cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5128105
title: Supplementary Material for: Increased Ocular Pulse Amplitude Associated with Unilateral Dysgenesis of the Orbital Roof

description: <b><i>Introduction:</i></b> Two patients (one with neurofibromatosis type 1) presented with unilateral ocular pulsation. <b><i>Methods:</i></b> A CT scan of the orbits revealed extensive dysgenesis of the orbital roof with herniation of the frontal lobe into the orbit in both cases. PASCAL dynamic contour tonometry was performed. <b><i>Results:</i></b> The ipsilateral ocular pulse amplitude (OPA) was greater than the contralateral side, and the ocular pulse waveform morphology more closely approximated the known intracranial waveform in these patients. <b><i>Conclusions:</i></b> We hypothesize that the greater OPA was due to stronger transmission of the intracranial pressure waveform amplitude and morphology in the absence of the orbital roof.
DOI: 10.6084/m9.figshare.5128108
title: Supplementary Material for: Sex-Biased Expression of Young Genes in <b><i>Silurana (Xenopus) tropicalis</i></b>

description: Sex-biased gene expression can evolve from sex-specific selection and is often associated with sex-linked genes. Gene duplication is a particularly effective mechanism for the generation of sex-biased genes, in which a new copy can help resolve intralocus sexual conflicts. This study assesses sex-biased gene expression in an amphibian with homomorphic ZW sex chromosomes, the Western clawed frog <i>Silurana (Xenopus)</i><i>tropicalis</i>. Previous work has shown that the sex chromosomes in this species are mainly undifferentiated and pseudoautosomal. Consistent with ongoing recombination between the sex chromosomes, this study detected little evidence for the general sexualization of sex-linked regions. A subset of genes closely linked to the sex determining locus displays a tendency for male-biased expression and elevated rates of evolution relative to genes in other genomic locations. This may be a symptom of an early stage of sex chromosome differentiation driven by, for example, chromosomal degeneration or natural selection on genes in this portion of the Z chromosome. Alternatively, it could reflect variation between the sexes in allelic copy number coupled with a lack of dosage compensation. Irrespective of the genomic location, lineage-specific genes and recently duplicated genes had significantly high levels of sex-biased expression, offering insights into the early transcriptional differentiation of young genes.
DOI: 10.6084/m9.figshare.5128102
title: Supplementary Material for: Renal Function and Long-Term Decline in Cognitive Function: The Baltimore Longitudinal Study of Aging

description: <b><i>Background:</i></b> Renal disease has been associated with greater risk of dementia and greater cognitive impairment. However, the relationship of lower renal function with long-term decline in specific domains of cognitive function remains unclear among community-dwelling, non-demented individuals. <b><i>Methods:</i></b> Stroke- and dementia-free participants (n = 2,116) were enrolled in the Baltimore Longitudinal Study of Aging, a community-based, prospective, longitudinal study. Renal function was estimated by the inverse of serum creatinine adjusted for age, sex and race and (in sensitivity analyses) estimated glomerular filtration rate (eGFR) using the MDRD formula. Outcome measures were changes in scores on 6 cognitive tests encompassing a range of cognitive functions, measured at 2-year intervals. Mixed-effects regression models examined the longitudinal relations of renal function with cognitive functions after adjusting for demographics, comorbidity and other potential confounders. <b><i>Results:</i></b> Mean age at initial testing was 53.9 years (SD 17.1), and 94 participants (4.4%) had an eGFR &lt;60 ml/min/1.73 m<sup>2</sup> and 18.5% had at least one comorbidity. With increasing age, longitudinal increases in creatinine concentrations were associated with more rapid decline in performance on several cognitive measures, including the learning slope of the California Verbal Learning Test, a test of verbal learning (p &lt; 0.01), and the Benton Visual Retention Test, a test of visual memory (p &lt; 0.01). Associations were similar for changes in eGFR<sub>MDRD</sub>, which was also associated with the rate of decline in verbal memory. <b><i>Conclusion:</i></b> In a community-based adult population, declines in renal function independently associated with greater long-term declines in visual memory and verbal memory and learning.
DOI: 10.6084/m9.figshare.5128108.v1
title: Supplementary Material for: Sex-Biased Expression of Young Genes in <b><i>Silurana (Xenopus) tropicalis</i></b>

description: Sex-biased gene expression can evolve from sex-specific selection and is often associated with sex-linked genes. Gene duplication is a particularly effective mechanism for the generation of sex-biased genes, in which a new copy can help resolve intralocus sexual conflicts. This study assesses sex-biased gene expression in an amphibian with homomorphic ZW sex chromosomes, the Western clawed frog <i>Silurana (Xenopus)</i><i>tropicalis</i>. Previous work has shown that the sex chromosomes in this species are mainly undifferentiated and pseudoautosomal. Consistent with ongoing recombination between the sex chromosomes, this study detected little evidence for the general sexualization of sex-linked regions. A subset of genes closely linked to the sex determining locus displays a tendency for male-biased expression and elevated rates of evolution relative to genes in other genomic locations. This may be a symptom of an early stage of sex chromosome differentiation driven by, for example, chromosomal degeneration or natural selection on genes in this portion of the Z chromosome. Alternatively, it could reflect variation between the sexes in allelic copy number coupled with a lack of dosage compensation. Irrespective of the genomic location, lineage-specific genes and recently duplicated genes had significantly high levels of sex-biased expression, offering insights into the early transcriptional differentiation of young genes.
DOI: 10.6084/m9.figshare.5128096
title: Supplementary Material for: Integrating a Web-Based Whole-Slide Imaging System and Online Questionnaires in a National Cytopathology Peer Comparison Educational Program in Taiwan

description: <b><i>Objective:</i></b> In a peer comparison educational program, transferring glass slides between laboratories and collecting responses are time- and cost-consuming. Integrating a web-based whole-slide imaging (WSI) system and online questionnaires may serve as a promising solution. <b><i>Study Design:</i></b> Five gynecologic Papanicolaou-stained smears and 5 nongynecologic slides were selected. The 10 whole-slide images were acquired by a Leica SCN-400 system and released via an Aperio eSlide Manager. Online questionnaires generated by Google Forms with access to the 10 whole-slide images were released to all the practitioners in Taiwan by e-mail. After closing the program, an online posttest feedback survey was conducted. <b><i>Results:</i></b> A total of 302 participants joined the gynecologic test, and 291 joined the nongynecologic test. The correct interpretation rates were 81.8-93.7% in the former and 28.5-93.1% in the latter. In the posttest feedback survey, there were 63.2% of the participants reporting first-time WSI experience, and 97.9% of them said they would like to participate in a similar program again. <b><i>Conclusion:</i></b> Integrating a web-based WSI system and online questionnaires is an easy method to access nationwide practitioners. Participants can make interpretations using WSI even without prior experience. The model is valuable for those who want to initiate a large-scale cytopathology peer comparison educational program.
DOI: 10.6084/m9.figshare.5128099
title: Supplementary Material for: TIR-Domain-Containing Adaptor-Inducing Interferon-β (TRIF) Mediates Antibacterial Defense during Gram-Negative Pneumonia by Inducing Interferon-γ

description: <i>Klebsiella pneumoniae</i> is an important cause of Gram-negative pneumonia and sepsis. Mice deficient for TIR-domain-containing adaptor-inducing interferon-β (TRIF) demonstrate enhanced bacterial growth and dissemination during <i>Klebsiella </i>pneumonia. We show here that the impaired antibacterial defense of TRIF mutant mice is associated with absent interferon (IFN)-γ production in the lungs. IFN-γ production by splenocytes in response to <i>K. pneumoniae </i>in vitro was critically dependent on Toll-like receptor 4 (TLR4), the common TLR adaptor myeloid differentiation primary response gene (MyD88) and TRIF. Reconstitution of TRIF mutant mice with recombinant IFN-γ via the airways reduced bacterial loads in lungs and distant body sites to levels measured in wild-type mice, and partially restored pulmonary cytokine levels. The IFN-γ-induced, improved, enhanced antibacterial response in TRIF mutant mice occurred at the expense of increased hepatocellular injury. These data indicate that TRIF mediates antibacterial defense during Gram-negative pneumonia, at least in part, by inducing IFN-γ at the primary site of infection.
DOI: 10.6084/m9.figshare.5128105.v1
title: Supplementary Material for: Increased Ocular Pulse Amplitude Associated with Unilateral Dysgenesis of the Orbital Roof

description: <b><i>Introduction:</i></b> Two patients (one with neurofibromatosis type 1) presented with unilateral ocular pulsation. <b><i>Methods:</i></b> A CT scan of the orbits revealed extensive dysgenesis of the orbital roof with herniation of the frontal lobe into the orbit in both cases. PASCAL dynamic contour tonometry was performed. <b><i>Results:</i></b> The ipsilateral ocular pulse amplitude (OPA) was greater than the contralateral side, and the ocular pulse waveform morphology more closely approximated the known intracranial waveform in these patients. <b><i>Conclusions:</i></b> We hypothesize that the greater OPA was due to stronger transmission of the intracranial pressure waveform amplitude and morphology in the absence of the orbital roof.
DOI: 10.6084/m9.figshare.5128090
title: Supplementary Material for: Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing

description: Poultry contamination can be largely attributed to the presence of chicken feces during the production process. Fecal contamination is often found in raw chicken products sold for human consumption. Quantitative analysis of the fecal microbial community of chickens using next-generation sequencing techniques is the focus of this study. Fecal samples were collected from 30 broiler chickens at two time points: days 1 and 35 of development. 454 pyrosequencing was conducted on 16S rRNA extracted from each sample, and microbial population dynamics were investigated using various automated bioinformatics pipelines. Diversity of the microbial community at the genus level increased during the 5-week growth period. Despite this growth, only a few dominant bacteria groups (over 80%) were identified in each fecal sample, with most groups being unique and only a few were shared between samples. Population analysis at the genus level showed that microbial diversity increased with chicken growth and development. Classification and phylogenetic analysis of highly represented microbes (over 1%) clearly showed high levels of sequence similarity between groups such as Firmicutes and Proteobacteria. These results suggest that the chicken fecal excreted microbiome is a dynamic system with a differentiated population structure that harbors a highly restricted number of higher taxa.
DOI: 10.6084/m9.figshare.5128093
title: Supplementary Material for: Lifestyle Factors and Indices of Kidney Function in the Framingham Heart Study

description: <b><i>Background and Objectives:</i></b> Lifestyle characteristics are modifiable factors that could be targeted as part of chronic kidney disease (CKD) prevention. We sought to determine the association of lifestyle characteristics with incident estimated glomerular filtration rate (eGFR) &lt;60 ml/min/1.73 m<sup>2</sup> and rapid eGFR decline in older adults in the United States. <b><i>Methods:</i></b> Prospective cohort study of Framingham Offspring participants with baseline eGFR &lt;60 ml/min/1.73 m<sup>2</sup> (n = 1,802) who attended the seventh (1998-2001; baseline) and eighth (2005-2008; follow-up) examinations (mean age = 59 years, 54.8% women). Predictors included measures of diet quality, physical activity, alcohol intake, and current smoking status assessed during baseline. Outcomes were based on creatinine-based eGFR at baseline and follow-up and included incident eGFR &lt;60 ml/min/1.73 m<sup>2</sup> (at follow-up) and rapid eGFR decline (annual eGFR decrease ≥3 ml/min/1.73 m<sup>2</sup>). <b><i>Results:</i></b> Over an average follow-up of 6.6 years, 9.5% (n = 171) of participants developed incident eGFR &lt;60. A trend was observed across quartiles of diet quality, with higher levels of diet quality associated with a decreased odds ratio (OR) of incident eGFR &lt;60 (p trend = 0.045). Higher diet quality was associated with decreased odds of rapid eGFR decline (p trend = 0.03) and was attenuated with additional adjustment (p trend = 0.07). In sensitivity analysis for rapid eGFR decline using a secondary definition (annual eGFR decrease ≥3 and incident eGFR &lt;60), diet associations remained significant with additional adjustment (p trend = 0.04). No associations were observed with physical activity, smoking status, or alcohol intake with incident eGFR &lt;60 or rapid eGFR decline (all p &gt; 0.19). <b><i>Conclusions:</i></b> Higher diet quality may be associated with a decreased risk of incident eGFR &lt;60 ml/min/1.73 m<sup>2</sup>, and rapid eGFR decline. Whether adherence to a healthy diet can prevent reduction in kidney function warrants further study.
DOI: 10.6084/m9.figshare.5128084
title: Supplementary Material for: A Multicenter Randomized Controlled Trial of Rituximab versus Cyclosporine in the Treatment of Idiopathic Membranous Nephropathy (MENTOR)

description: <b><i>Background:</i></b> Idiopathic membranous nephropathy remains the leading cause of nephrotic syndrome in Caucasian adults. Immunosuppressive therapy with cyclosporine (CSA) is often successful in reducing proteinuria, but its use is associated with a high relapse rate. Rituximab, a monoclonal antibody that specifically targets CD20 on the surface of B-cells, is effective in achieving a complete remission of proteinuria in patients with idiopathic membranous nephropathy. However, whether rituximab is as effective as CSA in inducing and maintaining complete or partial remission of proteinuria in these patients is unknown. The membranous nephropathy trial of rituximab (MENTOR) hypothesizes that B-cell targeting with rituximab is non-inferior to CSA in inducing long-term remission of proteinuria. <b><i>Methods and Design:</i></b> Patients with idiopathic membranous nephropathy, proteinuria ≥5 g/24 h, and a minimum of 3 months of Angiotensin-II blockade will be randomized into a 12-month treatment period with IV rituximab, 1,000 mg (2 infusions, 14 days apart; repeated at 6 months if a substantial reduction in proteinuria (equal to or &gt;25%) is seen at 6 months) or oral CSA 3.5-5 mg/kg/day for 6 months (continued for another 6 months if a substantial reduction in proteinuria (equal to or &gt;25%) is seen at 6 months). The efficacy of treatment will be assessed by the remission status (based on changes in proteinuria) at 24 months from randomization. Patient safety will be assessed via collection of adverse event data and evaluation of pre- and posttreatment laboratory data. At the 6-month post-randomization visit, patients who have been randomized to either CSA or rituximab but who do not have a reduction in proteinuria ≥25% (confirmed on repeat measurements within 2 weeks) will be considered treatment failures and exit the study. <b><i>Discussion:</i></b> This study will test for the first time whether treatment with rituximab is non-inferior to CSA in inducing long-term remission (complete or partial) of proteinuria in patients with idiopathic membranous nephropathy.
DOI: 10.6084/m9.figshare.5128087
title: Supplementary Material for: Early-Life Stress Perturbs Key Cellular Programs in the Developing Mouse Hippocampus

description: Conflicting reports are available with regard to the effects of childhood abuse and neglect on hippocampal function in children. While earlier imaging studies and some animal work have suggested that the effects of early-life stress (ELS) manifest only in adulthood, more recent studies have documented impaired hippocampal function in maltreated children and adolescents. Additional work using animal modes is needed to clarify the effects of ELS on hippocampal development. In this regard, genomic, proteomic, and molecular tools uniquely available in the mouse make it a particularly attractive model system to study this issue. However, very little work has been done so far to characterize the effects of ELS on hippocampal development in the mouse. To address this issue, we examined the effects of brief daily separation (BDS), a mouse model of ELS that impairs hippocampal-dependent memory in adulthood, on hippocampal development in 28-day-old juvenile mice. This age was chosen because it corresponds to the developmental period in which human imaging studies have revealed abnormal hippocampal development in maltreated children. Exposure to BDS caused a significant decrease in the total protein content of synaptosomes harvested from the hippocampus of 28-day-old male and female mice, suggesting that BDS impairs normal synaptic development in the juvenile hippocampus. Using a novel liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM) assay, we found decreased expression of many synaptic proteins, as well as proteins involved in axonal growth, myelination, and mitochondrial activity. Golgi staining in 28-day-old BDS mice showed an increase in the number of immature and abnormally shaped spines and a decrease in the number of mature spines in CA1 neurons, consistent with defects in synaptic maturation and synaptic pruning at this age. In 14-day-old pups, BDS deceased the expression of proteins involved in axonal growth and myelination, but did not affect the total protein content of synaptosomes harvested from the hippocampus, or protein levels of other synaptic markers. These results add two important findings to previous work in the field. First, our findings demonstrate that in 28-day-old juvenile mice, BDS impairs synaptic maturation and reduces the expression of proteins that are necessary for axonal growth, myelination, and mitochondrial function. Second, the results suggest a sequential model in which BDS impairs normal axonal growth and myelination before it disrupts synaptic maturation in the juvenile hippocampus.
DOI: 10.6084/m9.figshare.5128081
title: Supplementary Material for: Pedigree-Free Descent-Based Gene Mapping from Population Samples

description: Segments of the genome inherited from a common ancestor by related individuals are said to be identical by descent (IBD). Modern genetic marker data provide information to infer such segments among multiple related members of a population, even when pedigree relationships are unknown. Previous methods have been proposed for the detection of pairwise IBD, but the computation of probabilities of trait data under many trait models requires an IBD estimate jointly consistent among individuals and slowly varying across genome locations; we refer to such an estimate as an ‘IBD graph'. In this paper, we develop a novel method that builds IBD graphs sequentially among related individuals from a population sample using either phased or unphased genetic marker data. We show how IBD graphs realized conditionally on marker data provide a form of linkage mapping score, analogous to a LOD score, and propose a permutation approach to normalize this mapping score. Using a simulated quantitative trait dependent on the (unobserved) genotype at a major locus, we apply the approach to two samples containing both closely and remotely related individuals, among whom there are complex patterns of IBD. We compare the results of our approach with an alternate approach based on the estimation of local kinship. We show that pairwise estimates derived from a joint IBD graph give significant improvements in LOD score estimation over estimates derived from an intrinsically pairwise approach.
DOI: 10.6084/m9.figshare.5128093.v1
title: Supplementary Material for: Lifestyle Factors and Indices of Kidney Function in the Framingham Heart Study

description: <b><i>Background and Objectives:</i></b> Lifestyle characteristics are modifiable factors that could be targeted as part of chronic kidney disease (CKD) prevention. We sought to determine the association of lifestyle characteristics with incident estimated glomerular filtration rate (eGFR) &lt;60 ml/min/1.73 m<sup>2</sup> and rapid eGFR decline in older adults in the United States. <b><i>Methods:</i></b> Prospective cohort study of Framingham Offspring participants with baseline eGFR &lt;60 ml/min/1.73 m<sup>2</sup> (n = 1,802) who attended the seventh (1998-2001; baseline) and eighth (2005-2008; follow-up) examinations (mean age = 59 years, 54.8% women). Predictors included measures of diet quality, physical activity, alcohol intake, and current smoking status assessed during baseline. Outcomes were based on creatinine-based eGFR at baseline and follow-up and included incident eGFR &lt;60 ml/min/1.73 m<sup>2</sup> (at follow-up) and rapid eGFR decline (annual eGFR decrease ≥3 ml/min/1.73 m<sup>2</sup>). <b><i>Results:</i></b> Over an average follow-up of 6.6 years, 9.5% (n = 171) of participants developed incident eGFR &lt;60. A trend was observed across quartiles of diet quality, with higher levels of diet quality associated with a decreased odds ratio (OR) of incident eGFR &lt;60 (p trend = 0.045). Higher diet quality was associated with decreased odds of rapid eGFR decline (p trend = 0.03) and was attenuated with additional adjustment (p trend = 0.07). In sensitivity analysis for rapid eGFR decline using a secondary definition (annual eGFR decrease ≥3 and incident eGFR &lt;60), diet associations remained significant with additional adjustment (p trend = 0.04). No associations were observed with physical activity, smoking status, or alcohol intake with incident eGFR &lt;60 or rapid eGFR decline (all p &gt; 0.19). <b><i>Conclusions:</i></b> Higher diet quality may be associated with a decreased risk of incident eGFR &lt;60 ml/min/1.73 m<sup>2</sup>, and rapid eGFR decline. Whether adherence to a healthy diet can prevent reduction in kidney function warrants further study.