", "CM"], ["Q0IIG7", "Ras-related protein Rab-5Aa", "", "−2.11", "", "CT"], ["A6QR11", "Protein kinase C-binding protein NELL2a", "", "−2.37", "", "CaM"], ["Q5E9B5", "Actin, gamma-enteric smooth muscleb", "", "", "−3.76", "S"]], "row_count": 182, "column_count": 6, "numeric_cells": 653, "header_rows": 1, "locator": "section[5]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:31676851:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ee0cf8f71af1d337684ae52f021f6d3dd5743011e1042233e8fefb18104ea14", "bytes": 717, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Sample groups, milk samples, and their characteristics.", "structure": {"pmcid": "PMC6825138", "section_index": 14, "section_title": "Animals and milk samples", "row_count": 15, "column_count": 3}, "table": {"label": "Table 1", "caption": "Sample groups, milk samples, and their characteristics.", "rows": [["Sample group", "SCCa (cells/mL × 103)", "Bacteriology"], ["Positive", "Mean value 5545 (CMTb + 3)", ""], ["1", "4091", "Staphylococcus aureus"], ["2", "3782", "Staphylococcus aureus"], ["3", "8440", "Staphylococcus aureus"], ["4", ">10000", "Non-aureus staphylococci"], ["5", "4035", "Non-aureus staphylococci"], ["6", "2924", "Non-aureus staphylococci"], ["Negative", "Mean value 23.5 (CMT Neg)", ""], ["7", "46", "Negative"], ["8", "37", "Negative"], ["9", "30", "Negative"], ["10", "14", "Negative"], ["11", "8", "Negative"], ["12", "6", "Negative"]], "row_count": 15, "column_count": 3, "numeric_cells": 27, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:PXD012355 not downloaded", "asset:data:geo:PXD012355 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018)."}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD012355"], "resolved_accessions": ["PXD012355"], "statements": ["The data have been deposited to the ProteomeXchange with identifier PXD012355."], "basis": "The paper names PXD012355 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. 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