gebhart/patrepeval huggingface dataset:
Evidence for a Domain-Swapped CD4 Dimer as the Coreceptor for Binding to Class II MHC (2006)

CD4 is a coreceptor for binding of T cells to APC and the primary receptor for HIV. The disulfide bond in the second extracellular domain (D2) of CD4 is reduced on the cell surface, which leads to formation of disulfide-linked homodimers. A large conformational change must take place in D2 to allow for formation of the disulfide-linked dimer. Domain swapping of D2 is the most likely candidate for the conformational change leading to formation of two disulfide-bonds between Cys130 in one monomer and Cys159 in the other one. Mild reduction of the extracellular part of CD4 resulted in formation of disulfide-linked dimers, which supports the domain-swapped model. The functional significance of dimer formation for coreceptor function was tested using cells expressing wild-type or disulfide-bond mutant CD4. Eliminating the D2 disulfide bond markedly impaired CD4's coreceptor function. Modeling of the complex of the TCR and domain-swapped CD4 dimer bound to class II MHC and Ag supports the domain-swapped dimer as the immune coreceptor. The known involvement of D4 residues Lys318 and Gln344 in dimer formation is also accommodated by this model. These findings imply that disulfide-linked dimeric CD4 is the preferred coreceptor for binding to APC.
A Vision for the Future Part 1: Targets 1-4 (1994)

A Vision for the Future (1) has been received with great enthusiasm by some, and great suspicion try others. In the first of three articles which aim to analyse the document’s implications for nurses and nursing, Professor Stephen Wright gives its background and ethos, and looks specifically at Targets 1 -4. Part 2 of the series appears in next week’s edition of Nursing Standard
Automatic Reconstruction of Textured 3D Models (2014)

Three dimensional modeling and visualization of environments is an increasingly important problem. This work addresses the problem of automatic 3D reconstruction and we present a system for unsupervised reconstruction of textured 3D models in the context of modeling indoor environments. We present solutions to all aspects of the modeling process and an integrated system for the automatic creation of large scale 3D models.
C9ORF72 repeat expansion causes vulnerability of motor neurons to Ca2+-permeable AMPA receptor-mediated excitotoxicity (2018)

Mutations in C9ORF72 are the most common cause of familial amyotrophic lateral sclerosis (ALS). Here, through a combination of RNA-Seq and electrophysiological studies on induced pluripotent stem cell (iPSC)-derived motor neurons (MNs), we show that increased expression of GluA1 AMPA receptor (AMPAR) subunit occurs in MNs with C9ORF72 mutations that leads to increased Ca<sup>2+</sup>-permeable AMPAR expression and results in enhanced selective MN vulnerability to excitotoxicity. These deficits are not found in iPSC-derived cortical neurons and are abolished by CRISPR/Cas9-mediated correction of the C9ORF72 repeat expansion in MNs. We also demonstrate that MN-specific dysregulation of AMPAR expression is also present in C9ORF72 patient post-mortem material. We therefore present multiple lines of evidence for the specific upregulation of GluA1 subunits in human mutant C9ORF72 MNs that could lead to a potential pathogenic excitotoxic mechanism in ALS.
Comparative analysis of intracellular trans-splicing ribozyme activity against hepatitis C virus internal ribosome entry site. (2004)

Internal ribosome entry site (IRES) of the hepatitis C virus (HCV) is known to be essential for HCV replication and most conserved among HCV variants. Hence, IRES RNA is a good therapeutic target for RNA-based inhibitors, such as ribozymes. We previously proposed a new anti-HCV modulation strategy based on trans-splicing ribozymes, which can selectively replace HCV transcripts with a new RNA that exerts anti-HCV activity. To explore this procedure, sites which are accessible to ribozymes in HCV IRES were previously determined by employing an RNA mapping method in vitro. In this study, we evaluate the intracellular accessibility of the ribozymes by comparing the trans-splicing activities in cells of several ribozymes targeting different sites of the HCV IRES RNA. We assessed the intracellular activities of the ribozymes by monitoring their target-specific induction degree of both reporter gene activity and cytotoxin expression. The ribozyme capable of targeting the most accessible site identified by the mapping studies then harbored the most active trans-splicing activity in cells. These results suggest that the target sites predicted to be accessible are truly the most accessible in the cells, and thus, could be applied to the development of various RNA-based anti-HCV therapies.
Recurrent neural network based language modeling in meeting recognition (2011)

We use recurrent neural network (RNN) based language models to improve the BUT English meeting recognizer. On the baseline setup using the original language models we decrease word error rate (WER) more than 1% absolute by n-best list rescoring and language model adaptation. When n-gram language models are trained on the same moderately sized data set as the RNN models, improvements are higher yielding a system which performs comparable to the baseline. A noticeable improvement was observed with unsupervised adaptation of RNN models. Furthermore, we examine the influence of word history on WER and show how to speed-up rescoring by caching common prefix strings. Index Terms: automatic speech recognition, language modeling, recurrent neural networks, rescoring, adaptation
Progress on and challenges of p-type formation for GaN power devices (2020)

The fabrication processes of p-type regions for vertical GaN power devices are investigated. A p-type body layer in a trench gate metal-oxide-semiconductor field-effect transistor requires precise control of the effective acceptor concentration, which is equal to the difference between the Mg acceptor concentration (Na) and the compensating donor concentration (Nd). The carbon atoms incorporated during growth via metalorganic vapor phase epitaxy substitute nitrogen sites (CN) and function as donor sources in a p-type GaN layer. Since interstitial H atoms (Hi) also compensate holes, their removal from an Mg-doped layer is crucial. Extended anneals to release H atoms cause the formation of extra hole traps. The p+ capping layer allows effective and rapid removal of H atoms from a p-type body layer owing to the electric field across the p+/p– junction. On the other hand, selective area p-type doping via Mg ion implantation is needed to control the electrical field distribution at the device edge. Ultrahigh-pressure annealing (UHPA) under a nitrogen pressure of 1 GPa enables post-implantation annealing up to 1753 K without thermal decomposition. Cathodoluminescence spectra and Hall-effect measurements suggest that the acceptor activation ratio improves dramatically by annealing above 1673 K as compared to annealing at up to 1573 K. High-temperature UHPA also induces Mg atom diffusion. We demonstrate that vacancy diffusion and the introduction of H atoms from the UHPA ambient play a key role in the redistribution of Mg atoms.
A pattern for an effective class responsibility collaborator (CRC) cards (2004)

Class responsibility collaborator (CRC) cards can be used in developing object-oriented models. They provide a simple and an easy to use way to explore objects in the development of a system. However, different problems might arise while adopting current CRC-Cards in identifying the system objects. In this paper, we discuss the main problems with current CRC-Cards. As a solution, we propose a new look at CRC-cards that try to avoid most of the problems presented in traditional cards.
Mechanical ventilation causes airway distension with proinflammatory sequelae in mice (2014)

The pathogenesis of ventilator-induced lung injury has predominantly been attributed to overdistension or mechanical opening and collapse of alveoli, whereas mechanical strain on the airways is rarely taken into consideration. Here, we hypothesized that mechanical ventilation may cause significant airway distension, which may contribute to the pathological features of ventilator-induced lung injury. C57BL/6J mice were anesthetized and mechanically ventilated at tidal volumes of 6, 10, or 15 ml/kg body wt. Mice were imaged by flat-panel volume computer tomography, and central airways were segmented and rendered in 3D for quantitative assessment of airway distension. Alveolar distension was imaged by intravital microscopy. Functional dead space was analyzed in vivo, and proinflammatory cytokine release was analyzed in isolated, ventilated tracheae. CT scans revealed a reversible, up to 2.5-fold increase in upper airway volume during mechanical ventilation compared with spontaneous breathing. Airway distension was most pronounced in main bronchi, which showed the largest volumes at tidal volumes of 10 ml/kg body wt. Conversely, airway distension in segmental bronchi and functional dead space increased almost linearly, and alveolar distension increased even disproportionately with higher tidal volumes. In isolated tracheae, mechanical ventilation stimulated the release of the early-response cytokines TNF-α and IL-1β. Mechanical ventilation causes a rapid, pronounced, and reversible distension of upper airways in mice that is associated with an increase in functional dead space. Upper airway distension is most pronounced at moderate tidal volumes, whereas higher tidal volumes redistribute preferentially to the alveolar compartment. Airway distension triggers proinflammatory responses and may thus contribute relevantly to ventilator-induced pathologies.
Macroreticular Resin Columns. I. Modeling of Bead and Filament Packings (1980)

Abstract The diffusion of solutes into spherical beads and cylindrical filaments of macroreticular resin is modeled for the ideal and nonideal cases. These results are then used to develop mathematical models for the operation of continuous flow columns packed with such resins. Effects of design and operating parameters on the breakthrough curves of the columns are calculated.
Computer Aided Detection of Breast Density and Mass, and Visualization of Other Breast Anatomical Regions on Mammograms Using Graph Cuts (2013)

Breast cancer mostly arises from the glandular (dense) region of the breast. Consequently, breast density has been found to be a strong indicator for breast cancer risk. Therefore, there is a need to develop a system which can segment or classify dense breast areas. In a dense breast, the sensitivity of mammography for the early detection of breast cancer is reduced. It is difficult to detect a mass in a breast that is dense. Therefore, a computerized method to separate the existence of a mass from the glandular tissues becomes an important task. Moreover, if the segmentation results provide more precise demarcation enabling the visualization of the breast anatomical regions, it could also assist in the detection of architectural distortion or asymmetry. This study attempts to segment the dense areas of the breast and the existence of a mass and to visualize other breast regions (skin-air interface, uncompressed fat, compressed fat, and glandular) in a system. The graph cuts (GC) segmentation technique is proposed. Multiselection of seed labels has been chosen to provide the hard constraint for segmentation of the different parts. The results are promising. A strong correlation (r = 0.93) was observed between the segmented dense breast areas detected and radiological ground truth.
Detention Diversion Advocacy Project (2017)

The Detention Diversion Advocacy Project (DDAP) is a program designed to provide youth with alternatives to court‐ordered detention through community‐based support and supervision. The DDAP strives to create empirically based, multilevel interventions that divert youth from secure detention facilities, to demonstrate that community‐based interventions are an effective and cost‐efficient alternative to secure custody, and to reduce disproportionate minority confinement. Two essential components for DDAP programs are disposition case advocacy and case management. Disposition case advocacy refers to the process of community members identifying youth who are eligible for the program; DDAP programs target youths who are currently detained or those who are likely to be detained pending adjudication. Case management refers to the collective process of coordinating community‐based services and opportunities for youthful offenders, which is an essential element for promoting effective service delivery to diverse target populations.
Involvement of autophagy in cervical, endometrial and ovarian cancer (2013)

Autophagy is an intracellular molecular pathway that maintains cellular homeostasis. A role for autophagy in the development as well as in the treatment of gynecologic malignancies, while still under-investigated, is receiving increased interest. Depending on concomitant factors, autophagy can either promote or suppress development of cervical, endometrial and ovarian cancer. Moreover, these cancer cells can utilize autophagy to promote its resistance to chemotherapeutic agents or, conversely, autophagy can enhance the efficacy of cytotoxic agents by promoting autophagic cell death. In this review the key autophagy-related mechanisms in development and treatment of cervical, endometrial and ovarian cancer are elucidated and evaluated.
A pulsed X-ray generator (1973)

A pulsed x-ray generator has been developed primarily for phonon scattering experiments in semiconductors. The design uses triode valves to switch the high voltage across the tube and a hot tungsten filament to provide electronic emission. An adjustable pulse duration of from 1 to 10 mu s is possible at a repetition rate of up to 100 Hz. At a tube voltage fo 50 kV and a pulse duration of 10 mu s, the monochromatic (Cu K alpha ) photon flux is 4 * 107 photons per pulse.
Tree-Based Minimization of TCAM Entries for Packet Classification (2010)

Packet classification is a fundamental task for network devices such as edge routers, firewalls, and intrusion detection systems. Currently, most vendors use Ternary Content Addressable Memories (TCAMs) to achieve high-performance packet classification. TCAMs use parallel hardware to check all rules simultaneously. Despite their high speed, TCAMs have a fundamental in dealing with ranges efficiently. Many packet classification rules contain range specifications, each of which needs to be translated into multiple prefixes to store in TCAMs. Such translation may result in an explosive increase in the number of required TCAM entries. In this paper, we propose a redundancy removal algorithm using a tree representation of rules. The proposed algorithm removes redundant rules and combines overlaying rules to build an equivalent, smaller rule set for a given packet classifier. This equivalent transformation can significantly reduce the number of required TCAM entries. Our experiments show a reduction of 70.9% in the number of TCAM entries. Besides, our algorithm eliminates requirement of priority encoder circuits. It can also be used as a preprocessor, in tandem with other methods, to achieve further performance improvement.
Structure and expression of a cDNA encoding a putative neoxanthin cleavage enzyme (NCE), isolated from a wilt-related tomato (<i>Lycopersicon esculentum</i>Mill.) library (1997)

Oxidative cleavage of a 9-cis xanthophyll probably represents the key regulatory step in abscisic acid (ABA) biosynthesis. A transposon tagged maize (Zea mays) mutant vp14, provided the original DNA sequence data needed to design a VP14 fusion protein capable of catalysing this reaction in vitro. A cDNA encoding a similar protein has now been isolated from a wilt-related tomato (Lycopersicon esculentum Mill.) library. The tomato cDNA and derived amino acid sequence have been compared to those of maize and of other enzymes catalysing broadly similar oxidative cleavage reactions. The results of Northern analysis in tomato indicated that mRNA levels of this vp14 homologue increased dramatically in response to water stress.
GA201 (RG7160): A Novel, Humanized, Glycoengineered Anti-EGFR Antibody with Enhanced ADCC and Superior <i>In Vivo</i> Efficacy Compared with Cetuximab (2012)

These data suggest that GA201 may be more effective than cetuximab in patients with EGFR-positive solid tumors and may also represent a first-in-class treatment of patients with KRAS-mutated tumors. Clin Cancer Res; 19(5); 1126-38. ©2012 AACR.
Placebo-Controlled Evaluation of Ritalin Side Effects (1993)

The BSEQ proved to be clinically effective in tracking Ritalin side effects and should be incorporated into the routine evaluation and monitoring of ADHD patients for whom stimulants are prescribed.
Arsenic Trioxide as a Vascular Disrupting Agent: Synergistic Effect with Irinotecan on Tumor Growth Delay in a CT26 Allograft Model (2013)

The mechanism of action of arsenic trioxide (ATO) has been shown to be complex, influencing numerous signal transduction pathways and resulting in a vast range of cellular effects. Among these mechanisms of action, ATO has been shown to cause acute vascular shutdown and massive tumor necrosis in a murine solid tumor model like vascular disrupting agent (VDA). However, relatively little is understood about this VDA-like property and its potential utility in developing clinical regimens. We focused on this VDA-like action of ATO. On the basis of the endothelial cell cytotoxicity assay and tubulin polymerization assay, we observed that higher concentrations and longer treatment with ATO reduced the level of α- and β-tubulin and inhibited the polymerization of tubulin. The antitumor action and quantitative tumor perfusion studies were carried out with locally advanced murine CT26 colon carcinoma grown in female BALB/c mice. A single injection of ATO intraperitoneally displayed central necrosis of the tumor tissue by 24 hours. T1-weighted dynamic contrast-enhanced magnetic resonance image revealed a significant decrease in tumor enhancement in the ATO-treated group. Similar to other VDAs, ATO treatment alone did not delay the progression of tumor growth; however, ATO treatment after injection of other cytotoxic agent (irinotecan) showed significant additive antitumor effect compared to control and irinotecan alone therapy. In summary, our data demonstrated that ATO acts as a VDA by means of microtubule depolymerization. It exhibits significant vascular shutdown activity in CT26 allograft model and enhances antitumor activity when used in combination with another cytotoxic chemotherapeutic agent.
Antioxidant Properties of Conjugated Bilirubin and Biliverdin: Biologically Relevant Scavenging of Hypochlorous Acid (1989)

Conjugated bilirubin at low micromolar concentrations strongly inhibits the luminol-enhanced chemiluminescence response of stimulated human polymorphonuclear leukocytes. In contrast, it does not inhibit either reduction of ferricytochrome c or lucigenin-mediated chemiluminescence of stimulated cells. Also, conjugated bilirubin and its metabolic precursor, biliverdin, do not inhibit the enzyme myeloperoxidase (MPO) since (i) the MPO-dependent oxidation of guaiacol is not affected by biliverdin and (ii) the spectral changes observed when conjugated bilirubin is oxidized by a MPO-H2O2-Cl(-)-system are very similar to those obtained with reagent HOCl. As judged from these spectroscopic studies, each molecule of conjugated bilirubin can scavenge one molecule of HOCl giving rise to an oxidation product that itself is capable of scavenging further molecules of HOCl. Importantly, at physiological pH, both bile pigments can efficiently protect the elastase-inhibitory capacity of alpha 1-antiprotease against inactivation by reagent HOCl.
Resistance Gene Analogs within an Introgressed Chromosomal Segment Derived from <i>Triticum ventricosum</i> That Confers Resistance to Nematode and Rust Pathogens in Wheat (2000)

A resistance (R) gene-rich 2S chromosomal segment from Triticum ventricosum contains a cereal cyst nematode (CCN; Heterodera avenae) R gene locus CreX and a closely linked group of genes (Sr38, Yr17, and Lr37) that confer resistance to stem rust (Puccinia graminis f. sp. tritici), stripe rust (P. striiformis f. sp. tritici), and leaf rust (P. recondita f. sp. tritici) when introgressed into wheat. The 2S chromosomal segment from T. ventricosum is further delineated in translocations onto chromosome 2A of bread wheat, where the rust genes are retained but not the CreX gene. Using these critical genetic stocks, we have isolated family members of R gene analogs that are associated with either the 2S segment from T. ventricosum carrying the CreX locus or the rust genes. Derivatives of the Cre3 candidate R gene sequence and a rice (Oryza sativa) R gene analog that mapped to the 2S homologous chromosome groups in wheat were used to isolate related gene sequences from T. ventricosum that contain a nucleotide binding site-leucine rich repeat domain. The potential of these gene sequences as entry points for isolating candidate genes or gene family members of the CreX or rust genes and their further applications to plant breeding are discussed.
vNUMA-mgr: Managing VM memory on NUMA platforms (2010)

Continuing improvements in the scale of many-core platforms are accompanied by increased asymmetry in their memory architectures. Such NUMA architectures, however, require systems software that understands this asymmetry to attain high levels of performance, leading to significant work in optimizing operating systems like Linux and Windows to increase locality of access to memory nodes and to consider differences in access latencies when accessing remote nodes. When running on today's virtualized hardware platforms, however, virtual machines (VMs) remain unaware of underlying memory architecture, leading to non-compliance with their operating system's (OS) policies for managing NUMA memory, and thereby, incurring undesirable performance overheads. This paper describes the vNUMA-mgr approach of dealing with the NUMA memory characteristics of future virtualized multicore architectures, which (1) properly manages VM memory at the hyper-visor (VMM) level through a set of VMM-level strategies, coupled with (2) 'enlightening' guest VM OSes, if possible, to aid their memory management, and also (3) provides mechanisms to maintain the distribution of VM memory (across physical nodes), even when memory is over-provisioned. The vNUMA-mgr implementation in the Xen VMM is evaluated with respect to each of its memory allocation strategies. The evaluation, which uses a set of memory-intensive benchmarks representative of many High-Performance Computing (HPC) applications, shows 30-50% performance improvement on our platform.
A lossless handover method for video transmission in mobile ATM networks and its subjective quality assessment (1999)

Cell loss is one of the major causes of degradation in quality of service in ATM mobile communication systems. It can be suppressed by employing buffer memories in the network; however, cell delay occurs as a consequence. This article proposes a lossless handover method for mobile ATM communication networks that both prevents cell loss and can suppress cell delay variation. The method was simulated on an experimental system to subjectively evaluate MPEG2 images relative to buffer memory size and the results obtained are presented.