gebhart/patrepeval huggingface dataset:
Hypertension and SARS-CoV-2 infection: is inflammation the missing link? (2020)

receptor The dramatic emergence of the pandemic coronavirus disease COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raised significant medical and public health concerns for the high disease mortality rate ranging from 1% to more than 5%. In this setting, patients with severe disease exhibit high serum levels of proinflammatory cytokines, including interleukin (IL)-1b and IL-6, and their elevated concentrations closely relate to worse outcome. 1 In addition to respiratory failure, cardiovascular system involvement and myocardial Figure 1 Alveolar epithelial cell internalize SARS-CoV-2 by ACE2. Viral PAMPs bind to TLR4 located on alveolar macrophage and activate adaptor protein MyD88-TNF receptor-associated factor (TRAF) 6 pathway, nuclear factor kappa B (NF-jB) translocation into the nucleus and pro-inflammatory cytokine release. TLR4-associated activation of TIR-domain-containing adapter-inducing interferon-b (TRIF) signalling results in a cascade similar to MyD88 pathway. Moreover, the NLRP3 inflammasome complex may be directly activated by NF-jB with IL-1b secretion and cytokine storm. The same mechanism may occur on endothelial cells inducing endothelial damage and subsequent hypertension.
Molecular Recognition between Azotobacter vinelandii Rhodanese and a Sulfur Acceptor Protein (2003)

The occurrence of rhodanese-like proteins in the major evolutionary phyla, together with the observed abundance of these proteins also within the same genome, suggests that their function cannot be limited to cyanide scavenging. The aim of the present study was to investigate whether Azotobacter vinelandii RhdA, an enzyme possessing unique biochemical and structural features with respect to other members of rhodanese homology superfamily, could recognize a suitable protein as a potential acceptor of the sulfane sulfur held on its catalytic Cys residue. Both the potential sulfur-delivery RhdA-S and the sulfur-deprived RhdA were found to interact with either holo- or apo-adrenodoxin, the 'substrate' protein used in this work. Interaction of RhdA-S with apo-adrenodoxin led to mobilization of RhdA-S sulfane sulfur. Under appropriate conditions, the sulfur released from RhdA-S was productively used for 2Fe-2S cluster reconstitution to yield holo-adrenodoxin from apo-adrenodoxin in the absence of any other sulfur source. A comparison of the reactivity of RhdA-S with protein and non-protein thiols allowed also some insights into the accessibility of the sulfane sulfur carried by RhdA.
Anatomical guided segmentation with non-stationary tissue class distributions in an expectation-maximization framework (2005)

High quality segmentation of brain MR images is a challenging task. To deal with this problem many automatic segmentation methods rely on atlas information of anatomical structures. We further investigate this line of research by introducing hierarchical representations of anatomical structures in an Expectation-Maximization framework. This new approach enables us to divide a complex segmentation scenario into less difficult sub-problems reducing the scenario's statistical complexity. We demonstrate the method's strength by segmenting a set of brain MR images into 31 different anatomical structures as well as comparing it to other methods.
Efficacy of Indirect Enzyme Immunosorbent Assay and Passive Haemagglutination Test for the Diagnosis of Bovine Herpes Virus-1 (BHV-1) Infection (2016)

A total of 255 sera were collected from unvaccinated crossbred (174) and indigenous (81) cattle and buffalo having history of respiratory and reproductive disorders. All the sera sample were subjected to indirect ELISA and passive haemagglutination (PHA) test for the detection of BHV-1 antibodies. Indirect ELISA and PHA test detected significantly (P<0.01) varied prevalence of BHV-1 antibody i.e. 60.39% and 35.69%, respectively. The sensitivity and specificity of PHA test in comparison with indirect ELISA was 55.19% and 94.06%, respectively. Moderate agreement (kappa = 0.442) was noticed between ELISA and PHA for the diagnosis of BHV-1 antibodies. Significantly (p< 0.01) higher prevalence of BHV-1 antibodies was observed in crossbred (70.11%) as compared to indigenous cattle and buffalo (46.91%). Hence, it is be concluded from present investigation that the indirect ELISA could be reliable and sensitive test than PHA test to screen BHV-1 antibody.
Luminescent probes for detergent solutions. A simple procedure for determination of the mean aggregation number of micelles (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLuminescent probes for detergent solutions. A simple procedure for determination of the mean aggregation number of micellesNicholas J. Turro and Ahmad YektaCite this: J. Am. Chem. Soc. 1978, 100, 18, 5951–5952Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/ja00486a062https://doi.org/10.1021/ja00486a062research-articleACS PublicationsRequest reuse permissionsArticle Views7264Altmetric-Citations866LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Generation of focal mutations and large genomic deletions in the pancreas using inducible <i>in vivo</i> genome editing (2019)

Beyond the nearly uniform presence of KRAS mutations, pancreatic cancer is increasingly recognized as a heterogeneous disease. Preclinical in vivo model systems exist, but with the advent of precision oncology, murine models with enhanced genetic flexibility are needed to functionally annotate genetic alterations found in the human malignancy. Here, we describe the generation of focal gene disruptions and large chromosomal deletions via inducible and pancreas-specific expression of Cas9 in adult mice. Experimental mice are derived on demand directly from genetically engineered embryonic stem cells, without the need for further intercrossing. To provide initial validation of our approach, we show that disruption of the E3 ubiquitin ligase Rnf43 accelerates KrasG12D-dependent tumourigenesis. Moreover, we demonstrate that this system can be used to rapidly interrogate the impact of complex cancer-associated alleles through the generation of a previously unstudied 1.2 megabase deletion surrounding the CDKN2A and CDKN2B tumour suppressors. Thus, our approach is capable of reproducibly generating biallelic and precise loss of large chromosomal fragments that, in conjunction with mutant Kras, leads to development of pancreatic ductal adenocarcinoma with full penetrance.
Expressions of Cell Cycle Regulators in Human Colorectal Cancer Cell Lines (1997)

To study the altered mechanisms of cell cycle regulation in colorectal cancer, the expressions of cyclins, cyclin-dependent kinases (CDKs), CDK inhibitors, p53 and retinoblastoma (Rb) protein were analyzed by western blotting in a series of human colorectal cancer cell lines. The colorectal cancer cell lines exhibited various expression patterns of cell cycle regulators, which may reflect differences in the biological characteristics of cancer cells and in the genetic backgrounds of carcinogenesis. A correlation was found between p53 gene alteration and p21 expression, suggesting that p53 gene mutation usually suppresses p21 expression, though p21 expression could be induced via both a p53-dependent and a p53-independent pathway in colorectal cancer. None of the cell lines studied expressed p16 protein, suggesting that inactivation of p16 may be a common alteration in colorectal cancer. Moreover, all the D-type cyclins, especially D2 and D3, were expressed at a high level in most of the cell lines. Loss of p16 expression and increased expression of D-type cyclins promote CDK-mediated Rb phosphorylation. All of the colorectal cancer cell lines studied herein expressed Rb protein, but the growth-suppressive properties of Rb may be inactivated by the loss of p16 expression and increased expressions of D-type cyclins. In view of the pivotal role of Rb in cell cycle regulation, loss of p16 expression and overexpression of D-type cyclins may be critical alterations in colorectal cancer.
Quick-Starting Fuel Processors - A Feasibility Study (2003)

Approach • Working with multiple national laboratories, universities, and commercial organizations, design a gasoline fuel processor that can meet DOE's performance targets. • Develop a start-up strategy that will enable the fuel processor to deliver >90% of its rated hydrogen production capacity in 60 seconds or less. • Demonstrate start-up performance of key fuel processor components and the performance of the integrated fuel processor in laboratory tests. • Analyze test results to evaluate performance.
The Products of the Herpes Simplex Virus Type 1 Immediate-Early U <sub>S</sub> 1/U <sub>S</sub> 1.5 Genes Downregulate Levels of S-Phase-Specific Cyclins and Facilitate Virus Replication in S-Phase Vero Cells (2006)

Herpes simplex virus type 1 ICP22-/U(S)1.5- mutants initiate viral gene expression in all cells; however, in most cell types, the replication process stalls due to an inability to express gamma2 late proteins. Although the function of ICP22/U(S)1.5 has not been established, it has been suggested that these proteins activate, induce, or repress the activity of cellular proteins during infection. In this study, we hypothesized that cell cycle-associated proteins are targets of ICP22/U(S)1.5. For this purpose, we first isolated and characterized an ICP22-/U(S)1.5- mutant virus, 22/n199. Like other ICP22-/U(S)1.5- mutants, 22/n199 replicates in a cell-type-specific manner and fails to induce efficient gamma2 late gene expression in restrictive cells. Although synchronization of restrictive human embryonic lung cells in each phase of the cell cycle did not overcome the growth restrictions of 22/n199, synchronization of permissive Vero cells in S phase rendered them less able to support 22/n199 plaque formation and replication. Consistent with this finding, expression of cellular S-phase cyclins was altered in an ICP22/U(S)1.5-dependent manner specifically when S-phase Vero cells were infected. Collectively, these observations support the notion that ICP22/U(S)1.5 deregulates the cell cycle upon infection of S-phase permissive cells by altering expression of key cell cycle regulatory proteins either directly or indirectly.
Computational investigations of structural changes resulting from point mutations in a collagen-like peptide (1999)

The results of 0.5-1.0 ns molecular dynamics simulations of the collagen-like peptides [(POG)4(POA)(POG)4]3 and [(POG)9]3 (POG: proline-hydroxyproline-glycine) are presented. All simulations were performed using the AMBER-94 molecular mechanical force field with a shell of TIP3P waters surrounding the peptides. The initial geometries for the collagen-like peptides included an x-ray crystallographic structure, a computer-generated structure, a [(POG)9]3 structure modeled from the x-ray structure, and the x-ray structure with crystallographic waters replaced with a shell of modeled TIP3P waters. We examined the molecular dynamics peptide residue rms deviation fluctuations, dihedral angles, molecular and chain end-to-end distances, helical parameters, and peptide-peptide and peptide-solvent hydrogen-bonding patterns. Our molecular dynamics simulations of [(POG)4(POA)(POG)4]3 show average structures and internal coordinates similar to the x-ray crystallographic structure. Our results demonstrate that molecular dynamics can be used to reproduce the experimental structures of collagen-like peptides. We have demonstrated the feasibility of using the AMBER-94 molecular mechanical force field, which was parameterized to model nucleic acids and globular proteins, for fibril proteins. We provide a new interpretation of peptide-solvent hydrogen bonding and a peptide-peptide hydrogen bonding pattern not previously reported in x-ray studies. Last, we report on the differences; in particular with respect to main-chain dihedral angles and hydrogen bonding, between the native and mutant collagen-like peptides.
Automatic classification of minelike targets buried underground using time-frequency signatures extracted by a stepped-frequency radar (2001)

Ultra-wideband radar systems are feasible for extracting signature infor-ma-tion use-ful for target recognition purposes. An ultra-wideband radar system emits either an extremely short pulse, impulse, or a frequency modulated signal. The frequency content of the emitted signals is designed to match the size and kind of typical targets and environments. We investigate the backscattered echoes from selected targets that are extracted by a stepped-frequency continuous wave (SFCW) radar system playing the role of ground penetrating radar (GPR). The targets are metal and non-metal objects buried in dry sand. The SFCW radar transmits 55 different frequencies from 300 to 3,000 MHz in steps of 50 MHz. The duration of each frequency is about 100 µs, which means that each transmitted waveform has an extremely narrow band. The in-phase (I) sampled signals and quadrature-phase (Q) sampled signals give information of both the amplitude and phase of the signal returned from the target. As a result a complex-valued line spectrum of the target is obtained that can be used for synthesizing real-valued repetitive waveforms, using the inverse Fourier transform. We analyze synthe-sized back-scat-tered echoes from each target in the joint time-frequency domain us-ing a pseudo-Wigner distribution (PWD). A classification method that we developed previously using the fuzzy C-means clustering technique is then used to reduce the number and kind of fea-tures in the derived target signatures. Using a template for each member of the class the classifier decides the membership of a given target based on best fit of the templates measured by a cost function. We also address the problem of how to select suitable waveforms for the templates used by the classification algorithm.
Dynamics of Social Interactions in a Network Game (2011)

We characterize the social dynamics of human players in a transactional online game. We introduce two new approaches for understanding temporal behavior: the introduction of entropy dynamics, where we measuring the change in the entropy of certain descriptive distributions over the course of a game, and the use of clustering to discover temporal dynamics in subpopulations of experimental subjects. Experiments were conducted in the context of the Social Ultimatum Game, a multi-agent multi-round extension of a classical game-theoretic domain, using two distinct populations. We show that we are able to extract temporal behavior from the use of entropy dynamics and identify unique subpopulation behavior with respect to generosity, reciprocity and fairness.
Graft rejection as a Th1-type process amenable to regulation by donor Th2-type cells through an interleukin-4/STAT6 pathway (2008)

Graft rejection has been defined as the mirror image of graft-versus-host disease, which is biologically characterized primarily as a Th1-type process. As such, we reasoned that graft rejection would represent a Th1 response amenable to Th2 modulation. Indeed, adoptive transfer of host Th1-type cells mediated rejection of fully MHC-disparate murine bone marrow allografts more effectively than host Th2-type cells. Furthermore, STAT1-deficient host T cells did not differentiate into Th1-type cells in vivo and failed to mediate rejection. We next hypothesized that donor Th2 cell allograft augmentation would prevent rejection by modulation of the host Th1/Th2 balance. In the setting of donor Th2 cell therapy, host-anti-donor allospecific T cells acquired Th2 polarity, persisted posttransplantation, and did not mediate rejection. Abrogation of rejection required donor Th2 cell IL-4 secretion and host T-cell STAT6 signaling. In conclusion, T cell-mediated marrow graft rejection primarily resembles a Th1-type process that can be abrogated by donor Th2 cell therapy that promotes engraftment through a novel mechanism whereby cytokine polarization is transferred to host T cells.
Highly ordered Pb(Zr<sub>0.52</sub>Ti<sub>0.48</sub>)O<sub>3</sub>piezoelectric nanorod arrays (2013)

One-dimensional (1D) piezoelectric nanostructures have attracted significant attention for a broad range of applications including optoelectronics, thermoelectrics, electrochemical and electromechanical converters. We demonstrate the synthesis of 1D nanostructures based upon Pb(Zr0.52Ti0.48)O3 (PZT) on conductive substrates via sol-gel template synthesis. The vertically aligned PZT nanostructures with heights around one micron were synthesized by vacuum infiltration of sol-gel precursors into highly ordered cylindrical pores of anodized aluminum oxide templates. The 1D nanostructures were developed on large scale platinized silicon wafers and exhibited dense rod-like structure with a uniform diameter of 90 nm and an aspect ratio of 10. Scanning probe microscopy conducted on individual nanorods demonstrated good electromechanical properties with a high piezoelectric magnitude of 41 pm V(-1). We believe that this study opens the possibility of developing high performance nanoscale piezoelectric sensors and transducers.
Random charge pulser: A diagnostic tool (1991)

Electronic instrumentation used in conjunction with germanium gamma‐ray detectors for astrophysics observations must be tested under conditions similar to those encountered during actual operations. Simulation of cosmic‐rays, gamma‐ray bursts and solar flares is necessary to validate the performance of the entire spectroscopy chain. A random charge pulser used in conjunction with other diagnostic pulsers, and the techniques developed to verify the performance with and without a germanium gamma‐ray detector are described.
Toward Better Formula Lower Bounds: An Information Complexity Approach to the KRW Composition Conjecture. (2013)

One of the major open problems in complexity theory is proving super-polynomial lower bounds for circuits with logarithmic depth (i.e., P ̸ ⊆ NC1). This problem is interesting for two reasons: first, it is tightly related to understanding the power of parallel computation and of small-space computation; second, it is one of the first milestones toward proving superpolynomial circuit lower bounds. Karchmer, Raz, and Wigderson [KRW95] suggested to approach this problem by proving the following conjecture: given two boolean functions f and g, the depth complexity of the composed function g ◦ f is roughly the sum of the depth complexities of f and g. They showed that the validity of this conjecture would imply that P ̸ ⊆ NC1. As a starting point for studying the composition of functions, they introduced a relation called “the universal relation”, and suggested to study the composition of universal relations. This suggestion proved fruitful, and an analogue of the KRW conjecture for the universal relation was proved by Edmonds et. al. [EIRS01]. An alternative proof was given later by H˚astad and Wigderson [HW93]. However, studying the composition of functions seems more difficult, and the KRW conjecture is still wide open. In this work, we make a natural step in this direction, which lies between what is known and the original conjecture: we show that an analogue of the conjecture holds for the composition of a function with a universal relation. We also suggest a candidate for the next step and provide initial results toward it. Our main technical contribution is developing an approach based on the notion of information complexity for analyzing KW relations – communication problems that are closely related to questions on circuit depth and formula complexity. Recently, information complexity has proved to be a powerful tool, and underlined some major progress on several long-standing open problems in communication complexity. In this work, we develop general tools for analyzing the information complexity of KW relations, which may be of independent interest. 1
PM-11 * DEVELOPMENT OF A NOVEL GENE TARGETING AND CLONE SCREENING PLATFORM TO ENGINEER COMMON PEDIATRIC GLIOMA MUTATIONS INTO MODEL CELL LINES (2015)

The utility of CRISPR/Cas9 gene targeting tools to alter endogenous genomic loci has revolutionized biomedical research across numerous disease focus areas, with especially large gains made in the development of disease models. However, the introduction of specific mutations using donor DNA templates can be associated with low yields of single cell clones harboring homozygous versus heterozygous mutations. Conventional clone screening methods can be a labor intensive and expensive process, and thus better approaches are needed to identify cells with the desired genotype(s). In parallel, there is a dearth of human tumor cell model systems for pediatric cancers. To address these needs, we recently designed and validated a platform which utilizes a novel, inducible Cas9 expression system coupled with a high-resolution DNA melt (HRM) analysis protocol to rapidly identify mutant clones. We applied our platform to model several common DIPG mutations, including the Lys27Met missense mutation within histone variant H3.3 (H3F3A), and truncating mutations within protein phosphatase 1D (PPM1D) exon 6. Using our HRM protocol, both heterozygous point mutations in H3F3A, and indels in PPM1D were detectable and grouped distinctly from wild-type samples. These findings were validated using conventional Sanger sequencing and topo cloning, which confirmed that this approach could differentiate between mutant and wild-type clones. Multiple clones were generated in under four weeks using this process-flow. These findings highlight the utility and power of our unique approach to rapidly create engineered mutant cell lines. Our platform likely will become an invaluable tool for the development of better pediatric glioma cell line models in the future.
Effect of Epitoge Density on the Induction of the IgE Immune Response in Mice (1980)

The effect of hapten density on benzylpenicilloyl (BPO)-protein conjugates upon the induction of BPO-specific IgE immune response was investigated in BALB/c and C3H mice. Bovine gamma-globulin (BGG) and ovalbumin (OA) were employed as carrier proteins. In both strains of mice, moderately substituted conjugates (BPO19-BGG, and BPO-OA with an epitope density from 2 to 7.5) elicited a persistent BPO-specific IgE, while heavily substituted conjugates (BPO38-BGG) induced only a transient response. In contrast, lightly substituted conjugates (BPO3.2-, BPO9.5-BGG, and BPO1-OA) failed to produce BPO-specific IgE antibodies. There was no significant difference in carrier-specific IgE immune response among these various conjugates. These results suggest that moderately substituted hapten-protein conjugates are one of the favorable conditions for eliciting hapten-specific IgE immune response in mice.
Antenna array errors calibration algorithm for digital beamforming array (2014)

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