gebhart/patrepeval huggingface dataset:
Genetic Modeling of Chemical Antagonists: Genome Scale Validation of Hematopoietic Disease Drug Targets by In Vivo Functional Analysis. (2004)

Abstract Clinical management remains elusive for a large number of patients with hematological and other disorders necessitating the development of new, more effective pharmaceutical agents. While the sequencing of the human genome has provided a list of all drug targets that will ever exist, in order to improve the speed and cost of drug development there is a critical need to identify the small subset of these targets whose modulation will lead to therapeutic outcomes. As a genetic model of a perfectly selective and potent chemical antagonist, the analysis of the phenotypes of knockout mice allows one to predict the mechanism based efficacy and side effect profile of modulators of a particular target in a physiologic mammalian setting without having to first develop a candidate drug with which to validate the target. The power of this approach has been demonstrated by studies examining the targets of the best-selling drugs and current pharmaceutical pipelines. These analyses have confirmed a strong (~85%) correlation between the target’s knockout phenotype and the efficacy and/or side effects of drugs that modulate them. We have implemented this target validation approach by developing systems and infrastructure to generate and comprehensively phenotype mutant mice at a rate of more than fifteen novel lines per week. The battery of tests encompassed by our analysis have been specifically selected to reveal those genes that encode key control points in mammalian physiology whose modulation may be used to treat major disease processes including hematologic disorders. Tests to detect hematologic phenotypes include complete blood count; immunophenotyping; blood chemistry; analysis of soluble factors (immunoglobulins, cytokines and inflammatory mediators); full histopathologic examination, and various in vivo and in vitro immune challenge and cell activation assays. In addition, selected lines are subjected to more extensive analyses including additional challenge assays, gene expression profiling, and bone marrow transplantation. Data will be presented describing one of the lines analyzed in this screen, the Abl2 knockout, which has an increased mean total white blood count relative to wild-type littermates, as well as smaller body size (decreased length and weight). In parallel with the identification of therapeutically relevant proteins, we are actively exploring pharmacologic methods, both with small molecules and therapeutic antibodies, to modify the function of these novel gene targets, and ultimately to treat human disease.
A nuclear radiation detector system with integrated readout for SPECT/MR small animal imaging (2007)

We have developed and constructed an MR-compatible single photon emission computed tomography (SPECT) system for small animal molecular imaging applications. The system consists of identical radiation imaging modules and a multi-pinhole collimator sleeve. The modular design results in a very compact system which allows for easy insertion into state-of-the-art small animal MRI systems. This development leads to a multi-modality system that allows one to accurately coregister SPECT and MR images in space and time. The MR-compatible SPECT unit has a barrel shape with 119-mm outer diameter designed to fit into an MRI system with a 120-mm diameter inner bore. The inner diameter of the SPECT unit is 35 mm which is large enough to fit a mouse, and provides a 30-mm diameter imaging field of view (FOV). The system does not require active cooling due to its low-power dissipation. The radiation sensor performance is not affected by the presence of the magnetic field from the MRI system. The results are very promising for applications of the SPECT/MR system to small animal imaging.
Attacks and Defenses Utilizing Cross-Layer Interactions in MANET (2004)

Cross-layer protocol design is one of the prevailing methodologies that have recently been adopted in networking research and leads to significant performance benefits. In this study, we assess the performance of cross-layer interaction and investigate its effects with regard to security and information assurance of mobile ad hoc wireless networks. Using attacks in realistic wireless networks as a prototype, we find that natural cross-layer interactions between physical, MAC and network layer protocols in MANET can turn out to be a weak point, causing various attacks and intrusions. However, by allowing a controlled synergy between layers affected by attacks, we facilitate timely detection of such attacks that are otherwise difficult to detect and may have devastating effects on network functionality and operation. 1
Design and Evaluation of Nano-Composite Core Inductors for Efficiency Improvement in High-Frequency Power Converters. (2020)

Abstract not provided.
Automatic adaptation of streaming multimedia content in a dynamic and distributed environment (2005)

The diversity of end-terminal and access network capabilities as well as the dynamic nature of wireless connections pose significant challenges to providers of multimedia streaming services. In this paper, we present a system based on MPEG-21 Digital Item Adaptation (DIA) technologies that automatically adapts scalable multimedia resources, like upcoming MPEG-4 Scalable Video Coding (SVC) streams, in a generic and transparent way to the user and session context. This context includes terminal and network capabilities as well as user characteristics. A server side adaptation engine reacts to context changes by dynamic decision taking and accordingly modified bitstream adaptation. Furthermore, novel concepts are presented that facilitate multimedia adaptation in a distributed fashion along the delivery path.
Molecular analysis of peripheral non-squamous non-small cell lung cancer sampled by radial EBUS (2016)

<b>Background:</b> Treatment optimization of non-squamous non-small-cell lung cancers (nonSq-NSCLC) relies on the molecular analysis of the tumour. <b>Objective:</b> We aimed to assess the predictive factors of molecular analysis feasibility (MAF) from samples of peripheral nonSq-NSCLC obtained by radial endobronchial ultrasound bronchoscopy (r-EBUS) and 1.5 mm microbiopsy forceps. <b>Methods:</b> we reviewed data from consecutive peripheral lung nodules sampled with r-EBUS between January 2012 and July 2014 at a single French University Hospital. nonSq-NSCLC were systematically analysed for <i>EGFR</i><i>, KRAS</i><i>, ALK</i><i>, HER</i><i>2, PI3K</i> and <i>BRAF</i> throughout the study, and <i>c-</i><i>MET</i> and <i>ROS</i><i>1</i> alterations for the last 10 months. <b>Results:</b> Of 111 nonSq-NSCLC diagnosed by r-EBUS (113 procedures, mean nodule diameter 28 ± 15 mm), 88 were analysed for <i>EGFR</i> and <i>ALK</i>, 87 for <i>KRAS</i><i>,</i> 86 for <i>HER</i><i>2, PI3K</i> and <i>BRAF</i> and 14 for c-<i>MET</i>. Forty-one mutations were identified (23 <i>KRAS</i>, 10 <i>EGFR</i>, 2 <i>BRAF</i>, 1 <i>HER</i><i>2</i> and 5<i>ALK</i> rearrangements). Four <i>c-</i><i>MET</i> overexpressions were noted. MAF rose from 67% for the first 57 procedures to 89% for the last 56 procedures (<i>P</i> = 0.02) likely due to a higher number of biopsies performed (2 ± 1 vs 3 ± 2, <i>P</i> = 0.005). Upper or middle lobe location (OR 1.19, 95% CI: 1.02–1.38, <i>P</i> = 0.03), and at least three biopsies (OR 1.20, 95% CI: 1.04–1.40, <i>P</i> = 0.02) were predictive factors of MAF. Percentage of tumour cells, size of lesion and distance to the pleura did not correlate with MAF. <b>Conclusion:</b> Multi-gene molecular analysis could be performed in nearly 80% of paraffin-embedded biopsies or smear specimens sampled by r-EBUS assisted bronchoscopy of peripheral tumoral lung nodules.
Order-disorder transition in a block copolyurethane (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrder-disorder transition in a block copolyurethaneAnthony J. Ryan, Christopher W. Macosko, and Wim BrasCite this: Macromolecules 1992, 25, 23, 6277–6283Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://doi.org/10.1021/ma00049a026RIGHTS & PERMISSIONSArticle Views607Altmetric-Citations82LEARN 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 InReddit PDF (953 KB) Get e-Alerts Get e-Alerts
Supplementary Figure 3 from Androgen Deprivation Followed by Acute Androgen Stimulation Selectively Sensitizes AR-Positive Prostate Cancer Cells to Ionizing Radiation (2023)

&lt;p&gt;Clonogenic survival of PC3 cells following IR and DHT treatments. Clonogenic survival fraction is shown for AR negative PC3 cells exposed to vehicle control, 100 nM DHT, 4 Gy of IR or the combination of both. NS, not significant.&lt;/p&gt;
Challenges and Research Directions for Blockchains in the Internet of Things (2019)

In this paper, we analyze the state of the art in distributed ledger technologies and blockchains and investigate potential applications in the Internet of Things (IoT) domain. Afterwards, we discuss interoperability of blockchains, and their use in smart contracts, and artificial intelligence.
Blunting age-associated chronic inflammation preserves hematopoiesis and immunity and reduces leukemogenesis (2017)

Abstract Aging is the single most important prognostic factor for the development of many cancers. While mutational accumulation may increase the risk of cancer in aged individuals, declining immunity due to chronic inflammation is also a likely contributing factor. We have demonstrated that reducing aging-associated chronic inflammation abrogates fitness declines in B-progenitor cells, and significantly reduces leukemogenesis in aged mice (Henry et al., JCI, 2015). In addition to preserving the function of B-progenitor cells, subsequent studies have revealed that reducing chronic inflammation in aged mice augments immune responses. Specifically, reducing inflammation in aged mice (≥22 months) results in a two-fold reduction in the number of splenic M2 macrophage and T-regulatory cell populations, as well as, a three-fold reduction in the surface expression of the inhibitory protein PD-L1 on innate immune cells. Reducing chronic inflammation in aged mice also results in a three-fold increase in the percentage of interferon-gamma producing CD4+ and CD8+ T-cell lymphocytes when stimulated. These phenotypes were observed in aged, anti-inflammatory transgenic mice (alpha-1-anti-trypsin and interleukin-37) and in geriatric mice (≥27 months) treated with recombinant interleukin-37. Overall, these findings suggest that reducing chronic inflammation in aged populations can rejuvenate hematopoiesis and immunity, while also creating a less permissive environment for leukemogenesis.
Influence of the sample preparation method of the ultra-small-angle x-ray scattering of lightly sulfonated polystyrenes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfluence of the sample preparation method of the ultra-small-angle x-ray scattering of lightly sulfonated polystyrenesB. P. Grady, H. Matsuoka, Y. Nakatani, S. L. Cooper, and N. IseCite this: Macromolecules 1993, 26, 15, 4064–4066Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/ma00067a055https://doi.org/10.1021/ma00067a055research-articleACS PublicationsRequest reuse permissionsArticle Views118Altmetric-Citations18LEARN 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
IQ Imbalance Estimation Scheme in the Presence of DC Offset and Frequency Offset in the Frequency Domain (2009)

Direct conversion receivers in orthogonal frequency division multiplexing (OFDM) systems suffer from direct current (DC) offset, frequency offset, and IQ imbalance. We have proposed an IQ imbalance estimation scheme in the presence of DC offset and frequency offset, which uses preamble signals in the time domain. In this scheme, the DC offset is eliminated by a differential filter. However, the accuracy of IQ imbalance estimation is deteriorated when the frequency offset is small. To overcome this problem, a new IQ imbalance estimation scheme in the frequency domain with the differential filter has been proposed in this paper. The IQ imbalance is estimated with pilot subcarriers. Numerical results obtained through computer simulation show that estimation accuracy and bit error rate (BER) performance can be improved even if the frequency offset is small.
Understanding Failures of Deep Networks via Robust Feature Extraction (2021)

Traditional evaluation metrics for learned models that report aggregate scores over a test set are insufficient for surfacing important and informative patterns of failure over features and instances. We introduce and study a method aimed at characterizing and explaining failures by identifying visual attributes whose presence or absence results in poor performance. In distinction to previous work that relies upon crowdsourced labels for visual attributes, we leverage the representation of a separate robust model to extract interpretable features and then harness these features to identify failure modes. We further propose a visualization method aimed at enabling humans to understand the meaning encoded in such features and we test the comprehensibility of the features. An evaluation of the methods on the ImageNet dataset demonstrates that: (i) the proposed workflow is effective for discovering important failure modes, (ii) the visualization techniques help humans to understand the extracted features, and (iii) the extracted insights can assist engineers with error analysis and debugging.
PD-L1 Expression in the Merkel Cell Carcinoma Microenvironment: Association with Inflammation, Merkel Cell Polyomavirus, and Overall Survival (2013)

Merkel cell carcinoma (MCC) is a lethal, virus-associated cancer that lacks effective therapies for advanced disease. Agents blocking the PD-1/PD-L1 pathway have demonstrated objective, durable tumor regressions in patients with advanced solid malignancies and efficacy has been linked to PD-L1 expression in the tumor microenvironment. To investigate whether MCC might be a target for PD-1/PD-L1 blockade, we examined MCC PD-L1 expression, its association with tumor-infiltrating lymphocytes (TILs), Merkel cell polyomavirus (MCPyV), and overall survival. Sixty-seven MCC specimens from 49 patients were assessed with immunohistochemistry for PD-L1 expression by tumor cells and TILs, and immune infiltrates were characterized phenotypically. Tumor cell and TIL PD-L1 expression were observed in 49% and 55% of patients, respectively. In specimens with PD-L1(+) tumor cells, 97% (28/29) demonstrated a geographic association with immune infiltrates. Among specimens with moderate-severe TIL intensities, 100% (29/29) demonstrated PD-L1 expression by tumor cells. Significant associations were also observed between the presence of MCPyV DNA, a brisk inflammatory response, and tumor cell PD-L1 expression: MCPyV(-) tumor cells were uniformly PD-L1(-). Taken together, these findings suggest that a local tumor-specific and potentially MCPyV-specific immune response drives tumor PD-L1 expression, similar to previous observations in melanoma and head and neck squamous cell carcinomas. In multivariate analyses, PD-L1(-) MCCs were independently associated with worse overall survival (hazard ratio 3.12; 95% CI, 1.28-7.61; p=0.012). These findings suggest that an endogenous immune response promotes PD-L1 expression in the MCC microenvironment when MCPyV is present, and provide a rationale for investigating therapies blocking PD-1/PD-L1 for patients with MCC.
The Use of Chatbots in Future Faculty Mentoring: A Case of the Engineering Professoriate (2020)

analytics, computer science education, broadening participation in computing and culturally relevant computing
Impact of tertiary Gleason pattern 5 on prostate cancer aggressiveness: Lessons from a contemporary single institution radical prostatectomy series (2015)

Our results emphasize the importance of TP5 and suggest that criteria for tertiary pattern reporting in prostate cancer should be standardized. Further studies are needed to evaluate the role of tertiary patterns in prognostic models.
Mechanism of nitric oxide action on inhibitory GABAergic signaling within the nucleus tractus solitarii (2006)

The cellular mechanisms mediating nitric oxide (NO) modulation of the inhibitory transmission in the nucleus tractus solitarii (NTS) remain unclear, even though this could be extremely important for various physiological and pathological processes. Specifically, in the NTS NO-evoked glutamate and gamma-aminobutyric acid (GABA) release might contribute to pathological hypertension. In cultured rat brainstem slices, NTS GABAergic neurons were targeted using an adenoviral vector to express enhanced green fluorescent protein and studied with a combination of patch clamp and confocal microscopy. Low nanomolar concentrations of NO increased intracellular Ca2+ concentration ([Ca2+]i) in somata, dendrites, and putative axons of GABAergic neurons, with axons being the most sensitive compartment. This effect was cGMP mediated and not related to depolarization or indirect presynaptic effects on glutamatergic transmission. Blockade of the cyclic adenosine diphosphate ribose (cADPR)/ryanodine-sensitive stores but not the inositol triphosphate-sensitive stores, inhibited NO effect. Since cADPR/ryanodine-sensitive stores are implicated in the Ca2+-induced Ca2+ release, NO can be expected to potentiate GABA release. In support of this notion, a cADPR antagonist abolished the NO-induced potentiation of GABAergic inhibitory postsynaptic potentials in the NTS. Thus, the NO-cGMP-cADPR-Ca2+ pathway, previously described in sea urchin eggs, also operates in mammalian GABAergic neurons. Potentiation of GABA release by NO may have implications for numerous brain functions.
Search for displaced vertices of oppositely charged leptons from decays of long-lived particles in pp collisions at s=13 TeV with the ATLAS detector (2019)

Search for displaced vertices of oppositely charged
Multiple Targets for Suppression of RNA Interference by Tomato Aspermy Virus Protein 2B (2008)

Viral suppressors of RNA interference (RNAi) appear to have evolved as a response to this innate genomic defense. We report the nucleic acid binding properties of the Cucumovirus RNAi suppressor tomato aspermy virus protein 2B (TAV 2B). Using total internal reflection fluorescence spectroscopy (TIRFS), we show that TAV 2B binds double-stranded RNA corresponding to siRNAs and miRNAs, as well as single-stranded RNA oligonucleotides. A number of positively charged residues between amino acids 20 and 30 are critical for RNA binding. Binding to RNA oligomerizes and induces a conformational change in TAV 2B, causing it to form a primarily helical structure and a 4:2 protein-RNA complex.
ChemInform Abstract: Liquid Crystals Carrying Stereodefined Vicinal Difluoro‐ and Trifluoroalkyl Motifs. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A 3D bioprinted complex structure for engineering the muscle–tendon unit (2015)

Three-dimensional integrated organ printing (IOP) technology seeks to fabricate tissue constructs that can mimic the structural and functional properties of native tissues. This technology is particularly useful for complex tissues such as those in the musculoskeletal system, which possess regional differences in cell types and mechanical properties. Here, we present the use of our IOP system for the processing and deposition of four different components for the fabrication of a single integrated muscle-tendon unit (MTU) construct. Thermoplastic polyurethane (PU) was co-printed with C2C12 cell-laden hydrogel-based bioink for elasticity and muscle development on one side, while poly(ϵ-caprolactone) (PCL) was co-printed with NIH/3T3 cell-laden hydrogel-based bioink for stiffness and tendon development on the other. The final construct was elastic on the PU-C2C12 muscle side (E = 0.39 ± 0.05 MPa), stiff on the PCL-NIH/3T3 tendon side (E = 46.67 ± 2.67 MPa) and intermediate in the interface region (E = 1.03 ± 0.14 MPa). These constructs exhibited >80% cell viability at 1 and 7 d after printing, as well as initial tissue development and differentiation. This study demonstrates the versatility of the IOP system to create integrated tissue constructs with region-specific biological and mechanical characteristics for MTU engineering.
Antigenic differences between the major glycoproteins of bovine herpesvirus type 1.1 and bovine encephalitis herpesvirus type 1.3 (1993)

Differences in the antigenic structure of the major glycoproteins, gI, gIII and gIV, of bovine herpesvirus type 1.1 (BHV1.1) and the neurovirulent BHV1.3 were demonstrated with a panel of monoclonal antibodies (MAbs) prepared against the BHV1.1 glycoproteins. Glycoprotein gIII of BHV1.3 was the most dissimilar, reacting with only four of 15 gIII-specific MAbs. Glycoproteins gI and gIV of BHV1.3 reacted with eight of 11 and eight of 12 specific MAbs, respectively. Monospecific bovine antisera to the two viruses supported findings from the MAb analysis in that gI and gIV glycoproteins were cross-recognized, but gIII was not. Virus-neutralizing MAbs reactive to each glycoprotein and which reacted with both viruses also neutralized both viruses. Previously undescribed glycoproteins which were antigenically related to the intact gIII glycoproteins, but of reduced sizes and lacking at least one gIII epitope, were found for both viruses. Tunicamycin inhibition experiments and immunoprecipitation data suggested that these proteins were intracellular degradation products. Comparisons of the peptide footprints of the glycoproteins from the two viruses using protease V8 digestion after immunoprecipitation with cross-reactive MAbs revealed distinctive footprint patterns for the respective glycoproteins.