gebhart/patrepeval huggingface dataset:
Engineered probiotics modulate the endocannabinoid system (2021)

Butyrate is a key microbial metabolite known to enhance host metabolic processes by reducing blood glucose levels and promoting energy metabolism, thereby potentially suppressing the risk of developing metabolic syndrome. In this study, we examined the activity of butyrate on modulating the endocannabinoid system, which regulates food intake and energy metabolism. Furthermore, we genetically engineered probiotics to produce butyrate to investigate their effects on the endocannabinoid system. Our study shows that the engineered probiotics exerted antagonistic effects on the endocannabinoid system by downregulating and upregulating the endocannabinoid-synthesizing and -degrading enzyme expression, respectively. Our results suggest that butyrate can modulate the endocannabinoid system, and incorporation of butyrate-producing bacteria into the gut microbiota can potentially aid in re-establishing homeostatic metabolic processes and alleviating metabolic syndrome.
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species (2013)

The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck's defense mechanisms against influenza infection have been optimized through the diversification of its β-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
Impact of dietary analyzed calcium to phosphorus ratios and standardized total tract digestible phosphorus to net energy ratios on growth performance, bone, and carcass characteristics of pigs (2023)

A total of 2,184 pigs (337 × 1,050, PIC; initially 12.4 ± 0.17 kg) were used in a 143-d study to evaluate the effects of feeding varying analyzed calcium to phosphorus ratios (Ca:P) at two standardized total tract digestible (STTD) phosphorus to net energy ratios (STTD P:NE). Pens of pigs (26 pigs per pen) were assigned to 1 of the 6 dietary treatments in a 2 × 3 factorial with main effects of STTD P:NE and Ca:P ratio. Diets consisted of two levels of STTD P:NE; High (1.80, 1.62, 1.43, 1.25, 1.10, and 0.99 g STTD P/Mcal NE from 11 to 22, 22 to 40, 40 to 58, 58 to 81, 81 to 104, and 104 to 129 kg, respectively); or Low (75% of the High levels), and three analyzed Ca:P ratios (0.90:1, 1.30:1, and 1.75:1). There were 14 pens per treatment. Diets were corn-soybean meal-based and contained a constant phytase concentration within each dietary phase with levels decreasing throughout the trial (phases 1 through 3, 500 FTU/kg, assumed release of 0.13% STTD P; phase 4, 400 FTU/kg, assumed release of 0.11% STTD P; phase 5, 290 FTU/kg, assumed release of 0.09% STTD P; and phase 6, 210 FTU/kg, assumed release of 0.07% STTD P). Overall, there was a Ca:P × STTD P:NE interaction (P < 0.05) observed for average daily gain (ADG), feed efficiency (G:F), final body weight (BW), hot carcass weight (HCW), bone mineral density, bone mineral content, and bone-breaking strength. When feeding Low STTD P:NE levels, increasing the analyzed Ca:P ratio decreased (linear, P < 0.001) ADG final BW, HCW, and tended to worsen G:F, bone mineral density, and bone mineral content (linear, P < 0.10). However, when feeding High STTD P:NE levels, increasing the analyzed Ca:P ratio significantly improved bone mineral content and bone mineral density (linear, P < 0.05), and tended to improve ADG and final BW (linear, P < 0.10) and G:F (quadratic P < 0.10). Additionally, increasing the analyzed Ca:P ratio worsened ADG, G:F, and bone mineralization with Low STTD P:NE but had marginal impacts when adequate STTD P:NE was fed.
P3‐207: Age correlates with cortical acetylcholinesterase decline in Alzheimer's disease patients: A PET study (2012)

Early-onset Alzheimer's disease (EOAD), defined by age of onset below 65, and late-onset Alzheimer's disease (LOAD), defined by age of onset above 65 differs in clinical manifestations, disease progression, genetic background and neuroimaging findings. Age seems to play an important role in the pathophysiology of Alzheimer's disease (AD). To elucidate the influence of age in the cholinergic function of AD, we measured brain acetylcholinesterase (AChE) activity by using positron emission tomography in patients with EOAD and LOAD. Participants were 22 EOAD (age 59.5 ± 5.3, MMSE 16.9 ± 4.2, duration 2.8 ± 1.6), 26 LOAD (age 74.0 ± 5.2, MMSE 18.3 ± 4.2, duration 1.5 ± 0.8) and 16 healthy control (HC: age 63.3 ± 11.0, MMSE 28.3 ± 1.1) (mean ± SD). Forty minutes dynamic scan with arterial blood sampling was conducted after intravenous injection of N [11 C]-methyl-4-piperidyl acetate ([11 C]MP4A). Realignment, spatial normalization and smoothing were performed by SPM2 and 2 tissue 3 parameter model non-linear least square estimation was used to calculate voxel-wise brain AChE activity. Brain mask excluding cerebellum and striatum was applied. Voxel-based group comparison and correlation analysis were performed followed by VOI analysis. Clusters were accepted as significant if Family-Wise Error corrected P values < 0.05 in cluster-level with extent threshold above 30 voxels. Parametric group comparison showed that AChE activity was widely attenuated in neocortex of EOAD group while the AChE reduction was relatively restricted to temporoparietal area in LOAD group. Significant differences between EOAD and LOAD groups were found in bilateral superior temporal and inferior parietal region. Regional AChE activity of left Wernicke's area was positively correlated with age in AD. VOI analysis showed, when compared with HC, mean cortical AChE activity was reduced by 19.0% in EOAD (P < 0.001) and 11.5% in LOAD (P < 0.001), different between EOAD and LOAD (P = 0.005).
Supplemental Figure 2 from A Phase I Trial of a Guadecitabine (SGI-110) and Irinotecan in Metastatic Colorectal Cancer Patients Previously Exposed to Irinotecan (2023)

&lt;p&gt;LINE1 changes in tumor CpG 1-3 on cycle 1 day 8 from baseline. LINE1 changes in tumor DNA in individual patient biopsy samples.&lt;/p&gt;
Electrochemical Control of the Enzymatic Polymerization of PEG Hydrogels: Formation of Spatially Controlled Biological Microenvironments (2013)

Control of pH gradient profile at the electrode-electrolyte interfaces allows the control of the enzymatic PEG-hydrogel polymerization. By tuning the solution pH, buffer capacity, and the applied current, the extent of the local inhibition and confinement of the Factor XIII-mediated polymerization of PEG are controlled. This technology opens new perspectives for the production of 3D-structured biological microenvironments.
Accelerating a Medical 3D Brain MRI Analysis Algorithm using a High-Performance Reconfigurable Computer (2007)

Many automatic algorithms have been proposed for analyzing magnetic resonance imaging (MRI) data sets. These algorithms allow clinical researchers to generate quantitative data analyses with consistently accurate results. With the increasingly large data sets being used in brain mapping, there has been a significant rise in the need for methods to accelerate these algorithms, as their computation time can consume many hours. This paper presents the results from a recent study on implementing such quantitative analysis algorithms on High-Performance Reconfigurable Computers (HPRCs). A brain tissue classification algorithm for MRI, the Partial Volume Estimation (PVE), is implemented on an SGI RASC RC100 system using the Mitrion-C High-Level Language (HLL). The CPU-based PVE algorithm is profiled and computationally intensive floating-point functions are implemented on FPGA-accelerators. The images resulting from the FPGA-based algorithm are compared to those generated by the CPU-based algorithm for verification. The Similarity Indexes (SI) for pure tissues are calculated to measure the accuracy of the images resulting from the FPGA-based implementation. The portion of the PVE algorithm thatwas implemented on hardware achieved a 11× performance improvement over the CPU-based implementation. The overall performance improvement of the FPGA-accelerated PVE algorithm was 3.5× with four FPGAs.
A General and Efficient Method for the Suzuki–Miyaura Coupling of 2‐Pyridyl Nucleophiles (2008)

Eines der allgemeinsten Systeme für die Kreuzkupplung von Aryl- und Heteroarylbromiden und -chloriden mit 2-Pyridyl-Nucleophilen wird vorgestellt. Als idealer Katalysator erwies sich [Pd2(dba)3] in Kombination mit Diaryl- (1) oder Dialkylphosphanoxiden (2) als Liganden (siehe Schema). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2008/z801465_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Stable Tin-Based Perovskite Solar Cells (2023)

The developments in halide perovskite research target the next era of semiconductors. Photovoltaic solar cells are only one of the technologies that could be exploiting the potential of perovskites soon. Stability and toxicity are two critical aspects of photovoltaic applications because of the long-lasting lifetime and large volumes of the targeted technologies, such as multijunction solar cells with high power conversion efficiency. In this Perspective piece, I discuss how stability and toxicity can be addressed now, incentivizing the research toward lead-free and low-lead formulations. Recent works demonstrated that tin is a possible way out of the toxicity and stability issues of current perovskite formulations. I give speculative directions for stable tin-based perovskite solar cells.
Memantine for AIDS Dementia Complex: Open-Label Report of ACTG 301 (2010)

Objective: To evaluate the long-term safety and effi cacy of memantine use as treatment of HIV-associated cognitive impairment.Background: The results of a 20-week, randomized, double-blind, placebo-controlled trial of memantine in HIV-infected participants with cognitive impairment (ACTG 301) were previously reported.We report the results of the up-to-60-week open-label phase following the double-blind phase.Method: Participants received open-label memantine and were escalated to a 40 mg/day dose or their maximum tolerated dose in the double-blind phase.Adverse experiences were used to evaluate safety, and changes in the mean of eight neuropsychological test scores (NPZ-8) were used to evaluate effi cacy.Results: Ninety-nine participants entered the initial 12-week openlabel phase and 45 in the additional 48-week extension.Twenty-seven participants reported severe adverse experiences.During the initial 12-week open-label phase, participants randomized to memantine in the double-blind phase had a statistically signifi cant higher improvement in NPZ-8 compared to those randomized to placebo in the double-blind phase.No statistically signifi cant NPZ-8 changes were detected during the 48-week extension.Conclusion: Long-term use of memantine appears safe and tolerable.Future randomized studies with longer follow-up are necessary to establish effi cacy of memantine for the treatment of HIV-associated cognitive impairment.
Brucella suis urease encoded by ure 1 but not ure 2 is necessary for intestinal infection of BALB/c mice (2007)

These findings suggest that the ure1 operon is necessary for optimal growth in culture, urease activity, resistance against low-pH killing, and in vivo persistence of B. suis when inoculated by gavage. The ure2 operon apparently enhances the resistance to low-pH killing in-vitro.
Conical Emission of a Femtosecond Pulse Undergoing Self-focusing and Ionization in Air (1997)

Recently, the phenomenon of intense femtosecond light pulse filamentation over distances of several tens of meters was observed [1,2]. The study of long-interaction-length intense laser pulses has interesting applications including laser-induced lightning, laser-pumped x-ray sources, and laser-plasma based accelerators.
COVID-19 Vaccination hesitancy in black Americans: need for trusted voices explaining justified concerns (2023)

COVID-19 Vaccination hesitancy in black Americans: need for trusted voices explaining justified concerns was published in Mathematics for Human Flourishing in the Time of COVID-19 and Post COVID-19 on page 1.
Toward automatic robot instruction from perception-temporal segmentation of tasks from human hand motion (1995)

This paper describes work on the temporal segmentation of grasping task sequences based on human hand motion. The segmentation process results in the identification of motion breakpoints separating the different constituent phases of the grasping task. A grasping task is composed of three basic phases: pregrasp phase, static grasp phase, and manipulation phase. We show that by analyzing the fingertip polygon area (which is an indication of the hand preshape) and the speed of hand movement (which is an indication of the hand transportation), we can divide a task into meaningful action segments such as approach object (which corresponds to the pregrasp phase), grasp object, manipulate object, place object, and depart (a special case of the pregrasp phase which signals the termination of the task). We introduce a measure called the volume sweep rate, which is the product of the fingertip polygon area and the hand speed. The profile of this measure is also used in the determination of the task breakpoints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RCM-Mediated Synthesis of Fluorinated Cyclic Hydrazines (2008)

A series of fluorinated cyclic hydrazine derivatives has been prepared in a straightforward manner using ring-closing me­tathesis (RCM) of fluorinated- and trifluoromethylated olefins as the key step.
Bedding-plane slip as a microseismic source during hydraulic fracturing (2016)

Microseismic source mechanisms in shales often show similar double-couple events with one vertical nodal plane aligned with the hydraulic fracture and the other nodal plane oriented horizontal. We interpret the horizontal nodal plane as the fault plane where the shearing represents bedding-plane slip driven by opening of a connected, vertical hydraulic fracture. Using precisely mapped microseismic source locations from a Barnett shale hydraulic-fracture completion, Rutledge et al. (2015) proposed a model of step-over or jog structures along bedding to describe bedding plane slip and sense-of-slip reversals driven by vertical fracture opening. However, common step-over features will usually be too small to create a detectable microseismic signal, and if large, will terminate vertical growth. Chuprakov and Prioul (2015) describe a model of hydraulic-fracture growth through weak bedding interfaces where tensile crack growth can arrest at interfaces encountered. Fluid invasion and pressure can weaken the interface which can then shear from the added stress of adjacent crack opening. Under certain conditions, with subsequent net pressure recovery and gain, tensile fracture propagation can continue across the interface. Invoking this model, at least qualitatively, makes a more consistent explanation of the continuity and time-space development of the microseismic structures, as well as explaining the observed patterns of shear-fracture first motions. Presentation Date: Tuesday, October 18, 2016 Start Time: 10:20:00 AM Location: 144/145 Presentation Type: ORAL
Metal Debris From Titanium Spinal Implants (1999)

Wear debris is generated by the use of titanium spinal instrumentation in patients with a pseudarthrosis. These particles activate a macrophage cellular response in the spinal tissues similar to that seen in surrounding joint prostheses. Patients with a solid spinal fusion have negligible levels of particulate matter.
An assay for the detection of the dna genome of hepatitis b virus in serum (1982)

Abstract An assay based on nucleic acid hybridization detects and quantitates hepatitis B virus (HBV) DNA in particles present in serum. This assay allows rapid examination of multiple samples and is sensitive and reproducible; serum samples are treated with proteolytic enzyme and detergent and then extracted with phenol and chloroform. The deproteinized extracts which may contain HBV DNA are made alkaline to denature the DNA, neutralized, and bound to nitrocellulose filters in 3‐mm in diameter “spots” in a special 96‐well filtration apparatus. HBV DNA is detected by its ability to hybridize with 32 P‐labeled DNA prepared from recombinant plasmids containing the complete HBV genome. After hybridization, the nitrocellulose is washed and autoradiographed; samples containing HBV produce spots on X‐ray film whose intensity (in the linear exposure range of the film) is proportional to the amount of HBV DNA in the serum sample. The assay is specific and sensitive, correlates with infectivity of sera titered in chimpanzees as well as biophysical parameters, and is in agreement with serological indicators of HBV presence.
Electron spin resonance of TOAC labeled peptides: Folding transitions and high frequency spectroscopy (2000)

The unnatural, conformationally constrained nitroxide amino acid TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) stabilizes helical structure and provides a means for studying rigidly spin labeled peptides by electron spin resonance (ESR). Two new directions in TOAC research are described. The first investigates intermediates formed during alpha-helix unfolding. Double TOAC labeled alpha-helical peptides were unfolded at low temperature in aqueous solution with increasing concentrations of guanidine hydrochloride. Comparison of ESR spectra from two doubly labeled peptides suggests that 3(10)-helix emerges as an intermediate. The second research direction involves the use of high frequency ESR (140 GHz) at low temperature to assess dipolar couplings and, hence, distances between TOAC pairs in a series of 3(10)-helical peptides. Preliminary simulations suggest that high frequency ESR is able to extract correct distances between 6 and 11 A. In addition, the spectra appear to be very sensitive to the relative orientation of the TOAC labels.
Development of Patent Infection in Immunosuppressed C57BL/6 Mice with a Single Cryptosporidium meleagridis Oocyst (2003)

The ability of Cryptosporidium meleagridis to produce patent infection was studied in adult C57BL/6 mice that were immunosuppressed with dexamethasone phosphate provided in the drinking water at a dosage of 16 microg/ml. Four days after the onset of immunosuppression, mice were orally challenged with 1, 3, 10, or 1,000 C. meleagridis TU1867 oocysts per mouse. The mice were monitored daily for 18 days postinoculation for oocyst shedding. Five of 10 mice given a single oocyst, 4 of 5 mice given 3 oocysts, and all 9 mice given either 10 or 1,000 oocysts became infected and began shedding oocysts 5-7 days after challenge and continued to shed oocysts until the end of the experiment on day 18 postchallenge. Approximately 10(7) oocysts per mouse per day were excreted, regardless of the challenge dose. Neither the noninfected, immunosuppressed nor the inoculated, nonimmunosuppressed control mice shed oocysts. The excreted oocysts were confirmed to be those of C. meleagridis by polymerase chain reaction-restriction fragment length polymorphism analysis. We show that C. meleagridis, originally classified as an avian pathogen but recently found in humans with cryptosporidiosis, can produce patent infection in mice infected with a single oocyst. Moreover, we demonstrate that the immunosuppressed C57BL/6 adult mouse is an ideal host for the propagation of clonal populations of C. meleagridis isolates for laboratory studies.
Discrete Distribution Estimation under Local Privacy (2016)

The collection and analysis of user data drives improvements in the app and web ecosystems, but comes with risks to privacy. This paper examines discrete distribution estimation under local privacy, a setting wherein service providers can learn the distribution of a categorical statistic of interest without collecting the underlying data. We present new mechanisms, including hashed K-ary Randomized Response (KRR), that empirically meet or exceed the utility of existing mechanisms at all privacy levels. New theoretical results demonstrate the order-optimality of KRR and the existing RAPPOR mechanism at different privacy regimes.
Time-space tradeoffs for undirected graph traversal (2002)

Time-space tradeoffs for traversing undirected graphs are proved. One of these tradeoffs is a quadratic lower bound on a deterministic model that closely matches the probabilistic upper bound of A.Z. Broder et al. (1989). The models used are variants of S.A. Cook and C.W. Rackoff's (1980) jumping automata for graphs. Some open problems are stated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High-resolution tomographic imaging of a human cerebellum: comparison of absorption and grating-based phase contrast (2010)

Human brain tissue belongs to the most impressive and delicate three-dimensional structures in nature. Its outstanding functional importance in the organism implies a strong need for brain imaging modalities. Although magnetic resonance imaging provides deep insights, its spatial resolution is insufficient to study the structure on the level of individual cells. Therefore, our knowledge of brain microstructure currently relies on two-dimensional techniques, optical and electron microscopy, which generally require severe preparation procedures including sectioning and staining. X-ray absorption microtomography yields the necessary spatial resolution, but since the composition of the different types of brain tissue is similar, the images show only marginal contrast. An alternative to absorption could be X-ray phase contrast, which is known for much better discrimination of soft tissues but requires more intricate machinery. In the present communication, we report an evaluation of the recently developed X-ray grating interferometry technique, applied to obtain phase-contrast as well as absorption-contrast synchrotron radiation-based microtomography of human cerebellum. The results are quantitatively compared with synchrotron radiation-based microtomography in optimized absorption-contrast mode. It is demonstrated that grating interferometry allows identifying besides the blood vessels, the stratum moleculare, the stratum granulosum and the white matter. Along the periphery of the stratum granulosum, we have detected microstructures about 40 µm in diameter, which we associate with the Purkinje cells because of their location, size, shape and density. The detection of individual Purkinje cells without the application of any stain or contrast agent is unique in the field of computed tomography and sets new standards in non-destructive three-dimensional imaging.
High prevalence of Chlamydophila psittaci subclinical infection in Italian patients with Sjögren's syndrome and parotid gland marginal zone B-cell lymphoma of MALT-type. (2014)

In the light of accepted models of MALT B-cell lymphomagenesis and considering previous data implicating Cp infection in ocular adnexa MALT lymphoma, our results suggest that Cp infection could be involved also in a fraction of patients with SS developing lymphoma. The potential therapeutic implications of these findings appear worthwhile.