gebhart/patrepeval huggingface dataset:
Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium (2020)

Vancomycin-resistant <i>Enterococcus faecium</i> (VREfm) is an emerging antibiotic-resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonization, in particular following antibiotic treatment, remains largely unknown. We employed amplicon 16S rRNA gene sequencing and metabolomics in a murine model system to try and investigate functional roles of the gut microbiome during VREfm colonization. First-order taxonomic shifts between <i>Bacteroidetes</i> and <i>Tenericutes</i> within the gut microbial community composition were detected both in response to pretreatment using ceftriaxone and to subsequent VREfm challenge. Using neural networking approaches to find cooccurrence profiles of bacteria and metabolites, we detected key metabolome features associated with butyric acid during and after VREfm colonization. These metabolite features were associated with <i>Bacteroides</i>, indicative of a transition toward a preantibiotic naive microbiome. This study shows the impacts of antibiotics on the gut ecosystem and the progression of the microbiome in response to colonization with VREfm. Our results offer insights toward identifying potential nonantibiotic alternatives to eliminate VREfm through metabolic reengineering to preferentially select for <i>Bacteroides</i> <b>IMPORTANCE</b> This study demonstrates the importance and power of linking bacterial composition profiling with metabolomics to find the interactions between commensal gut bacteria and a specific pathogen. Knowledge from this research will inform gut microbiome engineering strategies, with the aim of translating observations from animal models to human-relevant therapeutic applications.
Table S2 from Functional Silencing of <i>HSD17B2</i> in Prostate Cancer Promotes Disease Progression (2023)

&lt;p&gt;Tandem mass spectrometry parameter for targeted steroids and internal standards (IS).&lt;/p&gt;
Optogenetic Protein Cleavage in Zebrafish Embryos (2022)

Abstract A wide array of optogenetic tools is available that allow for precise spatiotemporal control over many cellular processes. These tools have been especially popular among zebrafish researchers who take advantage of the embryo’s transparency. However, photocleavable optogenetic proteins have not been utilized in zebrafish. We demonstrate successful optical control of protein cleavage in embryos using PhoCl, a photocleavable fluorescent protein. This optogenetic tool offers temporal and spatial control over protein cleavage events, which we demonstrate in light-triggered protein translocation and apoptosis.
Structure-based design of a highly stable, covalently-linked SARS-CoV-2 spike trimer with improved structural properties and immunogenicity (2021)

SUMMARY The continued threat of SARS-CoV-2 to global health necessitates development of improved research tools and vaccines. We present an improved SARS-CoV-2 spike ectodomain, “VFLIP”, bearing five proline substitutions, a flexible cleavage site linker, and an inter-protomer disulfide bond. VFLIP displays significantly improved stability, high-yield production and retains its trimeric state without exogenous trimerization motifs. High-resolution cryo-EM and glycan profiling reveal that the VFLIP quaternary structure and glycosylation mimic the native spike on the viral surface. Further, VFLIP has enhanced affinity and binding kinetics relative to other stabilized spike proteins for antibodies in the Coronavirus Immunotherapeutic Consortium (CoVIC), and mice immunized with VFLIP exhibit potent neutralizing antibody responses against wild-type and B.1.351 live SARS-CoV-2. Taken together, VFLIP represents an improved tool for diagnostics, structural biology, antibody discovery, and vaccine design.
Simple transfer from spin coating to blade coating through processing aggregated solutions (2017)

We observe that thin film solar cells based on poly[5-(2-hexyldecyl)-1,3-thieno[3,4-<italic>c</italic>]pyrrole-4,6-dione-<italic>alt</italic>-5,5-(2,5-bis(3-dodecylthiophen-2-yl)-thiophene)] [P(T3-TPD)] blended with phenyl-C<sub>71</sub>-butyric acid methyl ester (PC<sub>71</sub>BM) are remarkably robust to process variations, optimizing under identical conditions for both spin and blade coating.
Mesoscopic self-assembly of gold islands on diblock-copolymer films (1994)

We describe the fabrication and characterization of self-assembled gold island arrays on diblock-copolymer thin films. The natural tendency of these polymers to form ordered phases is used to induce selective aggregation of evaporated gold metal during an annealing process. We obtain well-defined, nanoscale island arrays aligned with one of the copolymer blocks. Near perfect segregation is achieved between the two domains. Two types of diblock-copolymer systems are discussed, together with the resulting island patterns.
ChemInform Abstract: Functionalization of Saturated Hydrocarbons. Part 14. Further Studies on the Mechanism of Gif‐Type Systems. (1989)

Abstract The photolysis of the acyl derivatives (I) in Py‐AcOH is examined to study the partitioning of sec. radicals between oxygen, pyridine, and the thione functions (results are given in the scheme only for (Ia) as an example).
Scaled fixed-point frequency selective extrapolation for fast image error concealment (2017)

Image and video signal processing demands in many areas for error concealment algorithms, whereby the execution time plays an important role. Within this paper, we introduce the scaled fixed-point Frequency Selective Extrapolation for fast image error concealment. This algorithm is based on the complex-valued Frequency Selective Extrapolation, but reduces computational complexity. It is shown that a fixed-point realization of the state-of-the-art algorithm requires an impracticable word-length, which makes it necessary to design a novel, scaled Frequency Selective Extrapolation that reduces the required word-length. Regarding the new approach, execution time can be reduced on average by 22.84 % and at best by up to 40.45 % compared to the state-of-the-art floating point Frequency Selective Extrapolation at the same reconstruction quality. Moreover, platforms can be exploited, which support fixed-point arithmetic only.
ChemInform Abstract: Amino Acids and Peptides. Part 224. Analogues of Cholecystokinin Methylated in the Side Chain of Carboxyterminal Phenylalanine. (1992)

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.
Development of climbing configuration space database for predicting children's interaction with products in everyday situations (2018)

A million of children die of a preventable injury every year all over the world. One of effective methods is product improvement. Product improvement should be done in the manner that will reduce the risk of injury by predicting child interactions with products. However, it is still very difficult even for advanced simulation systems to precisely predict how children interact with consumer products in every-day life situations. In this study, the authors are exploring a data-driven method as one of promising approaches. The authors collected children's climbing behavioral data and developed a children's climbing behavior database using RGB-D cameras for clarifying a climbing configuration space, which allows us to predict and simulate possible climbing postures of children.
Non-Causal Time-Domain Filters for Single-Channel Noise Reduction (2012)

In many existing time-domain filtering methods for noise reduction in, e.g., speech processing, the filters are causal. Such causal filters can be implemented directly in practice. However, it is possible to improve the performance of such noise reduction filtering methods in terms of both noise suppression and signal distortion by allowing the filters to be non-causal. Non-causal time-domain filters require knowledge of the future, and are therefore not directly implementable. If the observed signal is processed in blocks, however, the non-causal filters are implementable. In this paper, we propose such non-causal time-domain filters for noise reduction in speech applications. We also propose some performance measures that enable us to evaluate the performance of non-causal filters. Moreover, it is shown how some of the filters can be updated recursively. Using the recursive expressions, it is also shown that the output SNRs of the filters always increase as we increase the length of the filter when the desired signal is stationary. From both the theoretical and practical evaluations of the filters, it is clearly shown that the performance of time-domain filtering methods for noise reduction can be improved by introducing non-causality.
Semi-transparent low-donor content organic solar cells employing cyclopentadithiophene-based conjugated molecules (2018)

Considering the facile synthesis of the cyclopentadithiophene (CPDT) building block, this study aims to synthesize and characterize two donor–acceptor type conjugated molecules, 2EH-CPDT(FBTTh<sub>2</sub>)<sub>2</sub> and 5EN-CPDT(FBTTh<sub>2</sub>)<sub>2</sub>, with different branching points from the backbone.
Highly Reliable Coding Methods for Emerging Applications: Archive and Enterprise Solid-State Drives (SSDs) (2015)

This paper proposes highly reliable coding methods for applications in two extreme conditions. n-out-of-8 level cell (nLC) is proposed for archival applications which require significantly long data-retention time with small write/erase cycle. On the other hand, for applications with large write/erase cycle and short data-retention time (enterprise application, etc.), universal asymmetric coding (UAC) is proposed. nLC reduces the number of memory states to improve the reliability with low cost overhead. In 7LC, the bit-error rate (BER) reduction will be 79% after 1k-year data retention while seven memory states are efficiently used out of eight states. By considering nLC with error-correcting codes (ECCs), the optimum number of cell levels (n) can be determined to minimize the bit-cost with given acceptable data-retention time. In UAC, the coding method is changed according to the write/erase cycle and data-retention time to keep the BER low. As a result, BER is reduced by 52% at maximum, compared with the original random pattern.
Characteristics of charged networks under an electric stimulus (1994)

Abstract The electrokinetic phenomena of poly(2‐acrylamido‐2‐methyl‐1‐propane sulfonic acid‐co‐ n ‐butylmethacrylate) were examined to investigate physical changes of the gel under an applied electric current. When an electrical stimulus was applied to a piece of the gel, without being in contact with an electrode, reversible gel bending was observed. The bending degree was directly proportional to the intensity of the applied electric stimulus. This was explained by ‘depletion polarization’ of ionic species under the stimulus. The swelling of the gel surface facing the anode increased, due to the decreased ionic strength of the boundary layer upon electric stimulation, while gel shrinking occurred at the cathode. When the gel is in direct contact with electrodes, deswelling of the gel was observed at the anode side, while water seepage occurred at the cathode side. This observation was attributed to the electro‐osmosis inside the gel, combined with local pH changes around the electrodes resulting from electrochemical reactions, particularly water electrolysis. © 1994 John Wiley &amp; Sons, Inc.
Resolution of 1:1 Electron Stepper with Patterned Cold Cathode (2002)

We investigated the feasibility of 1:1 electron stepper lithography based on a patterned cold cathode. We fabricated metal-semiconductor-insulator cold cathodes and measured the energy distribution of the emitted electrons. Based on the finite width of the energy distribution, we simulated the emission of the electron beam from one point on the cold cathode broadens at the wafer surface by solving the equation of motion. The simulation showed that when the energy width was 360 meV, the beam spread was estimated to be approximately 23 nm. This indicates that if we fabricate a 20-nm-wide emission area, the electron beam width on the wafer could be approximately 43 nm. Therefore, we conclude that the 1:1 electron stepper can achieve a 50-nm resolution.
A broken market: can increased access to broken rice decrease food insecurity in Haiti? (2022)

Abstract Haiti is a unique rice market in the sense that, despite the high poverty rates and dependency on rice as a staple, it relies on imports (80% of total consumption) of high-quality milled rice for which it pays a premium price. Haiti requires that all imported rice have a maximum of 4% broken kernels, which results in Haiti importing one of the most expensive non-fragrant long grain rice in the world. This study implements a non-hypothetical field experiment (300 observations) to elicit which rice attributes Haitians valued as revealed by their purchasing behavior in an open-air market setting. Specifically, we set out to estimate if Haitians would discount broken rice in such a manner that strict import regulations, which keeps cheaper imported broken rice out of domestic markets, continue to be warranted. Our findings suggest consumers (across locations and income groups) were not found to pay more for a reduced amount of broken rice, with the exception of the highest income group. This should signal to policy makers in Haiti that consumers are willing to consume rice with a higher percentage of brokens than the 4% importation standard. This is important from a food security standpoint as rice with a higher broken percentage provides the same nutritional value as rice with a lower broken rate, and can be sourced globally at a discounted price. Allowing imports of rice with higher broken rate could help alleviate food insecurity in Haiti by providing a cheaper alternative to relatively expensive domestic rice and imported rice, which currently has an inflated price due to its high-quality standards imposed by Haitian importers.
Green Bank Telescope 290 to 395 MHz Feed Analysis and Modification for Operation in the 140 to 175 MHz Band (2003)

A previously developed 290 to 395 MHz short backfire antenna feed for the Green Bank Telescope (GBT) has been modified for operation in the 140 to 175 MHz VHF band.The feed has been modeled with the Electromagnetic Surface Patch code, Version 5 (ESP5) software, developed at The Ohio State University (OSU) to predict the feed radiation patterns and with OSU SatCom Workbench software to predict the GBT radiation patterns.Measured feed radiation patterns are in good agreement with the electromagnetic model.This lower-fi-equency VHF feed is suitable for use as a receive anterma for the GBT.
Toward reliable multigenerational analysis of anatomical trees in 3D high-resolution CT images (2003)

Modern micro-CT and multidetector helical CT scanners can produce high-resolution 3D digital images of various anatomical tree structures, such as the coronary or hepatic vasculature and the airway tree. The sheer size and complexity of these trees make it essentially impossible to define them interactively. Automatic approaches, using techniques such as image segmentation, thinning, and centerline definition, have been proposed for a few specific problems. None of these approaches, however, can guarantee extracting geometrically accurate multigenerational tree structures. This limits their utility for detailed quantitative analysis of a tree. This paper proposes an approach for accurately defining 3D trees depicted in large 3D CT images. Our approach utilizes a three-stage analysis paradigm: (1) Apply an automated technique to make a "first cut" at defining the tree. (2) Analyze the automatically defined tree to identify possible errors. (3) Use a series of interactive tools to examine and correct each of the identified errors. At the end of this analysis, in principle, a more useful tree will be defined. Our paper will present a preliminary description of this paradigm and give some early results with 3D micro-CT images.
Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance (2015)

Our findings suggest that 20q11.22 is likely a risk region for bipolar disorder; they also highlight the informative value of integrating functional annotation of genetic variants for gene expression in advancing our understanding of the biological basis underlying complex disorders, such as bipolar disorder.
Production of Spherical Beads by JetCutting (2000)

Until now, the production of spherical and monodisperse small beads from higher-viscosity fluids was hardly possible. JetCutting is a new, simple and efficient technology for the production of monodisperse beads of small particle size from low- to high-viscosity fluids in large quantities. Since spherical beads are intermediates or products in various industries, e.g., the pharmaceutical, chemical and food industries, manifold applications are possible. Offering further advantages, the JetCutter has a great potential to replace conventional technologies for bead production.
Survey of full‐scale sidestream enhanced biological phosphorus removal (S2EBPR) systems and comparison with conventional EBPRs in North America: Process stability, kinetics, and microbial populations (2019)

Sidestream EBPR (S2EBPR) is an emerging alternative process to address common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. A systematic evaluation and comparison of the process performance and microbial community structure was conducted between conventional and S2EBPR facilities in North America. The statistical analysis suggested higher performance stability in S2EBPR than conventional EBPR, although possible bias associated with other plant-specific factors might have affected the comparison. Variations in stoichiometric values related to EBPR activity and discrepancies between the observed values and current model predictions suggested a varying degree of metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. Microbial community analysis using various techniques suggested comparable known candidate PAO relative abundances in S2EBPR and conventional EBPR systems, whereas the relative abundance of known candidate GAOs seemed to be consistently lower in S2EBPR facilities than conventional EBPR facilities. 16S rRNA gene sequencing analysis revealed differences in the community phylogenetic fingerprints between S2EBPR and conventional facilities and indicated statistically higher microbial diversity index values in S2EBPR facilities than those in conventional EBPRs. PRACTITIONER POINTS: Sidestream EBPR (S2EBPR) can be implemented with varying and flexible configurations, and they offer advantages over conventional configurations for addressing the common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. Survey of S2EBPR plants in North America suggested statistically more stable phosphorus removal performance in S2EBPR plants than conventional EBPRs, although possible bias might affect the comparison due to other plant-specific factors. The EBPR kinetics and stoichiometry of the S2EBPR facilities seemed to vary and are associated with metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. The abundance of known candidate PAOs in S2EBPR plants was similar to those in conventional EBPRs, and the abundance of known candidate GAOs was generally lower in S2EBPR than conventional EBPR facilities. Further finer-resolution analysis of PAOs and GAOs, as well as identification of other unknown PAOs and GAOs, is needed. Microbial diversity is higher in S2EBPR facilities compared with conventional ones, implying that S2EBPR microbial communities could show better resilience to perturbations due to potential functional redundancy.
Effect of Short-Term Exposure to Hexachlorophene on Rat Brain Marker Enzymes (1988)

Effect of Short-Term Exposure to Hexachlorophene on Rat Brain Cell Specific Marker Enzymes.KUNG, M-P., NICKERSON, P. A., SANSONE, F. M., OLSON, J. R., KOSTYNIAK, P. J., ADOLF, M. A., LIEN, P. J., AND ROTH, J. A. (1988). Fundam. Appl Toxicol 11, 519-527. Seven cell specific marker enzymes in brain and optic nerve and morphological evaluation by light microscopy were used to characterize the neurotoxicity associated with exposure of rats to hexachlorophene (HCP, 40 mg/kg/day, po, for 9 days). In vitro exposure to HCP at concentrations up to 100mm had no direct inhibitory effect on the marker enzymes, validating their use in evaluating brain function in vivo . Rats exhibited a reduction in body weight gain, weakness, and ataxia of the hind limbs by the ninth day of HCP exposure. At 24 hr following the last day of exposure to HCP, the activities of the three neuron specific enzymes, glutamic acid decarboxylase, tyrosine hydroxylase, and choline acetyltransferase, in rat brain were unchanged from 3 those of the vehicle-treated control group. Of the two astroglial enzyme markers measured, a small but significant increase was observed in the activity of nonneuronal enolase in the cerebellum and glutamine synthetase in the hippocampus of HCP-treated rats. The optic nerve appeared to be the most sensitive tissue in that the activity of both the astroglial marker, nonneuronal enolase, and the myelin marker, 2',3'-cyclic nuceleotide phosphohydrolase, was significantly decreased following HCP exposure. This decrease in enzyme activity is consistent with the histo-4 logical observations demonstrating extensive vacuolization and edema in the optic nerve after exposure to HCP.
The Role of Emission Layer Morphology on the Enhanced Performance of Light‐Emitting Diodes Based on Quantum Dot‐Semiconducting Polymer Hybrids (2016)

The influence of the morphology of quantum dot (QD)‐semiconducting polymer hybrid emission layers on the performance of quantum dot‐based light emitting diodes (QLEDs) is systematically investigated. Chemically grafted QD‐semiconducting polymer hybrids are fabricated by the ligand exchange procedure between CdSe/Cd x Zn 1− x S QDs and a new block copolymer consisting of a carbazole‐based electroactive block with a low highest occupied molecular orbital level and a disulfide‐based anchor block. The performance of QLEDs with hybrid emission layers is compared with QLEDs utilizing QD‐only and physically mixed QD/polymer emission layers. It is shown that only in the emission layers formed by chemically grafted hybrids QDs are evenly distributed throughout the semiconducting polymer matrix. This leads to improved charge transport balance and suppressed photoluminescence quenching of QDs. As a result, hybrid QLEDs with the peak external quantum efficiency of 5.6% and the peak luminance of 21 707 cd m −2 which outperform the conventional devices with QD‐only emission layers are fabricated.