gebhart/patrepeval huggingface dataset:
Death-defying acts: a meeting review on apoptosis. (1993)

Apoptosis, or programmed cell death, is the process by which a cell will actively commit suicide under tightly controlled circumstances. The apoptotic death process is associated with pronounced morphological changes in the cell as well as intranucleosomal DNA fragmentation. These criteria distinguish apoptosis from necrosis, which is cell death that occurs usually in response to physical injury. The last several years have produced an explosion of both interest in and information about apoptosis, not unlike that which occurred for the cell cycle in the 1980s. In the past, investigators did not appreciate the significance of cell death, and experiments with cell death as an outcome most often ended up in the trash. There was also a lack of molecular reagents with which to study cell death. Now, however, apoptosis is emerging as a key biological regulatory mechanism, possibly no less significant than regulation of cell growth and differentiation. Apoptosis is essential in many aspects of normal development and is required for maintaining homeostasis. Failure to regulate apoptosis negatively is associated with degenerative diseases, and failure to regulate apoptosis positively is associated with cancer and autoimmune disease. Thus, too much or to little cell death can have catastrophic consequences. Developing molecular approaches to study apoptosis in diverse systems is now the main objective of many laboratories. Some unifying themes have emerged: (1) Apoptosis may arise from incompatible or conflicting growth signals; (2) multiple pathways exist for induction of apoptosis; and (3) apoptosis can be a multistep process. This review is not meant to be comprehensive, but it is an attempt to highlight the most significant and interrelated developments presented by the participants at The Fifth Annual Pezcoller Symposium. 1
Preventing Phage Lysis of Lactococcus Lactis in Cheese Production Using A Neutralizing Heavy-Chain Antibody Fragment from Llama (2002)

Bacteriophage infection is still a persistent problem in large dairy processes despite extensive studies over the last decades. Consequently, new methods are constantly sought to prevent phage infection. In this paper, we show that phage neutralizing heavy-chain antibody fragments, obtained from Camelidae and produced at a large scale in the generally regarded as safe microorganism Saccharomyces cerevisiae, can effectively be used to impede phage induced lysis during a cheese process. The growth inhibition of the cheese starter culture by 10(5) pfu/ml cheese-milk of the small isometric-headed 936-type phage p2 was prevented by the addition of only 0.1 microg/ml (7 nM) of the neutralizing antibody fragment. The use of such antibody fragments in cheese manufacturing are a realistic and interesting option because of the small amount of antibody fragments that are needed. Moreover the antibodies are produced in a food grade microorganism and can easily be isolated from the fermentation liquid in a pure and DNA free form.
Liquid Fertility Management Bait Uptake by Urban Rats within New York City Subway Refuse Rooms (2014)

Traditional rodent management tools, such as traps and lethal rodenticides, are acute measures to reduce commensal rodent populations. Given the growing concerns regarding effectiveness, environmental safety, and animal welfare related to these tools, it has become imperative to find new methods. Fertility control is an emerging potential alternative to these tools as a safe, humane and effective method of long-term population management. SenesTech, Inc. has developed a liquid fertility management bait that causes follicle depletion in the ovaries of female Sprague Dawley rats and compromises sperm production in male Sprague Dawley rats in laboratory settings. These studies have shown significant decreases in litter sizes following bait consumption, but acceptance of this bait by wild rodents needed to be confirmed. Bait acceptance was tested within refuse rooms of the New York City subway system. Bait was provided ad libitum for 90 days. Uptake was evaluated by examining, via fluorescence microscopy, the presence of the bait marker rhodamine B, which manifests as fluorescent bands in whiskers. Presence of these bands indicated that 51% of the captured population had consumed the bait, and of these, 58% had taken the bait more than once. These results demonstrate that wild rats will consume a liquid fertility management bait, even in the presence of highly palatable and abundant food within the refuse rooms. This study establishes the successful acceptance of a bait by wild rats. Further investigation is needed to evaluate the effectiveness of this product for the management of urban Norway rat populations.
Pathophysiology of dystonia: A neuronal model (2002)

Dystonia has commonly been thought to represent a disorder of basal ganglia function. Although long considered a hyperkinetic movement disorder, the evidence to support such a classification was based on the presence of excessive involuntary movement, not on physiological data. Only recently, with the return of surgical procedures using microelectrode guidance for the treatment of dystonia, has electrophysiological data demonstrated an alteration in mean discharge rate, somatosensory responsiveness and the pattern of neuronal activity in the basal ganglia thalamocortical motor circuit. Previous models of dystonia suggested that reduced mean discharge rates in the globus pallidus internus (GPi) led to unopposed increases in activity in the thalamocortical circuit that precipitated the development of involuntary movement associated with dystonia. This model has subsequently been modified given the clear improvement in dystonic symptoms following lesions in the GPi, a procedure that is associated with a further reduction in pallidal output. The improvement in dystonia following pallidal lesions is difficult to reconcile with the "rate" hypothesis for hypokinetic and hyperkinetic movement disorders and has led to the development of alternative models that, in addition to rate, incorporate changes in pattern, somatosensory responsiveness and degree of synchronization of neuronal activity. Present models of dystonia, however, must not only take these changes into account but must reconcile these changes with the reported changes in cortical excitability reported with transcranial magnetic stimulation, the changes in metabolic activity in cortical and subcortical structures documented by positron emission tomography (PET), and the alterations in spinal and brainstem reflexes. A model incorporating these changes together with the reported changes in neuronal activity in the basal ganglia and thalamus is presented.
Variation in the expression of cell envelope proteins of coagulase-negative staphylococci cultured under iron-restricted conditions in human peritoneal dialysate (1991)

Summary: Strains of coagulase-negative staphylococci (CNS), including Staphylococcus epidermidis, S. hominis, S. warnerii, S. simulans, S. capitis, S. haemolyticus and S. saprophyticus, were isolated from patients with continuousambulatory-peritoneal-dialysis-related peritonitis. The cell wall and cytoplasmic membrane protein profiles of CNS strains cultured in either nutrient broth (NB) or pooled human peritoneal dialysate (HPD) were compared. Some interspecies variation in both the wall and membrane protein profiles was noted. However, the cell wall protein profiles of HPD-grown CNS strains differed markedly from those cultured in NB. Growth in HPD resulted in a marked reduction in the total number of cell-wall-associated proteins but up to three antigenically related proteins in the 40–56 kDa range, depending on the species, predominated. Growth in HPD also resulted in the induction of two iron-repressible cytoplasmic membrane proteins (IRMPs) of 32 and 36 kDa in S. epidermidis. Other CNS strains only appeared to express a single IRMP, which varied in molecular mass from 32 to 36 kDa. Whilst the IRMP in these CNS strains showed considerable antigenic homology with the 32 kDa IRMP, the S. warneri IRMP showed cross-reactivity with both the 32 and 36 kDa IRMPs of S. epidermidis. Immunoblotting experiments revealed that whilst the CNS cell wall proteins were poorly immunogenic, the IRMPs were the immunodominant CNS protein antigens, reacting strongly with antibodies present in HPD. This finding provides evidence to suggest that the IRMPs are expressed in vivo during infection.
ER chaperones in mammalian development and human diseases (2007)

The field of endoplasmic reticulum (ER) stress in mammalian cells has expanded rapidly during the past decade, contributing to understanding of the molecular pathways that allow cells to adapt to perturbations in ER homeostasis. One major mechanism is mediated by molecular ER chaperones which are critical not only for quality control of proteins processed in the ER, but also for regulation of ER signaling in response to ER stress. Here, we summarized the properties and functions of GRP78/BiP, GRP94/gp96, GRP170/ORP150, GRP58/ERp57, PDI, ERp72, calnexin, calreticulin, EDEM, Herp and co-chaperones SIL1 and P58(IPK) and their role in development and diseases. Many of the new insights are derived from recently constructed mouse models where the genes encoding the chaperones are genetically altered, providing invaluable tools for examining the physiological involvement of the ER chaperones in vivo.
Quality of Experience Oriented Video Streaming in Challenged Wireless Networks: Analysis, Protocol Design and Case Study (2012)

The effects of d1-2-(3'-t-butylamino-2'-hydroxypropylthio)-4-(5'-carbamoyl-2'-thi enyl) thiazole hydrochloride (S-596) were evaluated in 9 normal volunteers. Exercise echocardiography was performed in the semi-supine position before and 2, 4 and 24 hours after the oral administration of 15 mg of S-596. Two hours after administration, resting heart rate was unchanged, compared with control, but systolic blood pressure at rest was slightly decreased (114 +/- 6 vs 106 +/- 10 mmHg, p less than 0.05). Left ventricular dimensions were unchanged, but shortening fraction was increased in the resting state (30.3 +/- 4.6 vs 33.1 +/- 4.8%, p less than 0.05). During exercise on oral S-596, heart rate and systolic blood pressure responses were reduced (127 +/- 11 in control vs 108 +/- 6 beats/min on S-596, 198 +/- 25 vs 168 +/- 23 mmHg, p less than 0.001 and 0.05, respectively). Left ventricular end-diastolic dimension was not significantly altered by S-596 compared with the preceding control exercise test; however, end-systolic dimension was significantly larger after beta blockade with S-596 (2.6 +/- 0.4 vs 3.0 +/- 0.4 cm, p less than 0.05). Shortening fraction and cardiac output decreased significantly (43.7 +/- 3.7 vs 40.0 +/- 5.7%, 9.5 +/- 1.4 vs 8.4 +/- 1.3 L/min, p less than 0.05 and 0.01, respectively). These effects of S-596 were maximal at 2 hours after oral administration with reduced response of heart rate to exercise lasting for 24 hours. Compared with the effects of propranolol (30 mg, given orally) in the same subjects, beta-adrenergic blockade during exercise with S-596 was equivalent to or greater than that of propranolol. Thus, S-596 has little, if any, effect on resting left ventricular performance, but demonstrates potent negative chronotropic and inotropic effects during exercise in normal human subjects. Its beta-adrenergic blocking action also has long acting properties, especially its chronotropic effect.
Natural killer cell function and lymphocyte subpopulation profiles in inflammatory bowel disease. (1983)

Peripheral blood natural killer (NK) cell activity and lymphocyte subpopulation profiles were studied in 23 patients with inflammatory bowel disease (IBD) and in 16 healthy control subjects. NK activity was assessed by a 4-hr 51Cr release assay using K-562 erythroleukemia cell line targets. Both monocyte depleted and nondepleted lymphocyte preparations were tested using 50:1 and 25:1 effector to target cell ratios. Lymphocyte subpopulation profiles were determined by incubation of cell suspensions with the monoclonal anti-lymphocyte antibodies (OK-M1, OK-T4, Leu-4 and Leu-2) labeling with goat anti-mouse FITC and sorting by flow cytometry on the fluorescence-activated cell sorter (FACS). NK activity in patients with IBD showed wide variation, but mean activity was not significantly different from normal controls. Analysis of patient subgroups by disease activity, disease type, duration or treatment also failed to reveal significant differences from controls. Parallel measurements of peripheral blood lymphocyte subpopulations using these phenotypic markers revealed no significant differences between patients with IBD and control subjects.
Proteome Alterations in Gamma-Irradiated Human T-Lymphocyte Leukemia Cells (2005)

Analyses of the protein expression profiles of irradiated cells may be beneficial for identification of new biomolecules of radiation-induced cell damage. Therefore, in this study we exploited the proteomic approach to identify proteins whose expression is significantly altered in gamma-irradiated human T-lymphocyte leukemia cells. MOLT-4 cells were irradiated with 7.5 Gy and the cell lysates were collected at different times after irradiation (2, 5 and 12 h). The proteins were separated by two-dimensional electrophoresis and quantified using an image evaluation system. Proteins exhibiting significant radiation-induced alterations in abundance were identified by peptide mass fingerprinting. We identified 14 proteins that were either up- or down-regulated. Cellular levels of four of the proteins (Rho GDP dissociation inhibitor 1 and 2, Ran binding protein 1, serine/threonine protein kinase PAK2) were further analyzed by two-dimensional immunoblotting to confirm the data obtained from proteome analysis. All identified proteins were classified according to their cellular function, including their participation in biochemical and signaling pathways. Taken together, our results suggest the feasibility of the proteome method for monitoring of cellular radiation responses.
Dual Attention Networks for Multimodal Reasoning and Matching (2017)

We propose Dual Attention Networks (DANs) which jointly leverage visual and textual attention mechanisms to capture fine-grained interplay between vision and language. DANs attend to specific regions in images and words in text through multiple steps and gather essential information from both modalities. Based on this framework, we introduce two types of DANs for multimodal reasoning and matching, respectively. The reasoning model allows visual and textual attentions to steer each other during collaborative inference, which is useful for tasks such as Visual Question Answering (VQA). In addition, the matching model exploits the two attention mechanisms to estimate the similarity between images and sentences by focusing on their shared semantics. Our extensive experiments validate the effectiveness of DANs in combining vision and language, achieving the state-of-the-art performance on public benchmarks for VQA and image-text matching.
Arraying the Orchestration of Allograft Pathology (2004)

Microarrays, or gene chips, are exciting investigative tools for analyzing expression changes across thousands of genes in concert in tissues and cells of interest. Despite the relatively recent application of microarrays to transplant research, they hold great promise for unraveling the staging of rejection, stratifying patients towards more individualized treatment regimes, and discovering noninvasive biomarkers for monitoring of intragraft events. Bioinformatics tools are being developed to sift through the large data sets generated as "genomic fingerprints" of the underlying biologic pathways. Gene clustering and class prediction tools allow discovery of diagnostic and prognostic molecular signatures of health and disease. Oligonucleotide-based microarrays also have utility in genotyping polymorphic markers. This report reviews the current literature of microarray use in transplantation research, compares currently available array platforms, and discusses future application of this technology to clinical organ transplantation.
Heterogeneous Nuclear Ribonucleoprotein H Blocks MST2-Mediated Apoptosis in Cancer Cells by Regulating a-raf Transcription (2010)

A-Raf belongs to the family of oncogenic Raf kinases that are involved in mitogenic signaling by activating the mitogen-activated protein (MAP)/extracellular signal-regulated kinase (ERK) kinase (MEK)-ERK pathway. Low kinase activity of A-Raf toward MEK suggested that A-Raf might have alternative functions. Here, we show that A-Raf prevents cancer cell apoptosis contingent on the expression of the heterogeneous nuclear ribonucleoprotein H (hnRNP H) splice factor, which is required for the correct transcription and expression of a-raf. Apoptosis was prevented by A-Raf through sequestration and inactivation of the proapoptotic MST2 kinase. Small interfering RNA-mediated knockdown of hnRNP H or A-Raf resulted in MST2-dependent apoptosis. In contrast, enforced expression of either hnRNP H or A-Raf partially counteracted apoptosis induced by etoposide. In vivo expression studies of colon specimens corroborated the overexpression of hnRNP H in malignant tissues and its correlation with A-Raf levels. Our findings define a novel mechanism that is usurped in tumor cells to escape naturally imposed apoptotic signals.
Antigenic and immunologic characterization of an allogeneic colon carcinoma vaccine (2002)

We report the immunological characterization of three colon carcinoma cell lines, COLO 205, SW620 and SW403, which we selected to combine with cytokine-secreting fibroblasts for the development of an allogeneic tumour cell vaccine. The cell lines expressed HLA-A2 as well as shared tumour-associated antigens (TAAs) representative of colon carcinomas: CEA, Ep-CAM, MUC1, HER2/neu and MAGE antigens. They did not secrete high levels of the immunosuppressive factors TGF-beta, IL-10 or prostaglandins. The lines presented TAAs in a manner recognized by immune effector cells, which was demonstrated by the lysis of SW620 by HLA-A2-restricted anti-p53 cytotoxic T lymphocytes (CTL). COLO 205 and SW620 were genetically modified to express the co-stimulatory molecule CD80 (B7.1), which increased the ability of the cells to stimulate CTL in vitro. CTL clones derived from HLA-A2+ peripheral blood mononuclear cells stimulated with the CD80-expressing lines lysed the stimulator cell and an HLA-A2+ colon cancer cell line, but did not lyse an isogeneic fibroblast line or an HLA-A2- colon cancer cell line. CTL clones derived from colon carcinoma patients immunized with an allogeneic vaccine containing these lines demonstrated killing of autologous tumour cells, the vaccine cell lines and other HLA-A2+ colon cancer cell lines, but not fibroblasts isogeneic to certain of the target cell lines. Our studies demonstrate that these colon carcinoma cell lines express shared TAAs that can induce CTLs which recognize and lyse other colon carcinoma cells, and support the continued clinical evaluation of the CD80 gene modified allogeneic colon cell/cytokine-secreting fibroblast carcinoma vaccine.
Management of psoriasis in childhood (1999)

It is not unusual for psoriasis to start in childhood although a mild or atypical presentation sometimes makes it difficult to establish a confident diagnosis at this age. All adult forms occur but flexural psoriasis and guttate psoriasis are particularly common. Management involves education of the child and parents concerning the nature of psoriasis and the effects of treatment. Genetic counselling may be provided if needed based on population data. Environmental triggers of psoriasis should be sought particularly infection. Psoriasis can usually be treated effectively in children with topical agents including emollients, coal tar, corticosteroids, dithranol and calcipotriol according to age and the sites affected. In those who do not respond, consideration should be given first to day care or in-patient treatment which may be combined with UVB phototherapy. Systemic therapy should be used only under extreme circumstances such as resistant erythrodermic, pustular or arthropathic psoriasis. There are no controlled trials in this age group but the most experience has been with retinoids which are probably the second-line drug of choice for children. Methotrexate and cyclosporin appear to be effective in children but more efficacy and safety data are required.
Chronic Cerebral Vasospasm: Effect of Calcium Antagonists (1986)

The efficacy of the calcium antagonists nifedipine and nimodipine was evaluated in a multiinjection canine model of severe chronic cerebral vasospasm. Each of 21 adult mongrel dogs (15 to 20 kg) was assigned to one of four experimental groups. All animals received a total of 15 ml of fresh, unheparinized arterial blood via three cisterna magna injections. Selective left vertebral arteriography was performed 1 week before and exactly 7 days after the simulated subarachnoid hemorrhage. Treatment with calcium antagonists was initiated at 24 hours and continued for 7 consecutive days. Comparisons were based on the percentage of reduction in basilar artery diameter. On a milligram/kilogram basis, we used the manufacturer's maximal recommended daily dosages of nifedipine, whereas the dosages of nimodipine used were 3 to 7 times greater than that reported to be therapeutically effective in reducing the incidence of severe deficits from vasospasm in patients with aneurysmal subarachnoid hemorrhage. In this laboratory trial, systemic treatment with calcium antagonists did not prevent or significantly reduce chronic arterial narrowing. In the control group, spasm reduced basilar artery diameter an average of 71% +/- 11 (SD). In the group treated with nifedipine, 10 mg orally every 6 hours, vessel diameter was reduced an average of 58% +/- 13%. In those animals treated with nimodipine, 20 or 40 mg orally every 4 hours, the basilar artery diameter was decreased an average of 59% +/- 8 and 56% +/- 7, respectively. A preliminary trial using direct intracisternal administration of these agents demonstrated increased vessel diameter within 20 minutes in four of six animals, supporting other reports that this route of administration may prove more efficacious in the treatment of chronic cerebral vasospasm.
Feature-guided exploration with a robotic finger (2002)

Haptic exploration with robotic fingers is accomplished by feature-guided exploration, where information about surface features such as cracks and ridges is used to guide the finger in an exploratory procedure. A local exploration strategy uses contact trajectory information from a tactile sensor to identify features while moving over and around them. Using an algorithm based on the Voronoi diagram, an approximation of the medial axis of the feature is found, then pruned using an edge length threshold. Multiple feature skeletons are then used to create a global skeleton that partitions the surface into regions. The models resulting from these local and global explorations can be used to characterize objects for information storage and manipulation planning.
Maltotriose is the inducer of the maltose regulon of Escherichia coli (1987)

In a cell-free system programmed with a plasmid bearing a malP'-'lacZ gene fusion under the control of malPp, beta-galactosidase synthesis was strictly dependent on the presence of both the MalT activator protein and the inducer of the Escherichia coli maltose regulon. We show that, among all maltodextrins tested (from maltose to maltoheptaose), only maltotriose was able to induce beta-galactosidase synthesis. Likewise, in an in vitro transcription system, initiation of transcription at malPp required the presence of the MalT protein and maltotriose along with the RNA polymerase holoenzyme; neither maltose nor maltotetraose could substitute for maltotriose.