gebhart/patrepeval huggingface dataset:
Comparative Genomic Hybridizations Reveal Genetic Regions within theMycobacterium aviumComplex That Are Divergent fromMycobacterium aviumsubsp.paratuberculosisIsolates (2005)

Mycobacterium avium subsp. paratuberculosis is genetically similar to other members of the Mycobacterium avium complex (MAC), some of which are nonpathogenic and widespread in the environment. We have utilized an M. avium subsp. paratuberculosis whole-genome microarray representing over 95% of the predicted coding sequences to examine the genetic conservation among 10 M. avium subsp. paratuberculosis isolates, two isolates each of Mycobacterium avium subsp. silvaticum and Mycobacterium avium subsp. avium, and a single isolate each of both Mycobacterium intracellulare and Mycobacterium smegmatis. Genomic DNA from each isolate was competitively hybridized with DNA from M. avium subsp. paratuberculosis K10, and open reading frames (ORFs) were classified as present, divergent, or intermediate. None of the M. avium subsp. paratuberculosis isolates had ORFs classified as divergent. The two M. avium subsp. avium isolates had 210 and 135 divergent ORFs, while the two M. avium subsp. silvaticum isolates examined had 77 and 103 divergent ORFs. Similarly, 130 divergent ORFs were identified in M. intracellulare. A set of 97 ORFs were classified as divergent or intermediate in all of the nonparatuberculosis MAC isolates tested. Many of these ORFs are clustered together on the genome in regions with relatively low average GC content compared with the entire genome and contain mobile genetic elements. One of these regions of sequence divergence contained genes homologous to a mammalian cell entry (mce) operon. Our results indicate that closely related MAC mycobacteria can be distinguished from M. avium subsp. paratuberculosis by multiple clusters of divergent ORFs.
Immunophenotypic analysis of the Kaposi sarcoma herpesvirus (KSHV; HHV‐8)‐infected B cells in HIV+ multicentric Castleman disease (MCD) (2008)

Although both PEL and MCD originate from KSHV-infected pre-terminally differentiated B cells, these findings, with previously reported genetic studies, indicate HIV+ MCD may arise from extrafollicular B cells, whereas PELs may originate from cells that have traversed the germinal centre.
Influence of Plasma Treatment on Wheat and Oat Germination and Early Growth (2010)

The aim of this paper is to show and discuss the influence of cold plasma treatment on a germination enhancement of wheat and oat caryopses in wider context. Wheat and oat corns have been stimulated by cold plasma discharge under power of 500 W, air gas flow of 200 ml/min for different time durations (from 0 to 2400 s). Wheat seed coat showed an eroded surface after plasma treatment. Plasma treatment inhibited the germinating acceleration of wheat in first days but enhancement of footstalk was observed on plants grown from seeds treated for medium time. On the other hand, plasma treatment did not affect germination of oat seeds, but accelerated the rootlet generation at plants grown from treated seeds. The different content of phenolic compounds between control sprouts and sprouts from treated seedlings was discovered. The different contents illustrated changes in metabolism processes in both tested species. These phenomena indicate penetration of active species from plasma through the porous seed coat inside the seed where they react with seed cells.
An Efficient Iminophosphorane-Mediated Synthesis of Thieno[3,2-c]pyridine, Thieno[2,3-c]pyridine and Furo[3,2-c]-pyridine Derivatives (1987)

A number of thieno[3,2-c]pyridines 4, thieno[2,3-c]pyridines 7 and furo[3,2-c]pyridines 11 derivatives have been prepared by reaction of the appropriate iminophosphorane, available from ethyl azidoheteroarylacrylates and triphenylphosphine, with aromatic isocyanates.
The Emerging Infectious Challenge of Clostridium difficile-Associated Disease in Massachusetts Hospitals: Clinical and Economic Consequences (2007)

CDAD is widespread in Massachusetts hospitals. Rehospitalization with CDAD, if it occurs, generally happens within a few months and happens multiple times for some patients. Based on this study's findings, a conservative estimate of the annual US cost for CDAD management is $3.2 billion dollars.
Vasomodulation by Skeletal Muscle–Derived Nitric Oxide Requires α-Syntrophin–Mediated Sarcolemmal Localization of Neuronal Nitric Oxide Synthase (2003)

Neuronal nitric oxide synthase (nNOS) is abundantly expressed in skeletal muscle where it associates with the dystrophin complex at the sarcolemma by binding to the PDZ domain of alpha-syntrophin. Nitric oxide (NO) produced by skeletal muscle nNOS is proposed to regulate blood flow in exercising muscle by diffusing from the skeletal muscle fibers to the nearby microvessels where it attenuates alpha-adrenergic vasoconstriction. In the present study, we hypothesized that sarcolemmal localization of nNOS is a critical determinant of the vasoregulatory effect of skeletal muscle-derived NO. To test this hypothesis, we performed experiments in alpha-syntrophin null mice and in transgenic mice expressing a mutated alpha-syntrophin lacking the PDZ domain (DeltaPDZ), both of which are characterized by reduced sarcolemmal nNOS. We found that modulation of alpha-adrenergic vasoconstriction was greatly impaired in the contracting muscles of the alpha-syntrophin null mice and transgenic DeltaPDZ mice compared with wild-type mice and transgenic mice expressing full-length alpha-syntrophin. These in vivo mouse studies highlight the functional importance of appropriate membrane targeting of nNOS by the dystrophin-associated protein alpha-syntrophin and may have implications for the development of potential gene therapy strategies to treat muscular dystrophy or other muscle-related diseases.
Molecular cloning and sequence analysis of 3-hydroxy-3-methylglutaryl-coenzyme A reductase from the human parasite Schistosoma mansoni. (1989)

cDNA clones encoding the 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase [(S)-mevalonate:NADP+ oxidoreductase (CoA-acylating), EC 1.1.1.34] from the human parasite Schistosoma mansoni have been isolated and characterized. The composite 3459 base pairs of cDNA sequence contains a 2844-base-pair open reading frame corresponding to a protein of 948 amino acids. The predicted S. mansoni HMG-CoA reductase protein contains a hydrophobic amino terminus consisting of seven potential transmembrane domains that are structurally conservative but are not identical in amino acid sequence with HMG-CoA reductases from other species. The hydrophilic carboxyl terminus of the S. mansoni HMG-CoA reductase protein, however, shares 48-52% sequence identity with the carboxyl termini of other HMG-CoA reductases in a region that contains the catalytic domain. When expressed as a fusion protein in Escherichia coli, the carboxyl-terminal domain of the schistosome protein exhibits HMG-CoA reductase enzyme activity.
Blood group A cross-reacting epitope defined by monoclonal antibodies NCC-LU-35 and -81 expressed in cancer of blood group O or B individuals: its identification as Tn antigen. (1985)

Two monoclonal antibodies, NCC-LU-35 and NCC-LU-81, have been established after immunization of mice with membrane preparations of human lung cancer Lu65 tumor xenograft cells grown in vivo and intact cells cultured in vitro, respectively. These two antibodies react specifically with a majority of human adenocarcinomas, irrespective of the host's blood group ABO status, as well as with normal tissues and erythrocytes of blood group A individuals. The antigenicity is associated with a high molecular weight mucin-like glycoprotein separated by gel filtration of Lu65 tumor extracts. The epitope of the mucin-like glycoprotein has been identified as alpha-N-acetylgalactosaminyl residue directly linked O-glycosidically to serine or threonine residues of polypeptides. This epitope was serologically detected several years ago and given the name Tn. Our identification of the epitope is based on the following results: The antigen is sensitive to alpha-N-acetylgalactosaminidase, but not to sialidase or alpha-fucosidase. Various mono- and difucosyl A determinants, either type 1 or type 2 chain, cross-react with both antibodies. The reactivity with both antibodies can be created by treatment of glycophorin A of normal erythrocytes with sialidase followed by beta-galactosidase. N-[3H]acetylgalactosamine can be released by galactose oxidase/NaB3H4 treatment from the Lu65 mucin-like glycoprotein but not from the mucin-like glycoprotein of normal colonic mucosa upon reductive beta-elimination (alkaline borohydride treatment). The antigen may be one of the tumor-associated A cross-reacting antigens occurring in a wide variety of human adenocarcinomas of hosts belonging to all ABO blood groups.
The minimal ribosomal RNA gene promoter of Arabidopsis thaliana includes a critical element at the transcription initiation site (1995)

The genes encoding the precursor of 18S, 5.8S and 25S ribosomal RNAs are transcribed in the nucleolus by RNA polymerase I. Unlike rRNA gene promoters in animals which differ substantially across species boundaries, plant rRNA gene promoters share sequence similarity for several nucleotides upstream and downstream of the transcription start site (+ 1). The conserved sequence consists of a near-consensus TATA box, a critical promoter element of most genes transcribed by RNA polymerase II and certain genes transcribed by RNA polymerase III, followed by a cluster of four to six guanosines. Using transient expression of cloned promoter deletions in Arabidopsis thaliana protoplasts, it is shown that the 5' boundary of the Arabidopsis rRNA gene promoter is located between -55 and -33 and the 3' promoter boundary is approximately +6. The critical role of the TATA element at the initiation site was demonstrated by altering this region using tandem point mutations within constructs containing essentially complete intergenic spacer sequences from -2590 to +6. The initiation site mutations either abolished transcription or dramatically reduced transcript abundance relative to the wild-type promoter. In some mutants, transcription initiation was shifted to a new site, suggesting a role for the TATA-like initiator region in both start site selection and promoter strength. It is suggested that minimal rRNA gene promoters might be similar in design to minimal promoters of protein-encoding genes, many of which utilize an initiator element, or INR, as an important promoter element located directly at the transcription start site.
VSL#3 Probiotic-Mixture Induces Remission in Patients with Active Ulcerative Colitis (2005)

Treatment of patients with mild to moderate UC, not responding to conventional therapy, with VSL#3 resulted in a combined induction of remission/response rate of 77% with no adverse events. At least some of the bacterial species incorporated in the probiotic product reached the target site in amounts that could be detected.
Unsupervised intrinsic and extrinsic calibration of a camera-depth sensor couple (2014)

The availability of affordable depth sensors in conjunction with common RGB cameras (even in the same device, e.g. the Microsoft Kinect) provides robots with a complete and instantaneous representation of both the appearance and the 3D structure of the current surrounding environment. This type of information enables robots to safely navigate, perceive and actively interact with other agents inside the working environment. It is clear that, in order to obtain a reliable and accurate representation, not only the intrinsic parameters of each sensors should be precisely calibrated, but also the extrinsic parameters relating the two sensors should be precisely known. In this paper, we propose a human-friendly and reliable calibration framework, that enables to easily estimate both the intrinsic and extrinsic parameters of a camera-depth sensor couple. Real world experiments using a Kinect show improvements for both the 3D structure estimation and the association tasks.
Speech-Discrimination Scores Modeled as a Binomial Variable (1978)

Many studies have reported variability data for tests of speech discrimination, and the disparate results of these studies have not been given a simple explanation. Arguments over the relative merits of 25- vs 50-word tests have ignored the basic mathematical properties inherent in the use of percentage scores. The present study models performance on clinical tests of speech discrimination as a binomial variable. A binomial model was developed, and some of its characteristics were tested against data from 4120 scores obtained on the CID Auditory Test W-22. A table for determining significant deviations between scores was generated and compared to observed differences in half-list scores for the W-22 tests. Good agreement was found between predicted and observed values. Implications of the binomial characteristics of speech-discrimination scores are discussed.
The impact of environment and antimicrobial agents on the growth response of early-weaned pigs to spray-dried porcine plasma. (1995)

Four 28-d experiments involving 360 weanling pigs were conducted to investigate the effects of including spray-dried porcine plasma (SDPP) in diets from d 0 to 14 after weaning followed by feeding a common diet from d 14 to d 28. In Exp. 1, 80 weanling pigs (4.9 kg BW, 17 +/- 1 d of age) were used to determine the effects of substituting 0, 3, 6, 9, or 12% SDPP for dried skim milk (DSM) and L-lysine.HCl. Growth rate and feed intakes from d 0 to 14 and d 0 to 28 were not affected by increasing levels of SDPP, but feed/gain from d 0 to 14 increased linearly (P < .001) as the level of SDPP increased. In Exp. 2 and 3, 160 pigs (80 pigs in each trial; 5.4 kg BW, 18 +/- 2 d of age) were used to determine the effect of nursery environment on the performance of pigs fed a diet containing 20% DSM or 8.3% SDPP. Pigs were housed in either an off-site, environmental chamber in newly purchased pens (experimental nursery) or a more typical, on-farm, conventional nursery. Pigs in the experimental nursery performed superior to the pigs in the conventional nursery from d 0 to 14 and from d 0 to 28 (P < .001). Growth rate and feed intake were enhanced (P < .05) by feeding SDPP to pigs in the conventional nursery, but the responses to SDPP were of considerably less magnitude in pigs housed in the experimental nursery, resulting in environment x diet interactions (P < .05).(ABSTRACT TRUNCATED AT 250 WORDS)
Entero-hepatic pathobiology: histopathology and semi-quantitative bacteriology of the duodenum (2004)

Duodenum swabs were harvested from 80 broilers in 15 flocks of 8 broiler farms and were submitted to bacteriological evaluation. Five broiler breeders were sampled to obtain comparative data. Macro and microscopic lesions in the gut and the liver were evaluated in all birds submitted to swab harvesting and also broilers of two slaughter plants. Semiquantitative bacterial examination in duodenum swabs demonstrated higher microorganism growth in blood agar than in MacConkey medium. Staphylococcus sp, Enterococcus sp and Escherichia coli were found in some broiler flocks. An increased cellularity of the muscular mucosae of duodenum villi and/or the presence of some gametocytes or schizonts of coccidia were found in the lesioned gut in addition to high bacterial growth in blood agar. In some flocks, enlarged yellowish livers with vacuolated hepatocytes and/or increased reticuloendothelial response were seen in some birds. Liver and gut samples were collected in two slaughter plants in order to establish a pattern of response in broilers after withdrawal of growth promoters. Livers with macroscopic lesions presented microscopic lesions in the parenchyma such as increased leukocyte response in the sinusoidal space, vacuolar degeneration of hepatocytes or focal necrosis in the perilobular region, increased size or number of lymphoid nests in the perilobular region, the perivascular space and surrounding the biliary duct and increased extramedular granulocytopoiesis. Duodenum with hyperemic patches showed increased cellular response in the muscular mucosa of villi. These observations support the concept that semi-quantitative bacteriology and liver lesion evaluation could be used as a model to study gut bacterial imbalance in chickens.
Biomolecule-Assisted Synthesis of Water-Soluble Silver Nanoparticles and Their Biomedical Applications (2008)

The application of nanoparticles in the biomedical field is an exciting interdisciplinary research area in current materials science. In the present study, size-tunable and water-soluble noble metal silver nanoparticles (Ag NPs) have been successfully synthesized with the assistance of glutathione (GSH). The as-synthesized Ag NPs are ready to bind covalently with a model protein (bovine serum albumin) in mild conditions. The optical property of surface-modifiable Ag NPs was extremely sensitive to their size and the surface modification, suggesting a potential in the biomedical analysis and detection. Furthermore, Ag NPs with an average diameter of ca. 6 nm effectively suppress the proliferation of human leukemic K562 cells in the dose- and time-dependent manners, suggesting the promising potential of Ag NPs in cancer therapy.
The Pineal Gland and the Clinical Course of Multiple Sclerosis (1991)

Clinical, epidemiological, biochemical, immunological, and radiological studies suggest that the pineal gland may be implicated in the pathophysiology of multiple sclerosis (MS). The following communication is concerned with the association among MS, pregnancy, the postpartum period, and melatonin secretion and illustrates, based on a clinical case report, the influence of the pineal gland on the clinical course of MS. This association is noteworthy since MS may worsen during the postpartum period and melatonin secretion is reported to be altered most dramatically by pregnancy and delivery. Since melatonin secretion is cyclical, undergoing diurnal, weekly, seasonal, and annual variations, it is proposed that the pineal gland may be the "prime mover" underlying the spontaneous exacerbations and remissions in MS.
Functional Role for Cannabinoids in Respiratory Stability During Sleep (2002)

This study demonstrates potent suppression of sleep-related apnea by both exogenous and endogenous cannabinoids. These findings are of relevance to the pathogenesis and pharmacological treatment of sleep-related breathing disorders.
Dipeptide Monoester Ganciclovir Prodrugs for Treating HSV-1-Induced Corneal Epithelial and Stromal Keratitis: In Vitro and In Vivo Evaluations (2005)

Val-Val-GCV demonstrates excellent corneal permeability and chemical stability, high aqueous solubility, and substantial in vivo antiviral activity against the HSV-1.
CAUSAL RELATIONSHIPS BETWEEN ENDOCRINE-METABOLIC VARIABLES IN PATIENTS WITH ENDOMETRIAL CARCINOMA (1974)

Department of Obstetrics and Gynecology, School of Medicine, University of California at San Diego, La Jolla, California 92037
The design of 3D haptic widgets (1999)

D interaction with a computer is hard. As human interaction in the real world is quite dependent on haptics, we believe that adding haptics will alleviate many of the problems of 3D interaction with a computer. The naive approach to incorporating haptics would be to simply find existing objects and imitate them. This, however, would not seem to adequately leverage what is possible with a rea- sonably general force feedback device, as it does not take advantage of the ability to provide forces that are not physically based, or to simulate objects and behavior that could have been physically real- ized but weren't, or which would have been prohibitively difficult to physically realize. From our extensive experience with design- ing haptic computer user interfaces and using haptic interfaces in the real world we have abstracted from those interactions certain qualities which we present in this paper. In addition, this paper demonstrates how to use these qualities in the analysis and design of a suite of 3D haptic widgets, most of which are novel and many of which include non-physically based forces.
Optimization of distributed space-time filtering (2006)

Distributed space-time filtering (DSTF) has been re- cently proposed in (1) to increase the diversity in cooperative wire- less networks. In DSTF each node in the network is assigned a signature filter vector (SFV) and nodes cooperate without know- ing their partners. In this paper, we derive an approximation for the pairwise error probability of DSTF and use the result- ing expression for the optimization of SFVs. Two methods are provided for efficient filter calculation. Furthermore, unlike the original DSTF scheme in (1), we do not require the number of ac- tive nodes to be equal to the length of the SFVs, which is shown to result in additional performance gains. Simulation results show that the novel SFV designs outperform the previously proposed design even if non-ideal effects such as suboptimum equalization, imperfect channel estimation, and imperfect timing synchroniza- tion are taken into account.
Q Methodology, Textuality, and Tectonics (1997)

Along
 with the paper from Rex Stainton Rogers, and that from Simon Watts and 
Paul Stenner, this paper seeks to explain and illustrate to and why the Q
 work we are doing here (mainly in the UK, but also with some colleagues
 elsewhere) differs from the work with a much longer history which has 
been undertaken by Q scholars in the USA and their students and proteges
 (again, this includes work outside the primary geographical locus). 
While our work has much in common with the latter, there are significant
 differences both in our approach to carrying out Q studies and in our 
objectives. Our interest in Q arose from a theoretical location within a
 climate of perturbation framework, drawing from French Theory. Q 
met our need for an idiographic methodology, and offered us a highly 
effective means to conduct discourse analytic work. We use Q to address 
issues of power and knowledge, and their interplay, using analytics of 
textuality and tectonics. These terms are defined and an illustration is
 provided to show how Q can be used in this way.
Do self‐perpetuating B lymphocytes drive human autoimmune disease? (1999)

Normal immunological memory is thought to be underpinned by T lymphocytes. However, in rheumatoid arthritis there are indications that T-lymphocyte control has been subverted by self-perpetuating B lymphocytes. Potential mechanisms in other autoimmune states are less clear, but a number of observations suggest that misappropriation of immunological memory by B lymphocytes may be a common feature of human autoantibody-associated disease. Put simply, autoantibodies drive their own production. If so, the availability of safe B-lymphocyte-depleting agents provides a potential means for reversal of autoimmunity.
Akt Promotes Survival of Cardiomyocytes In Vitro and Protects Against Ischemia-Reperfusion Injury in Mouse Heart (2000)

These data are the first documentation that Akt functions to promote cellular survival in vivo, and they indicate that the activation of this pathway may be useful in promoting myocyte survival in the diseased heart.
Biology and Therapeutic Advances for Pediatric Osteosarcoma (2004)

Osteosarcoma is the most common malignant bone tumor in children and adolescents. Survival for these patients was poor with the use of surgery and/or radiotherapy. The introduction of multi-agent chemotherapy dramatically improved the outcome for these patients and the majority of modern series report 3-year disease-free survival of 60%-70%. This paper describes current strategies for treating patients with osteosarcoma as well as review of the clinical features, radiologic and diagnostic work-up, and pathology. The authors review the state of the art management for patients with osteosarcoma in North America and Europe including the use of limb-salvage procedures and reconstruction as well as discuss the etiologic and biologic factors associated with tumor development. Therapy-related sequelae and future directions in the biology and therapy for these patients are also discussed.