gebhart/patrepeval huggingface dataset:
Major histocompatibility complex binding and T cell recognition of a viral nonapeptide containing a minimal tetrapeptide (1991)

Abstract The primary immune response of cytotoxic T lymphocytes in H‐2 d and H‐2 q mice to infection with lymphocytic choriomeningitis virus is directed mostly towards the common major T cell epitope of amino acids 112–132 on the viral nucleoprotein (NP). The molecules responsible for presentation of the T cell epitope NP112‐132 are in both haplotypes the MHC class I L antigens (L d , L q ). Truncations of the amino and carboxy termini of the NP 112–132 sequence revealed the nonapeptide RPQASGVYM (NP118‐126) as a most effective peptide antigen, but even the tetrapeptide GVYM was recognized by CTL of both haplotypes in a class I antigen‐restricted specificity. When tyrosine (Y) or methionine (M) were substituted with alanine, CTL recognition of the altered nonamer required 10 6 to 10 8 times higher peptide concentrations and in one case (Y → A on L d ) the peptide was not recognized at all. Up‐modulation of the expression of L d and L q class I antigens as measured by flow cytometry correlated with the ability to present the peptide antigens. The only exception was peptide NP118‐126 (M → A), which was recognized by T cells on L‐L d and L‐L q target cells but failed to up‐regulate L d and L q antigens.
On the capacity of computer memory with defects (1983)

A computer memory with defects is modeled as a discrete memoryless channel with states that are statistically determined. The storage capacity is found when complete defect information is given to the encoder or to the decoder, and when the defect information is given completely to the decoder but only partially to the encoder. Achievable storage rates are established when partial defect information is provided at varying rates to both the encoder and the decoder. Arimoto-Blahut type algorithms are used to compute the storage capacity.
Human Immunodeficiency Virus Type 1 Recombinant Reverse Transcriptase Enzymes Containing the G190A and Y181C Resistance Mutations Remain Sensitive to Etravirine (2009)

Etravirine (ETR) is a second-generation nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI) active against common human immunodeficiency virus type 1 (HIV-1) drug-resistant strains. This study was designed to determine the extent to which each of the Y181C or G190A mutations in RT might confer resistance to ETR and other members of the NNRTI family of drugs. Recombinant HIV-1 RT enzymes containing either the Y181C or the G190A mutation, or both mutations in tandem, were purified. Both RNA- and DNA-dependent DNA polymerase assays were performed in order to determine the extent to which each of these mutations might confer resistance in cell-free biochemical assays against each of ETR, efavirenz, and nevirapine. Both the biochemical and the cell-based phenotypic assays confirmed the susceptibility of G190A-containing enzymes and viruses to ETR. The results of this study indicate that the G190A mutation is not associated with resistance to ETR.
Commercial Antivirus Software Effectiveness: An Empirical Study (2010)

Despite the widespread use of antivirus software, malware remains pervasive. A new study compares the effectiveness of six commercial AV products.
Recombinant Hepatocyte Growth Factor Accelerates Cutaneous Wound Healing in a Diabetic Mouse Model (2004)

We examined effects of recombinant hepatocyte growth factor (HGF) on cutaneous wound healing, using a full-thickness cutaneous excision model in diabetic mice. Topical administration of HGF, as well as basic fibroblast growth factor (bFGF), promoted the rate of wound closure and re-epithelialization. Both HGF and bFGF enhanced expansion of the granulation tissue and stimulated neovascularization on day 7 postwounding, wherein the increase in microvessel density in HGF-treated wounds was higher than that in bFGF-treated wounds. Matrix metalloproteinases (MMP-2 and MMP-9) activities involved in cell migration, angiogenesis, and extracellular matrix (ECM) remodeling, were enhanced by HGF-treatment on day 7. On day 28 postwounding (later stages of wound healing), granulation tissue in bFGF-treated wounds remained to a greater extent than that seen in saline- and HGF-treated wounds. Likewise, bFGF- but not HGF-treatment stimulated DNA synthesis of fibroblasts in granulation tissue, suggesting that HGF stimulates wound healing with lesser degree of susceptibility to cutaneous scarring. We propose that supplement of HGF may be a potential therapeutic approach for treatment of cutaneous ulcer.
Implications of the Human Genome Project for Medical Science (2001)

The year 2000 marked both the start of the new millennium and the announcement that the vast majority of the human genome had been sequenced. Much work remains to understand how this "instruction book for human biology" carries out its multitudes of functions. But the consequences for the practice of medicine are likely to be profound. Genetic prediction of individual risks of disease and responsiveness to drugs will reach the medical mainstream in the next decade or so. The development of designer drugs, based on a genomic approach to targeting molecular pathways that are disrupted in disease, will follow soon after. Potential misuses of genetic information, such as discrimination in obtaining health insurance and in the workplace, will need to be dealt with swiftly and effectively. Genomic medicine holds the ultimate promise of revolutionizing the diagnosis and treatment of many illnesses.
Sensing and repairing DNA double-strand breaks (2002)

The DNA double-strand break (DSB) is the principle cytotoxic lesion for ionizing radiation and radio-mimetic chemicals but can also be caused by mechanical stress on chromosomes or when a replicative DNA polymerase encounters a DNA single-strand break or other type of DNA lesion. DSBs also occur as intermediates in various biological events, such as V(D)J recombination in developing lymphoid cells. Inaccurate repair or lack of repair of a DSB can lead to mutations or to larger-scale genomic instability through the generation of dicentric or acentric chromosomal fragments. Such genome changes may have tumourigenic potential. In other instances, DSBs can be sufficient to induce apoptosis. Because of the threats posed by DSBs, eukaryotic cells have evolved complex and highly conserved systems to rapidly and efficiently detect these lesions, signal their presence and bring about their repair. Here, I provide an overview of these systems, with particular emphasis on the two major pathways of DSB repair: non-homologous end-joining and homologous recombination. Inherited or acquired defects in these pathways may lead to cancer or to other human diseases, and may affect the sensitivity of patients or tumour cells to radiotherapy and certain chemotherapies. An increased knowledge of DSB repair and of other DNA DSB responses may therefore provide opportunities for developing more effective treatments for cancer.
Single immunizing dose of recombinant adenovirus efficiently induces CD8+ T cell-mediated protective immunity against malaria (1997)

The immunogenicity of a recombinant replication defective adenovirus expressing a major malaria Ag, the circumsporozoite (CS) protein (AdPyCS), was determined using a rodent malaria model. A single immunizing dose of this construct induced a large number of CS-specific CD8+ and CD4+ T cells in the spleens of these animals, particularly when given by the s.c. or i.m. route. A single dose of AdPyCS also induced high titers of Abs to Plasmodium yoelii sporozoites in mice. No other form of presentation of the CS protein given as a single immunizing dose, i.e., irradiated sporozoites, recombinant vaccinia, or influenza virus, etc., elicits comparably high numbers of CS-specific CD8+ T cells. The high concentration of CS-specific CD8+ T cells in the spleen was relatively short-lived, decreasing to half of its original value by 4 wk and to one-third at 8 wk after AdPyCS inoculation. The decrease in splenic CS-specific CD4+ T cells was even more rapid. Most importantly, a single dose of inoculation of AdPyCS into mice rendered them highly resistant to sporozoite challenge, resulting in a 93% inhibition of liver stage development of the parasites. This protective effect was primarily mediated by CD8+ T cells, as shown by depletion of this T cell population, while depletion of the CD4+ T cell population had only a minor effect on anti-plasmodial activity. Moreover, the inoculation of mice with AdPyCS induces sterile immunity in a significant proportion of mice, preventing the occurrence of parasitemia.
Graphical inference for infovis (2010)

How do we know if what we see is really there? When visualizing data, how do we avoid falling into the trap of apophenia where we see patterns in random noise? Traditionally, infovis has been concerned with discovering new relationships, and statistics with preventing spurious relationships from being reported. We pull these opposing poles closer with two new techniques for rigorous statistical inference of visual discoveries. The "Rorschach" helps the analyst calibrate their understanding of uncertainty and "line-up" provides a protocol for assessing the significance of visual discoveries, protecting against the discovery of spurious structure.
Effect of hyperthermiain vitro andin vivo on adenine and pyridine nucleotide pools in human peripheral lymphocytes (1991)

Hyperthermia has been shown in vitro and in vivo to potentiate the effects of ionizing irradiation. Previous studies found that hyperthermia alters the metabolism of adenosine diphosphate (ADP)-ribose polymers required for recovery from DNA damage and that poly(ADP-ribose) polymerase activity is very sensitive to cellular nicotinamide-adenine dinucleotide (NAD) levels. Thus, the effect of 41.8 degrees C hyperthermia in vitro and in vivo on NAD and adenosine triphosphate (ATP) levels was studied in human peripheral lymphocytes. In vitro studies showed significant decreases in oxidized NAD (NAD+) and ATP levels after heating that simulated a clinical whole-body hyperthermia (WBH) treatment. This nucleotide depletion could not be attributed to nucleotide leakage or increased enzymatic NAD+ consumption. As the reduction of NAD observed was sufficient to decrease poly(ADP-ribose)polymerase activity by 50%, the studies were extended to clinica cases. Cellular NAD+ and ATP were measured in previously stored lymphocytes obtained from four patients before and after WBH; a statistically significant decrease in NAD+ was observed after WBH which quantitatively agreed with the in vitro results. Based on these results a prospective study was done in three patients; NAD+ was extracted immediately on sample collection, and the kinetics of WBH-induced NAD depletion were studied. These data, which agree quantitatively with the laboratory results, are presented.
System-level modeling for geological storage of CO2 (2006)

One way to reduce the effects of anthropogenic greenhouse gases on climate is to inject carbon dioxide (CO2) from industrial sources into deep geological formations such as brine formations or depleted oil or gas reservoirs. Research has and is being conducted to improve understanding of factors affecting particular aspects of geological CO2 storage, such as performance, capacity, and health, safety and environmental (HSE) issues, as well as to lower the cost of CO2 capture and related processes. However, there has been less emphasis to date on system-level analyses of geological CO2 storage that consider geological, economic, and environmental issues by linking detailed representations of engineering components and associated economic models. The objective of this study is to develop a system-level model for geological CO2 storage, including CO2 capture and separation, compression, pipeline transportation to the storage site, and CO2 injection. Within our system model we are incorporating detailed reservoir simulations of CO2 injection and potential leakage with associated HSE effects. The platform of the system-level modeling isGoldSim [GoldSim, 2006]. The application of the system model is focused on evaluating the feasibility of carbon sequestration with enhanced gas recovery (CSEGR) in the Rio Vista region of California. The reservoir simulations are performed using a special module of the TOUGH2 simulator, EOS7C, for multicomponent gas mixtures of methane and CO2 or methane and nitrogen. Using this approach, the economic benefits of enhanced gas recovery can be directly weighed against the costs, risks, and benefits of CO2 injection.
Why liquid membrane extraction is an attractive alternative in sample preparation (2004)

Abstract The use of liquid membrane-based extractions is increasingly seen as offering an alternative to conventional sample preparation procedures in analysis of chemical species in both environmental and biological media. In this article, emphasis is placed on the attractiveness of liquid membrane-based extraction techniques to a variety of analytical applications such as speciation of metal ions in biological fluids, time-weighted average field sampling, and time-weighted average passive field sampling. Further, the area of designing new and much simpler miniaturized configurations, which is enjoying much attention in liquid membrane-based extraction techniques, is discussed.
Calcium regulation of gene expression in neuronal cells (1994)

Long-term adaptive changes in neurons following brief periods of neuronal activity are likely to involve changes in gene expression. The mechanisms of activity-dependent gene expression have been explored in central neurons and the neuronal cell line PC12. Calcium influx through either NMDA receptors or voltage-sensitive calcium channels leads to the rapid induction of a number of immediate-early genes including c-fos. Promoter analysis indicates that Ca2+ influx through different calcium channels activates distinct signaling pathways that either target the serum response element (SRE) or the calcium response element (CaRE) within the c-fos promoter. Transcription through the CaRE requires the induced phosphorylation of the cAMP response element binding protein (CREB) at Ser133. This site on CREB is also phosphorylated in the suprachiasmatic nucleus in vivo upon light stimulation. These observations suggest Ca2+ can regulate gene expression by multiple signaling pathways including one that involves the Ca(2+)-dependent phosphorylation of the transcription factor CREB.
Recent progress in dengue vaccine research and development. (2010)

Recent data suggest that dengue immunity could be elicited via either humoral or cell-mediated routes. Directing the immune response to serotype-specific epitopes from domain (D)III of the dengue virus envelope protein (Env) may induce effective levels of neutralizing antibodies. Removing serotype-crossreactive epitopes from DIII, as well as DII, may reduce the potential for the vaccine to induce non-neutralizing antibodies associated with antibody-dependent enhancement (ADE) of infection. The use of consensus Env DIII sequences for each serotype, and perhaps even a single consensus sequence for all four serotypes of dengue virus, may direct the immune response to invariant neutralizing sequences, which might improve vaccine safety and long-term efficacy. Vaccines incorporating capsid and/or non-structural (NS) proteins may be capable of inducing tetravalent cell-mediated immunity without ADE. However, the potential of cell-mediated immunity to contribute to pathology is not well understood, and modifications of NS proteins, such as truncated NS1, may be necessary for optimal vaccine safety. This review discusses recent progress in the development of dengue vaccines.
[Patients' sleep in intensive care units and sleep-modifying factors]. (2000)

Patients admitted to intensive care units sleep poorly, generally because of the environmental conditions of these units. Sleep deprivation in critical patients has severe consequences and can contribute to deterioration of their condition. The quality of sleep of the patients in our unit was evaluated to identify factors that they considered disruptive of sleep. The study included 33 patients who were admitted between April 1998 and January 1999 and had remained conscious and oriented for at least 5 days before being included in the study. We asked them to evaluate how well they had slept during their stay in the unit and to score specific factors that could disrupt sleep (environment, admission to the unit, techniques and procedures) on a scale of 0 to 10. Most patients (63.6%) claimed that they "always" or "usually" slept well. The most disruptive environmental factor was the sound of alarms, pain bothered patients more than fear or anxiety, and endotracheal intubation and mechanical ventilation were the techniques that most interfered with sleep. The quality of sleep of patients in the unit was apparently uninfluenced by pre-admission sleep problems, the severity of the process, or the type of analgesia-sedation administered. The largest percentage of patients who slept poorly had been admitted to one of the wings of the unit, which should be studied specifically.
Pertuzumab Monotherapy After Trastuzumab-Based Treatment and Subsequent Reintroduction of Trastuzumab: Activity and Tolerability in Patients With Advanced Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer (2012)

Although pertuzumab has some activity in patients with HER2-positive breast cancer that progressed during therapy with trastuzumab, the combination of pertuzumab and trastuzumab seems to be more active than monotherapy.
Systematic micro-array based identification of placental mRNA in maternal plasma: towards non-invasive prenatal gene expression profiling (2004)

The discovery of fetal DNA in the plasma of pregnant women1 has led to the development of promising approaches for non-invasive prenatal diagnosis.2–6 However, as fetal and maternal DNA species co-exist in maternal plasma, these DNA based diagnostic applications depend largely on the use of genetic markers that would allow the discrimination between fetal and maternal DNA (for example, the Y chromosome of a male fetus), and thus, a particular genetic marker could generally only be used in a proportion of pregnancies. This situation has prompted a quest by many laboratories to develop fetal nucleic acid markers that are independent of sex or polymorphism.

The detection of fetal RNA in maternal plasma7 offers new possibilities for non-invasive prenatal investigation. This field has recently taken on new momentum as robust methods for plasma RNA extraction have been developed8 and circulating RNA has been shown to be surprisingly stable,9 possibly through an association with particulate matter.8 Furthermore, recent studies have identified the placenta as a significant source of such circulating fetal RNA.10 Hence, placental expressed mRNA transcripts, such as those coding for human placental lactogen ( hPL ), human chorionic gonadotropin β subunit ( βhCG ),10 and corticotropin releasing hormone ( CRH ),11 have been shown to be detectable in maternal plasma. Quantitative assays have been developed for the measurement of these circulating mRNA transcripts.8 The pregnancy specificity of these mRNA species has been demonstrated by their rapid clearance from maternal plasma after delivery.10,11 Thus, the detection in maternal plasma of mRNA transcripts derived from the plasma offers new avenues for the development of fetal specific nucleic acid markers that are independent of sex and polymorphism for the non-invasive prenatal assessment of all pregnancies.12 The clinical value of such an approach has …
Butyrate Specifically Down-Regulates Salmonella Pathogenicity Island 1 Gene Expression (2006)

Invasion of intestinal epithelial cells by Salmonella enterica is decreased after exposure to butyric acid. To understand the molecular mechanisms of this phenomenon, a comparative transcriptomic analysis of Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium grown in medium supplemented with butyrate was performed. We found that butyrate down-regulated the expression of 19 genes common to both serovars by a factor of twofold or more, and 17 of these genes localized to the Salmonella pathogenicity island 1 (SPI1). These included the SPI1 regulatory genes hilD and invF. Of the remaining two genes, ampH has 91% homology to an Escherichia coli penicillin-binding protein and sopE2 encodes a type III-secreted effector protein associated with invasion but located at a separate site on the chromosome from SPI1.
Comparative study of enteric viruses, coliphages and indicator bacteria for evaluating water quality in a tropical high-altitude system (2009)

Coliphages proved to be adequate faecal pollution indicators for the irrigation water studied. Viral presence in this tropical high-altitude system showed a similar trend to data previously reported for temperate zones.
[The clinical value of sialyl SSEA-1 antigen in patients with gynecologic tumors]. (1987)

In order to estimate the clinical significance of sialyl SSEA-1 antigen, the antigen was measured with an "FH-6" Otsuka Kit in sera from patients with various gynecologic tumors. Among the patients with uterine malignancies and benign ovarian tumors, the incidence of elevated sialyl SSEA-1 antigen levels was very low. However, among the patients with ovarian malignancies, serum sialyl SSEA-1 antigen was significantly increased in the following order: clinical stage I (40%), stage II (67%) and stage III (75%). The serum antigen values were also correlated with the effect of treatment. In addition, high antigen values were also observed in all 14 malignant ovarian cyst fluids tested. The immunohistochemical localization of sialyl SSEA-1 antigen was determined by an immunoperoxidase method using FH-6 monoclonal antibody. A weak positive reaction was observed in normal glands of female genital tracts. However, the intense staining was shown on the mocus materials or on the luminal surface of some malignant glands as well as in the cytoplasm of some adenocarcinoma cells of gynecologic malignancies, although there were few positive cases or positive cells. Thus, sialyl SSEA-1 antigen appears to be a useful marker in the diagnosis of ovarian malignancies.