cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5126272
title: Supplementary Material for: Expression Patterns of Neuroligin-3 and Tyrosine Hydroxylase across the Brain in Mate Choice Contexts in Female Swordtails

description: Choosing mates is a commonly shared behavior across many organisms, with important fitness consequences. Variations in female preferences can be due in part to differences in neural and cellular activity during mate selection. Initial studies have begun to identify putative brain regions involved in mate preference, yet the understanding of the neural processes regulating these behaviors is still nascent. In this study, we characterized the expression of a gene involved in synaptogenesis and plasticity <i>(neuroligin-3)</i> and one that codes for the rate-limiting enzyme in dopamine biosynthesis (<i>tyrosine hydroxylase</i>; TH1) in the female <i>Xiphophorus nigrensis </i>(northern swordtail) brain as related to mate preference behavior. We exposed females to a range of different mate choice contexts including two large courting males (LL), two small coercive males (SS), and a context that paired a large courting male with a small coercive male (LS). <i>Neuroligin-3</i> expression in a mate preference context (LS) showed significant correlations with female preference in two telencephalic areas (Dm and Dl), a hypothalamic nucleus (HV), and two regions associated with sexual and social behavior (POA and Vv). We did not observe any context- or behavior-specific changes in <i>tyrosine hydroxylase</i> mRNA expression concomitant with female preference in any of the brain regions examined. Analysis of TH and <i>neuroligin-3</i> expression across different brain regions showed that expression patterns varied with the male social environment only for <i>neuroligin-3</i>, where the density of correlated expression between brain regions was positively associated with mate choice contexts that involved a greater number of courting male phenotypes (LS and LL). This study identified regions showing presumed high levels of synaptic plasticity using <i>neuroligin-3</i>, implicating and supporting their roles in female mate preference, but we did not detect any relationship between <i>tyrosine hydroxylase</i> and mate preference with 30 min of stimulus presentation in <i>X. nigrensis</i>. These data suggest that information about potential mates is processed in select forebrain regions and the entire brain shows different degrees of correlated expression depending on the mate preference context.
DOI: 10.6084/m9.figshare.5126269
title: Supplementary Material for: Hypomagnesemia in Hemodialysis Patients: Role of Proton Pump Inhibitors

description: <b><i>Background:</i></b> Recent observations have associated hypomagnesemia with increased risk of cardiovascular morbidity and mortality in hemodialysis patients. <b><i>Methods:</i></b> We did a 3-month chart review of 62 chronic hemodialysis patients at a single US hospital. All were dialyzed using a dialysate [Mg] of 0.75-1.0 mEq/l. Patients were divided into two groups: hypomagnesemic (mean predialysis plasma [Mg] &lt;1.5 mEq/l) and non-hypomagnesemic (mean predialysis plasma [Mg] ≥1.5 mEq/l). <b><i>Results:</i></b> All patients were male; mean age was 64.3 ± 8.7 years and the majority (73%) diabetic. 24 patients (39%) had hypomagnesemia and 38 (61%) were not hypomagnesemic. There were no significant differences between the two groups in age, diabetes status, blood pressure, duration of dialysis, plasma calcium, phosphorus, albumin, intact parathyroid hormone (PTH), dialysis adequacy (Kt/V), or dietary protein intake (as estimated by normalized protein catabolic rate, nPCR). However, use of proton pump inhibitors (PPIs) was significantly associated with hypomagnesemia (plasma [Mg] 1.48 ± 0.16 mEq/l in the PPI group vs. 1.65 ± 0.26 mEq/l in the non-PPI group, p = 0.007). Adjustment for age, diabetes status, duration of dialysis, plasma albumin, Kt/V, nPCR, and diuretic use did not affect the association between PPI use and hypomagnesemia. <b><i>Conclusions:</i></b> Use of PPIs in patients dialyzed using a dialysate [Mg] of 0.75-1.0 mEq/l is associated with hypomagnesemia. We suggest monitoring plasma [Mg] in patients taking PPIs, with discontinuation of the medication if possible and/or adjustment of dialysate [Mg] to normalize plasma [Mg].
DOI: 10.6084/m9.figshare.5126281.v1
title: Supplementary Material for: Potassium-Binding Resins: Associations with Serum Chemistries and Interdialytic Weight Gain in Hemodialysis Patients

description: <b><i>Background:</i></b> Although potassium-binding sodium-based resins (K resins) have been prescribed to treat hyperkalemia for 50 years, there have been no large studies of their effects among hemodialysis (HD) patients. <b><i>Methods:</i></b> Data from 11,409 patients in the Dialysis Outcomes and Practice Patterns Study in Belgium, Canada, France, Italy, and Sweden (nations where ≥5% of patients were prescribed a sodium- based K resin; seven other countries had &lt;5% use) between 2002 and 2011 were analyzed. Linear mixed models examined associations between K resin use and interdialytic weight gain (IDWG) and serum electrolyte concentrations. Mortality was analyzed using Cox regression. An instrumental variable approach was used to partially account for unmeasured confounders. <b><i>Results:</i></b> The K resin prescription rate was 20% overall. As hypothesized, patients prescribed a K resin had greater IDWG and higher serum bicarbonate, phosphorus, and sodium (but not calcium) concentrations. Patients prescribed a K resin had higher serum K levels, but serum K levels were lower in an instrumental variable analysis limiting treatment by indication bias. K resin use was not associated with mortality risk. <b><i>Conclusion:</i></b> We report the first large study of K resin use and associated laboratory and clinical outcomes in HD patients. The prescription rate of K resins varied dramatically by country and dialysis center. The results suggest that K resin use may effectively lower serum K, although at the expense of somewhat higher phosphatemia and greater IDWG, and had no clear association with mortality. Further study is warranted to elucidate the optimal role for K resins in modern dialysis care.
DOI: 10.6084/m9.figshare.5126266
title: Supplementary Material for: Expansion of Urease- and Uricase-Containing, Indole- and p-Cresol-Forming and Contraction of Short-Chain Fatty Acid-Producing Intestinal Microbiota in ESRD

description: <b><i>Background:</i></b> Intestinal microbiome constitutes a symbiotic ecosystem that is essential for health, and changes in its composition/function cause various illnesses. Biochemical milieu shapes the structure and function of the microbiome. Recently, we found marked differences in the abundance of numerous bacterial taxa between ESRD and healthy individuals. Influx of urea and uric acid and dietary restriction of fruits and vegetables to prevent hyperkalemia alter ESRD patients' intestinal milieu. We hypothesized that relative abundances of bacteria possessing urease, uricase, and p-cresol- and indole-producing enzymes is increased, while abundance of bacteria containing enzymes converting dietary fiber to short-chain fatty acids (SCFA) is reduced in ESRD. <b><i>Methods:</i></b> Reference sets of bacteria containing genes of interest were compiled to family, and sets of intestinal bacterial families showing differential abundances between 12 healthy and 24 ESRD individuals enrolled in our original study were compiled. Overlap between sets was assessed using hypergeometric distribution tests. <b><i>Results:</i></b> Among 19 microbial families that were dominant in ESRD patients, 12 possessed urease, 5 possessed uricase, and 4 possessed indole and p-cresol-forming enzymes. Among 4 microbial families that were diminished in ESRD patients, 2 possessed butyrate-forming enzymes. Probabilities of these overlapping distributions were &lt;0.05.<b><i> Conclusions:</i></b> ESRD patients exhibited significant expansion of bacterial families possessing urease, uricase, and indole and p-cresol forming enzymes, and contraction of families possessing butyrate-forming enzymes. Given the deleterious effects of indoxyl sulfate, p-cresol sulfate, and urea-derived ammonia, and beneficial actions of SCFA, these changes in intestinal microbial metabolism contribute to uremic toxicity and inflammation.
DOI: 10.6084/m9.figshare.5126269.v1
title: Supplementary Material for: Hypomagnesemia in Hemodialysis Patients: Role of Proton Pump Inhibitors

description: <b><i>Background:</i></b> Recent observations have associated hypomagnesemia with increased risk of cardiovascular morbidity and mortality in hemodialysis patients. <b><i>Methods:</i></b> We did a 3-month chart review of 62 chronic hemodialysis patients at a single US hospital. All were dialyzed using a dialysate [Mg] of 0.75-1.0 mEq/l. Patients were divided into two groups: hypomagnesemic (mean predialysis plasma [Mg] &lt;1.5 mEq/l) and non-hypomagnesemic (mean predialysis plasma [Mg] ≥1.5 mEq/l). <b><i>Results:</i></b> All patients were male; mean age was 64.3 ± 8.7 years and the majority (73%) diabetic. 24 patients (39%) had hypomagnesemia and 38 (61%) were not hypomagnesemic. There were no significant differences between the two groups in age, diabetes status, blood pressure, duration of dialysis, plasma calcium, phosphorus, albumin, intact parathyroid hormone (PTH), dialysis adequacy (Kt/V), or dietary protein intake (as estimated by normalized protein catabolic rate, nPCR). However, use of proton pump inhibitors (PPIs) was significantly associated with hypomagnesemia (plasma [Mg] 1.48 ± 0.16 mEq/l in the PPI group vs. 1.65 ± 0.26 mEq/l in the non-PPI group, p = 0.007). Adjustment for age, diabetes status, duration of dialysis, plasma albumin, Kt/V, nPCR, and diuretic use did not affect the association between PPI use and hypomagnesemia. <b><i>Conclusions:</i></b> Use of PPIs in patients dialyzed using a dialysate [Mg] of 0.75-1.0 mEq/l is associated with hypomagnesemia. We suggest monitoring plasma [Mg] in patients taking PPIs, with discontinuation of the medication if possible and/or adjustment of dialysate [Mg] to normalize plasma [Mg].
DOI: 10.6084/m9.figshare.5126278.v1
title: Supplementary Material for: Assessment with Unenhanced MRI Techniques of Renal Morphology and Hemodynamic Changes during Acute Kidney Injury and Chronic Kidney Disease in Mice

description: <b><i>Background/Aims:</i></b> Changes in renal oxygenation and perfusion have been identified as common pathways to the development and progression of renal disease. Recently, the sensitivity of hemodynamic response imaging (HRI) was demonstrated; this is a functional magnetic resonance imaging (MRI) method combined with transient hypercapnia and hyperoxia for the evaluation of renal perfusion and vascular reactivity. The aim of this study was to utilize HRI for the noninvasive evaluation of changes in renal hemodynamics and morphology during acute, chronic and acute-on-chronic renal failures. <b><i>Methods:</i></b> Renal-HRI maps and true fast imaging with steady-state precession (True-FISP) images were used to evaluate renal perfusion, morphology and corticomedullary differentiation (CMD). MR images were acquired on two mouse models of kidney injury: adenine-induced chronic kidney disease (CKD) and rhabdomyolysis-induced acute kidney injury (AKI). Serum urea was measured from these mice in order to determine renal function. <b><i>Results:</i></b> Renal-HRI maps revealed a blunted response to hypercapnia and hyperoxia with evolving kidney dysfunction in both models, reflecting hampered renal vascular reactivity and perfusion. True-FISP images showed a high sensitivity to renal morphological changes, with different patterns characterizing each model. Calculated data obtained from HRI and True-FISP during the evolution of renal failure and upon recovery, with and without protective intervention, closely correlated with the degree of renal impairment. <b><i>Conclusions:</i></b> This study suggests the potential combined usage of two noninvasive MRI methods, HRI and True-FISP, for the assessment of renal dysfunction without the potential risk associated with contrast-agents administration. HRI may also serve as a research tool in experimental settings, revealing the hemodynamic changes associated with kidney dysfunction.
DOI: 10.6084/m9.figshare.5126257
title: Supplementary Material for: Tissue-Specific Patterning of Host Innate Immune Responses by <b><i>Staphylococcus aureus</i></b> α-Toxin

description: Immunomodulatory cytotoxins are prominent virulence factors produced by <i>Staphylococcus aureus</i>, a leading cause of bacterial sepsis, skin infection, and pneumonia. <i>S. aureus </i>α-toxin is a pore-forming toxin that utilizes a widely expressed receptor, ADAM10, to injure the host epithelium, endothelium, and immune cells. As each host tissue is characterized by a unique composition of resident cells and recruited immune cells, the outcome of α-toxin-mediated injury may depend on the infected tissue environment. Utilizing myeloid lineage-specific <i>Adam10</i> knockout mice, we show that α-toxin exerts tissue-specific effects on innate immunity to staphylococcal infection. Loss of ADAM10 expression exacerbates skin infection, yet affords protection against lethal pneumonia. These diverse outcomes are not related to altered immune cell recruitment, but rather correlate with a defect in toxin-induced IL-1β production. Extension of these studies through analysis of ADAM10 double-knockout mice affecting both the myeloid lineage and either the skin or lung epithelium highlight the prominence of toxin-induced injury to the epithelium in governing the outcome of infection. Together, these studies provide evidence of tissue specificity of pore-forming cytotoxin action in the modulation of host immunity, and illustrate that the outcome of infection is a collective manifestation of all effects of the toxin within the tissue microenvironment.
DOI: 10.6084/m9.figshare.5126251
title: Supplementary Material for: Increased Calcification in Osteoprotegerin-Deficient Smooth Muscle Cells: Dependence on Receptor Activator of NF-κB Ligand and Interleukin 6

description: <b><i>Objective:</i></b> Vascular calcification is highly correlated with cardiovascular disease morbidity and mortality. Osteoprotegerin (OPG) is a secreted decoy receptor for receptor activator of NF-κB ligand (RANKL). Inactivation of OPG in apolipoprotein E-deficient (ApoE-/-) mice increases lesion size and calcification. The mechanism(s) by which OPG is atheroprotective and anticalcific have not been entirely determined. We investigated whether OPG-deficient vascular smooth muscle cells (VSMCs) are more susceptible to mineralization and whether RANKL mediates this process. <b><i>Results:</i></b> Lesion-free aortas from 12-week-old ApoE-/-OPG-/- mice had spotty calcification, an appearance of osteochondrogenic factors and a decrease of smooth muscle markers when compared to ApoE-/-OPG+/+ aortas. In osteogenic conditions, VSMCs isolated from ApoE-/-OPG-/- (KO-VSMC) mice deposited more calcium than VSMCs isolated from ApoE-/-OPG+/+ (WT-VSMC) mice. Gene expression and biochemical analysis indicated accelerated osteochondrogenic differentiation. Ablation of RANKL signaling in KO-VSMCs rescued the accelerated calcification. While WT-VSMCs did not respond to RANKL treatment, KO-VSMCs responded with enhanced calcification and the upregulation of osteochondrogenic genes. RANKL strongly induced interleukin 6 (IL-6), which partially mediated RANKL-dependent calcification and gene expression in KO-VSMCs. <b><i>Conclusions:</i></b> OPG inhibits vascular calcification by regulating the procalcific effects of RANKL on VSMCs and is thus a possible target for therapeutic intervention.
DOI: 10.6084/m9.figshare.5126254
title: Supplementary Material for: Neural Correlates of Procedural Variants in Cognitive-Behavioral Therapy: A Randomized, Controlled Multicenter fMRI Study

description: <b><i>Background:</i></b> Cognitive behavioral therapy (CBT) is an effective treatment for panic disorder with agoraphobia (PD/AG). It is unknown, how variants of CBT differentially modulate brain networks involved in PD/AG. This study was aimed to evaluate the effects of therapist-guided (T+) versus self-guided (T-) exposure on the neural correlates of fear conditioning in PD/AG. <b><i>Method:</i></b> In a randomized, controlled multicenter clinical trial in medication-free patients with PD/AG who were treated with 12 sessions of manualized CBT, functional magnetic resonance imaging (fMRI) was used during fear conditioning before (t1) and after CBT (t2). Quality-controlled fMRI data from 42 patients and 42 healthy subjects (HS) were obtained. Patients were randomized to two variants of CBT (T+, n = 22, and T-, n = 20). <b><i>Results:</i></b> The interaction of diagnosis (PD/AG, HS), treatment group (T+, T-), time point (t1, t2) and stimulus type (conditioned stimulus: yes, no) revealed activation in the left hippocampus and the occipitotemporal cortex. The T+ group demonstrated increased activation of the hippocampus at t2 (t2 &gt; t1), which was positively correlated with treatment outcome, and a decreased connectivity between the left inferior frontal gyrus and the left hippocampus across time (t1 &gt; t2). <b><i>Conclusion:</i></b> After T+ exposure, contingency-encoding processes related to the posterior hippocampus are augmented and more decoupled from processes of the left inferior frontal gyrus, previously shown to be dysfunctionally activated in PD/AG. Linking single procedural variants to neural substrates offers the potential to inform about the optimization of targeted psychotherapeutic interventions.
DOI: 10.6084/m9.figshare.5126266.v1
title: Supplementary Material for: Expansion of Urease- and Uricase-Containing, Indole- and p-Cresol-Forming and Contraction of Short-Chain Fatty Acid-Producing Intestinal Microbiota in ESRD

description: <b><i>Background:</i></b> Intestinal microbiome constitutes a symbiotic ecosystem that is essential for health, and changes in its composition/function cause various illnesses. Biochemical milieu shapes the structure and function of the microbiome. Recently, we found marked differences in the abundance of numerous bacterial taxa between ESRD and healthy individuals. Influx of urea and uric acid and dietary restriction of fruits and vegetables to prevent hyperkalemia alter ESRD patients' intestinal milieu. We hypothesized that relative abundances of bacteria possessing urease, uricase, and p-cresol- and indole-producing enzymes is increased, while abundance of bacteria containing enzymes converting dietary fiber to short-chain fatty acids (SCFA) is reduced in ESRD. <b><i>Methods:</i></b> Reference sets of bacteria containing genes of interest were compiled to family, and sets of intestinal bacterial families showing differential abundances between 12 healthy and 24 ESRD individuals enrolled in our original study were compiled. Overlap between sets was assessed using hypergeometric distribution tests. <b><i>Results:</i></b> Among 19 microbial families that were dominant in ESRD patients, 12 possessed urease, 5 possessed uricase, and 4 possessed indole and p-cresol-forming enzymes. Among 4 microbial families that were diminished in ESRD patients, 2 possessed butyrate-forming enzymes. Probabilities of these overlapping distributions were &lt;0.05.<b><i> Conclusions:</i></b> ESRD patients exhibited significant expansion of bacterial families possessing urease, uricase, and indole and p-cresol forming enzymes, and contraction of families possessing butyrate-forming enzymes. Given the deleterious effects of indoxyl sulfate, p-cresol sulfate, and urea-derived ammonia, and beneficial actions of SCFA, these changes in intestinal microbial metabolism contribute to uremic toxicity and inflammation.
DOI: 10.6084/m9.figshare.5126245
title: Supplementary Material for: Review of Psychodynamic Psychotherapy Neuroimaging Studies

description: The clinical efficacy of psychodynamic psychotherapy (PDT) has undergone extensive study and review. Recently, researchers have studied the effects of this treatment on brain metabolic or synaptic activity, but the collective findings have never been reviewed. The objective of this review was to describe the findings of all neuroimaging studies of any form of PDT treatment. An extensive literature search through databases along with surveying of research groups were undertaken to acquire all available published studies. Eleven series were included in the final sample, consisting of 2 randomized controlled trials, 5 controlled trials and 4 case series, altogether involving 210 people: 94 healthy controls and 116 people with mood disorders, panic disorder, somatoform disorders and borderline personality disorder. A variety of neuroimaging techniques were used to examine regional metabolic activity and synaptic neurotransmission before and after treatment. The common finding was normalization of synaptic or metabolic activity in limbic, midbrain and prefrontal regions, occurring in association with improved clinical outcomes. PDT has demonstrable effects on brain function in diverse clinical populations as evidenced by a modest group of mixed neuroimaging studies.
DOI: 10.6084/m9.figshare.5126248
title: Supplementary Material for: Starchy Food Consumption in French Adults: A Cross-Sectional Analysis of the Profile of Consumers and Contribution to Nutritional Intake in a Web-Based Prospective Cohort

description: <b><i>Background:</i></b> French Nutritional Guidelines recommend eating starchy foods at each meal, according to appetite, and advise to vary sources. However, the proportion of energy from carbohydrates is currently too low in many Western European countries. <b><i>Methods:</i></b> Consumption of the different types of starchy foods was assessed among 80,209 adult participants in the French NutriNet-Santé cohort (78% women, mean age 42.9 ± 14.5). Description of starchy food consumption according to sociodemographics was provided as well as the contribution of starchy food to nutritional intake. Determinants of adherence to starchy food nutritional guidelines were estimated using multivariable polytomous logistic regression. <b><i>Results:</i></b> Starchy foods contributed approximately 22% of the energy intake, 75% of the complex carbohydrate intake and 36.1% of the fibre intake. About 43% of the subjects had intakes in line with the French Nutritional Guidelines concerning starchy foods. Men met the recommendation more frequently (55 vs. 33% for women), but were also more likely to exceed the recommendation (9.5 vs. 1.3%), even after adjustment for energy intake. According to our multivariable model, starchy food consumption increased also with age. <b><i>Conclusions:</i></b> A higher consumption of starchy foods should be promoted in the French population in order to increase the part of the energy intake coming from complex carbohydrates.