gebhart/patrepeval huggingface dataset:
Associations of Omega-3 Fatty Acid Supplement Use With Cardiovascular Disease Risks (2018)

This meta-analysis demonstrated that omega-3 fatty acids had no significant association with fatal or nonfatal coronary heart disease or any major vascular events. It provides no support for current recommendations for the use of such supplements in people with a history of coronary heart disease.
Bone marrow-generated dendritic cells pulsed with a class I-restricted peptide are potent inducers of cytotoxic T lymphocytes. (1995)

It has previously been shown that bone marrow-generated dendritic cells (DC) are potent stimulators in allogeneic mixed leukocyte reactions and are capable of activating naive CD4+ T cells in situ in an antigen-specific manner. In this study we have investigated whether bone marrow-generated DC are capable of inducing antigen-specific CD8+ T cell responses in vivo. Initial attempts to induce specific cytotoxic T lymphocyte (CTL) responses in mice injected with bone marrow-generated DC pulsed with ovalbumin (OVA) peptide were frustrated by the presence of high levels of nonspecific lytic activity, which obscured, though not completely, the presence of Ag-specific CTL. Using conditions that effectively differentiate between antigen-specific and nonspecific lytic activity, we have shown that bone marrow-generated DC pulsed with OVA peptide are potent inducers of OVA-specific CTL responses in vivo, compared with splenocytes or RMA-S cells pulsed with OVA peptide, or compared with immunization with free OVA peptide mixed with adjuvant. Antibody-mediated depletion experiments have shown that the cytotoxic effector cells consist primarily of CD8+ cells, and that induction of CTL in vivo is dependent on CD4+ as well as on CD8+ T cells. These results provide the basis for exploring the role of bone marrow-generated DC in major histocompatibility class I-restricted immune responses, and they provide the rationale for using bone marrow-generated DC in CTL-mediated immunotherapy of cancer and infectious diseases.
Treatment Selections of 239 Patients With Blepharospasm and Meige Syndrome Over 11 Years (1997)

BACKGROUND: A retrospective review of 239 patients with benign essential blepharospasm and Meige syndrome was performed in order to determine patients9 long term treatment preferences. METHODS: Of 239 patients evaluated, 228 received local injections of botulinum toxin, type A, into the eyelid and facial musculature over 11 years. RESULTS: Of 228 patients, 202 (72.1%) were still treated with botulinum toxin, type A. Eighteen patients (6.9%) no longer received botulinum toxin injections and sought no other treatment. Five patients (2.2%) had apparent remission of their disease after injection. Three patients (1.3%) ultimately obtained relief from orbicularis muscle extirpative surgery and required no additional treatment. Two of the 11 patients (4.6%) who chose not to receive botulinum toxin injections were successfully treated with other modalities: psychotherapy (one patient) and oral haloperidol (one patient). CONCLUSION: While botulinum toxin is the most highly effective treatment for benign essential blepharospasm and Meige syndrome over a long period of time, adjunctive oral drug therapy, including minor tranquillisers as well as eyelid surgery, may augment its effectiveness.
Multidimensional flow cytometric blood cell differentiation without erythrocyte lysis. (1991)

Forward light scattering, orthogonal light scattering, and the fluorescence intensities of unlysed peripheral blood cells, labeled with CD45-phycoerythrin and the nucleic acid dyes LDS-751 and thiazole orange, were measured simultaneously, utilizing a flow cytometer. Erythrocytes, reticulocytes, platelets, neutrophils, eosinophils, basophils, monocytes, lymphocytes, nucleated erythrocytes, and immature nucleated cells occupied unique positions in the five-dimensional space created by the listmode storage of the five independent parameters. A software program was developed which identified and enumerated each of these cell populations. Platelets in this study were identified by LDS-751 staining, in addition to their forward and orthogonal light-scattering characteristics. Validation of this approach was obtained by demonstrating that all CD41- or CD42-expressing platelets also stained with LDS-751. Furthermore, the staining by LDS-751 did not change following platelet activation with ADP. The quantification of erythrocytes, platelets, neutrophils, eosinophils, monocytes, and lymphocytes correlated well with data obtained with a commercial hematology whole blood analyzer (H-1). Reproducibility of the identification of these populations was shown by repeated measurement of the same sample and by staining and analysis of multiple aliquots of identical blood samples. Stability studies demonstrated that 8 hours after blood collection, the number of damaged cells increased. This could be measured by a greater thiazole orange uptake by the damaged cells. This investigation demonstrates the feasibility of multidimensional flow cytometric blood cell differentiation for an automated whole blood cell analysis without the necessity of erythrocyte lysis. The ability to simultaneously identify reticulocytes, nucleated erythrocytes, and immature nucleated cells in one measurement is unique and promises to be a powerful tool for the assessment of abnormal blood samples.
Learning to rank using gradient descent (2005)

We investigate using gradient descent methods for learning ranking functions; we propose a simple probabilistic cost function, and we introduce RankNet, an implementation of these ideas using a neural network to model the underlying ranking function. We present test results on toy data and on data from a commercial internet search engine.
Longitudinal brain activity changes in asymptomatic Alzheimer disease (2012)

Asymptomatic Alzheimer disease (ASYMAD) is characterized by normal cognition despite substantial AD pathology. To identify factors contributing to cognitive resilience, we compared early changes in regional cerebral blood flow (rCBF) in individuals subsequently diagnosed as ASYMAD with changes in cognitively impaired (CI) and normal older participants from the Baltimore Longitudinal Study of Aging. Participants underwent annual positron emission tomography (PET) rCBF measurements beginning 10.0 (SD 3.6) years before death and while cognitively intact. Based on clinical and autopsy information, subjects were grouped as cognitively normal (CN = 7), ASYMAD (n= 6), and CI (=6). Autopsy material was analyzed using CERAD and Braak scores and quantitative stereologic measures of tau and amyloid. ASYMAD and CI groups had similar CERAD and Braak scores, similar amounts of β-amyloid and tau in middle frontal (MFG), middle temporal (MTG), and inferior parietal (IP) regions, and more β-amyloid than CN in precuneus, MFG, and IP areas. Voxel-based PET analysis identified similarities and differences in longitudinal rCBF change among groups across a 7.2-year interval. Both ASYMAD and CI groups showed similar longitudinal rCBF declines in precuneus, lingual, and MTG regions relative to CN. The CI also showed greater rCBF decreases in anterior and posterior cingulate, cuneus, and brainstem regions relative to ASYMAD and CN, whereas ASYMAD showed greater relative rCBF increases over time in medial temporal and thalamic regions relative to CI and CN. Our findings provide evidence of early functional alterations that may contribute to cognitive resilience in those who accumulate AD pathology but maintain normal cognition.
Tangent Convolutions for Dense Prediction in 3D (2018)

We present an approach to semantic scene analysis using deep convolutional networks. Our approach is based on tangent convolutions - a new construction for convolutional networks on 3D data. In contrast to volumetric approaches, our method operates directly on surface geometry. Crucially, the construction is applicable to unstructured point clouds and other noisy real-world data. We show that tangent convolutions can be evaluated efficiently on large-scale point clouds with millions of points. Using tangent convolutions, we design a deep fully-convolutional network for semantic segmentation of 3D point clouds, and apply it to challenging real-world datasets of indoor and outdoor 3D environments. Experimental results show that the presented approach outperforms other recent deep network constructions in detailed analysis of large 3D scenes.
Absolute quantification of microRNAs by using a universal reference (2009)

MicroRNAs (miRNAs) are a species of small RNAs approximately 21-23-nucleotides long that have been shown to play an important role in many different cellular, developmental, and physiological processes. Accordingly, numerous PCR-, sequencing-, or hybridization-based methods have been established to identify and quantify miRNAs. Their short length results in a high dynamic range of melting temperatures and therefore impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here, we present a microarray-based approach for global and absolute quantification of miRNAs. The method relies on the parallel hybridization of the sample of interest labeled with Cy5 and a universal reference of 954 synthetic miRNAs in equimolar concentrations that are labeled with Cy3 on a microarray slide containing probes for all human, mouse, rat, and viral miRNAs (miRBase 12.0). Each single miRNA is quantified with respect to the universal reference canceling biases related to sequence, labeling, or hybridization. We demonstrate the accuracy of the method by various spike-in experiments. Furthermore, we quantified miRNA copy numbers in liver samples and CD34(+)/CD133(-) hematopoietic progenitor cells.
Salvia officinalis extract in the treatment of patients with mild to moderate Alzheimer's disease: a double blind, randomized and placebo-controlled trial (2003)

The results of this study indicate the efficacy of S. officinalis extract in the management of mild to moderate Alzheimer's disease. Moreover, S. officinalis may well reduce agitation of patients but this needs to be confirmed.
A phase I safety, tolerability, and pharmacokinetic study of enzastaurin combined with capecitabine in patients with advanced solid tumors (2008)

Enzastaurin, an oral inhibitor of protein kinase Cbeta, affects signal transduction associated with angiogenesis, proliferation, and survival. Capecitabine is converted to 5-fluoruracil by thymidine phosphorylase, a putative angiogenic factor. The all-oral combination of the two drugs offers the potential for targeting angiogenesis in capecitabine-sensitive tumors with nonoverlapping toxicities. Patients with advanced cancer initially received single-agent enzastaurin to achieve steady-state concentrations (cycle 1). In subsequent 21-day cycles, enzastaurin was given orally, once daily, on days 1-21 and capecitabine orally, twice daily (b.i.d.), on days 1-14 in three dose-level cohorts. Three dose-escalation cohorts were studied: cohort 1 (n=8), 350 mg of enzastaurin +capecitabine (750 mg/m2 b.i.d.); cohort 2 (n=7), enzastaurin (350 mg)+capecitabine (1000 mg/m2 b.i.d.); cohort 3 (n=12), 525-mg capsules or 500-mg enzastaurin+capecitabine (1000 mg/m2 b.i.d.). Further dose escalation was not pursued because of emerging data that enzastaurin systemic exposure did not increase at doses above 525 mg. Although a traditional toxicity-based maximum tolerated dose was not achieved, the highest dosing cohort represented a biologically relevant dose of enzastaurin, on the basis of preclinical data and correlative pharmacodynamic biomarker assays of protein kinase Cbeta inhibition in peripheral blood mononucleocytes, in combination with a standard dose of capecitabine. For the 500/525-mg dose, ratios of total enzastaurin analyte geometric means (i.e. enzastaurin alone versus enzastaurin with capecitabine) reflected a trend toward decreased enzastaurin exposure, but did not reach statistical significance. The pharmacokinetic parameters of capecitabine with enzastaurin were similar to those previously reported for single-agent capecitabine. The regimen was well tolerated, without any consistent pattern of drug-related grade 3 or grade 4 toxicities being observed. Although no objective tumor responses were documented, five patients maintained stable disease for >or=6 months (range: 6-9.7 months). The recommended phase II dose of this combination, based on the results of this study, is enzastaurin at a daily dose of 500 mg (tablet formulation) and capecitabine (1000 mg/m2, b.i.d.) on days 1-14 every 21 days. Further disease-directed studies are warranted, such as in malignancies in the treatment of which both capecitabine and inhibitors of angiogenesis have previously been benchmarked as being effective.
SFV: Reinforcement Learning of Physical Skills from Videos (2018)

Data-driven character animation based on motion capture can produce highly naturalistic behaviors and, when combined with physics simulation, can provide for natural procedural responses to physical perturbations, environmental changes, and morphological discrepancies. Motion capture remains the most popular source of motion data, but collecting mocap data typically requires heavily instrumented environments and actors. In this paper, we propose a method that enables physically simulated characters to learn skills from videos (SFV). Our approach, based on deep pose estimation and deep reinforcement learning, allows data-driven animation to leverage the abundance of publicly available video clips from the web, such as those from YouTube. This has the potential to enable fast and easy design of character controllers simply by querying for video recordings of the desired behavior. The resulting controllers are robust to perturbations, can be adapted to new settings, can perform basic object interactions, and can be retargeted to new morphologies via reinforcement learning. We further demonstrate that our method can predict potential human motions from still images, by forward simulation of learned controllers initialized from the observed pose. Our framework is able to learn a broad range of dynamic skills, including locomotion, acrobatics, and martial arts.
Generation of plasmacytomas with the chromosomal translocation t(12;15) in interleukin 6 transgenic mice. (1992)

The mechanisms through which pristane or mineral oil can induce plasmacytomas in BALB/c or NZB mice are not fully understood, but involvement of interleukin 6 (IL-6), a growth factor for plasmacytomas and myelomas, has been strongly suggested. To clarify the role of IL-6 in plasmacytomagenesis, a human IL-6 cDNA was introduced into mouse germ lines under the transcriptional control of the murine major histocompatibility complex class I (H-2Ld) promoter. IL-6 transgenic mice of C57BL/6 origin developed a massive plasmacytosis but not plasmacytomas. However, introduction of BALB/c genetic background into IL-6 transgenic mice could generate monoclonal transplantable plasmacytomas with the chromosomal translocation t(12;15). These results provide firm evidence of the critical role of IL-6 in the plasmacytoma development.
An interactive patient information and education system (Medical HouseCall) based on a physician expert system (Iliad). (1995)

Informed patients are better equipped to participate in their own health care decisions. We present Medical HouseCall (TM), a consumer expert system and medical information guide, derived in part from a diagnostic and treatment software used by physicians (Iliad). HouseCall(TM) generates a differential diagnosis based on the user symptoms and medical history. HouseCall(TM) also provides alerts for potentially harmful drug interactions, allows for the recording of personal medical history, and offers extensive but easy-to-read information about a variety of medical topics. Focus group evaluations of HouseCall (TM) have demonstrated the program's ease of use, as well as an appreciation of technology that can be used at home to investigate and understand health issues and participate in solving medical problems.
Contribution of hCAP-D2, a Non-SMC Subunit of Condensin I, to Chromosome and Chromosomal Protein Dynamics during Mitosis (2005)

Condensins are heteropentameric complexes that were first identified as structural components of mitotic chromosomes. They are composed of two SMC (structural maintenance of chromosomes) and three non-SMC subunits. Condensins play a role in the resolution and segregation of sister chromatids during mitosis, as well as in some aspects of mitotic chromosome assembly. Two distinct condensin complexes, condensin I and condensin II, which differ only in their non-SMC subunits, exist. Here, we used an RNA interference approach to deplete hCAP-D2, a non-SMC subunit of condensin I, in HeLa cells. We found that the association of hCAP-H, another non-SMC subunit of condensin I, with mitotic chromosomes depends on the presence of hCAP-D2. Moreover, chromatid axes, as defined by topoisomerase II and hCAP-E localization, are disorganized in the absence of hCAP-D2, and the resolution and segregation of sister chromatids are impaired. In addition, hCAP-D2 depletion affects chromosome alignment in metaphase and delays entry into anaphase. This suggests that condensin I is involved in the correct attachment between chromosome kinetochores and microtubules of the mitotic spindle. These results are discussed relative to the effects of depleting both condensin complexes.
Regulation of capsular polysaccharide synthesis in Escherichia coli K-12: characterization of three regulatory genes (1985)

The synthesis of the Escherichia coli capsular polysaccharide varies with growth medium, temperature of growth, and genetic background. lac fusions to genes necessary for capsule synthesis (cps) demonstrated that these genes are regulated negatively in vivo by the lon gene product. We have now isolated, characterized, and mapped mutations in three new regulatory genes (rcs, for regulator of capsule synthesis) that control expression of these same fusions. rcsA and rcsB are positive regulators of capsule synthesis. rcsA is located at min 43 on the E. coli map, whereas rcsB lies at 47 min. rcsC, a negative regulator of capsule synthesis, is located at min 47, close to rcsB. All three regulatory mutations are unlinked to either the structural genes cpsA-F or lon. Mutations in all three rcs genes are recessive to the wild type. We postulate that lon may regulate capsule synthesis indirectly, by regulating the availability of one of the positive regulators.
Bacillus subtilis genes for the utilization of sulfur from aliphatic sulfonates (1998)

A 5 kb region upstream of katA at 82 degrees on the Bacillus subtilis chromosome contains five ORFs organized in an operon-like structure. Based on sequence similarity, three of the ORFs are likely to encode an ABC transport system (ssuBAC) and another to encode a monooxygenase (ssuD). The deduced amino acid sequence of the last ORF (ygaN) shows no similarity to any known protein. B. subtilis can utilize a range of aliphatic sulfonates such as alkanesulfonates, taurine, isethionate and sulfoacetate as a source of sulfur, but not when ssuA and ssuC are disrupted by insertion of a neomycin-resistance gene. Utilization of aliphatic sulfonates was not affected in a strain lacking 3'-phosphoadenosine 5'-phosphosulfate (PAPS) sulfotransferase, indicating that sulfate is not an intermediate in the assimilation of sulfonate-sulfur. Sulfate or cysteine prevented expression of beta-galactosidase from a transcriptional ssuD::lacZ fusion. It is proposed that ssuBACD encode a system for ATP-dependent transport of alkanesulfonates and an oxygenase required for their desulfonation.
Large-Scale Application of High-Throughput Molecular Mechanics with Poisson−Boltzmann Surface Area for Routine Physics-Based Scoring of Protein−Ligand Complexes (2009)

We apply a high-throughput formulation of the molecular mechanics with Poisson-Boltzmann surface area (htMM-PBSA) to estimate relative binding potencies on a set of 308 small-molecule ligands in complex with the proteins urokinase, PTP-1B, and Chk-1. We observe statistically significant correlation to experimentally measured potencies and report correlation coefficients for the three proteins in the range 0.72-0.83. The htMM-PBSA calculations illustrate the feasibility of procedural automation of physics-based scoring calculations to produce rank-ordered binding-potency estimates for protein-ligand complexes, with sufficient throughput for realization of practical implementation into scientist workflows in an industrial drug discovery research setting.
Primary treatment of Crohn’s disease: combined antibiotics taking center stage (2011)

Although controversial, the use of properly chosen antibiotics in Crohn’s disease appears beneficial. Evidence supporting the use of targeted antibiotic therapy comes in two forms: statistical evidence derived from meta-analyses of multiple formal studies and the documented clinical and endoscopic responses in patients treated with antibiotic combinations outside of formal clinical studies. This article reviews evidence from both categories that support the use of properly chosen antibiotic regimens in treating Crohn’s disease, comments on the advantages and disadvantages of antibiotic therapy, and attempts to present a unifying hypothesis related to the role of enteric bacteria, mucosal immunity and antibiotic therapy. Relevant studies identified through a Medline search from 1976 to 2011 were assessed for inclusion by two independent observers who resolved any disagreements by consensus. References from all identified articles and recent review articles were cross-checked to ensure a thorough search. Papers were selected based on scientific merit as to which presented original contributions to the results.
A recombinant human RNASET2 glycoprotein with antitumorigenic and antiangiogenic characteristics (2006)

The current results suggested that RNASET2 represents a new class of antitumorigenic and antiangiogenic drugs, and the findings of this study emphasize the advantage of using agents like RNASET2 in combined therapy.
CSR, a scavenger receptor-like protein with a protective role against cellular damage causedby UV irradiation and oxidative stress (1998)

Oxidative stress is a pathogenic condition that causes cellular damage and, in a normally functioning cell, several transcription factors respond to this threat by modulating expression of genes whose products ameliorate the altered redox status in some way. We have isolated a novel macrophage scavenger receptor-like gene, CSR (cellular stress response), whose transcription in normal fibroblasts was significantly elevated by exposure to UV radiation or hydrogen peroxide, and pre-treatment with antioxidants prevented induction of CSR . Under conditions of oxidative stress, reactive oxygen species were significantly depleted in CSR -overexpressing cells, indicating that the CSR product protects cells by scavenging oxidative molecules or harmful products of oxidation. Further investigations into the regulation and function of CSR should open a way to understanding the cellular response and the pathogenic processes caused by oxidative stress.