gebhart/patrepeval huggingface dataset:
Cell cycle-dependent colocalization of BARD1 and BRCA1 proteins in discrete nuclear domains (1997)

Germ-line mutations of the BRCA1 gene predispose women to early-onset breast and ovarian cancer by compromising the gene's presumptive function as a tumor suppressor. Although the biochemical properties of BRCA1 polypeptides are not understood, their expression pattern and subcellular localization suggest a role in cell-cycle regulation. When resting cells are induced to proliferate, the steady-state levels of BRCA1 increase in late G1 and reach a maximum during S phase. Moreover, in S phase cells, BRCA1 polypeptides are hyperphosphorylated and accumulate into discrete subnuclear foci termed "BRCA1 nuclear dots." BRCA1 associates in vivo with a structurally related protein termed BARD1. Here we show that the steady-state levels of BARD1, unlike those of BRCA1, remain relatively constant during cell cycle progression. However, immunostaining revealed that BARD1 resides within BRCA1 nuclear dots during S phase of the cell cycle, but not during the G1 phase. Nevertheless, BARD1 polypeptides are found exclusively in the nuclear fractions of both G1- and S-phase cells. Therefore, progression to S phase is accompanied by the aggregation of nuclear BARD1 polypeptides into BRCA1 nuclear dots. This cell cycle-dependent colocalization of BARD1 and BRCA1 indicates a role for BARD1 in BRCA1-mediated tumor suppression.
Postoperative nausea and vomiting. (2012)

Postoperative nausea and vomiting (PONV) remains a significant clinical issue that can detract from patients' quality of life in hospital/treatment facility, as well as in the days immediately postdischarge. In addition, PONV may increase perioperative costs, increase perioperative morbidity, increase postanesthesia care unit stay, prolong hospital stays, length of stay/delay discharge, delay the time that the patient can go back to work, and lead to readmissions. Despite the existence of multiple tools to stratify patients according to their risk of developing PONV and multiple PONV treatment guidelines, clinicians do not appear to systematically address the treatment and/or prophylaxis of PONV in a uniform fashion with both pharmacologic and nonpharmacologic strategies in attempts to minimize PONV occurrences.
Survival of Apligraf in Acute Human Wounds (2004)

Apligraf consists of bovine collagen dermis seeded with allogeneic male fibroblasts and keratinocytes. It is been shown to promote healing, but the length of persistence and pathological features have not been characterized previously in acute wounds. Forty-eight deep dermal wounds were created and Apligraf, a split-skin graft (SSG), or a dressing was applied. Biopsies of wounds were taken for immunohistochemical analysis and polymerase chain reaction was performed to detect the Y chromosome from Apligraf cells in 14 female wounds. Male allogeneic DNA was detected in wounds for the first 4 weeks. All subsequent time points were negative apart from one biopsy at 6 weeks. The wounds took 4-9 weeks to heal, with the Apligraf exhibiting no features of engraftment. This was in contrast to the rapid healing seen in the SSG control group. Histology revealed a more intense cellular infiltrate, but less vascularization below Apligraf compared with controls. Evidence of an epidermal-mesenchymal interaction was observed. This is the first article to elucidate the survival of Apligraf allogeneic cells in acute wounds in immunocompetent human subjects for up to 6 weeks and demonstrates that in the management of acute surgical wounds, Apligraf has a role only as a temporary biological dressing.
Interactions of Nitrogen-Containing Xenobiotics with Monoamine Oxidase (MAO) Isozymes A and B:  SAR Studies on MAO Substrates and Inhibitors (2001)

ADVERTISEMENT RETURN TO ISSUEReviewNEXTInteractions of Nitrogen-Containing Xenobiotics with Monoamine Oxidase (MAO) Isozymes A and B: SAR Studies on MAO Substrates and InhibitorsAmit S. Kalgutkar, Deepak K. Dalvie, Neal Castagnoli,, and Timothy J. TaylorView Author Information Pharmacokinetics, Dynamics, and Metabolism Department, Pfizer Global Research and Development, Groton, Connecticut 06340, and Peters Center for the Study of Parkinson's Disease, Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 Cite this: Chem. Res. Toxicol. 2001, 14, 9, 1139–1162Publication Date (Web):July 20, 2001Publication History Received11 April 2001Published online20 July 2001Published inissue 1 September 2001https://pubs.acs.org/doi/10.1021/tx010073bhttps://doi.org/10.1021/tx010073breview-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1981Altmetric-Citations182LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Amines,Inhibition,Inhibitors,Oxidation,Selectivity Get e-Alerts
Multi-Scale Banking to 45 Degrees (2006)

In his text Visualizing Data, William Cleveland demonstrates how the aspect ratio of a line chart can affect an analyst's perception of trends in the data. Cleveland proposes an optimization technique for computing the aspect ratio such that the average absolute orientation of line segments in the chart is equal to 45 degrees. This technique, called banking to 45 degrees, is designed to maximize the discriminability of the orientations of the line segments in the chart. In this paper, we revisit this classic result and describe two new extensions. First, we propose alternate optimization criteria designed to further improve the visual perception of line segment orientations. Second, we develop multi-scale banking, a technique that combines spectral analysis with banking to 45 degrees. Our technique automatically identifies trends at various frequency scales and then generates a banked chart for each of these scales. We demonstrate the utility of our techniques in a range of visualization tools and analysis examples.
Programmable Assembly of DNA-Functionalized Liposomes by DNA (2011)

Bionanotechnology involves the use of biomolecules to control both the structure and property of nanomaterials. One of the most studied examples is DNA-directed assembly of inorganic nanoparticles such as gold nanoparticles (AuNPs). However, systematic studies on DNA-linked soft nanoparticles, such as liposomes, are still lacking. We herein report the programmable assembly and systematic characterization of DNA-linked liposomes as a function of liposome size, charge, fluidity, composition, DNA spacer, linker DNA sequence, and salt concentration for direct comparison to DNA-directed assembly of AuNPs. Similar to the assemblies of AuNPs, sharp melting transitions were observed for liposomes where the first derivative of the melting curve full width at half-maximum (fwhm) is equal to or less than 1 °C for all of the tested liposomes, allowing sequence specific DNA detection. We found that parameters such as liposome size, charge, and fluidity have little effect on the DNA melting temperature. Cryo-TEM studies showed that programmable assemblies can be obtained and that the majority of the liposomes maintained a spherical shape in the assembled state. While liposome and AuNP systems are similar in many aspects, there are also important differences that can be explained by their respective physical properties.
Fuzz Revisited: A Re-examination of the Reliability of UNIX Utilities and Services (1995)

We have tested the reliability of a large collection of basic UNIX utility programs, X-Window applications and servers, and network services. We used a simple testing method of subjecting these programs to a random input stream. Our testing methods and tools are largely automatic and simple to use. We tested programs on nine versions of the UNIX operating system, including seven commercial systems and the freely-available GNU utilities and Linux. We report which programs failed on which systems, and identify and categorize the causes of these failures. The result of our testing is that we can crash (with core dump) or hang (infinite loop) over 40% (in the worst case) of the basic programs and over 40% of the X-Window applications. We were not able to crash any of the network services that we tested nor any of X-Window servers. This study parallels our 1990 study (that tested only the basic UNIX utilities); all systems that we compared between 1990 and 1995 noticeably improved...
Designing human consensus antibodies with minimal positional templates. (1995)

A humanized antibody retains from the original murine antibody the variable region amino acid residues that are required for antigen binding. These generally include the grafted complementarity determining regions, as well as a few key framework residues. Although the remainder of the framework sequences are imported from a human antibody, they nevertheless differ at a few positions from the human consensus sequences. These atypical residues, which arose by somatic mutation during the affinity maturation of the chosen human antibody, could elicit an immune response in some of the patients receiving the humanized antibody. Thus, ideally one should, instead, choose human consensus frameworks for humanizing murine antibodies. Because there is a different consensus sequence for each of the subclasses of variable light and heavy chains, a method is needed to choose the most appropriate one. We are developing a minimal positional template for such a purpose. A minimal positional template indicates which positions in the variable region frameworks are absolutely required for maintaining the integrity of the binding domains. Therefore, to choose a human framework for humanization, one screens the available human consensus sequences for those that are most similar to the original murine sequence, specifically at the positions indicated by the template. In the subsequent humanization protocol, one then retains all of the murine residues found in the positions indicated in the template while humanizing the residues found at all other positions. A conservative positional template has been applied to the humanizations of the antibreast epithelial mucin antibodies BrE-3 and KC4-G3 without loss of binding affinity. Now we are using progressive cycles of computer modeling and laboratory testing to develop a minimal template. The first of such cycles produced template B, which has been used successfully in the humanization of the antibreast epithelial antigen BA46 antibody Mc3. This prompted us to design template C, which further approaches the desired minimal template. Future constructs will test the validity of this template as well as the validity of this novel humanization approach.
Semiconductor optical space switches (1996)

This paper reviews the various optical space switch structures on III-V semiconductor material. Their characteristics are discussed in the context of optical transport and switching network applications exploiting wavelength division multiplexing.
Changes in Forced Expiratory Volume in 1 Second over Time in COPD (2011)

The rate of change in FEV(1) among patients with COPD is highly variable, with increased rates of decline among current smokers, patients with bronchodilator reversibility, and patients with emphysema.
A model of colour vision for predicting colour appearance in various viewing conditions (1987)

Abstract A previously published model of colour vision predicted the hues, lightnesses, saturations, and chromas of colours seen under a medium photopic level of illumination. This model has now been extended to provide, in addition, predictions of brightness and colourfulness, for both related and unrelated colours, at any level of illumination, whether photopic, mesopic, or scotopic. The model has also been extended to cover a wider range of stimulus intensities and the use of various backgrounds.
BotHunter: detecting malware infection through IDS-driven dialog correlation (2007)

We present a new kind of network perimeter monitoring strategy, which focuses on recognizing the infection and coordination dialog that occurs during a successful malware infection. BotHunter is an application designed to track the two-way communication flows between internal assets and external entities, developing an evidence trail of data exchanges that match a state-based infection sequence model. BotHunter consists of a correlation engine that is driven by three malware-focused network packet sensors, each charged with detecting specific stages of the malware infection process, including inbound scanning, exploit usage, egg downloading, outbound bot coordination dialog, and outbound attack propagation. The BotHunter correlator then ties together the dialog trail of inbound intrusion alarms with those outbound communication patterns that are highly indicative of successful local host infection. When a sequence of evidence is found to match BotHunter’s infection dialog model, a consolidated report is produced to capture all the relevant events and event sources that played a role during the infection process. We refer to this analytical strategy of matching the dialog flows between internal assets and the broader Internet as dialog-based correlation, and contrast this strategy to other intrusion detection and alert correlation methods. We present our experimental results using BotHunter in both virtual and live testing environments, and discuss our Internet release of the BotHunter prototype. BotHunter is made available both for operational use and to help stimulate research in understanding the life cycle of malware infections. 1
Concurrent overexpression of ETS‐1 and C‐met correlates with a phenotype of high cellular motility in human esophageal cancer (2001)

Hepatocyte growth factor (HGF) stimulates cell motility as well as mitotic activity of cells. High concentrations of HGF or overexpression of its cellular receptor c-Met in cancer have been reported. We analyzed the expression status of c-Met immunohistochemically in 76 cases of human esophageal cancer. Overexpression of c-Met was noted at a considerably high frequency. Intriguingly, c-Met overexpression was frequent in a specific type of cell nest formation in tumors, i.e., the small nest type, in which tumors form small, dispersed cell nests. Further immunohistochemical analyses using serial sections revealed a striking coincidence between overexpression of c-Met and its transcriptional factor, Ets-1. Overexpression of c-Met and Ets-1 was statistically more frequent in small nest type tumors. The close correlation in expression status between Ets-1 and c-Met was also confirmed using 6 established human esophageal cancer cell lines. In addition, cells that expressed high levels of Ets-1 and c-Met exhibited an extremely motile phenotype by HGF stimulation in vitro. The presence of HGF in tissue sections was confirmed using similar immunohistochemical approaches. These observations suggest that in human esophageal cancer cells the transcriptional factor Ets-1 upregulates the expression of c-Met and, consequently, confers on cells a highly motile phenotype leading to a specific form of tumor development.
Carbon monoxide reverses established pulmonary hypertension (2006)

Pulmonary arterial hypertension (PAH) is an incurable disease characterized by a progressive increase in pulmonary vascular resistance leading to right heart failure. Carbon monoxide (CO) has emerged as a potently protective, homeostatic molecule that prevents the development of vascular disorders when administered prophylactically. The data presented in this paper demonstrate that CO can also act as a therapeutic (i.e., where exposure to CO is initiated after pathology is established). In three rodent models of PAH, a 1 hour/day exposure to CO reverses established PAH and right ventricular hypertrophy, restoring right ventricular and pulmonary arterial pressures, as well as the pulmonary vascular architecture, to near normal. The ability of CO to reverse PAH requires functional endothelial nitric oxide synthase (eNOS/NOS3) and NO generation, as indicated by the inability of CO to reverse chronic hypoxia-induced PAH in eNOS-deficient (nos3-/-) mice versus wild-type mice. The restorative function of CO was associated with a simultaneous increase in apoptosis and decrease in cellular proliferation of vascular smooth muscle cells, which was regulated in part by the endothelial cells in the hypertrophied vessels. In conclusion, these data demonstrate that CO reverses established PAH dependent on NO generation supporting the use of CO clinically to treat pulmonary hypertension.
The export of glutathione from human diploid cells in culture. (1979)

The export of glutathione from cultured human diploid fibroblasts into the surrounding medium was found by isotopic labeling experiments using [35S]cystine and by enzymatic measurements. The major part of the glutathione exported from the cells was found in normal culture medium as mixed disulfide of glutathione and cysteine. Radioactivity of 35S, mostly derived from cellular glutathione, was mainly located in glutathione moiety, not in cysteine moiety, of the mixed disulfide. Export of free glutathione was found when cystine-free medium was used. It was, therefore, concluded that mixed disulfide of glutathione and cysteine was formed in the medium by exported glutathione and medium cystine via sulfhydryl-disulfide exchange reaction. Amount of total glutathione exported from the cells was measured by enzymatic method and it was found that more than 10% of normal cellular glutathione was exported within 2 h. Apparent concentration of glutathione in the medium after a day of culture reached 3 to 4 micrometer, which was comparable to that observed in normal plasma by the same enzymatic method.
The GP64 envelope fusion protein is an essential baculovirus protein required for cell-to-cell transmission of infection (1996)

To demonstrate the essential nature of the baculovirus GP64 envelope fusion protein (GP64 EFP) and to further examine the role of this protein in infection, we inactivated the gp64 efp gene of Autographa californica multicapsid nuclear polyhedrosis virus (AcMNPV) and examined the biological properties of this virus in vivo. To provide GP64 EFP during construction of the recombinant GP64 EFP-null AcMNPV baculovirus, we first generated a stably transfected insect cell line (SfpOP64-6) that constitutively expressed the GP64 EFP of Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus (OpMNPV). The AcMNPV gp64 efp gene was inactivated by inserting the bacterial lacZ gene in frame after codon 131 of the gp64 efp gene. The inactivated gp64 gene was cloned into the AcMNPV viral genome by replacement of the wild-type gp64 efp locus. When propagated in the stably transfected insect cells (Sf9OP64-6 cells), budded virions produced by the recombinant AcMNPV GP64 EFP-null virus (vAc64z) contained OpMNPV GP64 EFP supplied by the Sf9OP64-6 cells. Virions propagated in Sf9OP64-6 cells were capable of infecting wild-type Sf9 cells, and cells infected by vAc64z exhibited a blue phenotype in the presence of X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside). Using cytochemical staining to detect vAc64z infected cells, we demonstrated that this GP64 EFP-null virus is defective in cell-to-cell propagation in cell culture. Although defective in cell-to-cell propagation, vAc64z produces occlusion bodies and infectious occlusion-derived virions within the nucleus. Occlusion bodies collected from cells infected by vAc64z were infectious to midgut epithelial cells of Trichoplusia ni larvae. However, in contrast to infection by a control virus, infection by vAc64z did not proceed into the hemocoel. Analysis of vAc64z occlusion bodies in a standard neonate droplet feeding assay showed no virus-induced mortality, indicating that occluded virions produced from vAc64z could not initiate a productive (lethal) infection in neonate larvae. Thus, GP64 EFP is an essential virion structural protein that is required for propagation of the budded virus from cell to cell and for systemic infection of the host insect.
Application of a Semiautomated Contour Segmentation Tool to Identify the Intervertebral Nucleus Pulposus in MR Images (2010)

The CS method is a semiautomated computer method able to segment the NP of the rabbit disk and detect disk degeneration. In addition, it could assist in clinical detection, assessment, and monitoring of early degeneration in human disks.
Transdermal testosterone gel: pharmacokinetics, efficacy of dosing and application site in hypogonadal men (2004)

The 3 g/2% dose applied to the skin daily resulted in serum testosterone in the normal reference range in most hypogonadal men. Dose adjustments to either a lower or higher dose should shift serum testosterone concentration to the desired range in those who do not achieve this range with this dose.
A photocleavable fluorescent nucleotide for DNA sequencing and analysis (2003)

DNA sequencing by synthesis during a polymerase reaction using laser-induced fluorescence detection is an approach that has a great potential to increase the throughput and data quality of DNA sequencing. We report the design and synthesis of a photocleavable fluorescent nucleoside triphosphate, one of the essential molecules required for the sequencing-by-synthesis approach. We synthesized this nucleoside triphosphate by attaching a fluorophore, 4,4-difluoro-5,7-dimethyl-4-bora-3alpha,4alpha-diaza-s-indacene propionic acid (BODIPY), to the 5 position of 2'-deoxyuridine triphosphate via a photocleavable 2-nitrobenzyl linker. We demonstrate that the nucleotide analogue can be faithfully incorporated by a DNA polymerase Thermo Sequenase into the growing DNA strand in a DNA-sequencing reaction and that its incorporation does not hinder the addition of the subsequent nucleotide. These results indicate that the nucleotide analogue is an excellent substrate for Thermo Sequenase. We also systematically studied the photocleavage of the fluorescent dye from a DNA molecule that contained the nucleotide analogue. UV irradiation at 340 nm of the DNA molecule led to the efficient release of the fluorescent dye, ensuring that a previous fluorescence signal did not leave any residue that could interfere with the detection of the next nucleotide. Thus, our results indicate that it should be feasible to use four different fluorescent dyes with distinct fluorescence emissions as unique tags to label the four nucleotides (A, C, G, and T) through the photocleavable 2-nitrobenzyl linker. These fluorescent tags can be removed easily by photocleavage after the identification of each nucleotide in the DNA sequencing-by-synthesis approach.