gebhart/patrepeval huggingface dataset:
Stargardt disease: clinical features, molecular genetics, animal models and therapeutic options (2016)

Stargardt disease (STGD1; MIM 248200) is the most prevalent inherited macular dystrophy and is associated with disease-causing sequence variants in the gene ABCA4 Significant advances have been made over the last 10 years in our understanding of both the clinical and molecular features of STGD1, and also the underlying pathophysiology, which has culminated in ongoing and planned human clinical trials of novel therapies. The aims of this review are to describe the detailed phenotypic and genotypic characteristics of the disease, conventional and novel imaging findings, current knowledge of animal models and pathogenesis, and the multiple avenues of intervention being explored.
Methods and algorithms for statistical analysis of protein sequences. (1992)

We describe several protein sequence statistics designed to evaluate distinctive attributes of residue content and arrangement in primary structure. Considered are global compositional biases, local clustering of different residue types (e.g., charged residues, hydrophobic residues, Ser/Thr), long runs of charged or uncharged residues, periodic patterns, counts and distribution of homooligopeptides, and unusual spacings between particular residue types. The computer program SAPS (statistical analysis of protein sequences) calculates all the statistics for any individual protein sequence input and is available for the UNIX environment through electronic mail on request to V.B. (volker/genomic@stanford.edu).
An Inhibitor of Cell Proliferation Associated with Adhesion Formation Is Suppressed by N,O-Carboxymethyl Chitosan (1998)

Surgical adhesions are a major cause of morbidity and mortality. The ideal barrier agent will both minimize adhesions and provide a milieu for the regeneration of the mesothelium lining of the abdominal and thoracic cavities. N,O-Carboxymethylchitosan (NOCC), a derivation of chitin that markedly reduces adhesions, may function to modulate intracellular signals such as growth factors and cytokines in the inflammatory exudate. Since transforming growth factor-beta is implicated in the fibrotic process, we investigated the possibility that NOCC's effects on adhesion formation reflects a modulation of TGF-beta activity. Using a biological assay for inhibition of cell proliferation to detect TGF-beta activity, we demonstrate that NOCC suppresses the levels of an inhibitor of cell proliferation released into serum and peritoneal exudates after cecal abrasion in the rat. However, this activity was distinct from known forms of TGF-beta as determined using both TGF-beta-neutralizing antisera and a TGF-beta-resistant cell proliferation assay. Thus at least one potential effect of NOCC involves a mechanism distinct from TGF-beta inhibition.
Capillary electrophoresis in 2 and 5 .mu.m diameter capillaries: application to cytoplasmic analysis (1990)

Capillary electrophoresis with electrochemical detection in 2- and 5-micron capillaries has been developed to study ultrasmall biological environments. Sample volumes as low as 270 fL have been injected into the electrophoresis capillary with subattomole detection limits for easily oxidized species. We have applied this method to the analysis of single cell cytoplasm. Sampling of the cytoplasm is accomplished by inserting one end of the electrophoresis capillary directly into a single nerve cell. The high-voltage end of the electrophoresis capillary has been etched with hydrofluoric acid to form a microinjector. This injection scheme represents an improvement over those previously used for similar applications. The excellent selectivity of this method is demonstrated for catecholamine and indolamine neurotransmitters and their metabolites found in the invertebrate system, the pond snail Planorbis corneus.
Frame Reflection: Toward the Resolution of Intractable Policy Controversies (1995)

(1995). Frame Reflection: Toward the Resolution of Intractable Policy Controversies. Journal of Economic Issues: Vol. 29, No. 3, pp. 965-968.
Foreign‐Body Reaction to the Bioabsorbable Suretac Device (2000)

Arthroscopic shoulder stabilization with the bioabsorbable Suretac device (Acufex Microsurgical, Mansfield, MA) offers some technical advantages compared with other approaches. However, in 4 patients (3 men, 1 woman; between 20 and 35 years of age) with 3 SLAP lesions grades 2 and 1 post-traumatic anterior shoulder instability, breakage and early loosening of the Suretac device was observed. All patients complained about shoulder pain and loss of active and passive motion. The arthroscopic examination revealed a massive synovitis without positive cultures. Loose fragments of the Suretac device spread in the joint cavity and induced a foreign-body reaction. Histologically, there was a massive infiltration of phagocytic cells (histiocytes, multinucleated giant cells) and birefringent polymeric particles surrounded by or within histiocytes and multinucleated giant cells. All patients underwent arthroscopic synovectomy. Because of instability, 2 of them required restabilization, which was performed with suture anchors (Fastak [Arthrex, Naples, FL], Mitek [Mitek Division, Ethicon, Norderstedt, Germany]). Postoperatively all patients were pain free, progressing to full active and passive range of motion. Our patients suffered from a mechanical failure rather than from a predisposition to exaggerated inflammatory response. According to this observation, the Suretac device seems to be prone to early failure in patients with SLAP lesions because of its biodegradability.
Multi-Level Liveness Verification for Face-Voice Biometric Authentication (2006)

In this paper we present the details of the multilevel liveness verification (MLLV) framework proposed for realizing a secure face-voice biometric authentication system that can thwart different types of audio and video replay attacks. The proposed MLLV framework based on novel feature extraction and multimodal fusion approaches, uncovers the static and dynamic relationship between voice and face information from speaking faces, and allows multiple levels of security. Experiments with three different speaking corpora VidTIMIT, UCBN and AVOZES shows a significant improvement in system performance in terms of DET curves and equal error rates (EER) for different types of replay and synthesis attacks.
The IETF Internet telephony architecture and protocols (1999)

Internet telephony was first used as a simple way to provide point-to-point voice transport between two IP hosts. However, the growing interest in providing integrated voice, data, and video services has caused its scope to be extended. Internet telephony now encompasses a range of services, including not only traditional conferencing, call control, multimedia, and mobility services, but also new ones that integrate Web, e-mail, presence, and instant messaging applications with telephony. Internet telephony and traditional circuit-switched telephony will coexist for quite some time, requiring interworking between the two. In this article we present a suite of protocols, developed in the IETF, which provide a partial solution to this complex problem.
Aliskiren inhibits atherosclerosis development and improves plaque stability in APOE*3Leiden.CETP transgenic mice with or without treatment with atorvastatin (2011)

Aliskiren inhibited atherosclerosis development and improved plaque stability alone and in combination with atorvastatin, possibly via a mechanism involving T cells. These results suggest a potential benefit of using aliskiren in a clinical setting, particularly in combination with statin treatment.
Characterization of Chiral Mesoporous Materials by Transmission Electron Microscopy (2004)

By using transmission electron microscopy (TEM), the chirality of novel mesoporous materials has been studied. In addition, a computer simulation that uses a simple structural model was employed. The existence of chiral channels inside a tubelike material was confirmed by the observation of fringes along the length of the tubes. The chiral pitch of the channels was measured from the intermittent period, the chirality (right- or left-handed) was determined from the tilt direction of a tube compared with the direction of incident electrons and the curvature direction of the curved intermitted fringes as viewed in the TEM images.
Evaluation of MRSA-Screen, a Simple Anti-PBP 2a Slide Latex Agglutination Kit, for Rapid Detection of Methicillin Resistance in Staphylococcus aureus (1999)

The MRSA-Screen test (Denka Seiken Co., Ltd., Tokyo, Japan), consisting of a slide latex agglutination kit that detects PBP 2a with a monoclonal antibody, was blindly compared to the oxacillin disk diffusion test, the oxacillin-salt agar screen, and PCR of the mecA gene for the detection of methicillin resistance in Staphylococcus aureus. A total of 120 methicillin-susceptible S. aureus (MSSA) and 80 methicillin-resistant S. aureus (MRSA) isolates, defined by the absence or presence of the mecA gene, respectively, were tested. The MRSA-Screen test, the oxacillin disk diffusion test, and the oxacillin-salt agar screening test showed sensitivities of 100, 61.3, and 82.5% and specificities of 99.2, 96.7, and 98.3%, respectively. We conclude that the MRSA-Screen is a very accurate, reliable, and fast test (15 min) for differentiation of MRSA from MSSA colonies on agar plates.
Analysis of translation using polysome profiling (2016)

During the past decade, there has been growing interest in the role of translational regulation of gene expression in many organisms. Polysome profiling has been developed to infer the translational status of a specific mRNA species or to analyze the translatome, i.e. the subset of mRNAs actively translated in a cell. Polysome profiling is especially suitable for emergent model organisms for which genomic data are limited. In this paper, we describe an optimized protocol for the purification of sea urchin polysomes and highlight the critical steps involved in polysome purification. We applied this protocol to obtain experimental results on translational regulation of mRNAs following fertilization. Our protocol should prove useful for integrating the study of the role of translational regulation in gene regulatory networks in any biological model. In addition, we demonstrate how to carry out high-throughput processing of polysome gradient fractions, for the simultaneous screening of multiple biological conditions and large-scale preparation of samples for next-generation sequencing.
Detection of the most common mutations causing beta-thalassemia in Mediterraneans using a multiplex amplification refractory mutation system (MARMS). (1992)

A rapid, simple, cost-effective, non-radioactive method for detection of the most common mutations causing beta-thalassemia in Mediterranean people has been developed by combining multiplexing with the amplification refractory system. This approach, the multiplex amplification refractory mutation system (MARMS), provides an easy assay for direct detection of normal and mutant beta-globin genes in homozygotes and heterozygotes. The strategy involves multiplex PCR of four of the five regions of interest within the beta-globin gene in a single reaction containing a common oligoprimer and either the normal or mutant oligonucleotides corresponding to IVS-1 nucleotide 1 or IVS-1 nucleotide 6, IVS-1 nucleotide 110, codon 39, and IVS-2 nucleotide 1 regions. Primers are chosen so that the sizes of the four PCR products differ, thereby facilitating detection on agarose gels following amplification. Patient samples are primed with either four normal or four mutant oligonucleotide mixtures and the common oligoprimer, and PCR products run in parallel on gels to detect band presence or absence. This approach simplifies mutation detection and shows promise for automation employing fluorescent-tagged primers.
Dietary Intake of Antioxidants and Risk of Alzheimer Disease (2002)

High dietary intake of vitamin C and vitamin E may lower the risk of Alzheimer disease.
Sampling bias and search space boundary extension in real coded genetic algorithms (2000)

In Real coded genetic algorithms, some crossover operators do not work well on functions which have their optimum at the corner of the search space. To cope with this problem, we have proposed boundary extension methods which allows individuals to be located within a limited space beyond the boundary of the search space. In this paper, we give an analysis of the boundary extension methods from a view point of the sampling bias and perform a comparative study on the effect of applying boundary extension methods, namely the BEM (boundary extension by mirroring, the BES (boundary extension with extended selection). We were able to confirm that to use sampling methods which have smaller sampling bias had good performance on both functions which have their optimum at or near the boundaries of the search space, and functions which have their optimum at the center of the search space. The BES/SD/A (BES by shortest distance selection with aging) had good performance on functions which have their optimum at or near the boundaries of the search space. We also confirmed that applying the BES/SD/A did not cause any performance degradation on functions which have their optimum at the center of the search space. This feature of the BES/SD/A is very useful because when we solve some function optimization problems, we do not know the position of their optimal point.
The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (2019)

We present Rsubread, a Bioconductor software package that provides high-performance alignment and read counting functions for RNA-seq reads. Rsubread is based on the successful Subread suite with the added ease-of-use of the R programming environment, creating a matrix of read counts directly as an R object ready for downstream analysis. It integrates read mapping and quantification in a single package and has no software dependencies other than R itself. We demonstrate Rsubread's ability to detect exon-exon junctions de novo and to quantify expression at the level of either genes, exons or exon junctions. The resulting read counts can be input directly into a wide range of downstream statistical analyses using other Bioconductor packages. Using SEQC data and simulations, we compare Rsubread to TopHat2, STAR and HTSeq as well as to counting functions in the Bioconductor infrastructure packages. We consider the performance of these tools on the combined quantification task starting from raw sequence reads through to summary counts, and in particular evaluate the performance of different combinations of alignment and counting algorithms. We show that Rsubread is faster and uses less memory than competitor tools and produces read count summaries that more accurately correlate with true values.
Set−Reset Flip-Flop Memory Based on Enzyme Reactions: Toward Memory Systems Controlled by Biochemical Pathways (2009)

The enzyme-based set-reset flip-flop memory system was designed with the core part composed of horseradish peroxidase and diaphorase biocatalyzing oxidation and reduction of redox species (2,6-dichloroindophenol or ferrocyanide). The biocatalytic redox reactions were activated by H(2)O(2) and NADH produced in situ by different enzymatic reactions allowing transformation of various biochemical signals (glucose, lactate, d-glucose-6-phosphate, ethanol) into reduced or oxidized states of the redox species. The current redox state of the system, controlled by the set and reset signals, was read out by optical and electrochemical means. The multiwell setup with the flip-flop units separately activated by various set/reset signals allowed encoding of complex information. For illustrative purposes, the words "Clarkson" and then "University" were encoded using ASCII character codes. The present flip-flop system will allow additional functions of enzyme-based biocomputing systems, thus enhancing the performance of multisignal biosensors and actuators controlled by logically processed biochemical signals. The integrated enzyme logic systems and flip-flop memories associated with signal-responsive chemical actuators are envisaged as basic elements of future implantable biomedical devices controlled by immediate physiological conditions.
Studies in Steroid Metabolism. V. The Problem of Walden Inversion in the Reactions of Steroid Hydrogen Sulfates and Steroid Sulfites1,2 (1948)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies in Steroid Metabolism. V. The Problem of Walden Inversion in the Reactions of Steroid Hydrogen Sulfates and Steroid Sulfites1,2Seymour Lieberman, Lucie B. Hariton, and David K. FukushimaCite this: J. Am. Chem. Soc. 1948, 70, 4, 1427–1432Publication Date (Print):April 1, 1948Publication History Published online1 May 2002Published inissue 1 April 1948https://pubs.acs.org/doi/10.1021/ja01184a040https://doi.org/10.1021/ja01184a040research-articleACS PublicationsRequest reuse permissionsArticle Views109Altmetric-Citations23LEARN 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
Mortality in the rheumatic diseases (1995)

Mortality has been found to be predicted in most instances by more severe clinical status, and therefore death should not be considered as "unrelated" to the rheumatic disease. These observations may have important implications for clinical care and health policies regarding patients with rheumatic diseases.
Adherence of Pseudomonas aeruginosa to human tracheobronchial mucin (1984)

A microtiter plate assay was developed to study the adherence of Pseudomonas aeruginosa to purified human tracheobronchial mucin. The wells of the plates were treated with silicon to minimize nonspecific binding of bacteria and then coated with a solution of purified human tracheobronchial mucin. Bacteria were added to the wells, and the plates were incubated at 37 degrees C. The wells were washed 15 times in an automated microtiter plate washer, and the bacteria bound to wells were desorbed with Triton X-100 and plated for enumeration. Scanning electron microscopy verified bacterial adherence to the mucin-coated wells and desorption of bacteria by Triton X-100. Adherence of P. aeruginosa increased as the concentration of mucin used to coat the wells was increased, with saturation occurring at 0.5 microgram of mucin protein per ml. Other parameters that affected adherence included the time of incubation and concentration of bacteria. Similar studies with strains of Escherichia coli and Klebsiella pneumoniae indicated a relative lack of binding of these bacteria to mucin. In comparing different strains of P. aeruginosa, there were small differences in binding between strains. It is inferred that there may be specific sites on human tracheobronchial mucin which facilitate this preferential binding.
Class-specific and polyvalent enzyme-linked immunosorbent assays for detection of antibodies to Borrelia burgdorferi in equids. (1989)

Class-specific and polyvalent ELISA were developed to detect IgM antibody or total immunoglobulins to Borrelia burgdorferi in equine sera. Analyses of 122 serum specimens, collected during 1985 from horses and ponies in tick-infested areas of Connecticut, revealed IgM antibody in 41 (34%) samples; titration end points ranged from 1:160 to 1:2,560. In polyvalent ELISA, 73 (16%) of 454 serum specimens contained IgM and/or IgG antibody. Seropositivity was highest (32%) for blood samples collected during May. Both ELISA procedures had comparable sensitivities.
Mammalian adipose tissue and muscle are major sources of lipid transfer protein mRNA (1991)

The plasma cholesteryl ester transfer protein (CETP) catalyzes the transfer of cholesteryl esters from high density lipoproteins (HDL) to triglyceride-rich lipoproteins and plays a major role in the catabolism of HDL. Lipoprotein lipase (LPL) is the rate-limiting enzyme for hydrolysis of circulating triglyceride and is involved in HDL formation. We show that tissues containing LPL are major sources of CETP mRNA in several mammalian species, including some with low cholesteryl ester transfer activity in plasma. In hamsters, adipose tissue and heart were found to be the richest sources of both CETP and LPL mRNA; in situ hybridization studies showed that the same cell types (i.e. adipocytes or myocytes) contained CETP and LPL mRNA in these tissues. Isolated adipocytes synthesized active CETP. Dietary studies revealed a complex pattern of response of CETP mRNA levels in different tissues, which showed partial similarity to the changes in LPL mRNA abundance. However, high cholesterol diets resulted in increased CETP mRNA abundance in adipose tissue, heart, and skeletal muscle, without equivalent changes in LPL mRNA. Plasma HDL cholesteryl ester levels showed strong inverse correlations with CETP mRNA abundance in adipose tissue. The results suggest a conserved function of CETP in adipose tissue and heart, such as a co-ordinate action with LPL to enhance HDL turnover. Although there is considerable overlap in the tissue- and cell-specific pattern of CETP and LPL gene expression, dietary studies revealed only limited parallelism in response at the mRNA level. The increase in CETP mRNA in peripheral tissues in response to increased dietary cholesterol suggests that local induction of CETP synthesis may help to recycle cholesterol deposited in these tissues during lipolysis of dietary lipoproteins.