gebhart/patrepeval huggingface dataset:
The effects of feeding mixed tocopherol oil on whole-blood respiratory burst and neutrophil immunometabolic-related gene expression in lactating dairy cows (2018)

The 4 major tocopherol isoforms differ in their biochemical reactivity and cellular effects due to basic chemical structural differences. Alpha-tocopherol has been well studied regarding effects on bovine polymorphonuclear leukocyte (PMN) function and its involvement in respiratory burst. However, no studies to date have identified the effects of supplementing a mixed tocopherol oil (Tmix) particularly enriched in non-α tocopherol isoforms (i.e., γ- and δ-isoforms) on fundamental immunometabolic changes in dairy cows. Therefore, the objectives of this study were to determine whether short-term feeding of vegetable oil-derived Tmix alters specific biomarkers of metabolism, whole-blood leukocyte populations, respiratory burst, immunometabolic-related gene expression of PMN, or gene expression of isolated PMN when challenged with lipopolysaccharides (LPS). Clinically healthy multiparous lactating Holstein cows (n = 12; 179 ± 17 d in milk, 40.65 ± 3.68 kg of milk yield) were fed Tmix (620 g/d) for 7 consecutive days. Jugular blood (EDTA anticoagulant) was collected from all cows on d 0 before treatment initiation and again on d 7 after Tmix feeding. Total stimulated respiratory burst activity (RBA) and leukocyte populations were assessed in whole blood, and tocopherol isoform concentrations, metabolites, and hormones were measured in plasma. For gene expression analysis, isolated PMN from cows before and after Tmix feeding were incubated with LPS at a final concentration of either 0.0 or 1.5 µg/mL. Feeding of Tmix for 7 d increased the concentrations of α- and γ-tocopherol. The Tmix did not alter plasma insulin but decreased cholesterol. The Tmix did not alter whole-blood RBA or the leukocyte populations. The LPS challenge increased the expression of proinflammatory genes TNFA and IL6. However, Tmix treatment did not alter the patterns of LPS-affected expression of genes (e.g., TNFA, ITGB2, PPARA, and RXRA) associated with the immune or metabolic response. In conclusion, short-term feeding of Tmix may have no negative effect on animal health as Tmix increased α- and γ-tocopherol concentrations in blood and did not impair whole-blood RBA or alter leukocyte populations. The data provide further support that the α- and γ-tocopherol isoforms do not interfere with normal immune or metabolic function.
Oxidized Substrates of APEH as a Tool to Study the Endoprotease Activity of the Enzyme (2021)

APEH is a ubiquitous and cytosolic serine protease belonging to the prolyl oligopeptidase (POP) family, playing a critical role in the processes of degradation of proteins through both exo- and endopeptidase events. Endopeptidase activity has been associated with protein oxidation; however, the actual mechanisms have yet to be elucidated. We show that a synthetic fragment of GDF11 spanning the region 48-64 acquires sensitivity to the endopeptidase activity of APEH only when the methionines are transformed into the corresponding sulphoxide derivatives. The data suggest that the presence of sulphoxide-modified methionines is an important prerequisite for the substrates to be processed by APEH and that the residue is crucial for switching the enzyme activity from exo- to endoprotease. The cleavage occurs on residues placed on the C-terminal side of Met(O), with an efficiency depending on the methionine adjacent residues, which thereby may play a crucial role in driving and modulating APEH endoprotease activity.
Modeling the dynamics of human hair cycles by a follicular automaton (2002)

The hair follicle cycle successively goes through the anagen, catagen, telogen, and latency phases, which correspond, respectively, to hair growth, arrest, shedding, and absence before a new anagen phase is initiated. Experimental observations collected over a period of 14 years in a group of 10 male volunteers, alopecic and nonalopecic, allowed us to determine the characteristics of scalp hair follicle cycles. On the basis of these observations, we propose a follicular automaton model to simulate the dynamics of human hair cycles. The automaton model is defined by a set of rules that govern the stochastic transitions of each follicle between the successive states anagen, telogen, and latency, and the subsequent return to anagen. The transitions occur independently for each follicle, after time intervals given stochastically by a distribution characterized by a mean and a variance. The follicular automaton model accounts both for the dynamical transitions observed in a single follicle and for the behavior of an ensemble of independently cycling follicles. Thus, the model successfully reproduces the evolution of the fractions of follicle populations in each of the three phases, which fluctuate around steady-state or slowly drifting values. We apply the follicular automaton model to the study of spatial patterns of follicular growth that result from a spatially heterogeneous distribution of parameters such as the mean duration of anagen phase. When considering that follicles die or miniaturize after going through a critical number of successive cycles, the model can reproduce the evolution to hair patterns similar to well known types of diffuse or androgenetic alopecia.
Abstract 2047: Discovery and molecular characterization of AGS-15/SLITRK6 as a novel target for antibody-mediated therapeutic development in bladder cancer. (2013)

Abstract Discovery efforts utilizing suppression subtractive hybridization identified AGS-15/SLITRK6 as a differentially expressed gene in bladder cancer. SLITRK6 encodes a cell surface type I transmembrane protein, a member of the SLITRK family of factors with neuronal function activities. Comprehensive SLITRK6 RNA expression analysis in patient specimens revealed limited restricted normal tissue expression and high frequent expression in bladder cancers, as well as expression in subsets of breast, lung and several other cancer types. Tissue immunohistochemical analysis validated SLITRK6 protein limited expression in normal tissues and high expression levels in cancers. SLITRK6 expression profiling in cancer cell lines and Agensys proprietary patient-derived xenografts (PDXs) identified model systems in relevant cancer indications for further target characterization and antibody therapeutics development. Genomic analyses, including whole exome next generation sequencing, chromosomal aberrations and gene copy number assessments, were performed to evaluate SLITRK6 gene status in model cell lines and PDXs. Thus, we discovered and characterized AGS-15/SLITRK6 as a novel target with high levels and selective expression in tumors, particularly in bladder cancer. This cell surface antigen's attractive expression profile is a major determinant of AGS-15/SLITRK6 as a suitable and preferential candidate for antibody drug conjugate therapeutic targeting in bladder cancer treatment and, potentially, in several other cancer indications. Citation Format: Yuriy Shostak, Suzanne Said, Deanna L. Russell, Michael D. Mattie, Mi Sook Chang, Ashley Christensen, Karen Morrison, Kendall Morrison, David Stover, Pia Challita-Eid. Discovery and molecular characterization of AGS-15/SLITRK6 as a novel target for antibody-mediated therapeutic development in bladder cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2047. doi:10.1158/1538-7445.AM2013-2047
Demystifying the medical management of nephrolithiasis. (2011)

Nephrolithiasis is a common problem associated with significant costs to the health care system. Its prevalence continues to increase, particularly in women, which is attributed to changes in diet and lifestyle. The costs associated with the evaluation and management of nephrolithiasis in the United States has been estimated to be $1.83 billion, and, without any intervention, the risk of recurrence is high. This article reviews the management options for nephrolithiasis including a new formulation of potassium citrate, Urocit®-K 15 mEq, that allows for dosing flexibility which can lead to improved compliance and tolerability.
THE ELECTRONIC STRUCTURE OF TRIGONAL AND AMORPHOUS Se AND Te (1974)

The electronic structure of trigonal and amorphous Se and Te is investigated using the empirical pseudopotential method (EPM), charge density calculations and simple tight binding models.Band structures and electronic densities of states are obtained which are in excellent agreement with recent photoemission measurements.a bonding charge can be defined which gives an estimate of the intra-vs inter-chain bonding strengths.The trigonal results along with model calculations to investigate the effects of bond angle variations on chains and the presence-of eight atid six-fold rings of bonds are used to interpret the chang~s observed in the experimental spectra of amorphous Se and Te.A new model of amorphous Se :is proposed.
The Development of a High-Content Screening Binding Assay for the Smoothened Receptor (2012)

In this study, the development of an image-based high-content screening (HCS) binding assay for the seven-transmembrane (7TM) receptor Smoothened (Smo) is described. Using BacMam-based gene delivery of Smo, BODIPY-cyclopamine as a fluorescent probe, and a confocal imaging system, a robust 384-well assay that could be used for high-throughput compound profiling activities was developed. The statistically robust HCS binding assay was developed through optimization of multiple parameters, including cell transduction conditions, Smo expression levels, the image analysis algorithm, and staining procedures. Evaluation of structurally diverse compounds, including functional Smo activators, inhibitors, and related analogs, demonstrated good compound potency correlations between high-content imaging binding, membrane fluorescence polarization binding, and gene reporter assays. Statistical analysis of data from a screening test set of compounds at a single 10-µM concentration suggested that the high-content imaging Smo binding assay is amenable for use in hit identification. The 384-well HCS assay was rapidly developed and met statistical assay performance targets, thus demonstrating its utility as a fluorescent whole-cell binding assay suitable for compound screening and profiling.
Morphological and optical properties of Si nanostructures imbedded in SiO2 and Si3N4 films grown by single source chemical vapor deposition (2002)

Luminescent Si nanocrystals imbedded in amorphous SiO2 and Si3N4 networks have been prepared using an approach based on deposition of Si-rich Si–O and Si–N films by ultrahigh vacuum-chemical vapor deposition reactions of the single-source precursors O(SiH3)2 and N(SiH3)3 respectively. The film growth is conducted on Si (100) at temperatures of 750–850 °C and at extremely high rates of 20–30 nm per min with complete hydrogen elimination. Rapid thermal annealing of the as-deposited films at 1100–1200 °C for 30–60 s generates Si nanocrystals with tunable sizes, discrete shapes, and uniform distributions. The phase, composition, and microstructure of the films are characterized by a variety of analytical techniques including high-resolution electron microscopy. The room temperature photoluminescence (PL) is blueshifted substantially with respect to pure Si and appears to be independent of the Si3N4 and SiO2 dielectric medium. The PL energy increases with decreasing crystal size in accordance with quantum confinement concepts. The key aspects of this approach include the use of completely inorganic (C–H free) and volatile siloxanes and silyl amines with built-in Si–N and Si–O atomic arrangements that allow stoichiometric control at the atomic level leading to formation of highly homogeneous crystallite profiles with adjustable densities and sizes throughout the amorphous matrix.
ChemInform Abstract: Synthesis of Dihydroisoxazole Nucleoside and Nucleotide Analogues. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fabrication and high-speed characterization of SU-8 shrouded two-dimensional microimpellers (2007)

In this study, the performance of shrouded two-dimensional microimpellers was measured for application to a micro centrifugal pump used in a portable fuel cell system. Two types of microimpellers were designed, and fabricated by a multi-layer photolithography process using an ultrathick photoresist (SU-8 3000). Microimpellers with a diameter of 10 mm were tested using an air spindle up to maximum rotation speeds determined by the destruction of the microimpellers, which are 350 000 rpm for a purely-radial-outlet blade impeller and 450 000 rpm for a backward blade impeller. The purely-radial-outlet blade impeller showed a higher pressure rise—2.8 kPa at 150 000 rpm, 5.1 kPa at 200 000 rpm and 12.5 kPa at 300 000 rpm. The measured performance satisfies the requirement of the micro centrifugal pump. However, the measured pressure rises are roughly half of the simulated values. The influence of the radial clearance and height difference between the impeller and the diffuser was investigated using an electromagnetic motor and impellers with a diameter of 16 mm. Against expectation, a better pumping performance was obtained with a larger tip clearance, and the height difference did not affect the pumping performance. These unexpected results suggest that the tip clearance and the clearance between the impeller shroud and the stationary housing act as a diffuser.
Probe design for large-scale molecular biology applications (2004)

Large-scale molecular biology technologies such as DNA microarrays and large-scale in situ hybridization (ISH) are used to gain an appreciation of global attributes in biological tissues and cells. Although many of these efforts use cDNA probes, an approach that makes use of designed oligo probes should offer improved consistency at uniform hybridization conditions and improved specificity, as demonstrated by various oligo microarray platforms. We describe a new Web-based application that takes FASTA-formatted sequences as input, and returns both a list of the best choices for probes and a full report containing possible alternatives. Probe design for microarrays may use a scoring routine that optimizes probe intensity based upon an artificial neural network (ANN) trained to predict the average probe intensity from the physical properties of the probe and a screen for possible cross-reactivity. This new tool should provide a reliable way to construct probes that maximize signal intensity while minimizing cross-reactivity.
Defect Level of the Carbon Vacancy-Carbon Antisite Pair Center in SI 4H SiC (2008)

The understanding of the structure and associated defect level of point defects in SiC is important because the material is to be used both as a semiconductor and semi-insulator. Production of the latter is achieved by compensation of unavoidable impurities using defects that require more energy for ionization than the unintentional donors or acceptors. The purpose of the present work is to measure the defect energy level of one center in high resistivity 4H SiC using photo-induced electron paramagnetic resonance (photo-EPR). The center is identified as SI-5, an EPR signal that others have attributed to the negative charge state of the carbon vacancy-carbon antisite pair, − C Si V C . Samples containing this defect exhibit two different photo thresholds, which depend on the resistivity activation energy, Ea. For samples with Ea less than 0.8 eV, a photothreshold at 0.75+/- 0.05 eV is observed, but for those with Ea greater than 0.8 eV, the threshold is between 2 and 2.5 eV. Previous work focused on the former case. Here, the SiC substrates with the larger Ea are emphasized, showing that the photo-threshold likely measures the neutral to negative defect level, − / 0 C Si V C .
BIOLOGICAL INTERACTIONS WITH POLYMER BIOMATERIALS EVALUATED AT MICROSCOPIC AND NANOSCOPIC LEVELS (2001)

Polymer biomaterials are used in a variety of blood-contacting medical devices. In particular, poly(urethaneurea) (PUU) based biomaterials have proven well-suited for devices due to their good mechanical properties and superior blood compatibility compared to other synthetic materials. This has largely been attributed to the phenomena of microphase separation, as the PUU copolymer separates into distinct “hard” and “soft” microphases. Although a variety of evidence relating microphase separation and blood compatibility exists in the literature, there is no direct evidence relating the two phenomena at a molecular level. We have attempted to leam more about the biological interactions with polymer biomaterials including PUU materials by utilizing high resolution fluorescence microscopy and atomic force microscopy (AFM). AFM was used to characterize the microphase structure of a series of PUU films of varying hard segment/soft segment ratio and to determine the interactions of proteins with synthetic polymer materials under aqueous buffer conditions. Fluorescence microscopy with immunohistochemical staining was used to study platelet interactions with PUU materials under in-vitro conditions as well as protein interactions with PUU blood sacs retrieved from total artificial heart implanted animals. AFM images demonstrated a characteristic microphase structure in the PUU films best described as randomly oriented cylinders with occasional spherical domains. High-resolution studies of individual plasma proteins on hydrophobic polymer materials reveal tertiary structures consistent with what others have observed previously on ultrasmooth model biomaterial surfaces. The fluorescence microscopy images demonstrated protein deposition aligned with the expected direction of blood flow in the implanted devices. Taken together, these data provide insight into the nature of biomaterial/biological interactions under physiologically relevant conditions.
Monolithic Sorbents for Carbon Dioxide Removal (2006)

&lt;div class="htmlview paragraph"&gt;The NASA objective of expanding the human experience into the far reaches of space will require the development of regenerable life support systems. On-board carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;) removal units play a key role in such systems ensuring high quality cabin air for crew members. Similar but more compact units are needed for extravehicular activities (space suit). The use of monolithic (e.g., honeycomb-shaped) rather than granular sorbents has the potential to result in a CO&lt;sub&gt;2&lt;/sub&gt;-removal system that possesses substantial weight, size, and power-requirement advantages over current systems (improved CO&lt;sub&gt;2&lt;/sub&gt; adsorption and lower pressure drop). The subject of this study was the use and manufacture of lightweight, porous carbon monoliths with controlled pore characteristics that will serve as support for the sorbent material (e.g., liquid amines). The objective was to demonstrate the technical feasibility of the above approach. Several high surface area, high pore volume carbon monoliths were produced, and the pressure-drop advantage of monolithic sorbents over granular material was demonstrated. Thermal conductivity of monolithic carbon was measured and found to be significantly higher than the currently used polymer-based amine support. Preliminary testing of sorbent performance with respect to CO&lt;sub&gt;2&lt;/sub&gt; adsorption capacity was performed and promising results were obtained.&lt;/div&gt;
Determination of Electronic Warfare Receiver's Instantaneous Dynamic Range Using Music Method (2008)

The purpose of this paper is to find the limit of instantaneous dynamic range (IDR) for electronic warfare (EW) receivers with two-signal detection capability. In order to make the limit independent of the order of music method, very high order is used. Two signal detection criterions are used. One criterion is through the eigenvalue distribution. The other is through the frequency identification using the music spectral analysis. General behavior of IDR vs. frequency shows a small IDR at small frequency separation and that IDR reaches a saturation value at some frequency separation. This is the expected result. In order to apply to practical EW receiver design, analog-to-digital converters (ADCs) with various numbers of bits are used to calculate the IDR. The calculated results for ADC with different number of bits are curve fitted to represent the IDR vs. frequency separation. These curves can be used as the limit for digital EW receiver designs.
Inducible and reversible breaching of the blood brain barrier by RNAi (2011)

Abstract Sequence‐specific knockdown of gene expression is a goal that has been long sought by both basic and clinical investigators. In this regard, the discovery of RNA interference (RNAi) in Caenorhabditis elegans was immediately recognized as a potential breakthrough for studying gene function (Fire et al, 1998 ). These findings demonstrated that double‐stranded (ds)RNAs are triggers for sequence‐specific, post‐transcriptional gene silencing via targeted degradation of messenger RNAs harbouring a complementary sequence to one of the two strands. Initially, it was thought that such post‐transcriptional regulation of gene expression could not be achieved in mammalian systems due to the strong induction of interferon by dsRNAs. This potential restriction was short lived with the demonstration that endonuclease processed dsRNAs of 21–25 nucleotides in length, designated small interfering RNAs (siRNAs), were able to elicit sequence‐specific degradation of mRNAs in mammalian cells without triggering interferon responses (Elbashir et al, 2001 ). These findings provided a huge impetus to develop RNAi as a therapeutic modality. The dream to selectively block the expression of deleterious proteins and treat formerly non‐drugable diseases led to the rapid establishment of new biotech companies and branches of major pharmaceutical companies devoted to RNAi therapeutics. See related article in EMBO Mol Med (Campbell et al. (2011) EMBO Mol Med 3: 228–238 )
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor (2015)

Ecogenomic investigation of a methanogenic bioreactor degrading terephthalate (TA) allowed elucidation of complex synergistic networks of uncultivated microorganisms, including those from candidate phyla with no cultivated representatives. Our previous metagenomic investigation proposed that Pelotomaculum and methanogens may interact with uncultivated organisms to degrade TA; however, many members of the community remained unaddressed because of past technological limitations. In further pursuit, this study employed state-of-the-art omics tools to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and reports the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments. Metabolic reconstruction revealed that these organisms perform fermentative, syntrophic and acetogenic catabolism facilitated by energy conservation revolving around H2 metabolism. Several of these organisms could degrade TA catabolism by-products (acetate, butyrate and H2) and syntrophically support Pelotomaculum. Other taxa could scavenge anabolic products (protein and lipids) presumably derived from detrital biomass produced by the TA-degrading community. The protein scavengers expressed complementary metabolic pathways indicating syntrophic and fermentative step-wise protein degradation through amino acids, branched-chain fatty acids and propionate. Thus, the uncultivated organisms may interact to form an intricate syntrophy-supported food web with Pelotomaculum and methanogens to metabolize catabolic by-products and detritus, whereby facilitating holistic TA mineralization to CO2 and CH4.