gebhart/patrepeval huggingface dataset:
Long-range mapping of the Philadelphia chromosome by pulsed-field gel electrophoresis (1988)

The Philadelphia chromosome (Ph1) of chronic myelogenous leukemia (CML) contains sequences from chromosome 9, including the ABL protooncogene, that have been translocated to the breakpoint cluster region (bcr) of chromosome 22, giving rise to a bcr-ABL fusion gene, whose product has been implicated in the genesis of CML. Although chromosome 22 translocation breakpoints in CML virtually always occur within the 5.8-kilobase (kb) bcr, chromosome 9 breakpoints have been identified within the known limits of ABL in only a few instances. For a better understanding of the variability of the breakpoints on chromosome 9, we studied the CML cell line BV173. Using pulsed-field gel electrophoresis (PFGE), large-scale maps of the t(9;22) junctions were constructed. The chromosome 9 breakpoint was shown to have occurred within an ABL intron, 160 kb upstream of the v-abl homologous sequences, but still 35 kb downstream of the 5'-most ABL exon. bcr-ABL and ABL-bcr fusion genes were demonstrated on the Ph1 and the 9q+ chromosomes, respectively; both of these genes are expressed. These results suggest that the 9;22 translocation breakpoints in CML consistently occur within the limits of the large ABL gene. RNA splicing, sometimes of very large regions, appears to compensate for the variability in breakpoint location. These studies show that PFGE is a powerful new tool for the analysis of chromosomal translocations in human malignancies.
The role of positive costimulatory molecules in transplantation and tolerance (2008)

These observations suggest that the therapeutic exploitation of strategies targeting costimulatory molecules will require carefully timed interventions directed against multiple pathways.
Botulinum toxin A and headache treatment. (2013)

The literature currently suggests a modest effect, if any, with the use of botulinum toxin A for the prophylactic treatment of chronic migraine and tension-type headache, and further prospective, randomized, double-blinded studies are needed.
Protecting enzymatic function through directed packaging into bacterial outer membrane vesicles (2016)

Bacteria possess innate machinery to transport extracellular cargo between cells as well as package virulence factors to infect host cells by secreting outer membrane vesicles (OMVs) that contain small molecules, proteins, and genetic material. These robust proteoliposomes have evolved naturally to be resistant to degradation and provide a supportive environment to extend the activity of encapsulated cargo. In this study, we sought to exploit bacterial OMV formation to package and maintain the activity of an enzyme, phosphotriesterase (PTE), under challenging storage conditions encountered for real world applications. Here we show that OMV packaged PTE maintains activity over free PTE when subjected to elevated temperatures (>100-fold more activity after 14 days at 37 °C), iterative freeze-thaw cycles (3.4-fold post four-cycles), and lyophilization (43-fold). We also demonstrate how lyophilized OMV packaged PTE can be utilized as a cell free reagent for long term environmental remediation of pesticide/chemical warfare contaminated areas.
Identification of Tumor-Suppressor Genes Using Human Melanoma Cell Lines UACC903, UACC903(+6), and SRS3 by Comparison of Expression Profiles (2000)

The development and progression of cancer are believed to be due to multiple genetic alterations resulting in complex changes in expression of many genes. The parental malignant melanoma cell line UACC903 displays anchorage-independent growth, and the chromosome 6-suppressed subline UACC903(+6) displays anchorage-dependent growth. The anchorage-independent revertant cell line SRS3 derived from UACC903(+6) by retroviral transduction resembles the phenotype of UACC903. In this study, we first compared the expression profiles of 3317 genes between these three cell lines in pairs by cDNA microarrays, resulting in identification of genes with known suppressor activities. We then demonstrated connexin 43 (Cx43)-suppressing anchorage-independent growth of UACC903 on overexpression. Of 3317 genes with informative expression detected by cDNA microarray, 321 (9.68%) showed expression changes between at least one pair of the three cell lines. Notably, 12 genes displayed higher levels of expression in UACC903(+6) than in both UACC903 and SRS3, providing candidates for further identification of melanoma-suppressor genes. Genes encoding Cx43 (suppressor activity), monocyte chemotactic protein 1 (suppressor activity), and cysteine proteinase P32alpha (apoptotic activity) were all upregulated in UACC903(+6), in contrast to both UACC903 and SRS3. Transfection of Cx43, encoded on human chromosome 6q21-q23, a region frequently altered in malignant melanoma, resulted in its overexpression and the suppression of anchorage-independent growth of UACC903. Thus, our result proves the principle that the combination of the ability to alter cellular phenotype by successive genetic alterations and the ability to examine the global expression profiles facilitates the identification of tumor suppressor genes. Mol. Carcinog. 28:119-127, 2000.
Control of G2 delay by the RAD9 gene of Saccharomyces cerevisiae (1989)

In response to DNA damage, Saccharomyces cerevisiae cells arrest the cell cycle in the G2 phase. Arrest is defective in rad9 mutants; rad9 cells divide and die without repairing the damage. Several cell cycle mutants that are defective in DNA replication arrest in G2 at the restrictive temperature; this arrest is due to the RAD9 control function. Thus RAD9 is responsible for the fact that mitosis is normally dependent upon DNA replication, a function we term a 'checkpoint'. Four additional genes have been identified that are also components of the RAD9 checkpoint.
Analysis of the transforming potential of the human H-ras gene by random mutagenesis. (1984)

Some tumor cells contain mutant ras genes that are capable of transforming NIH 3T3 cells. Those genes that have been analyzed arise from the wild-type, non-transforming ras genes by mutations producing single amino acid substitutions at position 12 or 61 of the encoded protein. We have performed random bisulfite-induced mutagenesis on the cloned wild-type human H-ras gene to find if mutations at other positions can activate the transforming potential of that gene. Most mutations are not activating, but mutations that specify single amino acid substitutions at position 12, 13, 59, or 63 of the encoded protein do activate the transforming potential of the H-ras gene. Some, but not all, mutant ras proteins show an altered electrophoretic mobility in NaDodSO4/polyacrylamide gels.
Zone electrophoresis in open-tubular glass capillaries (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTZone electrophoresis in open-tubular glass capillariesJames W. Jorgenson and Krynn DeArman. LukacsCite this: Anal. Chem. 1981, 53, 8, 1298–1302Publication Date (Print):July 1, 1981Publication History Published online1 May 2002Published inissue 1 July 1981https://pubs.acs.org/doi/10.1021/ac00231a037https://doi.org/10.1021/ac00231a037research-articleACS PublicationsRequest reuse permissionsArticle Views3863Altmetric-Citations1802LEARN 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 Get e-Alerts
Aspergillus Antigen in Serum, Urine and Bronchoalveolar Lavage Specimens of Neutropenic Patients in Relation to Clinical Outcome (2000)

We have used a new, commercial enzyme-linked immunosorbent assay (ELISA, Platelia Aspergillus) to detect Aspergillus antigen in serum, urine and bronchoalveolar lavage (BAL) samples of 105 haematological patients who received empirical amphotericin B treatment for suspected fungal infection. 14% (60/419) of serum and 5% (18/373) of urine samples were positive. Ten-fold concentration of urine increased the number of positive samples to 31 (8%). The antigen was detected in 5 of 20 BAL samples, but fungal culture was negative in all of them. 22 patients had positive antigen test. Serum was positive in 17, urine in 7 and concentrated urine in 12 patients. Six patients had confirmed invasive aspergillosis. In all these patients, antigen was detected in serum, but urine was positive in only 2 patients. Patients whose antigen test turned negative during the amphotericin B treatment had significantly lower mortality than patients with persistently positive antigen test (2/10 vs. 8/8, p = 0.002). We conclude that Aspergillus galactomannan can be detected by ELISA in serum, urine and BAL samples of haematological patients, but the higher sensitivity of serum testing makes it preferable for screening. Disappearance of the antigen during antifungal therapy seems to correlate with good, and persistence with poor, clinical outcome.
The DOE Wide Area Measurement System (WAMS) Project -- Demonstration of dynamic information technology for the future power system (1995)

In 1989 the Bonneville Power Administration (BPA) and the Western Power Administration (WAPA) joined the US Department of Energy (DOE) in an assessment of longer-term research and development needs for future electric power system operation. The effort produced a progressively sharper vision of a future power system in which enhanced control and operation are the primary means for serving new customer demands in an environment characterized by increased competition, a wider range of services and vendors, and much narrower operating margins. Technology and infrastructure for real time access to wide area dynamic information were identified as critical path elements in realizing that vision. In 1995 the DOE accordingly launched the Wide Area Measurement System (WAMS) Project jointly with the two Power Marketing Administrations (PMAs) to address these issues in a practical operating environment the western North America power system. The Project draws upon many years of PMA effort and related collaboration among the western utilities, plus an expanding infrastructure that includes regionally involved contractors, universities, and National Laboratories plus linkages to the Electric Power Research Institute (EPRI).
Adversarial Logit Pairing (2018)

In this paper, we develop improved techniques for defending against adversarial examples at scale. First, we implement the state of the art version of adversarial training at unprecedented scale on ImageNet and investigate whether it remains effective in this setting - an important open scientific question (Athalye et al., 2018). Next, we introduce enhanced defenses using a technique we call logit pairing, a method that encourages logits for pairs of examples to be similar. When applied to clean examples and their adversarial counterparts, logit pairing improves accuracy on adversarial examples over vanilla adversarial training; we also find that logit pairing on clean examples only is competitive with adversarial training in terms of accuracy on two datasets. Finally, we show that adversarial logit pairing achieves the state of the art defense on ImageNet against PGD white box attacks, with an accuracy improvement from 1.5% to 27.9%. Adversarial logit pairing also successfully damages the current state of the art defense against black box attacks on ImageNet (Tramer et al., 2018), dropping its accuracy from 66.6% to 47.1%. With this new accuracy drop, adversarial logit pairing ties with Tramer et al.(2018) for the state of the art on black box attacks on ImageNet.
Synergy between anti-CD40 MAb and Epstein-Barr virus in activation and transformation of human B lymphocytes (1997)

For human B lymphocytes, Epstein-Barr virus (EBV) is a polyclonal activator, inducing both proliferation and Ig secretion. It is also a transforming virus capable of generating immortalized B cell lines. These early and late functions of EBV are not apparently connected. The receptor for EBV, CD21, also serves as a receptor for some complement components and is called CR2. This molecule associates with CD19 and TAPA-1 on the surface of B cells. This complex is involved in signaling B cells and participates in many responses. We have observed that simultaneous ligation of CD40 and the CD21 complex, by exposure to anti-CD40 MAbs and EBV, enhances both the short-term proliferation as well as the long-term transformation rate of human B lymphocytes. B cell proliferation shows synergy between anti-CD40 MAb and EBV. CD19 also appears to be involved in the synergistic activation of B cells through CD40 and CD21, since ligation of CD19 with anti-CD19 MAbs, either prior to or concomitant with exposure to anti-CD40 and EBV, markedly inhibits both proliferation and subsequent B cell transformation. These observations do not elucidate the mechanisms of B cell transformation employed by EBV but the do suggest a relationship between early proliferation and later transformation induced by the virus. Anti-CD40 enhances both these effects and anti-CD19 is capable of inhibiting both.
Regulation of human immunodeficiency virus env expression by the rev gene product (1989)

A single simian virus 40 late replacement vector which expresses both the rev and envelope (env) genes of human immunodeficiency virus was used to examine the mechanism underlying the dependence of env gene expression on the rev protein. When rev was deleted from the vector, no envelope protein expression could be detected in transfected cells, and the levels of cytoplasmic env mRNA were dramatically reduced. In contrast to this, the levels of env RNA in total cellular RNA preparations were similar with or without rev coexpression, and analysis of nuclear RNA showed that the levels of nuclear env RNA were increased in the absence of rev. These results suggest that rev functions to regulate nuclear export of env mRNA. It was possible to restore env expression from the vector lacking rev by supplying rev in trans, provided that a cis-acting sequence was also present. This sequence was mapped to a 854-base-pair region within the env open reading frame, and it was shown that the sequence could be moved but that it worked only in its original orientation.
Spiking-based matrix computation by leveraging memristor crossbar array (2015)

As process technology continues scaling down, the memory barrier becomes more severe. Thus, spiking neuromorphic computing that can significantly enhance computing and communication efficiencies has been widely studied. Both conventional CMOS technology and emerging devices have been used in hardware implementation of spiking neuromorphic computing. Particularly, the memristor technology that can naturally emulate plasticity and energy efficiency of biological synapses have gained a lot of attention. However, the use of memristors in high density computation, such as matrix-vector operation, is still missing. In this work, a spiking (pulse-based) computing component that leverages memristor crossbar array is proposed for matrix-vector operation. We adopt the rate coding model and count the produced spike number during a given time period of T as the computation output. We carefully design the crossbar array structure and the integrate-and-fire circuit. The linear relationship between output spike numbers and the sum-of-production of input vector and matrix entries is observed in our simulation results. The proposed spiking computing design realizes matrix computation successfully and demonstrates good adaptability in neural network.
Recessive inheritance of a new point mutation of the PMP22 gene in Dejerine-Sottas disease (1999)

The existence of recessive transmission of Dejerine-Sottas disease, a severe demyelinating neuropathy of childhood, has been questioned, because only heterozygous mutations of the myelin proteins P0 or PMP22 genes have been identified in virtually all patients with this phenotype. We report on a family with 3 affected children with this phenotype, born to clinically and electrophysiologically unaffected parents. All 3 children carried a previously unknown homozygous missense point mutation (Arg157Trp) of the PMP22 gene. The parents were heterozygous for the same mutation. These findings demonstrate the occurrence of recessive transmission in this setting.
Hydrodynamic focusing in microstructures: Improved detection efficiencies in subfemtoliter probe volumes (2007)

We present a method for improving detection efficiencies in single molecule confocal fluorescence spectroscopy with subfemtoliter probe volumes within microfluidic channels. Our approach is based on hydrodynamically focusing an analyte stream within a microfluidic channel down to a width on the same order of magnitude as that of the confocal probe volume. Experiments are performed in which fluorescently labeled polystyrene microspheres (930 nm diameter) are motivated through a microchannel and passed through a focused laser beam at a variety of flow rates (0.1−11 μL∕min). Hydrodynamic focusing of the analyte stream is achieved by introduction of two sheath flow streams that flank the central analyte stream. Through variation of the relative flow rates in each input stream the analyte stream can be controlled with micron resolution. A maximum hydrodynamic focusing width of 3 μm was achieved within a 50 μm wide microfluidic channel; hence, a larger proportion of molecules traveling through the microfluidic device were detected. Furthermore, simple statistical methods are used to investigate the resulting fluorescence bursts and generate single-particle burst width and burst area distributions. From these data, the total detection efficiencies are shown to be an order of magnitude better than those achievable in conventional unfocused systems.
Dietary nitrate supplementation reduces the O2cost of walking and running: a placebo-controlled study (2010)

Dietary supplementation with beetroot juice (BR) has been shown to reduce resting blood pressure and the O(2) cost of submaximal exercise and to increase tolerance to high-intensity cycling. We tested the hypothesis that the physiological effects of BR were consequent to its high NO(3)(-) content per se, and not the presence of other potentially bioactive compounds. We investigated changes in blood pressure, mitochondrial oxidative capacity (Q(max)), and physiological responses to walking and moderate- and severe-intensity running following dietary supplementation with BR and NO(3)(-)-depleted BR [placebo (PL)]. After control (nonsupplemented) tests, nine healthy, physically active male subjects were assigned in a randomized, double-blind, crossover design to receive BR (0.5 l/day, containing ∼6.2 mmol of NO(3)(-)) and PL (0.5 l/day, containing ∼0.003 mmol of NO(3)(-)) for 6 days. Subjects completed treadmill exercise tests on days 4 and 5 and knee-extension exercise tests for estimation of Q(max) (using (31)P-magnetic resonance spectroscopy) on day 6 of the supplementation periods. Relative to PL, BR elevated plasma NO(2)(-) concentration (183 ± 119 vs. 373 ± 211 nM, P < 0.05) and reduced systolic blood pressure (129 ± 9 vs. 124 ± 10 mmHg, P < 0.01). Q(max) was not different between PL and BR (0.93 ± 0.05 and 1.05 ± 0.22 mM/s, respectively). The O(2) cost of walking (0.87 ± 0.12 and 0.70 ± 0.10 l/min in PL and BR, respectively, P < 0.01), moderate-intensity running (2.26 ± 0.27 and 2.10 ± 0.28 l/min in PL and BR, respectively, P < 0.01), and severe-intensity running (end-exercise O(2) uptake = 3.77 ± 0.57 and 3.50 ± 0.62 l/min in PL and BL, respectively, P < 0.01) was reduced by BR, and time to exhaustion during severe-intensity running was increased by 15% (7.6 ± 1.5 and 8.7 ± 1.8 min in PL and BR, respectively, P < 0.01). In contrast, relative to control, PL supplementation did not alter plasma NO(2)(-) concentration, blood pressure, or the physiological responses to exercise. These results indicate that the positive effects of 6 days of BR supplementation on the physiological responses to exercise can be ascribed to the high NO(3)(-) content per se.
Intercellular adhesion molecule-1 gene expression in human endothelial cells. Differential regulation by tumor necrosis factor-alpha and phorbol myristate acetate. (1992)

Intercellular adhesion molecule-1 (ICAM-1) is an inducible glycoprotein expressed on the surface of inflamed endothelium which mediates in part the extravasation of granulocytes into sites of infection or injury. ICAM-1 mRNA is not detected in unstimulated human umbilical vein endothelial cells (HUVECs), but accumulates transiently following tumor necrosis factor-alpha (TNF-alpha) or phorbol myristate acetate (PMA) treatment with maximal steady state levels occurring at 2 or 4 h, respectively. Pretreating HUVECs with PMA for 72 h down-regulates protein kinase C and inhibits the subsequent induction of ICAM-1 mRNA by PMA, but does not affect TNF-alpha-induced message accumulation. Nuclear run-on assays showed that the ICAM-1 gene is transcribed under basal conditions in HUVECs, and that TNF-alpha stimulates transcriptional activity 3- to 4-fold within 30 min of treatment. In contrast, PMA has little effect on ICAM-1 gene transcription up to 4 h following stimulation. Message stability studies established that ICAM-1 mRNA induced by PMA has a longer half-life than the TNF-alpha-induced message. These results suggest that PMA acts through protein kinase C to up-regulate ICAM-1 expression primarily at a post-transcriptional level by stabilizing ICAM-1 mRNA, whereas TNF-alpha transcriptionally regulates ICAM-1 gene expression through an undefined, protein kinase C-independent pathway.
Amino acid sequence and secondary structural analysis of the corn inhibitor of trypsin and activated Hageman Factor. (1984)

The amino acid sequence of a corn inhibitor for trypsin and activated Hageman Factor (Factor XIIa) was determined by automated Edman degradation from the intact inhibitor and two fragments generated by specific cleavage of the inhibitor. The 112-residue sequence is unique at each position except 91, where both Ala and Glu were found. The structural heterogeneity suggests the occurrence of two genes (possibly allelic) for the inhibitor. Based on analysis of fragments produced by the interaction of the inhibitor with trypsin-agarose, the reactive site peptide bond is identified as Arg 36-Leu 37. There is no strong similarity between the sequence of the corn inhibitor and the sequences published for other serine protease inhibitors. Thus, the corn inhibitor represents a new family of protease inhibitors. Circular dichroism measurements and a theoretical prediction of secondary structure indicate that the inhibitor has helix and beta sheet contents of approximately 40 and 20%, respectively.