gebhart/patrepeval huggingface dataset:
High incidence of septic shock caused by Streptococcus pneumoniae serotype 3 - a retrospective epidemiological study (2013)

S. pneumoniae serotype 3 more often caused septic shock compared to serotype 14. Our results support the hypothesis that serotypes with high invasiveness mainly cause IPD in younger patients with less co-morbidities. In contrast, serogroups with low and intermediate invasive potential mostly cause IPD in the elderly with defined co-morbidities, and thus can be considered as opportunistic.
Riboprint and virulence gene patterns for Bacillus cereus and related species. (2008)

A total of 72 Bacillus cereus strains and 5 Bacillus thuringiensis strains were analyzed for their EcoRI ribogroup by ribotyping and for the presence or absence of seven virulence-associated genes. From these 77 strains, 42 distinctive ribogroup were identified using EcoRI, but the two species could not be discriminated by their EcoRI ribogroup. The 77 strains were also examined by PCR for the presence of seven virulence-associated genes, cerAB, pi-plc, entFM, bceT, hblA, hblC, and hblD. All five Bacillus thuringiensis strains were positive for these genes. Although differences in the patterns of virulence genes were observed among the different B. cereus strains, within any given ribogroup the patterns of the seven virulence genes was the same. Pulsed-field gel electrophoresis (PFGE) analysis in combination with available chromosomal maps for a selected group of B. cereus strains revealed significant differences in their chromosome size and the placement of virulence genes. Evidence for significant rearrangements within the B. cereus chromosome suggests the mechanism through which the pattern of virulence-associated genes varies. The results suggest linkage between ribogroups and virulence gene patterns as well as no apparent containment of the latter within any particular species boundary.
Selection for Early Flowering in Corn: Seven Late Synthetics (1976)

Seven corn ( Zea mays L.) synthetics adapted to southern Iowa were grown in southern Minnesota at high plant density, and the earliest 5% to flower were sibmated for five generations. The original populations and the five selected cycles were then compared in performance trials at three plant densities over 2 years. Selection effect per cycle averaged: 1.1 q/ha yield increase, 2.2 ears/100 p.lants increase (1‐year data), 1.6 percentage points grain moisture decrease, 2.8% stalk breakage increase, 6.1 cm plant height decrease, 4.1 cm ear height decrease, 1.7 days less to flower, and 0.4 days less silk delay. We observed a cycle‐by‐density interaction wherein advanced cycles exhibited prolificacy at a low density after selection against barrenness at high densities. The decrease in silk delay and increase in ears per plant indicate that selection for early flowering during stress is effective in adapting materials to high plant densities. Flowering date is highly heritable and responds readily to selection. Selection for early flowering is an effective way to adapt late corns to an earlier area. It provides more genetic divergence than the pedigree method or other breeding schemes that use early germplasm as donor of maturity genes. Strong correlated responses to selection for early flowering were found for lower kernel moisture, lower plant and ear height, and higher stalk breakage. Earlier flowering increased yields among late flowering corns and decreased yields among early ones. Earlier flowering increased yields in a short, cool season and decreased yields in a long, warm season. These phenomena can be explained by the contrasting relationships of flowering date with plant size and length of grain filling period: earlier flowering increases yield when longer grain filling period is critical and decreases yield when larger plant size is more important.
Maximizing antibody production in a targeted integration host by optimization of subunit gene dosage and position (2020)

Historically, therapeutic protein production in Chinese hamster ovary (CHO) cells has been accomplished by random integration (RI) of expression plasmids into the host cell genome. More recently, the development of targeted integration (TI) host cells has allowed for recombination of plasmid DNA into a predetermined genomic locus, eliminating one contributor to clone-to-clone variability. In this study, a TI host capable of simultaneously integrating two plasmids at the same genomic site was used to assess the effect of antibody heavy chain and light chain gene dosage on antibody productivity. Our results showed that increasing antibody gene copy number can increase specific productivity, but with diminishing returns as more antibody genes are added to the same TI locus. Random integration of additional antibody DNA copies in to a targeted integration cell line showed a further increase in specific productivity, suggesting that targeting additional genomic sites for gene integration may be beneficial. Additionally, the position of antibody genes in the two plasmids was observed to have a strong effect on antibody expression level. These findings shed light on vector design to maximize production of conventional antibodies or tune expression for proper assembly of complex or bispecific antibodies in a TI system.
Synthesis of Group 4 Complexes that Contain the Diamidoamine Ligands, [(2,4,6-Me3C6H2NCH2CH2)2NR]2- ([Mes2N2NR]2-; R = H or CH3), and Polymerization of 1-Hexene by Activated [Mes2N2NR]ZrMe2 Complexes (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis of Group 4 Complexes that Contain the Diamidoamine Ligands, [(2,4,6-Me3C6H2NCH2CH2)2NR]2- ([Mes2N2NR]2-; R = H or CH3), and Polymerization of 1-Hexene by Activated [Mes2N2NR]ZrMe2 ComplexesLan-Chang Liang, Richard R. Schrock, William M. Davis, and David H. McConvilleView Author Information Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Exxon Chemical Company 5200 Bayway Dr., Baytown, Texas 77522 Cite this: J. Am. Chem. Soc. 1999, 121, 24, 5797–5798Publication Date (Web):June 5, 1999Publication History Received16 October 1998Published online5 June 1999Published inissue 1 June 1999https://pubs.acs.org/doi/10.1021/ja983636nhttps://doi.org/10.1021/ja983636nrapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views959Altmetric-Citations120LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amines,Chemical structure,Ligands,Monomers,Nitrogen Get e-Alerts
Gefitinib induces myeloid differentiation of acute myeloid leukemia (2005)

Cure rates for patients with acute myeloid leukemia (AML) remain low despite ever-increasing dose intensity of cytotoxic therapy. In an effort to identify novel approaches to AML therapy, we recently reported a new method of chemical screening based on the modulation of a gene expression signature of interest. We applied this approach to the discovery of AML-differentiation-promoting compounds. Among the compounds inducing neutrophilic differentiation was DAPH1 (4,5-dianilinophthalimide), previously reported to inhibit epidermal growth factor receptor (EGFR) kinase activity. Here we report that the Food and Drug Administration (FDA)-approved EGFR inhibitor gefitinib similarly promotes the differentiation of AML cell lines and primary patient-derived AML blasts in vitro. Gefitinib induced differentiation based on morphologic assessment, nitro-blue tetrazolium reduction, cell-surface markers, genome-wide patterns of gene expression, and inhibition of proliferation at clinically achievable doses. Importantly, EGFR expression was not detected in AML cells, indicating that gefitinib functions through a previously unrecognized EGFR-independent mechanism. These studies indicate that clinical trials testing the efficacy of gefitinib in patients with AML are warranted.
Automatic Static Bug Detection for Machine Learning Libraries: Are We There Yet? (2023)

Automatic detection of software bugs is a critical task in software security. Many static tools that can help detect bugs have been proposed. While these static bug detectors are mainly evaluated on general software projects call into question their practical effectiveness and usefulness for machine learning libraries. In this paper, we address this question by analyzing five popular and widely used static bug detectors, i.e., Flawfinder, RATS, Cppcheck, Facebook Infer, and Clang static analyzer on a curated dataset of software bugs gathered from four popular machine learning libraries including Mlpack, MXNet, PyTorch, and TensorFlow with a total of 410 known bugs. Our research provides a categorization of these tools' capabilities to better understand the strengths and weaknesses of the tools for detecting software bugs in machine learning libraries. Overall, our study shows that static bug detectors find a negligible amount of all bugs accounting for 6/410 bugs (0.01%), Flawfinder and RATS are the most effective static checker for finding software bugs in machine learning libraries. Based on our observations, we further identify and discuss opportunities to make the tools more effective and practical.
<title>Design techniques for surface-micromachining MEMS processes</title> (1995)

This paper describes design techniques and structural components for building surface- micromachined polycrystalline silicon microelectromechanical systems (MEMS). The devices presented in this paper were fabricated thorugh the ARPA-sponsored multi-user MEMS process (MUMPS), but the ideas are applicable to other surface-micromachining polycrystalline silicon (polysilicon) processes. Specific devices are not discussed; instead, generic design and assembly techniques are presented to give novice or experienced MEMS designers new tools and ideas to improve their own designs. The topological effects which result from the fabrication of surface-micromachined polysilicon structures can be detrimental to many designs. However, these same effects can be turned into an advantage for the MEMS designer. Design techniques are presented for using conformal layer topologies to shape structures for guide rails, bossing, or to obtain closer tolerances than the design rules would seen to imply. Methods are also described for wiring hinged devices and large systems. These techniques were developed from the experience gained by the faculty and students at the Air Force Institute of Technology from the design of over 200 different devices and test structures on over 25 MUMPS die in the past two years.
Modeling and Evaluating the Environmental Degradation of UHTCs under Hypersonic Flow (2014)

Abstract : Recent advances in understanding the mechanisms of degradation of Ultra-High Temperature Ceramics (UHTCs) under hypersonic flight conditions are reviewed. Experimental and modeling efforts using leading edge samples of HfB2-20% (vol) SiC within a scramjet rig are presented. Other experimental efforts to study the behavior of UHTCs under simulated hypersonic conditions are reviewed.
Investigation into the effect of transcranial direct current stimulation on cardiac pacemakers (2019)

Results in this small series of cases found no evidence that tDCS interferes with the function of the pacemakers and suggests tDCS can be delivered to patients equipped with a cardiac pacemaker. Further studies are needed to generalize these results to other pacemakers.
Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis (2019)

Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. In this study, the Axiom Microbiome Array was evaluated to determine its sensitivity, specificity and utility in microbiome analysis of veterinary clinical samples. The array contains probes designed to detect more than 12,000 species of viruses, bacteria, fungi, protozoa and archaea, yielding the most comprehensive microbial detection platform built to date. The array was able to detect Shigella and Aspergillus at 100 genome copies, and vaccinia virus DNA at 1,000 genome copies. The Axiom Microbiome Array made correct species-level calls in mock microbial community samples. When tested against serum, tissue, and fecal samples from pigs experimentally co-infected with porcine reproductive and respiratory syndrome virus and porcine circovirus type 2, the microarray correctly detected these two viruses and other common viral and bacterial microbiome species. This cost-effective and high-throughput microarray is an efficient tool to rapidly analyze large numbers of clinical and environmental samples for the presence of multiple viral and bacterial pathogens.
Lumbar Spine Fractures in Undercarriage Impacts: Analysis of 1997-2015 NASS-CDS (2018)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Objective: This is a descriptive study of the incidence of spinal injury by crash type using NASS-CDS. It provides an understanding of impacts to the undercarriage of the vehicle and injuries to the lumbar spine by reviewing electronic cases in NASS-CDS to determine crash circumstances for fractures of the lumbar spine with undercarriage impacts.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Methods: 1997-2015 NASS-CDS was evaluated for serious injury (MAIS 3 + F) to front-seat occupants by seatbelt use and crash type in 1994+ MY vehicles. Undercarriage impacts were defined by GAD1 = U without a rollover. Serious injury was defined as MAIS 3 + F. Spinal injuries AIS 3+ were separated into cervical, thoracic and lumbar regions. Weighted data was determined using ratio weight. NASS-CDS electronic cases were downloaded from NHTSA with AIS 3+ lumbar spine injuries in undercarriage impacts.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Results: There were 2,160 MAIS 3 + F injured occupants in undercarriage impacts. This was 0.23% of all serious injury. There were 914 (42.3%) AIS 3+ spinal injuries in undercarriage impacts with 88.3% in the lumbar spine. The 807 lumbar spine injuries represented 4.1% of all AIS 3+ spinal injury. There were six electronic cases with AIS 3+ lumbar spine injury in undercarriage impacts. They involved off-road excursions at high speed with undercarriage impacts from changes in terrain. All involved front airbag deployments. Four of the six cases involved multiple lumbar fractures from compression of the spine.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Conclusions: Serious spinal injuries are rare in undercarriage impacts. Based on NASS-CDS cases, they are primarily compression (burst) fractures of the lumbar spine from vertical loads on the spine.&lt;/div&gt;&lt;/div&gt;
Building γ-secretase – the bits and pieces (2008)

gamma-Secretase is a promiscuous aspartyl protease responsible for the final intramembrane cleavage of various type I transmembrane proteins after their large ectodomains are shed. The vast functional diversity of its substrates, which are involved in cell fate decisions, adhesion, neurite outgrowth and synapse formation, highlights the important role gamma-secretase plays in development and neurogenesis. The most renowned substrates are the amyloid precursor protein and Notch, from which gamma-secretase liberates amyloid beta peptides and induces downstream signalling, respectively. gamma-Secretase is a multiprotein complex containing presenilin (which harbours the catalytic site), nicastrin, APH1 and PEN2. Its assembly occurs under tight control of ER-Golgi recycling regulators, which allows defined quantities of complexes to reach post-Golgi compartments, where gamma-secretase activity is regulated by multiple other factors. 3D-EM rendering reveals a complex with a translucent inner space, suggesting the presence of a water-filled cavity required for intramembrane proteolysis. Despite huge efforts, we are now only beginning to unravel the assembly, stoichiometry, activation and subcellular location of gamma-secretase.
Integrated genomic characterization of endometrial carcinoma (2013)

We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array-and sequencing-based technologies. Uterine serous tumours and â¼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours. Â© 2013 Macmillan Publishers Limited. All rights reserved.
Interaction of Streptococcus pyogenes with extracellular matrix components resulting in immunomodulation and bacterial eradication (2020)

<i>Streptococcus pyogenes</i> is a major human pathogen that causes a variety of diseases ranging from mild skin and throat infections to fatal septicemia. In severe invasive infections, <i>S. pyogenes</i> encounters and interacts with components of the extracellular matrix (ECM), including small leucine rich-proteoglycans (SLRPs). In this study, we report a novel antimicrobial role played by SLRPs biglycan, decorin, fibromodulin and osteoadherin, specifically in promoting the eradication of <i>S. pyogenes</i> in a human sepsis model of infection. SLRPs can be released from the ECM and de novo synthesized by a number of cell types. We reveal that infection of human monocytes by <i>S. pyogenes</i> induces the expression of decorin. Furthermore, we show that the majority of genetically distinct and clinically relevant <i>S. pyogenes</i> isolates interact with SLRPs resulting in decreased survival in blood killing assays. Biglycan and decorin induce TLR2 and TLR4 signaling cascades resulting in secretion of proinflammatory and chemotactic molecules and recruitment of professional phagocytes. Surprisingly, SLRP-mediated elimination of <i>S. pyogenes</i> occurs independently of TLR activation. Our results indicate that SLRPs act in concert with human serum, enhancing deposition of complement activation fragments and the classical activator C1q on the bacterial surface, facilitating efficient microbial eradication. Addition of the complement C3 inhibitor compstatin significantly reverses SLRP-induced blood killing, confirming active complement as a key mediator in SLRP-mediated bacterial destruction. Taken together our results add to the functional repertoire of SLRPs, expanding to encompass their role in controlling bacterial infection.
ChemInform Abstract: From Conception to Realization: An Historial Account of Graphene and Some Perspectives for Its Future. (2011)

Abstract Review: 146 refs.
Design and implementation of modern production renderers (2018)

Over the past decade, production rendering has moved from primarily using Reyes-based algorithms to being based on path tracing and physically based approaches. The developers of five of the most significant production renderers have each recently written comprehensive systems papers on their renderers, describing the challenges of modern production rendering and the systems they have respectively built to solve them. In May 2018, these papers were published in a special issue of ACM Transactions on Graphics.
Frequency-based modulation of diverse species in a nucleic acid library (2023)

A method of processing a collection of nucleic acid sequences is provided including connecting an adaptor to one or more or each nucleic acid sequence in the collection to create a processed nucleic acid template library, wherein the adaptor includes a first DNA sequence encoding a PAM sequence and at least a tracr mate.
Data from Tasquinimod Is an Allosteric Modulator of HDAC4 Survival Signaling within the Compromised Cancer Microenvironment (2023)

&lt;div&gt;Abstract&lt;p&gt;Tasquinimod is an orally active antiangiogenic drug that is currently in phase III clinical trials for the treatment of castration-resistant prostate cancer. However, the target of this drug has remained unclear. In this study, we applied diverse strategies to identify the histone deacetylase HDAC4 as a target for the antiangiogenic activity of tasquinimod. Our comprehensive analysis revealed allosteric binding (Kd 10–30 nmol/L) to the regulatory Zn&lt;sup&gt;2+&lt;/sup&gt; binding domain of HDAC4 that locks the protein in a conformation preventing HDAC4/N-CoR/HDAC3 complex formation. This binding inhibited colocalization of N-CoR/HDAC3, thereby inhibiting deacetylation of histones and HDAC4 client transcription factors, such as HIF-1α, which are bound at promoter/enhancers where epigenetic reprogramming is required for cancer cell survival and angiogenic response. Through this mechanism, tasquinimod is effective as a monotherapeutic agent against human prostate, breast, bladder, and colon tumor xenografts, where its efficacy could be further enhanced in combination with a targeted thapsigargin prodrug (G202) that selectively kills tumor endothelial cells. Together, our findings define a mechanism of action of tasquinimod and offer a perspective on how its clinical activity might be leveraged in combination with other drugs that target the tumor microenvironment. &lt;i&gt;Cancer Res; 73(4); 1386–99. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;