gebhart/patrepeval huggingface dataset:
Unusual Multiple Recoding Events Leading to Alternative Forms of Hepatitis C Virus Core Protein from Genotype 1b (2003)

In addition to its involvement in the formation of the capsid shell of the virus particles, the core protein of hepatitis C virus (HCV) is believed to play an important role in the pathogenesis and/or establishment of persistent infection. We describe here alternative forms of genotype 1b HCV core protein identified after purification of various products of core protein segment 1-169 expressed in Escherichia coli and their analysis by proteolysis, mass spectrometry, and amino acid sequencing. These proteins all result from a +1 frameshift at codon 42 (a different position than that previously reported in genotype 1a) and, for some of them, from a rephasing in the normal open reading frame at the termination codon 144 in the +1 open reading frame. To test the relevance of these recoding events in a eukaryotic translational context, the nucleotide sequences surrounding the two shift sites were cloned in the three reading frames into expression vectors, allowing the production of a C-terminally fused green fluorescent protein, and expressed both in a reticulocyte lysate transcription/translation assay and in culture cells. Both recoding events were confirmed in these expression systems, strengthening the hypothesis that they might occur in HCV-infected cells. Moreover, sera from HCV-positive patients of genotype 1a or 1b were shown to react differently against synthetic peptides encoded in the +1 open reading frame. Together, these results indicate the occurrence of distinct recoding events in genotypes 1a and 1b, pointing out genotype-dependent specific features for F protein.
The sequences of the human and mouse c-cbl proto-oncogenes show v-cbl was generated by a large truncation encompassing a proline-rich domain and a leucine zipper-like motif. (1991)

The murine Cas NS-1 retrovirus carries the v-cbl oncogene and induces pre-B cell lymphomas and myeloid leukemias. The cellular homolog of v-cbl has been identified in mouse and human DNA, and was recently mapped to mouse chromosome 9 and human chromosome 11q23. To determine the coding sequences of the human and mouse c-cbl proto-oncogenes cDNA clones were isolated from libraries prepared from the human T cell leukemia lines CCRF-CEM and HUT 78, and the mouse pre-B cell line 70Z/3. DNA sequencing revealed an open reading frame encoding 906 amino acids in the human cDNAs and 896 amino acids in 70Z/3. The sequence showed that v-cbl is a markedly truncated form of murine c-cbl containing 355 N-terminal amino acids. The nucleotide sequence of v-cbl is identical to murine c-cbl in this region, and the human sequence has only five amino acid changes in the v-cbl portion. The most notable features of the sequence which was lost in the generation of v-cbl is a C-terminal leucine zipper and a stretch of 208 amino acids containing 23% proline and 19% serine/threonine residues. This proline-rich sequence has similarities to the transcriptional activation domains of some transcription factors, and v-cbl's transforming potential may be due to the loss of this region and the leucine zipper.
Molecular Cloning of Human Alpha and Beta Interferon Genes from Namalwa Cells (1982)

A cDNA library constructed from poly(A)+RNA of Sendai virus-induced human lymphoblastoid (Namalwa) cells was screened with a synthetic oligonucleotide specific for interferon genes. Recombinant plasmids containing sequences derived from alpha and beta interferon (IFN) mRNAs were obtained. The clones were characterized by RNA transfer hybridization, translation of hybrid-isolated RNA, and DNA sequencing. One alpha interferon (IFN-alpha) clone obtained is a variant differing from previously described clones in the location of its polyadenylation site.
A new amino protecting group removable by reduction. Chemistry of the dithiasuccinoyl (Dts) function (1977)

Purpose\nTo evaluate the long-term refractive and visual, anterior chamber depth, and axial length (AL) changes and complications after rigid iris-fixated phakic intraocular lens (pIOL) implantation to treat myopia or astigmatism.\n\nSetting\nUniversity Eye Clinic Maastricht, Maastricht UMC+, the Netherlands.\n\nDesign\nProspective case series.\n\nMethods\nThe study evaluated patients who had implantation of an Artisan myopic or toric iris-fixated pIOL as of January 1998. Changes were measured annually and reported after 1, 5, and 10 years postoperatively.\n\nResults\nThe study comprised 460 eyes (250 patients; mean age 41.1 years ± 10.7 [SD]). Over 10 years, the mean myopization was −0.79 diopters (D) (P &amp;lt; .001), with 52% of eyes within ±1.0 D of target. The mean increase in the logarithm of the minimum angle of resolution (logMAR) corrected distance visual acuity (CDVA) over 10 years was 0.05 (P &amp;lt; .001); 95% of eyes had a CDVA of 20/40 or more and 7% lost 2 or more lines of CDVA. The mean logMAR uncorrected visual acuity (UDVA) increased by 0.14 over 10 years (P &amp;lt; .001); 96% had a UDVA 20/40 or better. The AL increased by 1.14 mm over 10 years (P = .009). Ten percent of pIOLs were explanted because of cataract formation after a mean of 97.9 ± 34.9 months. A higher preoperative age (hazard ratio [HR], 1.08; P &amp;lt; .001) and longer AL (HR, 1.34; P &amp;lt; .001) were risk factors for shorter survival because of cataract formation.\n\nConclusion\nTen years after rigid iris-fixated pIOL implantation, the CDVA and UDVA decreased significantly as a result of significant myopization caused by an increased AL unrelated to the pIOL.
Effect of phytase from Aspergillusniger on plant growth and mineral assimilation in wheat (Triticumaestivum Linn.) and its potential for use as a soil amendment (2012)

Phytase from A. niger showed improvement in phytate phosphorus and mineral availability. Besides a plant growth-promoting effect, reduction in use of chemical fertilizers and soil improvement could be achieved simultaneously for maintaining the sustainability of agriculture.
A practical approach for evaluating new antibodies in the clinical immunohistochemistry laboratory. (2001)

Paraffin section immunohistochemistry (IHC) is widely used in diagnostic surgical pathology. Today, it is difficult to imagine the practice of surgical pathology without IHC. The availability of automated immunostainers with reagent rental contracts makes this technology commonplace. One potential danger is that many laboratories are now offering immunostains without significant prior knowledge or experience in IHC. As part of its mission, the Cell Markers Committee of the College of American Pathologists offers this manuscript as a basic guide to introducing new antibodies in the clinical IHC laboratory. Issues relating to regulatory developments, antibody selection, staining optimization, and test validation are addressed.
Mouse Genome Database (MGD) 2019 (2018)

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for the laboratory mouse. MGD is the authoritative source for biological reference data sets related to mouse genes, gene functions, phenotypes, and mouse models of human disease. MGD is the primary outlet for official gene, allele and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multi Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the Phenotype-Gene Expression matrix which was developed in collaboration with the Gene Expression Database (GXD) and allows researchers to compare gene expression and phenotype annotations for mouse genes. Other recent improvements include enhanced efficiency of our literature curation processes and the incorporation of Transcriptional Start Site (TSS) annotations from RIKEN's FANTOM 5 initiative.
Data compression and harmonic analysis (1998)

In this paper we review some recent interactions between harmonic analysis and data compression. The story goes back of course to Shannon's R(D) theory in the case of Gaussian stationary processes, which says that transforming into a Fourier basis followed by block coding gives an optimal lossy compression technique; practical developments like transform-based image compression have been inspired by this result. In this paper we also discuss connections perhaps less familiar to the information theory community, growing out of the field of harmonic analysis. Recent harmonic analysis constructions, such as wavelet transforms and Gabor transforms, are essentially optimal transforms for transform coding in certain settings. Some of these transforms are under consideration for future compression standards. We discuss some of the lessons of harmonic analysis in this century. Typically, the problems and achievements of this field have involved goals that were not obviously related to practical data compression, and have used a language not immediately accessible to outsiders. Nevertheless, through an extensive generalization of what Shannon called the "sampling theorem", harmonic analysis has succeeded in developing new forms of functional representation which turn out to have significant data compression interpretations. We explain why harmonic analysis has interacted with data compression, and we describe some interesting recent ideas in the field that may affect data compression in the future.
A Comparison of Subcutaneous Low-Molecular-Weight Heparin with Warfarin Sodium for Prophylaxis against Deep-Vein Thrombosis after Hip or Knee Implantation (1993)

Our data demonstrate that the small reduction in the incidence of venous thrombosis with low-molecular-weight heparin, as compared with warfarin, was offset by an increase in bleeding complications. Although the use of low-molecular-weight heparin is simpler, because it is administered subcutaneously without the need for monitoring, it may be more costly than warfarin. Warfarin is inexpensive, but the overall cost of its use is increased by the need to monitor the intensity of anticoagulation. At this time it is unclear which of these approaches is the most cost effective.
Reversible and irreversible current induced domain wall motion in CoFeB based spin valves stripes (2007)

The authors present results on current induced domain wall motion in Co∕Cu∕CoFeB trilayered stripes. The threshold current densities are around 106A∕cm2 at zero field, i.e., about two orders of magnitude smaller than in single NiFe stripes. The domain wall motion is assisted when the field torque acts in the same direction as the spin torque. When the field torque is opposed to the spin transfer one and above a threshold field, the authors observe a reversible displacement of the domain wall (peak in the dV∕dI measurements). This can be ascribed to the onset of domain wall fluctuations, which is confirmed by micromagnetic simulations.
Protein-linked DNA strand breaks induced in mammalian cells by camptothecin, an inhibitor of topoisomerase I. (1989)

Camptothecin was recently identified as an inhibitor of mammalian topoisomerase I. Similar to inhibitors of topoisomerase II, camptothecin produces DNA single-strand breaks (SSB) and DNA-protein cross-links (DPC) in mammalian cells. However, their one-to-one association, expected for trapped topoisomerase complexes, has not previously been demonstrated. We have studied camptothecin-induced SSB and DPC in Chinese hamster DC3F cells and their isolated nuclei, using the DNA alkaline elution technique. It was found that the SSB and DPC frequencies detected following camptothecin treatment depend upon the conditions used for lysis. When lysis was with sodium dodecyl sulfate, the observed frequencies of SSB and DPC were 2- to 3-fold greater than when sodium dodecyl sarkosinate (Sarkosyl) was used. In either case, the SSB:DPC ratio was close to 1. All of the camptothecin-induced SSB were protein linked, as indicated by the absence of DNA elution under nondeproteinizing conditions. DNA cleavage assays with purified topoisomerase I also indicated that the weaker Sarkosyl detergent fails to trap all of the enzyme-DNA complexes. In contrast, lysis conditions had little effect on levels of SSB or DPC produced by 4'-(9-acridinylamino)-methanesulfon-m-anisidide, suggesting that trapping of topoisomerase II complexes occurs equally well with either detergent. In experiments using isolated nuclei, it was found that the camptothecin-induced SSB, in contrast to trapped topoisomerase II complexes, can form and reverse within minutes at 4 degrees C. The activity of camptothecin at low temperature was also seen with purified topoisomerase I. These results support the hypothesis that the SSB and DPC induced by camptothecin in mammalian cells are due to an action on topoisomerase I.
Does enoxaparin interfere with HMGB1 signaling after TBI? A potential mechanism for reduced cerebral edema and neurologic recovery (2015)

Mirroring ENX, HMGB1 signaling blockade reduces LEU recruitment, cerebrovascular permeability, and cerebral edema following TBI. ENX further reduced lung edema indicating a multifaceted effect beyond HMGB1 blockade. Further study is needed to determine how ENX may play a role in blunting HMGB1 signaling in brain injury patients.
Primary chromosomal rearrangements of leukemia are frequently accompanied by extensive submicroscopic deletions and may lead to altered prognosis (2001)

BCR/ABL fluorescent in situ hybridization study of chronic myeloid leukemia (CML) and Philadelphia(+) (Ph(+)) acute lymphoid leukemia (ALL) indicated that approximately 9% of patients exhibited an atypical hybridization pattern consistent with a submicroscopic deletion of the 5' region of ABL and the 3' region of the BCR genes on the 9q(+) chromosome. The CML patients with deletions had a shorter survival time and a high relapse rate following bone marrow transplant. Since deletions are associated with both Ph(+) CML and ALL, it seemed probable that other leukemia-associated genomic rearrangements may also have submicroscopic deletions. This hypothesis was confirmed by the detection of deletions of the 3' regions of the CBFB and the MLL genes in AML M4 patients with inv(16) and in patients with ALL and AML associated with MLL gene translocations, respectively. In contrast, analysis of the AML M3 group of patients and AML M2 showed that similar large deletions were not frequently associated with the t(15;17) or t(8;21) translocations. Analysis of sequence data from each of the breakpoint regions suggested that large submicroscopic deletions occur in regions with a high overall density of Alu sequence repeats. These findings are the first to show that the process of deletion formation is not disease specific in leukemia and also implicate that the presence of repetitive DNA in the vicinity of breakpoint regions may facilitate the generation of submicroscopic deletions. Such deletions could lead to the loss of one or more genes, and the associated haploinsufficiency may result in the observed differences in clinical behavior. (Blood. 2001;97:3581-3588)
Comparison between fluorescence in situ hybridization and classical cytogenetics in human tumors. (1998)

Cytogenetic and fluorescence in situ hybridization (FISH) studies permit analyses of structural and numerical chromosome abnormalities. We compared modal chromosome count in cancer cells by FISH and classical cytogenetics (CC). Our cytogentic studies for chromosomes 3 and 17 on 134 human solid tumor cultures ¿57 small cell lung cancer (SCLC) and 77 non small cell lung cancers (NSCLC)¿, indicated a high incidence of numerical changes in these tumors. Using centromeric probes for chromosomes 3 and 17 we compared 15 tumor and 3 lymphoblastoid cultures, both by FISH (> 100 interphase nuclei) and by CC using trypsin-Giemsa G banding (> 20 metaphases). Although some intra-tumor heterogeneity was seen by FISH, we observed a high degree of concordancy (78%) in modal count by the two techniques.
[Implication of VEGF, steroid hormones and neuropeptides in hair follicle cell responses]. (2002)

Human hair follicles progress independently through the anagen, catagen, telogen and latency phases that correspond to growth arrest and hair shedding before initiation of a new anagen phase. Hair follicles are self-renewing and contain reservoirs of multi-potent stem cells. Identification of the messenger molecules and pathways operating in the growth and cycling of hair follicles, have provided substantial data. However, only a limited number of these signals is well understood. The specific response of hair follicle cells to these signals is correlated with the expression of their corresponding receptors. What regulates these responses? In this review, we will focus on the hair cycle and its control mechanisms. We will provide some elements in answer to these questions and present some of the markers of hair follicle cells, and hormonal and vascular growth factors, which may regulate respectively hair follicle cell metabolism and cycle, and the neuropeptide impact on hair follicle response and hair growth. The results of our study show the modifications in various expression patterns of receptors in dermal papilla cells, and demonstrate the cross-interaction between these different components. In conclusion, we present an accumulation of evidence suggesting that the regulation of hair growth requires a combination of hormonal, vascular and neuropeptide approaches that will provide further insight in defining new treatments for hair loss.
A facile preparation of 2,6-diarylpyrazines (1998)

2,6-Diarylpyrazines were prepared in good yields by a novel method of condensing methoxycarbonylhydrazine with N,N-bis(arylcarbonylmethyl)-p-toluenesulfonamides, unsymmetrical derivatives of which were synthesized by a new (or different) procedure. The structures of these 2,6-diarylpyrazines were established by spectral data and X-ray diffraction analysis. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:341–345, 1998
Cancer screening in the United States, 2015: A review of current American Cancer Society guidelines and current issues in cancer screening (2015)

Each year, the American Cancer Society (ACS) publishes a summary of its guidelines for early cancer detection along with a report on data and trends in cancer screening rates and select issues related to cancer screening. In this issue of the journal, we summarize current ACS cancer screening guidelines. The latest data on utilization of cancer screening from the National Health Interview Survey (NHIS) also is described, as are several issues related to screening coverage under the Affordable Care Act, including the expansion of the Medicaid program.
Hardware Aspects of Secure Computing (1970)

It makes no sense to discuss software for privacy-preserving or secure time-shared computing without considering the hardware on which it is to run. Software access controls rely upon certain pieces of hardware. If these can go dead or be deliberately disabled without warning, then all that remains is false security.
Design and implementation of a distributed virtual machine for networked computers (1999)

This paper describes the motivation, architecture and performance of a distributed virtual machine (DVM) for networked computers. DVMs rely on a distributed service architecture to meet the manageability, security and uniformity requirements of large, heterogeneous clusters of networked computers. In a DVM, system services, such as verification, security enforcement, compilation and optimization, are factored out of clients and located on powerful network servers. This partitioning of system functionality reduces resource requirements on network clients, improves site security through physical isolation and increases the manageability of a large and heterogeneous network without sacrificing performance. Our DVM implements the Java virtual machine, runs on x86 and DEC Alpha processors and supports existing Java-enabled clients.
A study of the homogeneity of the trabecular bone mineral density in the calcaneus (1987)

In the past our laboratory has reported a method of measuring trabecular bone mineral density (TBMD) in the calcaneus in vivo by using the coherent-to-Compton scattering ratio. In the present work the distribution of TBMD in the calcaneus has been studied, and the reproducibility of this technique in vivo has been determined. It is found that although the TBMD may vary within the calcaneus, a region exists over which the variation in density is not large. This region coincides with the midportion of the heel and is the site chosen for the measurement of TBMD by the coherent-to-Compton scattering ratio technique. The reproducibility of this technique in vivo has been determined to be 3.4%.
An Industrial Single‐Slice Si‐MBE Apparatus (1989)

A new, single‐slice MBE machine for industrial application is presented. The basic unit of the modular concept consists of a storage chamber, which accommodates 25 wafers of 150 mm diam and a growth chamber with up to four E‐beam evaporators' and six effusion cells. A technical description of the key components of the fully microprocessor‐controlled system is given. Preliminary results concerning the performance of the apparatus are reported. Crystal quality and electrical characteristics of nominally undoped, epitaxial Si layers grown in the new system are discussed.
Visual-lidar odometry and mapping: low-drift, robust, and fast (2015)

Here, we present a general framework for combining visual odometry and lidar odometry in a fundamental and first principle method. The method shows improvements in performance over the state of the art, particularly in robustness to aggressive motion and temporary lack of visual features. The proposed on-line method starts with visual odometry to estimate the ego-motion and to register point clouds from a scanning lidar at a high frequency but low fidelity. Then, scan matching based lidar odometry refines the motion estimation and point cloud registration simultaneously.We show results with datasets collected in our own experiments as well as using the KITTI odometry benchmark. Our proposed method is ranked #1 on the benchmark in terms of average translation and rotation errors, with a 0.75% of relative position drift. In addition to comparison of the motion estimation accuracy, we evaluate robustness of the method when the sensor suite moves at a high speed and is subject to significant ambient lighting changes.
Evaluation of a behavioral measure of risk taking: The Balloon Analogue Risk Task (BART). (2002)

The present study (N = 86) sought to evaluate a laboratory-based behavioral measure of risk taking (the Balloon Analogue Risk Task; BART) and to test associations between this measure and self-report measures of risk-related constructs as well as self-reported real-world risk behaviors. The BART evidenced sound experimental properties, and riskiness on the BART was correlated with scores on measures of sensation seeking, impulsivity, and deficiencies in behavioral constraint. Also, riskiness on the BART was correlated with the self-reported occurrence of addictive, health, and safety risk behaviors, with the task accounting for variance in these behaviors beyond that accounted for by demographics and self-report measures of risk-related constructs. These results indicate that the BART may be a useful tool in the assessment of risk taking.