gebhart/patrepeval huggingface dataset:
Lymphogranuloma venereum emerging in men who have sex with men in Germany (2006)

A resurgence of lymphogranuloma venereum (LGV) has been observed in several European countries. LGV is not a mandatorily notifiable disease in Germany. Reports of LGV cases have actively been collected by the Robert Koch-Institut since 2004 to describe the outbreak and estimate the extent of the LGV problem in Germany. Updates on the LGV outbreak were published in the German national epidemiological bulletin. Physicians were asked to send their samples to a laboratory for genotyping. A possible case was defined as a person with symptoms of proctitis and/or inguinal lymph node swelling and a positive chlamydia serology. A probable case had in addition a positive chlamydia rectal or urinary PCR test. A case was confirmed if the genotype L1-L3 was identified based on sequence analysis of omp1 gene sequences. Since 2003, LGV has been reported in 78 male patients in Germany. Of these, 61 patients were confirmed as genotype L2. Fifty eight out of 78 patients (74%) are known to be men who have sex with men (MSM). Fifty five patients (71%) had rectal symptoms and 49 (63%) knew they were HIV positive. Sixty two (79%) of the patients were residents of Berlin or Hamburg. LGV has emerged in MSM in Germany at the same time as in other European countries. It is thought that LGV may become endemic in the MSM community in German metropolitan areas, because the number of reported patients with LGV continues to increase. The increase in the number of LGV cases and the high HIV prevalence in LGV patients are of great public health concern. Clinicians and MSM may not be sufficiently aware of the disease, and existing efforts to promote awareness and prevention of sexually transmitted infections and HIV need to be strengthened.
HIV-1 THERAPEUTIC VACCINE: A RAY OF HOPE (2003)

The human immunodeficiency virus (HIV) epidemic is still in its early stages, and a marked increase in global prevalence is projected for the next coming years. Neither behavioural therapies nor current antiretroviral drugs are likely to have an impact on this silent epidemic. Current antiretroviral drugs are too expensive for the developing countries, and there are major problems of adherence, resistance and toxicity, which limit their application and efficacy. The main problem facing us, as inhabitants of a single world, is to prevent further infections regardless of where they occur, and this requires a vaccine programme. A successful immunotherapeutic HIV vaccine has the potential to overcome these problems, and would be a valuable advance. To accelerate the development of an HIV vaccine, additional candidate vaccines must be evaluated in parallel in both industrialized and developing countries. This will require international collaboration and coordination and critical ethical issues will need to be addressed. The probable triple cocktail of the future for global HIV prevention will be vaccination, anti-retroviral therapy, and not the least, behavioural therapy.
A syllable-based name transliteration system (2009)

This paper describes the name entity transliteration system which we conducted for the "NEWS2009 Machine Transliteration Shared Task" (Li et al 2009). We get the transliteration in Chinese from an English name with three steps. We syllabify the English name into a sequence of syllables by some rules, and generate the most probable Pinyin sequence with the mapping model of English syllables to Pinyin (EP model), then we convert the Pinyin sequence into a Chinese character sequence with the mapping model of Pinyin to characters (PC model). And we get the final Chinese character sequence. Our system achieves an ACC of 0.498 and a Mean F-score of 0.786 in the official evaluation result.
Age-Related Impairment of Synaptic Transmission But Normal Long-Term Potentiation in Transgenic Mice that Overexpress the Human APP695SWE Mutant Form of Amyloid Precursor Protein (2001)

We have studied synaptic function in a transgenic mouse strain relevant to Alzheimer's disease (AD), overexpressing the 695 amino acid isoform of human amyloid precursor protein with K670N and M671L mutations (APP(695)SWE mice), which is associated with early-onset familial AD. Aged-transgenic mice had substantially elevated levels of Abeta (up to 22 micromol/gm) and displayed characteristic Abeta plaques. Hippocampal slices from 12-month-old APP(695)SWE transgenic animals displayed reduced levels of synaptic transmission in the CA1 region when compared with wild-type littermate controls. Inclusion of the ionotropic glutamate receptor antagonist kynurenate during preparation of brain slices abolished this deficit. At 18 months of age, a selective deficit in basal synaptic transmission was observed in the CA1 region despite treatment with kynurenate. Paired-pulse facilitation and long-term potentiation (LTP) were normal in APP(695)SWE transgenic mice at both 12 and 18 months of age. Thus, although aged APP(695)SWE transgenic mice have greatly elevated levels of Abeta protein, increased numbers of plaques, and reduced basal synaptic transmission, LTP can still be induced and expressed normally. We conclude that increased susceptibility to excitotoxicity rather than a specific effect on LTP is the primary cause of cognitive deficits in APP(695)SWE mice.
Reversal of myofibroblasts by amniotic membrane stromal extract (2008)

Myofibroblasts play an important role in morphogenesis, inflammation, and fibrosis in most tissues. The amniotic membrane stroma can maintain keratocytes in cultures and prevent them from differentiating into myofibroblasts. However, it is unknown whether the AM stroma can also reverse differentiated myofibroblasts. In this study, we found that amniotic membrane stromal cells (AMSCs), which adopted fibroblastic phenotype in vivo, quickly and completely differentiated into myofibroblasts during ex vivo culture in DMEM/FBS on plastic within 2 passages. When cultured on type I collagen, the myofibroblasts maintained their phenotype, however, when these myofibroblasts were re-seeded onto a cryopreserved amniotic membrane stromal surface, they reversed to the fibroblast phenotype. Moreover, we found that the amniotic membrane stromal extract not only helps maintain primary AMSCs fibroblastic phenotype in vitro, but also can reverse differentiated myofibroblasts back to fibroblasts. This reversal was not coupled with cell proliferation. We concluded that the amniotic membrane stroma contains soluble factors that can regulate the mesenchymal cell differentiation. Further investigation into the identity of these factors and the control mechanisms may unravel a new scar-reversing strategy.
Measurement of MAP kinase activation by flow cytometry using phospho‐specific antibodies to MEK and ERK: Potential for pharmacodynamic monitoring of signal transduction inhibitors (2001)

Cancer cells frequently show abnormal signaling via the mitogen activated protein kinase (MAP kinase) pathway due to increased activity of surface receptors for growth factors, or as a result of ras mutations. The development of potent anti-cancer agents that target this pathway prompts the need for analytical methods that allow pharmacodynamic monitoring of drug effects in patients during early phase clinical trial. We describe such a method, based on the activation of T-lymphocytes in undiluted peripheral blood using phorbol myristate acetate (PMA). Following rapid hypotonic lysis and formaldehyde fixation, activation of the MAP kinase pathway can then be demonstrated using phospho-specific antibodies that recognize the activated mediators MEK or ERK, followed by surface labeling with anti-CD3 to identify T-lymphocytes. This method was used to investigate the effects of a MEK inhibitor, U0126, and a new raf kinase inhibitor BAY 37-9751 in blood samples from normal donors. Dose-dependent inhibition of pERK activation was demonstrated for both agents. Furthermore, differential effects on pMEK activation allowed the molecular targets of the two inhibitors to be distinguished. In addition to monitoring drug effects in patients during treatment with inhibitors of the MAP kinase pathway, the general methodology described in this paper has the potential for wide application to the study of signal transduction at the single cell level using flow cytometry.
Increase of Plasma VEGF after Intravenous Administration of Bevacizumab Is Predicted by a Pharmacokinetic Model (2010)

Vascular endothelial growth factor (VEGF) is one of the most potent cytokines targeted in antiangiogenic therapies. Bevacizumab, a recombinant humanized monoclonal antibody to VEGF, is being used clinically in combination with chemotherapy for colorectal, non-small cell lung and breast cancers, and as a single agent for glioblastoma and is being tested for other types of cancer in numerous clinical trials. It has been reported that the intravenous injection of bevacizumab leads to an increase of plasma VEGF concentration in cancer patients. The mechanism responsible for this counterintuitive increase has not been elucidated, although several hypotheses have been proposed. We use a multiscale systems biology approach to address this problem. We have constructed a whole-body pharmacokinetic model comprising three compartments: blood, normal tissue, and tumor tissue. Molecular interactions among VEGF-A family members, their major receptors, the extracellular matrix, and an anti-VEGF ligand are considered for each compartment. Diffusible molecules extravasate, intravasate, are removed from the healthy tissue through the lymphatics, and are cleared from the blood.
Gastrointestinal Mucus (1989)

The sections in this article are: 1 Adherent Mucus Gel 1.1 In Vivo Continuity and Thickness 1.2 Physical and Permeability Properties 2 Isolated Mucin Glycoprotein 2.1 Technology 2.2 Mucin Carbohydrate Chain Structure 2.3 Protein Core of Mucins and Macromolecular Polymeric Structure 2.4 Gel-Formation and Physical Properties of Mucins 2.5 Lipid and Protein Components of Mucus Secretions 3 Biosynthesis and Secretion of Mucus: Cellular Aspects 3.1 Mucus-Secreting Cells 3.2 Mucin Biosynthesis 3.3 Secretion of Mucus 4 Secretion of Mucus: Measurement and Control 4.1 Measurement 4.2 Control of Secretion of Gastric Mucus 4.3 Control of Secretion of Intestinal and Colonic Mucus 5 Degradation of Mucus 6 Function of Mucus
New reference equation of state for associating liquids (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew reference equation of state for associating liquidsWalter G. Chapman, Keith E. Gubbins, George Jackson, and Maciej RadoszCite this: Ind. Eng. Chem. Res. 1990, 29, 8, 1709–1721Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/ie00104a021https://doi.org/10.1021/ie00104a021research-articleACS PublicationsRequest reuse permissionsArticle Views5869Altmetric-Citations1765LEARN 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
Web Links as User Artefacts (1996)

The Distributed Link Service, a distributed system of link services for the World Wide Web [Carr et al 95, Carr et al 96], has been used to impose configurable navigation structures upon suites of static document resources in the World-Wide Web. This paper describes the integration of the link service functionality into a Web proxy server, and examines the implications for the service&amp;apos;s user interface in terms of including, representing, discriminating, prioritising and traversing links.
Induction of interleukin 1 and tumor necrosis factor by mycobacterial proteins: the monocyte western blot. (1990)

Infection with Mycobacterium tuberculosis involves mononuclear phagocytic cells as hosts to intracellular parasites, accessory cells in the induction of the immune response, effector cells for mycobacterial killing, and targets of cytotoxic lymphocytes. When stimulated by whole mycobacteria or various mycobacterial preparations, monocytes and macrophages produce the cytokines interleukin 1 and tumor necrosis factor, which possess multiple functions, including immune induction, and may be responsible for the fever and cachexia prominent in tuberculosis. To identify mycobacterial proteins that may directly activate production of these cytokines, culture filtrate of M. tuberculosis that had been subjected to gel electrophoresis and transferred to nitrocellulose paper was used to stimulate monocyte production of cytokines. Fractions representing molecular weights of 46,000 and 20,000 consistently induced both interleukin 1 and tumor necrosis factor. The magnitude of the monocyte responses to these fractions was similar to that to intact mycobacteria or optimal concentrations of lipopolysaccharide. This stimulatory effect was not due to contamination with either bacterial lipopolysaccharide or mycobacterial lipoarabinomannan, as it was abolished by digestion with Streptomyces griseus protease but was unaffected by ammonium sulfate precipitation, preincubation with polymyxin B, or depletion of lipoarabinomannan by immunoaffinity chromatography. Proteins identified by this system may have considerable potential as immunogens, as the capacity to directly stimulate mononuclear phagocyte production of cytokines is an essential property of adjuvants.
Intravitreal injection of crystalline cortisone as adjunctive treatment of proliferative vitreoretinopathy (2000)

This pilot study suggests that intravitreal injection of crystalline cortisone with most of the vehicle removed is not toxic to intraocular structures, reduces postoperative intraocular inflammation, and may be a potentially useful additional tool in the treatment of proliferative vitreoretinopathy.
Retinal imaging using adaptive optics technology (2014)

Adaptive optics (AO) is a technology used to improve the performance of optical systems by reducing the effect of wave front distortions. Retinal imaging using AO aims to compensate for higher order aberrations originating from the cornea and the lens by using deformable mirror. The main application of AO retinal imaging has been to assess photoreceptor cell density, spacing, and mosaic regularity in normal and diseased eyes. Apart from photoreceptors, the retinal pigment epithelium, retinal nerve fiber layer, retinal vessel wall and lamina cribrosa can also be visualized with AO technology. Recent interest in AO technology in eye research has resulted in growing number of reports and publications utilizing this technology in both animals and humans. With the availability of first commercially available instruments we are making transformation of AO technology from a research tool to diagnostic instrument. The current challenges include imaging eyes with less than perfect optical media, formation of normative databases for acquired images such as cone mosaics, and the cost of the technology. The opportunities for AO will include more detailed diagnosis with description of some new findings in retinal diseases and glaucoma as well as expansion of AO into clinical trials which has already started.
Double-stranded RNA is a trigger for apoptosis in vaccinia virus-infected cells (1997)

The vaccinia virus E3L gene codes for double-stranded RNA (dsRNA) binding proteins which can prevent activation of the dsRNA-dependent, interferon-induced protein kinase PKR. Activated PKR has been shown to induce apoptosis in HeLa cells. HeLa cells infected with vaccinia virus with the E3L gene deleted have also been shown to undergo apoptosis, whereas HeLa cells infected with wild-type vaccinia virus do not. In this report, using virus recombinants expressing mutant E3L products or alternative dsRNA binding proteins, we show that suppression of induction of apoptosis correlates with functional binding of proteins to dsRNA. Infection of HeLa cells with ts23, which leads to synthesis of increased dsRNA at restrictive temperature, induced apoptosis at restrictive but not permissive temperatures. Treatment of cells with cytosine arabinoside, which blocks the late buildup of dsRNA in vaccinia virus-infected cells, prevented induction of apoptosis by vaccinia virus with E3L deleted. Cells transfected with dsRNA in the absence of virus infection also underwent apoptosis. These results suggest that dsRNA is a trigger that can initiate a suicide response in virus-infected and perhaps uninfected cells.
Cytotoxic T lymphocyte responsiveness after resolution of chronic hepatitis B virus infection. (1996)

Clearance of the hepatitis B virus (HBV) during acute hepatitis is associated with a strong, polyclonal, multispecific cytotoxic T lymphocyte (CTL) response to the viral envelope, nucleocapsid and polymerase proteins that persists for decades after clinical recovery. In contrast, chronically infected patients usually fail to mount a strong CTL response to this virus. In this study we demonstrate that chronically infected patients who experience a spontaneous or interferon-induced remission develop a CTL response to HBV that is similar in strength and specificity to patients who have recovered from acute hepatitis. The results suggest that specific immunotherapeutic enhancement of the CTL response to HBV should be possible in chronically infected patients, and that it could lead to viral clearance in these individuals with resolution of chronic liver disease.
Molecular Characterization of the PhoP-PhoQ Two-Component System in Escherichia coli K-12: Identification of Extracellular Mg 2+ -Responsive Promoters (1999)

We identified Mg2+-responsive promoters of the phoPQ, mgtA, and mgrB genes of Escherichia coli K-12 by S1 nuclease analysis. Expression of these genes was induced by magnesium limitation and depended on PhoP and PhoQ. The transcription start sites were also determined, which allowed us to find a (T/G)GTTTA direct repeat in their corresponding promoter regions.
The R6/2 transgenic mouse model of Huntington's disease develops diabetes due to deficient β-cell mass and exocytosis (2005)

Diabetes frequently develops in Huntington's disease (HD) patients and in transgenic mouse models of HD such as the R6/2 mouse. The underlying mechanisms have not been clarified. Elucidating the pathogenesis of diabetes in HD would improve our understanding of the molecular mechanisms involved in HD neuropathology. With this aim, we examined our colony of R6/2 mice with respect to glucose homeostasis and islet function. At week 12, corresponding to end-stage HD, R6/2 mice were hyperglycemic and hypoinsulinemic and failed to release insulin in an intravenous glucose tolerance test. In vitro, basal and glucose-stimulated insulin secretion was markedly reduced. Islet nuclear huntingtin inclusions increased dramatically over time, predominantly in beta-cells. beta-cell mass failed to increase normally with age in R6/2 mice. Hence, at week 12, beta-cell mass and pancreatic insulin content in R6/2 mice were 35+/-5 and 16+/-3% of that in wild-type mice, respectively. The normally occurring replicating cells were largely absent in R6/2 islets, while no abnormal cell death could be detected. Single cell patch-clamp experiments revealed unaltered electrical activity in R6/2 beta-cells. However, exocytosis was virtually abolished in beta- but not in alpha-cells. The blunting of exocytosis could be attributed to a 96% reduction in the number of insulin-containing secretory vesicles. Thus, diabetes in R6/2 mice is caused by a combination of deficient beta-cell mass and disrupted exocytosis.
Intranasal administration of nerve growth factor (NGF) rescues recognition memory deficits in AD11 anti-NGF transgenic mice (2005)

Nerve growth factor (NGF) delivery to the brain of patients appears to be an emerging potential therapeutic approach to neurodegenerative disease, such as Alzheimer's disease (AD). The intranasal route of administration could provide an alternative to intracere-broventricular infusion and gene therapy. We previously showed that intranasal administration of NGF determined an amelioration of cholinergic deficit and a decrease in the number of phosphotau-positive neurons and of beta-amyloid accumulation in AD11 mice, which express transgenic antibodies neutralizing NGF action and exhibit a progressive Alzheimer-like neurodegeneration. In this study, we report that the Alzheimer-like neurodegeneration in AD11 mice is linked to progressive behavioral deficits in visual recognition memory and spatial memory starting from 4 months of age. To establish whether intranasal administration of NGF, started after the appearance of the first memory deficits, could revert the cognitive deficits in AD11 mice, we assessed the performance of NGF-treated or control AD11 mice in the object recognition test and in a test of memory for place and context. Deficits exhibited by untreated AD11 mice could be rescued by the intranasal administration of NGF. Thus, this route of administration provides a promising way to deliver NGF to the brain in a therapeutic perspective.
Using distributed topology update and preplanned configurations to achieve trunk network survivability (1991)

The authors present a new approach for trunk network survivability. This modular approach is intended for a telephone trunk network consisting of high-bandwidth fiber-optic links connected through reconfigurable digital cross-connect nodes. It works for both node and link failures. This approach comprises a distributed protocol with two parts. First, the surviving digital cross-connect nodes are caused to converge to an agreement on the topology (i.e., what is up and what is down). Second, based on the agreed topology and on a precomputed plan for that topology, the digital cross-connect nodes are reconfigured to restore as much call-carrying capacity as possible. The modularity of this approach comes from separating the problem of devising a distributed fault-tolerant protocol to determine what the failure is from the problem of designing a network reconfiguration for that failure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A stepwise framework for the normalization of array CGH data (2005)

The proposed stepwise normalization framework preserves the minute copy number changes while removing the observed systematic biases.