What's in a Badge? A Computational Reproducibility Investigation of the Open Data Badge Policy in One Issue of Psychological Science.

In April 2019, Psychological Science published its first issue in which all Research Articles received the Open Data badge. We used that issue to investigate the effectiveness of this badge, focusing on the adherence to its aim at Psychological Science: sharing both data and code to ensure reproducibility of results. Twelve researchers of varying experience levels attempted to reproduce the results of the empirical articles in the target issue (at least three researchers per article). We found that all 14 articles provided at least some data and six provided analysis code, but only one article was rated to be exactly reproducible, and three were rated as essentially reproducible with minor deviations. We suggest that researchers should be encouraged to adhere to the higher standard in force at Psychological Science. Moreover, a check of reproducibility during peer review may be preferable to the disclosure method of awarding badges.

Hydrogen motional disorder in crystalline iron group chloride dihydrates.

The principal components and the relative orientation of the 2H paramagnetic shift and quadrupolar coupling tensors have been measured for the MCl2·2D2O family of compounds, M = Mn, Fe, Co, Ni, and Cu, using the two-dimensional shifting-d echo nuclear magnetic resonance experiment in order to determine (1) the degree of unpaired electron delocalization and (2) the number and location of crystallographically distinct hydrogen sites around oxygen and their fractional occupancies. Expressions for the molecular susceptibility of 3d ion systems, where the spin-orbit coupling is a weak perturbation onto the crystal field, are derived using the generalized Van Vleck equation and used to predict molecular susceptibilities. These predicted molecular susceptibilities are combined with various point dipole source configurations modeling unpaired electron delocalization to predict 2H paramagnetic shift tensors at potential deuterium sites. The instantaneous deuterium quadrupolar coupling and shift tensors are then combined with parameterized motional models, developed for trigonally (M = Mn, Fe, Co, and Cu) and pyramidally (M = Ni) coordinated D2O ligands, to obtain the best fit of the experimental 2D spectra. Dipole sources placed onto metal nuclei with a small degree of delocalization onto the chlorine ligands yield good agreement with the experiment for M = Mn, Fe, Co, and Ni, while good agreement for CuCl2·2D2O is obtained with additional delocalization onto the oxygen. Our analysis of the salts with trigonally coordinated water ligands (M = Mn, Fe, Co, and Cu) confirms the presence of bisector flipping and the conclusions from neutron scattering measurements that hydrogen bonding to chlorine on two adjacent chains leads to the water molecule in the [M(D2O)2Cl4] cluster being nearly coplanar with O-M-Cl involving the shortest metal-chlorine bonds of the cluster. In the case of NiCl2·2D2O, the experimental parameters were found to be consistent with a motional model where the D2O ligands are pyramidally coordinated to the metal and undergo bisector flipping while the water ligand additionally hops between two orientations related by a 120° rotation about the Ni-O bond axis. The position of the three crystallographically distinct hydrogen sites in the unit cell was determined along with fractional occupancies. This restricted water ligand motion is likely due to van der Waals interactions and is concerted with the motion of neighboring ligands.

Exercise increases lactoferrin, but decreases lysozyme in salivary granulocytes.

INTRODUCTION: Intracellular lactoferrin (Lac) and lysozyme (Lys) content play an important role in regulating inflammation and promoting host protection. While exercise has demonstrated an increase in Lac and Lys concentration in exocrine solutions, little is known regarding intracellular concentration changes in response to exercise. PURPOSE: To quantify intracellular Lac and Lys concentration before and after exercise in salivary CD45+CD15+ cells. METHODS: 11 males (20.3 ± 0.8 years, 57.2 ± 7.6 mL/kg/min V̇O2pk, 11.1 ± 3.9% body fat) ran for 45 min at 75% of VO2pk. 12 mL of stimulated saliva were collected pre and immediately post exercise. Saliva was filtered through a 30-µm filter before analysis of leukocytes (CD45+) and granulocytes (CD45+CD15+) using flow cytometry. RESULTS: Median fluorescent intensity (MFI) of Lac increased from pre (64,268 ± 46,036 MFI) to post (117,134 ± 88,115 MFI) exercise (p <0.05). Lys MFI decreased with exercise (pre: 16,933 ± 8249; post: 11,616 ± 6875) (p <0.05). CONCLUSION: Acute running resulted in an increased Lac concentration which could lead to a decrease in inflammation, adding further evidence of the anti-inflammatory effects of exercise. Conversely, the exercise-associated decrease of intracellular Lys content could be the cause of increased Lys in exocrine solutions.

Exercise does not increase salivary lymphocytes, monocytes, or granulocytes, but does increase salivary lysozyme.

An increase in salivary leukocytes may contribute to the exercise-induced increase in salivary antimicrobial proteins (AMPs). However, exercise-induced changes in salivary leukocytes have not been studied. The purpose of the study was to describe salivary leukocyte changes with exercise. Participants (n = 11, 20.3 ± 0.8 years, 57.2 ± 7.6 ml kg-1 min-1 peak oxygen uptake ((VO) ̇2peak), 11.1 ± 3.9% body fat) ran for 45 min at 75% of VO2peak. Stimulated saliva (12 mL) was collected pre- and immediately post exercise. Saliva was filtered through a 30 µm filter before analysis of leukocytes (CD45+), granulocytes (CD45+CD15+), monocytes (CD45+CD14+), T-cells (CD45+CD3+), and B-cells (CD45+CD20+) using flow cytometry. Saliva was analysed for Lysozyme (Lys) using ELISA. Exercise did not alter any leukocyte subset. The major constituent of leukocytes pre-exercise were granulocytes (57.9 ± 30.3% compared with monocytes: 5.1 ± 2.7%, T-cells: 17.1 ± 8.9%, B-cells: 12.1 ± 10.2%) (P < 0.05). In a subset of n = 6, Lys secretion rate increased after exercise (pre: 5,170 ± 5,215 ng/min; post: 7,639 ± 4,140 ng/min) (P < 0.05). Exercise does not result in increased granulocytes, but does increase Lys. Further, these data suggest that an increase in salivary leukocytes is not needed to increase Lys.

Exercise, but not acute sleep loss, increases salivary antimicrobial protein secretion.

Sleep deficiencies may play a role in depressing immune parameters. Little is known about the impact of exercise after sleep deprivation on mucosal immunity. The purpose of this study was to quantify salivary antimicrobial proteins (AMPs) in response to sleep loss before and after exercise. Four men and 4 women (age: 22.8 ± 2; : 49.1 ± 7.1 ml · kg(-1) · min(-1)) completed 2 exercise trials consisting of 45 minutes of running at 75% VO2peak after a normal night of sleep (CON) and after a night without sleep (WS). Exercise trials were separated by 10 ± 3 days. Saliva was collected before, immediately after, and 1 hour after exercise. LL-37, HNP1-3, Lactoferrin (Lac), and Lysozyme (Lys) were measured. Sleep loss did not affect the concentration or secretion rate of AMPs before or in response to exercise. However, exercise increased the concentration from pre- to post-exercise of LL-37 (pre: 15.5 ± 8.7; post: 22.3 ± 16.2 ng · ml(-1)), HNP1-3 (pre: 2.2 ± 2.3; post: 3.3 ± 2.5 µg · ml(-1)), Lac (pre: 5,234 ± 4,202; post: 12,283 ± 10,995 ng · ml(-1)), and Lys (pre: 5,831 ± 4,465; post: 12,542 ± 10,755 ng · ml(-1)), p <= 0.05. The secretion rates were higher immediately after and 1 hour after exercise compared with before exercise for LL-37 (pre: 3.1 ± 2.1; post: 5.1 ± 3.7; +1: 6.9 ± 8.4 ng · min(-1)), HNP1-3 (pre: 0.38 ± 0.38; post: 0.80 ± 0.75; +1: 0.84 ± 0.67 µg · min(-1)), Lac (pre: 1,096 ± 829; post: 2,948 ± 2,923; +1: 2,464 ± 3,785 ng · min(-1)), and Lys (pre: 1,534 ± 1,790; post: 3,042 ± 2,773; +1: 1,916 ± 1,682 ng · min-(1)), p <= 0.05. These data suggest that the major constituents of the mucosal immune system are unaffected by acute sleep loss and by exercise after acute sleep loss. Exercise increased the concentration and secretion rate of each AMP suggesting enhanced immunity and control of inflammation, despite limited sleep.

Prostate specific membrane antigen produces pro-angiogenic laminin peptides downstream of matrix metalloprotease-2.

Prostate specific membrane antigen (PSMA) is a pro-angiogenic cell-surface protease that we previously demonstrated regulates blood vessel formation in a laminin and integrin ß1-dependent manner. Here, we examine the principal mechanism of PSMA activation of integrin ß1. We show that digesting laminin sequentially with recombinant matrix metalloprotease-2 (MMP-2) and PSMA generates small peptides that enhance endothelial cell adhesion and migration in vitro. We also provide evidence that these laminin peptides activate adhesion via integrin α6ß1 and focal adhesion kinase. Using an in vivo Matrigel implant assay, we show that these MMP/PSMA-derived laminin peptides also increase angiogenesis in vivo. Together, our results reveal a novel mechanism of PSMA activation of angiogenesis by processing laminin downstream of MMP-2.

Differential expression of tissue repair genes in the pathogenesis of chronic obstructive pulmonary disease.

RATIONALE: The airflow limitation that defines severity of chronic obstructive pulmonary disease (COPD) is caused by a combination of small airway obstruction and emphysematous lung destruction. OBJECTIVES: To examine the hypothesis that small airway obstructive and emphysematous destructive lesions are produced by differential expression of genes associated with tissue repair. METHODS: The expression of 54 genes associated with repair of repetitively damaged tissue was measured in 136 paired samples of small bronchioles and surrounding lung tissue separated by laser capture microdissection. These samples were collected from 63 patients at different levels of disease severity who required surgery for either lung cancer or lung transplantation for very severe COPD. Gene expression was measured by quantitative polymerase chain reaction in these paired samples and compared with the FEV(1) by linear regression analysis. MEASUREMENTS AND MAIN RESULTS: After corrections for false discovery rates, only 2 of 10 genes (serpin peptidase inhibitor/plasminogen activator inhibitor member 2 and matrix metalloproteinase [MMP] 10) increased, whereas 8 (MMP2, integrin-alpha1, vascular endothelial growth factor, a disintegrin and metallopeptidase domain 33, scatter factor/hepatocyte growth factor, tissue inhibitor of matrix metalloproteinase-2, fibronectin, and collagen 3alpha1) decreased in small airways in association with FEV(1). In contrast, 8/12 genes (early growth response factor 1, MMP1, MMP9, MMP10, plasminogen activator urokinase, plasminogen activator urokinase receptor, tumor necrosis factor, and IL13) increased and 4/12 (MMP2, tissue inhibitor of matrix metalloproteinase-1, collagen 1alpha1, and transforming growth factor-beta3) decreased in the surrounding lung tissue in association with progression of COPD. CONCLUSIONS: The progression of COPD is associated with the differential expression of a cluster of genes that favor the degradation of the tissue surrounding the small conducting airways.