gebhart/patrepeval huggingface dataset:
Individualized Mutation Detection in Circulating Tumor DNA for Monitoring Colorectal Tumor Burden Using a Cancer-Associated Gene Sequencing Panel (2016)

This panel of 50 cancer-associated genes appeared to be sufficient to identify individual, tumor-unique, mutated ctDNA markers in cancer patients. The MMs showed the clinical utility in monitoring curatively-treated colorectal tumor burden if the allele frequency of MMs in plasma DNA is above 0.1%.
Run-time Updating of Network Device Drivers (2009)

Recent operating systems are capable of using dynamic loadable module functions to update the device driver programs without shutting down the entire system. However, even if a system continues to operate, some services provided by the device driver will be temporarily unavailable during the run-time update. To reduce the period during which the services are unavailable, we propose a new method for run-time updating of device drivers; this method uses context migration from an old driver to an updated one. In this study, we describe the implementation of a network-device driver using our method. In addition, we have shown some advantages of our method by performing a trial on the FreeBSD operating system.
Nuclear envelope breakdown in mammalian cells involves stepwise lamina disassembly and microtubule-driven deformation of the nuclear membrane (1997)

We have studied nuclear envelope disassembly in mammalian cells by morphological methods. The first signs of nuclear lamina depolymerization become evident in early prophase as A-type lamins start dissociating from the nuclear lamina and diffuse into the nucleoplasm. While B-type lamins are still associated with the inner nuclear membrane, two symmetrical indentations develop on antidiametric sites of the nuclear envelope. These indentations accommodate the sister centrosomes and associated astral microtubules. At mid- to late prophase, elongating microtubules apparently push on the nuclear surface and eventually penetrate the nucleus. At this point the nuclear envelope becomes freely permeable to large ligands, as indicated by experiments with digitonin-treated cells and by the massive release of solubilized A-type lamins into the cytoplasm. At the prophase/prometaphase transition, the B-type lamina is fragmented, but 'islands' of lamin B polymer can still be discerned on the tips of congressing chromosomes. Finally, at metaphase, the lamin B polymer breaks down into small pieces, which tend to concentrate in the area of the mitotic spindle. Nuclear envelope breakdown is not prevented when the microtubules are depolymerized by nocodazole; however, the mode of nuclear lamina fragmentation in the absence of microtubules is markedly different from the normal one and involves multiple raffles and gaps, which develop rapidly along the entire surface of the nuclear envelope. These data suggest that nuclear envelope disassembly is a stepwise process in which the microtubules play an important part.
Profibrotic Effect of IL-9 Overexpression in a Model of Airway Remodeling (2007)

IL-9 overexpression protects against alveolar fibrosis induced by crystalline silica particles. This cytokine is also involved in allergic asthma. In the present study, we examined the effect of IL-9 overexpression on the subepithelial fibrotic response, a feature of asthmatic remodeling, induced by chronic exposure to Alternaria alternata extract. IL-9-overexpressing mice (Tg5) and their wild-type counterparts (FVB) were intranasally exposed to A. alternata extract or PBS (controls) twice a week during 3 mo. At the end of the allergic challenge, enhanced pause (Penh) measured in response to methacholine and fibrotic parameters, such as collagen and fibronectin lung content, were significantly higher in Tg5 compared with FVB. Staining of lung sections with Masson's Trichrome also showed more collagen fibers in peribronchial areas of treated Tg5 mice. A similar recruitment of inflammatory cells was observed in challenged FVB and Tg5 mice, except for eosinophils, which were significantly more abundant in the lung of Tg5. High serum levels of IgE and IgG1 in both strains indicated that FVB and Tg5 developed a strong type 2 immune response. The concentration of the eosinophil chemoattractant RANTES and the profibrotic mediator connective tissue growth factor (CTGF) was higher in the BAL of challenged Tg5 than FVB. These results demonstrate a profibrotic role of IL-9 in an airway remodeling model, possibly involving eosinophils and CTGF. These data also highlight a dual role of IL-9 in lung fibrosis, being anti- or profibrotic depending on the alveolar or airway localization of the process, respectively.
Design of Asynchronous Sequential Networks Using Read-Only Memories (1975)

The application of microprogrammed READ-ONLY memories in the design of asynchronous sequential networks is investigated. Variations of single-transition time (STT) state assignments are shown to be applicable to the problem of assigning memory addresses to a memory representation of an asynchronous network. Design algorithms are developed which allow the implementation of an asynchronous sequential network as a READ-ONLY memory. Two operating modes are considered: normal asynchronous operation and a self-clocked mode in which sequential outputs are allowed on a single-input change, thus providing a means of implementing functions normally achieved with synchronous (clocked) networks. In addition the practical timing constraints of the proposed methods are considered.
Epitaxial growth of MgO nanowires by pulsed laser deposition (2007)

We fabricated single-crystalline MgO nanowires epitaxially grown on MgO single crystal substrate using the Au catalyst-assisted pulsed laser deposition (PLD). Controlling appropriately the amount of Au catalyst and the substrate temperature was found to be crucial for the MgO nanowire growth using the catalyst-assisted PLD. In addition, (100) oriented MgO nanowires were epitaxially grown on (100), (110), and (111) oriented substrates, allowing the limited growth directions. The possible growth mechanism of MgO nanowires in PLD is discussed. This feasibility of PLD for fabricating MgO nanowires would contribute to incorporating the rich functionalities of various transition metal oxides into nanowires via in situ construction of heterostructures in oxide nanowires.
Bacterial Lipopolysaccharide Can Enter Monocytes Via Two CD14-Dependent Pathways (1998)

Host recognition and disposal of LPS, an important Gram-negative bacterial signal molecule, may involve intracellular processes. We have therefore analyzed the initial pathways by which LPS, a natural ligand of glycosylphosphatidylinositol (GPI)-anchored CD14 (CD14-GPI), enters CD14-expressing THP-1 cells and normal human monocytes. Exposure of the cells to hypertonic medium obliterated coated pits and blocked 125I-labeled transferrin internalization, but failed to inhibit CD14-mediated internalization of [3H]LPS monomers or aggregates. Immunogold electron microscope analysis found that CD14-bound LPS moved principally into noncoated structures (mostly tubular invaginations, intracellular tubules, and vacuoles), whereas relatively little moved into coated pits and vesicles. When studied using two-color laser confocal microscopy, internalized Texas Red-LPS and BODIPY-transferrin were found in different locations and failed to overlap completely even after extended incubation. In contrast, in THP-1 cells that expressed CD14 fused to the transmembrane and cytosolic domains of the low-density lipoprotein receptor, a much larger fraction of the cell-associated LPS moved into coated pits and colocalized with intracellular transferrin. These results suggest that CD14 (GPI)-dependent internalization of LPS occurs predominantly via noncoated plasma membrane invaginations that direct LPS into vesicles that are distinct from transferrin-containing early endosomes. A smaller fraction of the LPS enters via coated pits. Aggregation, which greatly increases LPS internalization, accelerates its entry into the nonclathrin-mediated pathway.
Azz(0°)for the charge-symmetricHe3(d→,p)He4andH3(d→,n)He4reactions below 6.75 MeV (1980)

The tensor analyzing power of ${A}_{\mathrm{zz}}(0\ifmmode^\circ\else\textdegree\fi{})$ has been measured for the charge symmetric $^{3}\mathrm{He}(d,p)^{4}\mathrm{He}$ and $^{3}\mathrm{H}(d,n)^{4}\mathrm{He}$ reactions as a function of incident deuteron energy from 0.24 to 6.75 MeV. The measurements were performed in a nearly simultaneous fashion to ensure that a meaningful comparison of ${A}_{\mathrm{zz}}(0\ifmmode^\circ\else\textdegree\fi{})$ for the two reactions could be made. The absolute scale of the $^{3}\mathrm{He}(d,p)^{4}\mathrm{He}$ analyzing power was calibrated at four energies using the isospin forbidden $^{16}\mathrm{O}(d,{\ensuremath{\alpha}}_{1})^{14}\mathrm{N}$ reaction. Large differences in ${A}_{\mathrm{zz}}(0\ifmmode^\circ\else\textdegree\fi{})$ for the two reactions were observed for energies both below 1.65 MeV and above 4 MeV. The $^{3}\mathrm{H}(d,n)^{4}\mathrm{He}$ data reported here resolve discrepancies in published data of other authors; the $^{3}\mathrm{He}(d,p)^{4}\mathrm{He}$ results confirm previously reported measurements, except for a small scale shift.NUCLEAR REACTIONS $^{3}\mathrm{He}(\stackrel{\ensuremath{\rightarrow}}{d},p)^{4}\mathrm{He}$, $^{3}\mathrm{H}(\stackrel{\ensuremath{\rightarrow}}{d},n)^{4}\mathrm{He}$, $E=0.24\ensuremath{-}6.75$ MeV; measured ${A}_{\mathrm{zz}}(0\ifmmode^\circ\else\textdegree\fi{})$; calibrated beam polarization by $^{16}\mathrm{O}(\stackrel{\ensuremath{\rightarrow}}{d},{\ensuremath{\alpha}}_{1})^{14}\mathrm{N}$ reaction.
Plantar fasciitis: diagnosis and therapeutic considerations. (2005)

Plantar fasciitis is the most common cause of inferior heel pain. The pain and discomfort associated with this condition can have a dramatic impact on physical mobility. The etiology of this condition is not clearly understood and is probably multi-factorial in nature. Weight gain, occupation-related activity, anatomical variations, poor biomechanics, overexertion, and inadequate footwear are contributing factors. Although plantar fasciitis is generally regarded as a self-limited condition, it can take months to years to resolve, presenting a challenge for clinicians. Many treatment options are available that demonstrate variable levels of efficacy. Conservative therapies include rest and avoidance of potentially aggravating activities, stretching and strengthening exercises, orthotics, arch supports, and night splinting. Other considerations include use of anti-inflammatory agents, ultrasonic shockwave therapy, and, in the most extreme cases, surgery. This article reviews plantar fasciitis, presents the most effective treatment options currently available, and proposes nutritional considerations that may be beneficial in the management of this condition.
Studies on transfer ribonucleic acids and related compounds. 23. Synthesis of a heptanucleotide corresponding to a eukaryotic initiator tRNA loop sequence (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on transfer ribonucleic acids and related compounds. 23. Synthesis of a heptanucleotide corresponding to a eukaryotic initiator tRNA loop sequenceE. Ohtsuka, S. Tanaka, and M. IkeharaCite this: J. Am. Chem. Soc. 1978, 100, 26, 8210–8213Publication Date (Print):December 1, 1978Publication History Published online1 May 2002Published inissue 1 December 1978https://doi.org/10.1021/ja00494a031RIGHTS & PERMISSIONSArticle Views140Altmetric-Citations29LEARN 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 (537 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The Recognition of Maltodextrins by Escherichia coli (1980)

1. Escherichia coli can accumulate 14C-labelled (alpha 1 leads to 4)-linked D-glucose oligomers up to maltoheptaose. Longer maltodextrins are not transported and are not utilized as carbon sources. 2. Maltodextrins too large to be transported are nevertheless bound by the outer envelope of intact E. coli. This binding is saturable (Kd for maltodecaose = 3-4 microM) and the binding sites are inducible by maltose. Each bacterium has approximately 30,000 sites when fully induced. 3. Using mutants devoid of various components of the maltose transport system, the high-affinity binding of maltodextrins by intact bacteria has been shown to be dependent on the presence of both lambda receptor (an outer membrane protein) and periplasmic maltose binding protein. 4. The same binding sites are accessible to both utilizable and non-utilizable maltodextrins. Maltodecapentaose is a competitive inhibitor of maltose transport (Ki 1.5-2.5 microM). 5. These results show that the periplasmic maltose binding protein is readily accessible to substrates of at least 2500 molecular weight. The inability to transport dextrins larger than maltoheptaose is, therefore, due to the inability of E. coli to transfer large substrates from the binding protein to the cytoplasm and not to lack of access through the outer membrane.
Hire me: Computational Inference of Hirability in Employment Interviews Based on Nonverbal Behavior (2014)

Understanding the basis on which recruiters form hirability impressions for a job applicant is a key issue in organizational psychology and can be addressed as a social computing problem. We approach the problem from a face-to-face, nonverbal perspective where behavioral feature extraction and inference are automated. This paper presents a computational framework for the automatic prediction of hirability. To this end, we collected an audio-visual dataset of real job interviews where candidates were applying for a marketing job. We automatically extracted audio and visual behavioral cues related to both the applicant and the interviewer. We then evaluated several regression methods for the prediction of hirability scores and showed the feasibility of conducting such a task, with ridge regression explaining 36.2% of the variance. Feature groups were analyzed, and two main groups of behavioral cues were predictive of hirability: applicant audio features and interviewer visual cues, showing the predictive validity of cues related not only to the applicant, but also to the interviewer. As a last step, we analyzed the predictive validity of psychometric questionnaires often used in the personnel selection process, and found that these questionnaires were unable to predict hirability, suggesting that hirability impressions were formed based on the interaction during the interview rather than on questionnaire data.
Strain-dependent differences in malignant conversion of mouse skin tumors is an inherent property of the epidermal keratinocyte (2004)

The multistage evolution of squamous skin tumors induced by chemical or viral carcinogens on mice from different genetic backgrounds has been a valuable model to define low penetrance loci that determine cancer susceptibility or resistance. Susceptibility determinants are multigenic, stage-specific, dependent on the carcinogenesis protocol, and in the case of initiating events, intrinsic properties of keratinocytes. In this study we examined the malignant conversion frequency of keratinocytes derived from FVB/N, inbred SENCARA/Pt, BALB/c or C57BL/6 mouse strains that differ substantially in the frequency of progression from papilloma to carcinoma. Keratinocytes were cultured from newborn mice and tested in an in vitro malignant conversion assay induced by a chemical carcinogen or immortalized by infection with replication defective human papillomavirus type 16 (HPV-16) E6/E7 retroviruses and tested for malignancy by grafting immortalized cell lines to nude mice. In vitro, FVB/N keratinocytes were 10-fold more sensitive to chemically induced malignant conversion than keratinocytes from other strains, consistent with the known sensitivity of this strain to pre-malignant progression in vivo. The E6/E7 genes induced immortalization of keratinocytes from FVB/N, SENCARA/Pt or C57BL/6 mice more efficiently than BALB/c, and HPV-16-immortalized FVB/N keratinocytes formed tumors more frequently (64%) than SENCARA/Pt (31%) BALB/c (1.9%) or C57BL/6 (2.5%). Furthermore, 78% of the tumors formed by FVB/N keratinocytes progressed to squamous carcinomas compared with 46% for SENCARA/Pt-derived cells and <3% for the others. In F(1) offspring of crosses from SENCARA/Pt and FVB/N mice, both the papilloma incidence and frequency of malignant conversion reflected the SENCARA/Pt parent indicating that predisposition to pre-malignant progression is not a dominant characteristic. This predisposition is an intrinsic property of the target keratinocytes and as such should be amenable to further study in isolated cells.
Einsatz von dBASE IV in lokalen Netzwerken (1990)

Wie bereits dBASE III Plus läßt sich auch dBASE IV, die entsprechende Hard- und Softwareumgebung vorausgesetzt, alternativ sowohl im Einzel- als auch Mehrbenutzerbetrieb einsetzen. Die Benutzeroberfläche, die Generatoren und Hilfsprogramme sowie der Sprachumfang sind in beiden Bereichen identisch. Jeder Anwender, der bereits Erfahrung im Umgang mit der Einzelplatzversion von dBASE IV gesammelt hat, kann sofort mit der Netzwerk-Lösung ohne zusätzliche Schulung arbeiten. Der einzige Unterschied besteht darin, daß er beim Zugriff auf den in einem lokalen Netzwerk (LAN) zentral gespeicherten Datenbestand mit anderen Anwendern konkurriert.
Infectious Bronchitis Virus Subpopulations in Vaccinated Chickens After Challenge (2012)

Infectious bronchitis coronavirus (IBV) shows extensive genotypic and phenotypic variability. The evolutionary process involves generation of genetic diversity by mutations and recombination followed by replication of those phenotypes favored by selection. In the current study, we examined changes occurring in a wild Arkansas (Ark) challenge strain in chickens that were vaccinated either ocularly with commercially available attenuated ArkDPI-derived vaccines or in ovo with a replication-defective recombinant adenovirus expressing a codon-optimized IBV Ark S1 gene (AdArkIBV.S1(ck)). Commercial IBV Ark vaccines A, B, and C provided slightly differing levels of protection against homologous challenge. Most importantly for the current study, chickens vaccinated with the different vaccines displayed significant differences in specific B-lymphocyte responses in the Harderian gland (i.e., the challenge virus encountered differing immune selective pressure during invasion among host groups). Based on S1 sequences, five predominant populations were found in different individual vaccinated/challenged chickens. Chickens with the strongest immune response (vaccine A) were able to successfully impede replication of the challenge virus in most chickens, and only the population predominant in the challenge strain was detected in a few IBV-positive birds. In contrast, in chickens showing less than optimal specific immune responses (vaccines B and C) IBV was detected in most chickens, and populations different from the predominant one in the challenge strain were selected and became predominant. These results provide scientific evidence for the assumption that poor vaccination contributes to the emergence of new IBV strains via mutation and/or selection. In ovo vaccination with a low dose of AdArkIBV.S1(ck) resulted in a mild increase of systemic antibody and reduced viral shedding but no protection against IBV signs and lesions. Under these conditions we detected only virus populations identical to the challenge virus. Possible explanations are discussed. From a broad perspective, these results indicate that selection is an important force driving IBV evolution.
Rett syndrome like phenotypes in the R255X Mecp2 mutant mouse are rescued by MECP2 transgene (2015)

Rett syndrome (RTT) is a severe neurodevelopmental disorder that is usually caused by mutations in Methyl-CpG-binding Protein 2 (MECP2). Four of the eight common disease causing mutations in MECP2 are nonsense mutations and are responsible for over 35% of all cases of RTT. A strategy to overcome disease-causing nonsense mutations is treatment with nonsense mutation suppressing drugs that allow expression of full-length proteins from mutated genes with premature in-frame stop codons. To determine if this strategy is useful in RTT, we characterized a new mouse model containing a knock-in nonsense mutation (p.R255X) in the Mecp2 locus (Mecp2(R255X)). To determine whether the truncated gene product acts as a dominant negative allele and if RTT-like phenotypes could be rescued by expression of wild-type protein, we genetically introduced an extra copy of MECP2 via an MECP2 transgene. The addition of MECP2 transgene to Mecp2(R255X) mice abolished the phenotypic abnormalities and resulted in near complete rescue. Expression of MECP2 transgene Mecp2(R255X) allele also rescued mTORC1 signaling abnormalities discovered in mice with loss of function and overexpression of Mecp2. Finally, we treated Mecp2(R255X) embryonic fibroblasts with the nonsense mutation suppressing drug gentamicin and we were able to induce expression of full-length MeCP2 from the mutant p.R255X allele. These data provide proof of concept that the p.R255X mutation of MECP2 is amenable to the nonsense suppression therapeutic strategy and provide guidelines for the extent of rescue that can be expected by re-expressing MeCP2 protein.
Novel Peptidyl α-Keto Amide Inhibitors of Calpains and Other Cysteine Proteases (1996)

A series of new dipeptidyl alpha-keto amides of the general structure R1-L-Leu-D,L-AA-CONH-R2 were synthesized and evaluated as inhibitors for the cysteine proteases calpain I, calpain II, and cathepsin B. They combine 10 different N-protecting groups (R1), 3 amino acids residues in P1 (AA), and 44 distinct substituents on the alpha-keto amide nitrogen (R2). In general, calpain II was more sensitive to these inhibitors than calpain I, with a large number of inhibitors displaying dissociation constants (Ki) in the 10-100 nM range. Calpain I was also effectively inhibited, but very low Ki values were observed with a smaller number of inhibitors than with calpain II. Cathepsin B was weakly inhibited by most compounds in this study. The best inhibitors for calpain II were Z-Leu-Abu-CONH-CH2-CHOH-C6H5 (Ki = 15 nM), Z-Leu-Abu-CONH-CH2-2-pyridyl (Ki = 17 nM), and Z-Leu-Abu-CONH-CH2-C6H3(3,5(OMe)2) (Ki = 22 nM). The best calpain I inhibitor in this study was Z-Leu-Nva-CONH-CH2-2-pyridyl (Ki = 19 nM). The peptide alpha-keto amide Z-Leu-Abu-CONH-(CH2)2-3-indolyl was the best inhibitor for cathepsin B (Ki = 31 nM). Some compounds acted as specific calpain inhibitors, with comparable activity on both calpains I and II and a lack of activity on cathepsin B (e.g., 40, 42, 48, 70). Others were specific inhibitors for calpain I (e.g., 73) or calpain II (e.g., 18, 19, 33, 35, 56). Such inhibitors may be useful in elucidating the physiological and pathological events involving these proteases and may become possible therapeutic agents.