gebhart/patrepeval huggingface dataset:
Ornithine Decarboxylase G316A Genotype Is Prognostic for Colorectal Adenoma Recurrence and Predicts Efficacy of Aspirin Chemoprevention (2008)

The ODC G316A genotype is prognostic for CRA recurrence and predictive of an enhanced response to aspirin in preventing recurrence. This variant has the potential to be a clinically useful genetic marker to identify individuals likely to derive the greatest benefit from aspirin chemoprevention.
CandidTree: visualizing structural uncertainty in similar hierarchies (2007)

Most visualization systems fail to convey uncertainty within data. To provide a way to show uncertainty in similar hierarchies, we interpreted the differences between two tree structures as uncertainty. We developed a new interactive visualization system called CandidTree that merges two trees into one and visualizes two types of structural uncertainty: location and sub-tree structure uncertainty. Since CandidTree can visualize the differences between two tree structures, we conducted a series of user studies with tree-comparison tasks. First a usability study was conducted to identify major usability issues and evaluate how our system works. Another qualitative user study was conducted to see if biologists, who regularly work with hierarchically organized names, are able to use CandidTree, and to assess the 'uncertainty' metric we used. A controlled experiment with software engineers was conducted to compare CandidTree with WinDiff, a traditional files and folders comparison tool. The results showed that users performed better with CandidTree. Furthermore, CandidTree received better satisfaction ratings and all users preferred CandidTree to WinDiff.
Development of novel assays for botulinum type A and B neurotoxins based on their endopeptidase activities (1996)

A novel assay method based on the endopeptidase activities of the botulinum neurotoxins has been developed and applied to the detection of botulinum type A and B toxins. An assay system developed for the detection of botulinum type B neurotoxin (BoNT/B) is based on the cleavage of a synthetic peptide substrate representing amino acid residues 60 to 94 of the intracellular target protein for the toxin, VAMP (vesicle-associated membrane protein, or synaptobrevin). In this assay system, immobilized VAMP (60-94) peptide substrate is cleaved by BoNT/B at the Gln-76-Phe-77 bond, leaving the C-terminal cleavage fragment on the solid phase. This fragment is then detected by the addition of an antibody-enzyme reagent which specifically recognizes the newly exposed N terminus of the cleavage product. The developed assay was specific to BoNT/B, showing no cross-reactivity with other clostridial neurotoxins, and had a sensitivity for BoNT/B of 0.6 to 4.5 ng/ml, which could be increased to 0.1 to 0.2 ng/ml by using an assay amplification system based on catalyzed reporter deposition. Trypsin treatment of BoNT/B samples, which converts the single-chain toxin to the active di-chain form, was found to increase the sensitivity of the endopeptidase assay from 5- to 10-fold. An endopeptidase assay for BoNT/A, based on the cleavage of a peptide substrate derived from the protein SNAP-25 (synaptosome-associated protein), was also developed and characterized.
Re-targeting T-cells against cancer by gene-transfer of tumor-reactive receptors (2009)

Clinical trials report so far only limited efficacy of adoptively transferred genetically modified T-cells. However, the recent progress in engineering tumor-reactive T cells is providing a promising basis to further explore this treatment modality.
Proteomics of the Retinal Pigment Epithelium Reveals Altered Protein Expression at Progressive Stages of Age-Related Macular Degeneration (2006)

These results provide the first direct evidence of AMD stage-specific changes in human RPE protein expression and provide a basis for functional investigation of AMD that may ultimately suggest new therapeutic strategies.
Minimal/measurable residual disease in AML: a consensus document from the European LeukemiaNet MRD Working Party (2018)

Measurable residual disease (MRD; previously termed minimal residual disease) is an independent, postdiagnosis, prognostic indicator in acute myeloid leukemia (AML) that is important for risk stratification and treatment planning, in conjunction with other well-established clinical, cytogenetic, and molecular data assessed at diagnosis. MRD can be evaluated using a variety of multiparameter flow cytometry and molecular protocols, but, to date, these approaches have not been qualitatively or quantitatively standardized, making their use in clinical practice challenging. The objective of this work was to identify key clinical and scientific issues in the measurement and application of MRD in AML, to achieve consensus on these issues, and to provide guidelines for the current and future use of MRD in clinical practice. The work was accomplished over 2 years, during 4 meetings by a specially designated MRD Working Party of the European LeukemiaNet. The group included 24 faculty with expertise in AML hematopathology, molecular diagnostics, clinical trials, and clinical medicine, from 19 institutions in Europe and the United States.
8.3: Design of a Compact Light Engine for FLCOS Microdisplays in a p‐HMPD System (2008)

Abstract We have designed a compact light engine for a ferroelectric Liquid‐crystal‐on‐Silicon (FLCOS) microdisplay used in a polarized head mounted projection display (p‐HMPD). In the light engine, the polarization of the light is manipulated in order to achieve a compact structure and a mirror based tapered light pipe is designed to improve the light efficiency and image uniformity. The performance of the light engine is analyzed based on the simulation results using LightTools.
Aortic Development and Anomalies (2007)

Development of the aorta takes place during the third week of gestation. It is a complex process that can lead to a variety of congenital variants and pathological anomalies. In diagnostic and interventional radiology, knowledge of aortic abnormalities and variant branching sequence is crucially important. This article gives a systematic overview of anatomical variability of the aorta.
Calcium dependence of rapid astrocyte death induced by transient hypoxia, acidosis, and extracellular ion shifts (2001)

Exposure to hypoxic, acidic, ion-shifted Ringer (HAIR) for 15-40 min has been shown to cause rapid astrocyte death upon reperfusion with normal media. The ion shifts of the HAIR solution included a rise in extracellular K(+) (e.g., [K(+)](o)) and a fall in [Na(+)](o), [Cl(-)](o), and [Ca(2+)](o), characteristic of ischemic-traumatic brain insults. We investigated the ionic basis of the HAIR-induced injury. After HAIR exposure, reperfusion in 0 Ca(2+)/EGTA media completely protected astrocytes. Preincubation of cells in BAPTA-AM ester was also protective, indicating that the injury was triggered by Ca(2+) influx during reperfusion. Neither nimodipine, CNQX, APV, nor TTX reduced injury. Astrocyte death could be blocked by 100 microM Ni(2+) or 100 microM benzamil, suggesting involvement of Na(+)-Ca(2+) exchange. KB-R7943, which preferentially inhibits reverse Na(+)-Ca(2+) exchange, also protected astrocytes. Elevation of [K(+)](o) was not necessary for astrocyte death. However, when [Na(+)](o) was maintained at 151 mM throughout the HAIR protocol, cell death was markedly reduced. We postulate that [Na(+)](o) shifts aid reversal of Na(+)-Ca(2+) exchange by favoring cytosolic Na(+) loading. Possible means of astrocytic Na(+) accumulation are discussed.
Defining the Normal Bacterial Flora of the Oral Cavity (2005)

More than 700 bacterial species or phylotypes, of which over 50% have not been cultivated, have been detected in the oral cavity. Our purposes were (i) to utilize culture-independent molecular techniques to extend our knowledge on the breadth of bacterial diversity in the healthy human oral cavity, including not-yet-cultivated bacteria species, and (ii) to determine the site and subject specificity of bacterial colonization. Nine sites from five clinically healthy subjects were analyzed. Sites included tongue dorsum, lateral sides of tongue, buccal epithelium, hard palate, soft palate, supragingival plaque of tooth surfaces, subgingival plaque, maxillary anterior vestibule, and tonsils. 16S rRNA genes from sample DNA were amplified, cloned, and transformed into Escherichia coli. Sequences of 16S rRNA genes were used to determine species identity or closest relatives. In 2,589 clones, 141 predominant species were detected, of which over 60% have not been cultivated. Thirteen new phylotypes were identified. Species common to all sites belonged to the genera Gemella, Granulicatella, Streptococcus, and Veillonella. While some species were subject specific and detected in most sites, other species were site specific. Most sites possessed 20 to 30 different predominant species, and the number of predominant species from all nine sites per individual ranged from 34 to 72. Species typically associated with periodontitis and caries were not detected. There is a distinctive predominant bacterial flora of the healthy oral cavity that is highly diverse and site and subject specific. It is important to fully define the human microflora of the healthy oral cavity before we can understand the role of bacteria in oral disease.
Histological evaluation of an impacted bone graft substitute composed of a combination of mineralized and demineralized allograft in a sheep vertebral bone defect (2007)

Demineralized bone matrix (DBMs) preparations are a potential alternative or supplement to autogenous bone graft, but many DBMs have not been adequately tested in clinically relevant animal models. The aim of current study was to compare the efficacy of a new bone graft substitute composed of a combination of mineralized and demineralized allograft, along with hyaluronic acid (AFT Bone Void Filler) with several other bone graft materials in a sheep vertebral bone void model. A drilled defect in the sheep vertebral body was filled with either the new DBM preparation, calcium sulfate (OsteoSet), autologous bone graft, or left empty. The sheep were euthanized after 6 or 12 weeks, and the defects were examined by histology and quantitative histomorphometry. The morphometry data were analyzed by one-way analysis of variance with the post hoc Tukey-Kramer test or the Student's t-test. All of the bone defects in the AFT DBM preparation group showed good new bone formation with variable amounts of residual DBM and mineralized bone graft. The DBM preparation group at 12 weeks contained significantly more new bone than the defects treated with calcium sulfate or left empty (respectively, p < 0.05, p < 0.01). There was no significant difference between the DBM and autograft groups. No adverse inflammatory reactions were associated with any of the three graft materials. The AFT preparation of a mixture of mineralized and demineralized allograft appears to be an effective autograft substitute as tested in this sheep vertebral bone void model.
Study of Moderately Rapid Chemical Exchange Reactions by Means of Nuclear Magnetic Double Resonance (1963)

A nuclear magnetic double-resonance method for the determination of chemical exchange rates has been developed. The method is applicable to systems in which a nuclear spin is reversibly transferred between two nonequivalent sites, A and B. The lifetime (τA) and spin—lattice relaxation time (T1A) in Site A are obtained through the study of the decay to a new equilibrium value of Signal A upon the sudden saturation of Signal B. The converse experiment permits the determination of τB and T1B. A number of data for cross checks are furthermore obtained through the study of the recovery of the signals upon the release of various combinations of saturating rf fields. A simple theory based on the Bloch equations as modified by McConnell to incorporate the effects of chemical exchange is given. Experimental results on the hydroxyl proton exchange in the system salicylaldehyde and 2-hydroxyacetophenone are well described by this simple theory. The present method, which can readily be extended to systems with several sites, offers a complement to the Gutowsky—Saika single-resonance method and is particularly suited to the study of exchange rates slower than those accessible by the single-resonance method.
THE ASSESSMENT OF DISEASE ACTIVITY IN RHEUMATOID ARTHRITIS USING A MULTIVARIATE ANALYSIS (1981)

A simple method of assessing 'index of disease activity' (IDA) in rheumatoid arthritis (RA) using a multivariate analysis (MVA) comprising morning stiffness (MS), pain scale (PS), grip strength (GS), articular index (AI), haemoglobin (Hb) and erythrocyte sedimentation rate (ESR) is described. The IDA of 99 patients with RA was assessed using MVA. The method could be used reliably and readily for random or longitudinal assessment, in drug trials and for comparing disease activity with other objective indices.
Engineering the Microstructure of Electrospun Fibrous Scaffolds by Microtopography (2013)

Controlling the structure and organization of electrospun fibers is desirable for fabricating scaffolds and materials with defined microstructures. However, the effects of microtopography on the deposition and, in turn, the organization of the electrospun fibers are not well understood. In this study, conductive polydimethylsiloxane (PDMS) templates with different micropatterns were fabricated by combining photolithography, silicon wet etching, and PDMS molding techniques. The fiber organization was varied by fine-tuning the microtopography of the electrospinning collector. Fiber conformity and alignment were influenced by the depth and the slope of microtopography features, resulting in scaffolds comprising either an array of microdomains with different porosity and fiber alignment or an array of microwells. Microtopography affected the fiber organization for hundreds of micrometers below the scaffold surface, resulting in scaffolds with distinct surface properties on each side. In addition, the fiber diameter was also affected by the fiber conformity. The effects of the fiber arrangement in the scaffolds on the morphology, migration, and infiltration of cells were examined by in vitro and in vivo experiments. Cell morphology and organization were guided by the fibers in the microdomains, and cell migration was enhanced by the aligned fibers and the three-dimensional scaffold structure. Cell infiltration was correlated with the microdomain porosity. Microscale control of the fiber organization and the porosity at the surface and through the thickness of the fibrous scaffolds, as demonstrated by the results of this study, provides a powerful means of engineering the three-dimensional structure of electrospun fibrous scaffolds for cell and tissue engineering.
ISCOMs: an adjuvant with multiple functions (1998)

Aluminum salts are currently the only widely used adjuvant for human vaccines. Over the past 10-15 years, a large research effort has attempted to find novel adjuvants with ability to induce a broad range of immune responses, including cell-mediated immunity. The immunostimulating complex or ISCOM is one adjuvant with multiple adjuvant properties. ISCOMs are open cage-like complexes typically with a diameter of about 40 nm that are built up by cholesterol, lipid, immunogen, and saponins from the bark of the tree Quillaia saponaria Molina. ISCOMs have been demonstrated to promote antibody responses and induce T helper cell as well as cytotoxic T lymphocyte responses in a variety of experimental animal models, and have now progressed to phase I and II human trials. This review describes recent developments in the understanding of the structure, composition, and preparation of ISCOMs and will cover important aspects of the understanding of the adjuvant functions of ISCOMs and how they act on the immune system.
Establishment and characterization of a human acute monocytic leukemia cell line (THP‐1) (1980)

A human leukemic cell line (THP-1) cultured from the blood of a boy with acute monocytic leukemia is described. This cell line had Fc and C3b receptors, but no surface or cytoplasmic immunoglobulins. HLA haplotypes of THP-1 were HLA-A2, -A9, -B5, -DRW1 and -DRW2. The monocytic nature of the cell line was characterized by: (1) the presence of alpha-naphthyl butyrate esterase activities which could be inhibited by NaF; (2) lysozyme production; (3) the phagocytosis of latex particles and sensitized sheep erythrocytes; and (4) the ability to restore T-lymphocyte response to Con A. The cells did not possess Epstein-Barr virus-associated nuclear antigen. These results indicate that THP-1 is a leukemia cell line with distinct monocytic markers. During culture, THP-1 maintained these monocytic characteristics for over 14 months.
The periplasmic dipeptide permease system transports 5-aminolevulinic acid in Escherichia coli (1993)

In a genetic screen designed to generate Escherichia coli strains completely devoid of the heme precursor 5-aminolevulinic acid (ALA), we isolated a class of mutants which were defective for exogenous ALA uptake. The mutations, designated alu (ALA uptake), mapped to the 80-min region of the E. coli chromosome. They were complemented by a recombinant plasmid containing the dpp operon, which encodes a dipeptide permease transport system. Alu mutants displayed a severe reduction in ALA import, as did a strain with a chromosomal insertion in the first gene of the dpp operon. A recognized substrate of Dpp transport, prolyl-glycine, effectively competed with ALA for uptake. E. coli strains defective in ALA biosynthesis (hemA or hemL) require exogenous ALA to achieve wild-type growth but show limited aerobic and anaerobic growth in the absence of ALA. The presence of an alu or dpp mutation in hemA or hemL strains abolishes growth in the absence of ALA and requires increased levels of ALA for normal growth. We conclude that the alu mutations are within the dpp operon and that the dipeptide transport system mediates uptake of the important metabolite ALA.
Multiple attenuation by explicit wave extrapolation to an interpreted horizon (1999)

One of the oldest approaches to multiple attenuation is to predict the multiples using their periodic nature as their identifying trait and then simply subtract them from the original data. It is done routinely as a trace-by-trace, time-axis deconvolution on nearly every exploration seismic data set to attenuate the short-period multiples. This simple prediction method loses its effectiveness, however, when the multiple period gets to be significantly longer than the source wavelet. The problem is that the longer-period multiples do not occur in an evenly spaced train. The delay between cycles depends on the wave propagation angle and the dip of the multiple-generating reflectors. Thus the period varies both with source-receiver offset and the subsurface geology.
The second international reference preparation of erythropoietin, human, urinary, for bioassay. (1972)

A collaborative study of the second international Reference Preparation of Erythropoietin, Human, Urinary, for Bioassay was carried out in 10 laboratories. Combined potency estimates obtained by comparison with the International Reference Preparation, indicate that ampoules of the second Preparation contain 10.0 IU (weighted mean potency) or, taking the unweighted mean potency, 9.8 IU, with fiducial limits (P=0.95) of 8.4-11.5 IU. The second Preparation could be used as a standard in estimating the potency of a preparation of sheep plasma erythropoietin (68/307) although, as with the International Reference Preparation, there was a tendency for the sheep plasma preparation to produce log-dose-log-response regression lines that were steeper than those produced by the second Preparation.In accelerated degradation studies of the second Preparation stored as the dry product in ampoules for up to 1 year, there was no consistent trend to indicate instability of the preparation.Following its establishment in 1971, the Second International Reference Preparation was allocated a potency of 10 IU/ampoule.
Accurate and efficient regression modeling for microarchitectural performance and power prediction (2006)

We propose regression modeling as an efficient approach for accurately predicting performance and power for various applications executing on any microprocessor configuration in a large microarchitectural design space. This paper addresses fundamental challenges in microarchitectural simulation cost by reducing the number of required simulations and using simulated results more effectively via statistical modeling and inference.Specifically, we derive and validate regression models for performance and power. Such models enable computationally efficient statistical inference, requiring the simulation of only 1 in 5 million points of a joint microarchitecture-application design space while achieving median error rates as low as 4.1 percent for performance and 4.3 percent for power. Although both models achieve similar accuracy, the sources of accuracy are strikingly different. We present optimizations for a baseline regression model to obtain (1) application-specific models to maximize accuracy in performance prediction and (2) regional power models leveraging only the most relevant samples from the microarchitectural design space to maximize accuracy in power prediction. Assessing sensitivity to the number of samples simulated for model formulation, we find fewer than 4,000 samples from a design space of approximately 22 billion points are sufficient. Collectively, our results suggest significant potential in accurate and efficient statistical inference for microarchitectural design space exploration via regression models.
What Judges Want and Need: User-Friendly Foundations for Effective Judicial Education (2014)

This article evaluates the connection between judicial education and judges’ needs and preferences. In Part I, we begin by discussing the history, purpose, and form of judicial education, charting its evolution over time. In Part II, we examine current judicial education programs and scholarship, highlighting differences and similarities between federal and state programming. In Part III, we analyze the limitations of existing scholarship and programming, arguing judicial education programs are insufficiently tied to evidence of judicial demands. We conclude in Parts IV and V by suggesting two proposals to align programming with needs: (1) an annual needs-based assessment of judicial education offerings and (2) a voucher system for judges to attend their choice of judicial education programs.
Coexpression of Mutant p53 and p193 Renders Embryonic Stem Cell–Derived Cardiomyocytes Responsive to the Growth-Promoting Activities of Adenoviral E1A (2001)

Expression of adenoviral E1A in cardiomyocytes results in the activation of DNA synthesis followed by apoptosis. In contrast, expression of simian virus 40 large T antigen induces sustained cardiomyocyte proliferation. Previous studies have shown that T antigen binds to 2 proapoptotic proteins in cardiomyocytes, namely the p53 tumor suppressor and p193 (a new member of the BH3-only proapoptosis subfamily). Structure-function analyses identified a p193 C-terminal truncation mutant that encodes prosurvival activity. This mutant was used to test the role of p193 in E1A-induced cardiomyocyte apoptosis. E1A induced apoptosis in cardiomyocytes derived from differentiating embryonic stem cells. Expression of the prosurvival p193 mutant alone or a mutant p53 alone did not block E1A-induced apoptosis. In contrast, combinatorial expression of mutant p193 and mutant p53 blocked E1A-induced apoptosis, resulting in a proliferative response indistinguishable from that seen with T antigen. These results confirm the hypothesis that there are 2 proapoptotic pathways, encoded by p53 and p193, respectively, which restrict cardiomyocyte cell cycle activity in differentiating embryonic stem cell cultures. Furthermore, these results explain in molecular terms the phenotypic differences of E1A versus T-antigen gene transfer in cardiomyocytes.