gebhart/patrepeval huggingface dataset:
Low Thermal Conductivity in Heteroanionic Materials with Layers of Homoleptic Polyhedra (2022)

Although BiAgOSe, an analogue of a well-studied thermoelectric material BiCuOSe, is thermodynamically stable, its synthesis is complicated by the low driving force of formation from the stable binary and ternary intermediates. Here we have developed a "subtraction strategy" to suppress byproducts and produce pure phase BiAgOSe using hydrothermal methods. Electronic structure calculations and optical characterization show that BiAgOSe is an indirect bandgap semiconductor with a bandgap of 0.95 eV. The prepared sample exhibits lower lattice thermal conductivities (0.61 W·m<sup>-1</sup>·K<sup>-1</sup> at room temperature and 0.35 W·m<sup>-1</sup>·K<sup>-1</sup> at 650 K) than BiCuOSe. Lattice dynamical simulations and variable temperature diffraction measurements demonstrate that the low lattice thermal conductivity arises from both the low sound velocity and high phonon-phonon scattering rates in BiAgOSe. These in turn result primarily from the soft Ag-Se bonds in the edge-sharing AgSe<sub>4</sub> tetrahedra and large sublattice mismatch between the quasi-two-dimensional [Bi<sub>2</sub>O<sub>2</sub>]<sup>2+</sup> and [Ag<sub>2</sub>Se<sub>2</sub>]<sup>2-</sup> layers. These results highlight the advantages of manipulating the chemistry of homoleptic polyhedra in heteroanionic compounds for electronic structure and phonon transport control.
Diet Networks: Thin Parameters for Fat Genomics (2016)

Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer: each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
Perlecan Domain IV Peptide Stimulates Salivary Gland Cell Assembly In Vitro (2009)

Treatment of xerostomia would benefit from development of a functional implantable artificial salivary gland. Salivary gland tissue from surgical patients was assessed by histology and immunohistochemistry to establish the phenotype of normal salivary gland cells including the native basement membranes. Ductal and acinar cells were identified in tissue and cultured cells from dispersed tissue. High levels of laminin and perlecan/HSPG2 (heparan sulfate proteoglycan 2) were noted in basement membranes, and perlecan also was secreted and organized by cultured acinar populations, which formed lobular structures that mimicked intact glands when cultured on Matrigel or a bioactive peptide derived from domain IV of perlecan. On either matrix, large acini-like lobular structures grew and formed connections between the lobes. alpha-Amylase secretion was confirmed by staining and activity assay. Biomarkers, including tight junction protein E-cadherin and water channel protein aquaporin 5 found in tissue, were expressed in cultured acinar cells. Cells cultured on Matrigel or domain IV of perlecan peptide organized stress fibers and activated focal adhesion kinase. We report a novel technique to isolate acinar cells from human salivary gland and identify a human peptide sequence in perlecan that triggers differentiation of salivary gland cells into self-assembling acini-like structures that express essential biomarkers and which secrete alpha-amylase.
Shielding, a new pathogen defence mechanism against PMNs (2009)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Time dependence of biomarkers: Non-proportional effects of immunohistochemical panels predicting relapse risk in early breast cancer (2015)

Background:We investigated the impact of follow-up duration to determine whether two immunohistochemical prognostic panels, IHC4 and Mammostrat, provide information on the risk of early or late distant recurrence using the Edinburgh Breast Conservation Series and the Tamoxifen vs Exemestane Adjuvant Multinational (TEAM) trial.Methods:The multivariable fractional polynomial time (MFPT) algorithm was used to determine which variables had possible non-proportional effects. The performance of the scores was assessed at various lengths of follow-up and Cox regression modelling was performed over the intervals of 0-5 years and >5 years.Results:We observed a strong time dependence of both the IHC4 and Mammostrat scores, with their effects decreasing over time. In the first 5 years of follow-up only, the addition of both scores to clinical factors provided statistically significant information (P<0.05), with increases in R 2 between 5 and 6% and increases in D-statistic between 0.16 and 0.21.Conclusions:Our analyses confirm that the IHC4 and Mammostrat scores are strong prognostic factors for time to distant recurrence but this is restricted to the first 5 years after diagnosis. This provides evidence for their combined use to predict early recurrence events in order to select those patients who may/will benefit from adjuvant chemotherapy.
Acute Renal Failure in Critically Ill Patients (2007)

Results Of 29269 critically ill patients admitted during the study period, 1738 (5.7%; 95% confidence interval [CI], 5.5%-6.0%) had ARF during their ICU stay, including 1260 who were treated with RRT. The most common contributing factor to ARF was septic shock (47.5%; 95% CI, 45.2%-49.5%). Approximately 30% of patients had preadmission renal dysfunction. Overall hospital mortality was 60.3% (95% CI, 58.0%62.6%). Dialysis dependence at hospital discharge was 13.8% (95% CI, 11.2%16.3%) for survivors. Independent risk factors for hospital mortality included use of vasopressors (odds ratio [OR], 1.95; 95% CI, 1.50-2.55; P.001), mechanical ventilation (OR, 2.11; 95% CI, 1.58-2.82; P.001), septic shock (OR, 1.36; 95% CI, 1.031.79; P=.03), cardiogenic shock (OR, 1.41; 95% CI, 1.05-1.90; P=.02), and hepatorenal syndrome (OR, 1.87; 95% CI, 1.07-3.28; P=.03). Conclusion In this multinational study, the period prevalence of ARF requiring RRT in theICUwasbetween5%and6%andwasassociatedwithahighhospitalmortalityrate.
Direct and Indirect Effects of Insulin to Inhibit Hepatic Glucose Output in Obese Subjects (1987)

The effects of small increases in plasma insulin on hepatic glucose production are incompletely understood. To partially elucidate this issue we have studied seven obese subjects with the euglycemic clamp technique with a low-dose insulin infusion rate of 15 mU X m-2 X min-1 over 3 h. Basal insulin levels were 24 +/- 7 microU/ml and increased to steady-state levels of 35 +/- 3 microU/ml during insulin infusion. Endogenous insulin secretion, quantitated by C-peptide measurements, decreased by 58% of the basal value after peripheral insulin infusion. Based on C-peptide measurements and the contribution of the peripheral insulin infusion to the circulating insulin concentrations, calculated portal insulin levels either decreased or remained unchanged during the clamp studies. Basal glucagon levels were 165 +/- 18 and did not change during the insulin infusion. The basal glucose disposal rate was 86 +/- 2 mg X m-2 X min-1 and did not increase significantly during the clamp studies. In contrast, hepatic glucose output (HGO) was suppressed by 82 +/- 5% of the basal value. In summary, in a group of insulin-resistant obese subjects, glucose-clamp studies were performed at peripheral insulin levels of 35 +/- 3 microU/ml; glucose disposal did not increase, whereas HGO was suppressed by 82%. At the same time, glucagon levels remained constant and estimated portal insulin levels either decreased or remained unchanged. These findings suggest that insulin can suppress HGO through indirect extrahepatic actions.
Reduced speed of microvascular blood flow in hemodialysis patients versus healthy controls: a coherent hemodynamics spectroscopy study (2014)

We present a pilot clinical application of coherent hemodynamics spectroscopy (CHS), a technique to investigate cerebral hemodynamics at the microcirculatory level. CHS relies on frequency-resolved measurements of induced cerebral hemodynamic oscillations that are measured with near-infrared spectroscopy (NIRS) and analyzed with a hemodynamic model. We have used cyclic inflation (200 mmHg) and deflation of a pneumatic cuff placed around the subject's thigh at seven frequencies in the range of 0.03 to 0.17 Hz to generate CHS spectra and to obtain a set of physiological parameters that include the blood transit times in the cerebral microcirculation, the cutoff frequency for cerebral autoregulation, and blood volume ratios across the three different compartments. We have investigated five hemodialysis patients, during the hemodialysis procedure, and six healthy subjects. We have found that the blood transit time in the cerebral microcirculation is significantly longer in hemodialysis patients with respect to healthy subjects. No significant differences were observed between the two groups in terms of autoregulation efficiency and blood volume ratios. The demonstration of the applicability of CHS in a clinical setting and its sensitivity to the highly important cerebral microcirculation may open up new opportunities for NIRS applications in research and in medical diagnostics and monitoring.
Geologically Inspired Monoliths for Sustainable Release of Essential Minerals into Drinking Water (2019)

Decreasing mineral content in drinking water is a serious concern especially due to the proliferation of desalination technologies. We present an approach to remineralize water with essential minerals such that their concentrations are at the recommended daily dose. We accomplished this using composite materials whose composition and surface area were tuned to achieve constant release of minerals into water over a prolonged period of time. We developed a nature-mimicking tectosilicate porous composite matrix and used it as a structural framework to incorporate leachable minerals to the extent of 40% of the whole mass, which were released into the water during its functional working life. Release of not only the common macro minerals but also the vital trace minerals was possible in this work. Compacted composites of this kind have been used to create mineralization cartridges. The greenness of these composites evaluated from several sustainability metrics shows that the manufacturing process has minimum or negligible carbon emission, E-factor, and energy consumption. This methodology may be extended to encompass all the essential minerals expected to be present in water.
Population differentiation between Australian and ChineseHelicoverpa armigeraoccurs in distinct blocks on the Z-chromosome (2018)

Over the last 40 years, many types of population genetic markers have been used to assess the population structure of the pest moth species Helicoverpa armigera. While this species is highly vagile, there is evidence of inter-continental population structure. Here, we examine Z-chromosome molecular markers within and between Chinese and Australian populations. Using 1352 polymorphic sites from 40 Z-linked loci, we compared two Chinese populations of moths separated by 700 km and found virtually no population structure (n = 41 and n = 54, with <1% of variation discriminating between populations). The levels of nucleotide diversity within these populations were consistent with previous estimates from introns in Z-linked genes of Australian samples (π = 0.028 vs. 0.03). Furthermore, all loci surveyed in these Chinese populations showed a skew toward rare variants, with ten loci having a significant Tajima's D statistic, suggesting that this species could have undergone a population expansion. Eight of the 40 loci had been examined in a previous study of Australian moths, of which six revealed very little inter-continental population structure. However, the two markers associated with the Cyp303a1 locus that has previously been proposed to be a target of a selective sweep, exhibited allele structuring between countries. Using a separate dataset of 19 Australian and four Chinese moths, we scanned the molecular variation distributed across the entire Z-chromosome and found distinct blocks of differentiation that include the region containing Cyp303a1. We recommend some of these loci join those associated with insecticide resistance to form a set of genes best suited to analyzing population structure in this global pest.
Effect of Reconstruction Parameters in High-Definition PET/CT on Assessment of Lymph Node Metastases in Head and Neck Squamous Cell Carcinoma (2013)

For lymph node assessment on a high-resolution PET/CT scanner, we consider the OSEM algorithm with 3 iterations and 24 subsets, combined with 3-dimensional 3-mm gaussian postfiltering, to be optimal. The continuous application of presently established PET protocols in patients with HNSCC will prove whether current acquisition and reconstruction methods are valuable and should be maintained.
Interactive Vulnerability Analysis Enhancement Results (2012)

Interactive Application Security Testing (IAST) is an innovative new approach to application security vulnerability detection.This investigation focused on making performance improvements to this technology to allow deployments of the technology in production systems, to enable automatic generation of protection rules for the vulnerabilities discovered, and expanding the range of applications supported from JavaEE web based applications to other non-web based Java programs.Technology developed in this effort should be generally applicable to other IAST tools.
Effects of the knockdown of hypoxia inducible factor-1α expression by adenovirus-mediated shRNA on angiogenesis and tumor growth in hepatocellular carcinoma cell lines (2010)

These data suggest that adenovirus-mediated inhibition of HIF-1α inhibits the invasion, tube formation, and cell growth in HUVECs and HCC cells.
Leptin‐Target Neurones of the Rat Hypothalamus Express Somatostatin Receptors (2003)

Hypothalamic leptinoceptive neurones can be visualized by histochemical demonstration of leptin-induced nuclear translocation of the signalling molecule STAT3. We investigated the relationship of the leptinoceptive neurones to the somatostatin signalling system. With double-labelling immunohistochemistry, we studied the colocalization of leptin-activated transcription factor, STAT3, with somatostatin receptor subtypes, sst1, sst2A, sst2B, sst3 and sst4, or the neuropeptide itself, in the rat hypothalamus. Immunoreactivity for all the entities was widely distributed throughout the entire hypothalamus. Despite the wide distribution, only few cases of colocalization of somatostatin with leptin-activated STAT3 were detected in the paraventricular, arcuate and dorsomedial nuclei. A moderate to high degree of colocalization of nuclear STAT3 and all investigated subtypes of somatostatin receptors was found in the lateral and dorsal hypothalamic areas and in the dorsomedial hypothalamic nucleus. Immunoreactivity for sst1, sst2B and sst4 was present in STAT3-containing nuclei of the paraventricular, periventricular, arcuate and ventromedial hypothalamic neurones, as well as in the retrochiasmatic and posterior hypothalamic areas. Despite the wide distribution of sst2A in the rat hypothalamus, few events of colocalization with leptin-activated STAT3 were observed in the dorsomedial nucleus and in the lateral and dorsal hypothalamic areas only. Many leptin-responsive neurones of the dorsal, lateral, periarcuate, perifornical and posterior hypothalamic areas, as well as in the ventromedial and dorsomedial hypothalamic nuclei, displayed sst3 immunoreactivity at their neuronal cilia. These results provide strong anatomical evidence for the direct interaction of leptin and the somatostatin systems in neuroendocrine control loops such as the energy homeostasis, growth or stress response.
Efficacy of Three Vaccines in Protecting Western Scrub-Jays ( Aphelocoma californica ) from Experimental Infection with West Nile Virus: Implications for Vaccination of Island Scrub-Jays ( Aphelocoma insularis ) (2011)

The devastating effect of West Nile virus (WNV) on the avifauna of North America has led zoo managers and conservationists to attempt to protect vulnerable species through vaccination. The Island Scrub-Jay (Aphelocoma insularis) is one such species, being a corvid with a highly restricted insular range. Herein, we used congeneric Western Scrub-Jays (Aphelocoma californica) to test the efficacy of three WNV vaccines in protecting jays from an experimental challenge with WNV: (1) the Fort Dodge West Nile-Innovator(®) DNA equine vaccine, (2) an experimental DNA plasmid vaccine, pCBWN, and (3) the Merial Recombitek(®) equine vaccine. Vaccine efficacy after challenge was compared with naïve and nonvaccinated positive controls and a group of naturally immune jays. Overall, vaccination lowered peak viremia compared with nonvaccinated positive controls, but some WNV-related pathology persisted and the viremia was sufficient to possibly infect susceptible vector mosquitoes. The Fort Dodge West Nile-Innovator DNA equine vaccine and the pCBWN vaccine provided humoral immune priming and limited side effects. Five of the six birds vaccinated with the Merial Recombitek vaccine, including a vaccinated, non-WNV challenged control, developed extensive necrotic lesions in the pectoral muscle at the vaccine inoculation sites, which were attributed to the Merial vaccine. In light of the well-documented devastating effects of high morbidity and mortality associated with WNV infection in corvids, vaccination of Island Scrub-Jays with either the Fort Dodge West Nile-Innovator DNA vaccine or the pCBWN vaccine may increase the numbers of birds that would survive an epizootic should WNV become established on Santa Cruz Island.
The Effect of Dissolved CO2 and O2 on the Corrosion of Iron (1990)

Reports concerning the effects of dissolved carbon dioxide on the corrosion of iron have ranged from “no effect” to a catalytic mechanism for the observed corrosion processes. Pedagogical references indicate that dissolved carbon dioxide is benign towards iron corrosion. Contrary to this, our results suggest that carbon dioxide does indeed play an active role in the corrosion of iron much as chloride and other aggressive ions. Visual, spectral, and electrochemical results all support the significance of the effect of dissolved carbon dioxide on the corrosion of iron.
Comparison and Clinical Implementation of Quality of Life Tools in Patients with Small Bowel Neuroendocrine Tumors Treated with Lu-DOTA-TATE PRRT (2019)

Aim: This study assesses if clinically developed quality of life (QoL) tools are as effective in small bowel neuroendocrine tumors (NETs) as NET-specific research questionnaires. Methods: QoL in patients with small bowel NETs treated with Lu-DOTA-TATE was assessed with The European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30, QLQ-GI.NET21 and Edmonton Symptom Assessment System Revised (ESAS-r) at baseline and after four treatments. Repeated measures ANOVA was performed. Results: Both EORTC and ESAS-r demonstrated maintained overall QoL. EORTC demonstrated statistically and clinically significant improvement in insomnia, diarrhea, gastrointestinal, endocrine symptoms and social function. ESAS-r demonstrated statistically and clinically significant improvement in overall total symptom distress score. Conclusion: ESAS-r is quick and easy to interpret. It is not as sensitive to individual symptoms but does track overall function. EORTC assessment is more complex, but better reflects QoL for NET specific symptoms.
Autosensitization of Lymphocytes against Thymus Reticulum Cells (1972)

Lymph nodes of normal rats contain lymphocytes that can be induced in vitro to mediate a specific cellular immune reaction against reticulum cells derived from syngeneic adult thymus glands. It is likely that these lymphocytes had access to reticulum cell antigens during the period in which they developed immunocompetence within the thymus. This suggests that contact with self-antigens during development may not eliminate self-reactive lymphocytes. These findings are in conflict with the theory that natural tolerance to self-antigens depends upon elimination of lymphocyte clones.
Catalytic Conjugate Additions of Carbonyl Anions under Neutral Aqueous Conditions. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
MoA-1-4 EFFECT OF HEAD-DISK INTERFACE BIASING ON HEAD WEAR OF THERMAL FLYING HEIGHT CONTROL SLIDERS (2015)

In this investigation, we study head wear as a function of a dc bias voltage applied across the head-disk interface (HDI). Head-wear is determined by measuring the change in the heater touch-down power before and after 10 minute wear tests. It is found that applying a positive bias to the disk with respect to the slider results in reduced head wear.
Erratum: “Effects of calibration methods on quantitative material decomposition in photon‐counting spectral computed tomography using a maximum a posteriori estimator” [Med. Phys., 44(10): 5187‐5197 (2017)] (2018)

[https://doi.org/10.1002/mp.12457] The authors thank Yirong Yang of Tsinghua University for bringing this error to our attention. National Science Foundation (DMR-1309587). Kelly Cares Foundation. St. Joseph Regional Medical Center. University of Notre Dame Equipment Renewal and Restoration Program.