gebhart/patrepeval huggingface dataset:
DNA methylation profiling in human Huntington's disease brain (2016)

Despite extensive progress in Huntington's disease (HD) research, very little is known about the association of epigenetic variation and HD pathogenesis in human brain tissues. Moreover, its contribution to the tissue-specific transcriptional regulation of the huntingtin gene (HTT), in which HTT expression levels are highest in brain and testes, is currently unknown. To investigate the role of DNA methylation in HD pathogenesis and tissue-specific expression of HTT, we utilized the Illumina HumanMethylation450K BeadChip array to measure DNA methylation in a cohort of age-matched HD and control human cortex and liver tissues. In cortex samples, we found minimal evidence of HD-associated DNA methylation at probed sites after correction for cell heterogeneity but did observe an association with the age of disease onset. In contrast, comparison of matched cortex and liver samples revealed tissue-specific DNA methylation of the HTT gene region at 38 sites (FDR < 0.05). Importantly, we identified a novel differentially methylated binding site in the HTT proximal promoter for the transcription factor CTCF. This CTCF site displayed increased occupancy in cortex, where HTT expression is higher, compared with the liver. Additionally, CTCF silencing reduced the activity of an HTT promoter-reporter construct, suggesting that CTCF plays a role in regulating HTT promoter function. Overall, although we were unable to detect HD-associated DNA methylation alterations at queried sites, we found that DNA methylation may be correlated to the age of disease onset in cortex tissues. Moreover, our data suggest that DNA methylation may, in part, contribute to tissue-specific HTT transcription through differential CTCF occupancy.
Development and Validation of a Clinical Risk Score to Predict the Occurrence of Critical Illness in Hospitalized Patients With COVID-19 (2020)

In this study, a risk score based on characteristics of COVID-19 patients at the time of admission to the hospital was developed that may help predict a patient's risk of developing critical illness.
Actions of Estrogens and Progestins on Nerve Cells (1983)

Estrogens and progestins alter electrical and chemical features of nerve cells, particularly in hypothalamus. Temporally, these events follow nuclear receptor occupation by these steroids, although not all effects have been proved to depend on translocation of receptors to the nucleus. Narrowing studies to focus on particular medial hypothalamic cells has been useful for understanding some of the actions of these steroids in brain. The variety of morphological, chemical, and electrical effects allow for a multiplicity in the cellular functions controlled by these hormones.
Clinical activity, safety, and biomarkers of MPDL3280A, an engineered PD-L1 antibody in patients with locally advanced or metastatic melanoma (mM). (2013)

9010 Background: mM is an immunotherapy responsive disease where PD-L1 overexpression is prevalent. MPDL3280A, a human monoclonal antibody containing an engineered Fc-domain designed to optimize efficacy and safety, targets PD-L1, blocking PD-L1 from binding its receptors, including PD-1 and B7.1. Initial antitumor activity observed during dose escalation supported further expansion in mM with MPDL3280A as monotherapy and in combination with targeted therapy. Methods: Pts with mM of any histologic subtype received MPDL3280A administered IV q3w for up to 1 y. Objective response rate (ORR) was assessed by RECIST v1.1. Reported ORR includes u/cCR and u/cPR. In addition, a separate Ph 1b was initiated to evaluate the safety and efficacy of MPDL3280A with vemurafenib (vem) in pts with BRAF-V600 mutated mM. Results: As of Jan 10, 2013, 45 mM pts were treated at ≤1 (n=4), 10 (n=10), 25 (n=20) and 20 mg/kg (n=11) and evaluable for safety. Median pt age was 63 y (range 21-83 y), 100% were PS 0-1, 91% had prior surgery and 64% received prior systemic therapy. Pts received MPDL3280A treatment for a median duration of 127 days (range 1-282). The incidence of all G3/4 AEs, regardless of attribution, was 33%, including hyperglycemia (7%), elevated ALT (7%) and elevated AST (4%). No G3-5 pneumonitis was reported. No treatment-related deaths occurred on study. 35 mM pts who initiated treatment at doses of 1-20 mg/kg and enrolled prior to Jul 1, 2012, were evaluable for efficacy. An ORR of 26% (9/35) was observed, with all RECIST responses ongoing or improving. Further, some responding pts experienced tumor shrinkage within days of initial treatment. The 24-week PFS was 35%. Several additional pts had delayed antitumor activity after apparent radiographic progression and were counted as PD for the above analyses. Analysis of mandatory archival tumors showed a correlation between PD-L1 status and efficacy. Further, of three initial pts treated with MPDL3280A and vem, 2 experienced tumor shrinkage, including 1 CR. Conclusions: MPDL3280A was well tolerated as monotherapy, and durable ORs were observed. Therefore, further assessment of MPDL3280A as monotherapy and combination therapy is warranted. Clinical trial information: NCT01375842.
Outbreak of vancomycin-, ampicillin-, and aminoglycoside-resistant Enterococcus faecium bacteremia in an adult oncology unit (1994)

An outbreak of bacteremia caused by Enterococcus faecium with high-level resistance to vancomycin (MIC of > or = 256 micrograms/ml), ampicillin (MIC of > or = 64 micrograms/ml), and gentamicin or streptomycin (MIC of > or = 2,000 micrograms/ml) occurred in an adult oncology unit from June 1991 to May 1992. Active surveillance for the presence of this organism in stool or perianal cultures was begun in September 1991. Between June 1991 and May 1992, seven patients with bacteremia and 22 noninfected carriers of the organism in stool were identified. The vanA gene, tested for by PCR and gene probe, was present in all isolates evaluated. All bacteremic patients also had resistant E. faecium present in a stool or perianal culture; the stool isolates tested were closely related to the respective blood isolates as determined by pulsed-field gel electrophoresis. Antibiotic regimens using high-dose ampicillin and an aminoglycoside were ineffective with four patients. Five patients (71%) had multiple positive blood cultures; four of these patients died. Following a multiple logistic regression analysis, it was found that bacteremic patients received a significantly greater number of total antibiotic days compared with noninfected stool carriers (P = 0.019). The emergence of E. faecium with high-level resistance to vancomycin, ampicillin, and aminoglycosides underscores the importance of performing susceptibility testing on all clinically significant isolates. In the neutropenic adult oncology patient, bacteremia with this organism is of probable gastrointestinal origin, is often persistent, and is refractory to treatment with ampicillin in combination with an aminoglycoside. Prolonged use of antibiotics may predispose patients with gastrointestinal colonization to develop bacteremia.
Monoclonal Antibody Against Human Ovarian Tumor-Associated Antigens (1986)

Mouse monoclonal antibodies (OV-TL 3) were raised against human ovarian tumor-associated antigens for diagnostic purposes. A cloned hybridoma cell line was obtained by fusion of murine myeloma cells with spleen lymphocytes from BALB/c mice immunized with a tumor cell suspension prepared from an ovarian endometrioid carcinoma. The antibodies were initially screened for their ability to bind on frozen sections of human ovarian carcinoma tissue and a negative reaction on gastric carcinoma tissue by indirect immunofluorescence. The reactivity of the selected OV-TL 3 clone (IgG1 subclass) was studied on normal and neoplastic tissues as well as on a cell line derived from the original tumor cell suspension used for immunization. OV-TL 3 antibodies stained frozen sections of human ovarian carcinomas of the following histological types: serous, mucinous, endometrioid, and clear cell. No reaction was found with breast cancers or other nongynecological tumors. No differences in staining pattern were observed between primary and metastatic ovarian carcinomas. OV-TL 3 antibodies brightly stained ovarian carcinoma cell clusters in ascitic fluids and left unstained mesothelial cells and peripheral blood cells. The OV-TL 3-defined antigen also remained strongly expressed on a cell line derived from the endometrioid ovarian carcinoma originally used for generation of OV-TL 3 clone. Reactivity was weak and irregular in a few ovarian cysts, while traces of fluorescence were sometimes detected in epithelial cells lining the female genital tract. In only 3 specimens of 15 endometrium carcinomas was weak focal reactivity with OV-TL 3 antibodies observed. The results of the immunofluorescence study were confirmed by the more sensitive avidin-biotin method and by 125I-labeled OV-TL 3 antibodies. Thus OV-TL 3 recognizes a common antigen for most ovarian carcinomas and may be a useful tool for rapid diagnosis of ovarian carcinomas.
C-C chemokine receptor type five (CCR5): An emerging target for the control of HIV infection (2013)

When HIV was initially discovered as the causative agent of AIDS, many expected to find a vaccine within a few years. This has however proven to be elusive; it has been approximately 30 years since HIV was first discovered, and a suitable vaccine is still not in effect. In 2009, a paper published by Hutter et al. reported on a bone marrow transplant performed on an HIV positive individual using stem cells that were derived from a donor who was homozygous for a mutation in the CCR5 gene known as CCR5 delta-32 (Δ32) (Hütter et al., 2009). The HIV positive individual became HIV negative and remained free of viral detection after transplantation despite having halted anti-retroviral (ARV) treatment. This review will focus on CCR5 as a key component in HIV immunity and will discuss the role of CCR5 in the control of HIV infection.
Training a Binary Classifier with the Quantum Adiabatic Algorithm (2008)

This paper describes how to make the problem of binary classification amenable to quantum computing. A formulation is employed in which the binary classifier is constructed as a thresholded linear superposition of a set of weak classifiers. The weights in the superposition are optimized in a learning process that strives to minimize the training error as well as the number of weak classifiers used. No efficient solution to this problem is known. To bring it into a format that allows the application of adiabatic quantum computing (AQC), we first show that the bit-precision with which the weights need to be represented only grows logarithmically with the ratio of the number of training examples to the number of weak classifiers. This allows to effectively formulate the training process as a binary optimization problem. Solving it with heuristic solvers such as tabu search, we find that the resulting classifier outperforms a widely used state-of-the-art method, AdaBoost, on a variety of benchmark problems. Moreover, we discovered the interesting fact that bit-constrained learning machines often exhibit lower generalization error rates. Changing the loss function that measures the training error from 0-1 loss to least squares maps the training to quadratic unconstrained binary optimization. This corresponds to the format required by D-Wave's implementation of AQC. Simulations with heuristic solvers again yield results better than those obtained with boosting approaches. Since the resulting quadratic binary program is NP-hard, additional gains can be expected from applying the actual quantum processor.
Antiplatelet Therapy and Vascular Grafts (1986)

Antiplatelet therapy is currently recommended in an effort to improve patency rates of small-caliber vascular grafts. The effect of aspirin and heparin on acute platelet deposition was studied in a baboon ex vivo shunt. Two grafts, expanded polytetrafluoroethylene and knitted Dacron, were exposed to a flow rate of 25 mL/min after administration of aspirin or heparin. Indium 111-labeled platelet uptake by the grafts was determined over 2 1/2 hours. The amount of platelet deposition in the treated groups was significantly less than that of controls after 2 1/2 hours. There was no difference between the aspirin and heparin groups. The finding that heparin inhibited platelet deposition to a degree comparable with aspirin suggests that it may not be necessary to start antiplatelet therapy preoperatively. Intraoperative systemic heparinization will provide sufficient inhibition of platelet deposition. A protocol for perioperative antiplatelet therapy is outlined.
HeLa cell DNA polymerase alpha is tightly associated with tryptophanyl-tRNA synthetase and diadenosine 5',5"'-P1,P4-tetraphosphate binding activities. (1981)

The purified high molecular weight form of HeLa cell DNA polymerase alpha (deoxynucleosidetriphosphate: DNA deoxynucleotidyltransferase, EC 2.7.7.7) was shown to associate tightly with several aminoacyl-tRNA synthetase activities. Fractionation of the high molecular weight enzyme on hexylagarose followed by gel filtration, chromatography on phosphocellulose, or polyacrylamide gel electrophoresis under nondenaturing conditions demonstrated copurification of only tryptophanyl-tRNA synthetase [L-tryptophan:tRNATrp ligase (AMP-forming), EC 6.1.1.2] along with DNA polymerase alpha. The high molecular weight (660,000) and low molecular weight (145,000) forms of DNA polymerase alpha were shown to possess a highly specific, noncovalent, diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) binding activity. The dissociation constants were determined to be 16 and 22 microM, respectively, by utilization of a charcoal adsorption procedure. No high-affinity binding of ATP could be detected. These findings suggest a link between the amino acid activation process and DNA replication in mammalian cells.
Photonic band structure and defects in one and two dimensions (1993)

We present an experimental and numerical study of electromagnetic wave propagation in one-dimensional (1D) and two-dimensional (2D) systems composed of periodic arrays of dielectric scatterers. We demonstrate that there are regions of frequency for which the waves are exponentially attenuated for all propagation directions. These regions correspond to band gaps in the calculated band structure, and such systems are termed photonic band-gap (PBG) structures. Removal of a single scatterer from a PBG structure produces a highly localized defect mode, for which the energy density decays exponentially away from the defect origin. Energy-density measurements of defect modes are presented. The experiments were conducted at 6–20 GHz, but we suggest that they may be scaled to infrared frequencies. Analytic and numerical solutions for the band structure and the defect states in 1D structures are derived. Applications of 2D PBG structures are briefly discussed.
Oxidative metabolism deficiencies in brains of patients with Alzheimer's disease (1996)

Glucose metabolism in the brain has an important influence on many normal cellular processes. It contributes to the synthesis of acetylcholine, glutamate, aspartate, gamma-aminobutyric acid, glycine, and ATP production (the driving force behind almost all cellular and molecular activity). Neuronal glucose metabolism is controlled antagonistically by insulin and cortisol. Desensitization of the neuronal insulin receptor causes abnormalities in oxidative energy metabolism. During normal aging, the cerebral energy pool is slightly diminished, but its level increases after stressful events. In age-related sporadic late-onset dementia of the Alzheimer type (SDAT), glucose metabolism and formation of cellular energy are severely reduced. Desensitization of the neuronal insulin receptor seems to be an early event in the pathogenesis or even etiology of SDAT causing disturbances in oxidative glucose metabolism and energy failure in insulin-sensitive brain structures. These abnormalities appear to induce a cascade of disturbances that leads to abnormal APP processing and amyloid formation, membrane damage, and neuronal death.
Micro-speculation, Micro-sandboxing, and Self-Correcting Assertions: Support for Self-Healing Software and Application Communities (2005)

Software faults and vulnerabilities continue to present significant obstacles to achieving reliable and secure software. The critical problem is that systems currently lack the capability to respond intelligently and automatically to attacks – especially attacks that exploit previously unknown vulnerabilities or are delivered by previously unseen inputs. Therefore, the goal of this thesis is to provide an environment where both supervision and automatic remediation can take place. Also provided is a mechanism to guide the supervision environment in detection and repair activities. This thesis supports the notion of Self-Healing Software by introducing three novel techniques: micro-sandboxing, micro-speculation, and self-correcting assertions. These techniques are combined in a kernel-level emulation framework to speculatively execute code that may contain faults or vulnerabilities and automatically repair such faults or exploited vulnerabilities. The framework, VPUF, introduces the concept of computation as an operating system service by providing control for an array of virtual processors in the Linux kernel (creating the concept of an endolithic kernel). This thesis introduces ROAR (Recognize, Orient, Adapt, Respond) as a conceptual workflow for Self-healing Software systems. This thesis proposal outlines a 17 month program for developing the major components of the proposed system, implementing them on a COTS operating system and programming language, subjecting them to a battery of evaluations for performance and efficacy, and publishing the results. In addition, this proposal looks forward to several areas of follow-on work, including implementing some of the proposed techniques in hardware and leveraging the general kernel-level framework to support Application Communities.
Advances in the changing patterns of aetiology of head and neck cancers (2006)

This review tries to summarize the most recent advances in the field of cancerogenesis in head and neck cancer.
The Development of Risk Analysis: A Personal Perspective (2012)

This article reflects on my experiences observing and participating in the development of risk analysis for environmental and health hazards since the 1970s with emphasis on its critical role in informing decisions with potentially high consequences, even for very low probability events once ignored or simply viewed as "acts of God." I discuss how modern society wants to protect itself from hazards with limited or no immediate historical precedent such that prediction and protective actions must depend on models that offer varying degrees of reliability. I believe that we must invest in understanding risks and risk models to ensure health in the future and protect ourselves from large challenges, including climate change, whether anthropogenic or otherwise, terrorism, and perhaps even cosmic change.
Superficial Punctate Fluorescein Staining of the Ocular Surface (2008)

This review highlights major challenges in attempting to extrapolate from the clear importance of gross corneal staining down to the meaning of observation of superficial punctate staining, and should promote greater circumspection in interpreting this phenomenon. The literature reflects that superficial punctate corneal staining does not reflect corneal injury or toxicity. More work is required to elucidate the various mechanisms underlying superficial punctate staining, and to provide clinicians with a rational interpretation algorithm for this observation.
Autoimmunity in Chagas' disease. Identification of cardiac myosin-B13 Trypanosoma cruzi protein crossreactive T cell clones in heart lesions of a chronic Chagas' cardiomyopathy patient. (1996)

Heart tissue destruction in chronic Chagas' disease cardiomyopathy (CCC) may be caused by autoimmune recognition of heart tissue by a mononuclear cell infiltrate decades after Trypanosoma cruzi infection. Indirect evidence suggests there is molecular mimicry between T. cruzi and heart tissue. In murine models of CCC, antibodies and CD4+ T cells recognize myosin, the major heart protein. We recently identified a heart-specific epitope of cardiac myosin heavy chain (residues 1442-1447, AAALDK) that is crossreactive with a homologous sequence (AAAGDK) of the immunodominant T. cruzi antigen B13. Furthermore, cardiac myosin-B13 crossreactive antibodies are present in 100% CCC patients vs 14% asymptomatic T. cruzi-seropositive individuals (P = 2.3 x 10(-6)), suggesting a role for molecular mimicry between cardiac myosin and B13 in CCC pathogenesis. In this paper, we obtained heart-infiltrating T cell clones from CCC patients to assess whether molecular mimicry between cardiac myosin and B13 is directly involved in the genesis of heart lesions. We identified T cell clones derived from CCC heart lesions simultaneously responsive to cardiac myosin heavy chain (but not skeletal myosin heavy chain) and B13 T. cruzi protein, but could not find T cell clones primarily reactive to any T. cruzi antigen. Together with the association of myosin-B13 crossreactive antibodies with CCC, the present data strongly suggest the relevance of molecular mimicry between cardiac myosin and the T. cruzi protein B13 in the pathogenesis of heart lesions in chronic Chagas' disease cardiomyopathy.
Experimental evaluation of the JenaClip transcatheter aortic valve (2009)

In this study, we demonstrate feasibility of a leaflet-fixation device in nondiseased aortic valves. The JenaClip provides an effective concept of fixation with positioning feelers that allows exact positioning without outflow obstruction and anchoring the valve to the native leaflets. Further studies are necessary to investigate this concept in diseased aortic valves.
New Glycosphingolipids from the Marine Sponge Halichondria panicea (1992)

A novel sphingolipid containing an iso-fatty acid, (4E,8E)-N-13'-methyltetradecanoyl-1-O-beta-D-glucopyra nosyl-4-sphingadiene, was isolated from the Oregon marine sponge Halichondria panicea and its structure determined using a combination of spectroscopic and chemical degradation techniques. A second galactosyl-ceramide, which contained an unusually long chain fatty acid amide component, was also isolated from H. panicea.
Reduction of Organic Compounds by Lithium Aluminum Hydride. I. Aldehydes, Ketones, Esters, Acid Chlorides and Acid Anhydrides (1947)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReduction of Organic Compounds by Lithium Aluminum Hydride. I. Aldehydes, Ketones, Esters, Acid Chlorides and Acid AnhydridesRobert F. Nystrom and Weldon G. BrownCite this: J. Am. Chem. Soc. 1947, 69, 5, 1197–1199Publication Date (Print):May 1, 1947Publication History Published online1 May 2002Published inissue 1 May 1947https://pubs.acs.org/doi/10.1021/ja01197a060https://doi.org/10.1021/ja01197a060research-articleACS PublicationsRequest reuse permissionsArticle Views5743Altmetric-Citations251LEARN 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