gebhart/patrepeval huggingface dataset:
Instruction Balance, Energy Consumption and Program Performance (2001)

A computer processor consists of multiple functional units that carry out dierent sets of instructions. At each time of execution, a program may have a varied number of instructions for each functional unit. Recent studies have exploited this dierence to save energy. The idea is to slow functional units that have a lower load. As a result, the number of idle CPU cycles is reduced and so is the waste of power. Symmetrical to recon guring hardware is reorganizing software. For each program segment, we can alter its demands for dierent functional units by exchanging its instructions with those from other parts of the program. In other words, we can change the balance of instructions in dierent parts of a program. This paper explores the theoretical lower bound of the energy consumption assuming that both a program and a machine are fully adjustable. It shows that a program with a consistent instruction balance always consumes less power than the same program with an uneven balance. In...
Low-Carbohydrate Diets and Prostate Cancer: How Low Is “Low Enough”? (2010)

Previous studies indicate that carbohydrate intake influences prostate cancer biology, as mice fed a no-carbohydrate ketogenic diet (NCKD) had significantly smaller xenograft tumors and longer survival than mice fed a Western diet. As it is nearly impossible for humans to consume and maintain NCKD, we determined whether diets containing 10% or 20% carbohydrate kcal showed similar tumor growth as NCKD. A total of 150 male severe combined immunodeficient mice were fed a Western diet ad libitum, injected with the human prostate cancer cell line LAPC-4, and then randomized 2 weeks later to one of three arms: NCKD, 10% carbohydrate, or 20% carbohydrate diets. Ten mice not injected were fed an ad libitum low-fat diet (12% fat kcal) serving as the reference in a modified-paired feeding protocol. Mice were sacrificed when tumors reached 1,000 mm(3). Despite consuming extra calories, all mice receiving low-carbohydrate diets were significantly lighter than those receiving a low-fat diet (P < 0.04). Among the low-carbohydrate arms, NCKD-fed mice were significantly lighter than the 10% or 20% carbohydrate groups (P < 0.05). Tumors were significantly larger in the 10% carbohydrate group on days 52 and 59 (P < 0.05), but at no other point during the study. Diet did not affect survival (P = 0.34). There were no differences in serum insulin-like growth factor-I or insulin-like growth factor binding protein-3 at sacrifice among the low-carbohydrate arms (P = 0.07 and P = 0.55, respectively). Insulin was significantly lower in the 20% carbohydrate arm (P = 0.03). LAPC-4 xenograft mice fed a low-carbohydrate diet (10-20% carbohydrate kcal) had similar survival as mice consuming NCKD (0% carbohydrate kcal).
Netprobe (2007)

Given a large online network of online auction users and their histories of transactions, how can we spot anomalies and auction fraud? This paper describes the design and implementation of NetProbe, a system that we propose for solving this problem. NetProbe models auction users and transactions as a Markov Random Field tuned to detect the suspicious patterns that fraudsters create, and employs a Belief Propagation mechanism to detect likely fraudsters. Our experiments show that NetProbe is both efficient and effective for fraud detection. We report experiments on synthetic graphs with as many as 7,000 nodes and 30,000 edges, where NetProbe was able to spot fraudulent nodes with over 90% precision and recall, within a matter of seconds. We also report experiments on a real dataset crawled from eBay, with nearly 700,000 transactions between more than 66,000users, where NetProbe was highly effective at unearthing hidden networks of fraudsters, within a realistic response time of about 6 minutes. For scenarios where the underlying data is dynamic in nature, we propose IncrementalNetProbe, which is an approximate, but fast, variant of NetProbe. Our experiments prove that Incremental NetProbe executes nearly doubly fast as compared to NetProbe, while retaining over 99% of its accuracy.
High Throughput Screening Technologies for Direct Cyclic AMP Measurement (2003)

A study comparing five different cAMP detection technologies in terms of sensitivity, robustness, and feasibility for HTS is presented. In this report, the following methods are described: a nonhomogeneous DELFIA, and the homogeneous methods based on time-resolved fluorescence (HTRF), luminescent singlet oxygen channeling or ALPHAScreen, FP, and high-affinity enzyme complementation. DELFIA had the highest sensitivity, whereas ALPHAScreen and HTRF shared several advantages, including high sensitivity, broad dynamic range, and minimal reagent addition steps. For G(s)-coupled antagonist screens, we found HTRF and ALPHAScreen the more sensitive and HTS-compatible techniques.
Tracking Non-Stationary Appearances and Dynamic Feature Selection (2005)

Since the appearance changes of the target jeopardize visual measurements and often lead to tracking failure in practice, trackers need to be adaptive to non-stationary appearances or to dynamically select features to track. However, this idea is threatened by the risk of adaptation drift that roots in its ill-posed nature, unless good constraints are imposed. Different from most existing adaptation schemes, we enforce three novel constraints for the optimal adaptation: (1) negative data, (2) bottom-up pair-wise data constraints, and (3) adaptation dynamics. Substantializing the general adaptation problem as a subspace adaptation problem, this paper gives a closed-form solution as well as a practical iterative algorithm. Extensive experiments have shown that the proposed approach can largely alleviate adaptation drift and achieve better tracking results.
Axonal growth of embryonic stem cell-derived motoneurons in vitro and in motoneuron-injured adult rats (2004)

We generated spinal motoneurons from embryonic stem (ES) cells to determine the developmental potential of these cells in vitro and their capacity to replace motoneurons in the adult mammalian spinal cord. ES cell-derived motoneurons extended long axons, formed neuromuscular junctions, and induced muscle contraction when cocultured with myoblasts. We transplanted motoneuron-committed ES cells into the spinal cords of adult rats with motoneuron injury and found that approximately 3,000 ES cell-derived motoneurons (25% of input) survived for >1 month in the spinal cord of each animal. ES cell-derived axonal growth was inhibited by myelin, and this inhibition was overcome by administration of dibutyryl cAMP (dbcAMP) or a Rho kinase inhibitor in vitro and in vivo. In transplanted rats infused with dbcAMP, approximately 80 ES cell-derived motor axons were observed within the ventral roots of each animal, whereas none were observed in transplanted rats not treated with dbcAMP. Because these cells replicate many of the developmental and mature features of true motoneurons, they are an important biological tool to understand formation of motor units in vitro and a potential therapeutic tool to reconstitute neural circuits in vivo.
Affinity-Tuned ErbB2 or EGFR Chimeric Antigen Receptor T Cells Exhibit an Increased Therapeutic Index against Tumors in Mice (2015)

Target-mediated toxicity is a major limitation in the development of chimeric antigen T-cell receptors (CAR) for adoptive cell therapy of solid tumors. In this study, we developed a strategy to adjust the affinities of the scFv component of CAR to discriminate tumors overexpressing the target from normal tissues that express it at physiologic levels. A CAR-expressing T-cell panel was generated with target antigen affinities varying over three orders of magnitude. High-affinity cells recognized target expressed at any level, including at levels in normal cells that were undetectable by flow cytometry. Affinity-tuned cells exhibited robust antitumor efficacy similar to high-affinity cells, but spared normal cells expressing physiologic target levels. The use of affinity-tuned scFvs offers a strategy to empower wider use of CAR T cells against validated targets widely overexpressed on solid tumors, including those considered undruggable by this approach.
PHOSPHOLIPID METABOLISM IN INTACT AND MODIFIED ERYTHROCYTE MEMBRANES (1971)

Erythrocyte membranes incorporated labeled phosphate from gamma-adenosine triphosphate (AT(32)P) into phosphatidic acid and the polyphosphoinositides. Inositol-(3)H and palmitate-(14)C were also incorporated into the phospholipids but alpha-glycerophosphate-(32)P was not. The incorporation of gamma-AT(32)P into phospholipids was increased when the erythrocyte ghosts were incubated in hypotonic media which lysed the cells. Lysis had little or no effect on the incorporation of inositol-(3)H and palmitate-(14)C into the phospholipids. If erythrocyte membranes were prepared in 1 mM ethylenediaminetetraacetate (EDTA), instead of 1 mM MgCl(2), then the tonicity of the incubating medium did not influence the incorporation of gamma-AT(32)P into the phospholipids. Erythrocyte ghosts, prepared by lysis in water, EDTA, or 1 mM calcium, lead, mercury, zinc, or cadmium, failed to reconstitute when placed in isotonic medium, inasmuch as they did not retain potassium against a chemical gradient. Ghosts prepared by lysis in 1 mM magnesium, barium, or strontium could be reconstituted. Ghosts which failed to reconstitute incorporated more labeled phosphate from gamma-AT(32)P into the phospholipids than did intact or reconstituted ghosts. The larger incorporation of labeled phosphate by leaky ghosts was not due to a greater entrance of gamma-AT(32)P into those cells. Primaquine phosphate and digitonin, at concentrations which are known to cause cells to form smaller vesicles or to lyse cells by removing cholesterol, did not increase the incorporation of labeled phosphate into the phospholipids. It is suggested that the increased metabolism of phospholipids may be involved in a membrane repair mechanism.
ETS transcription factor ETV2 directly converts human fibroblasts into functional endothelial cells (2014)

Transplantation of endothelial cells (ECs) is a promising therapeutic approach for ischemic disorders. In addition, the generation of ECs has become increasingly important for providing vascular plexus to regenerated organs, such as the liver. Although many attempts have been made to generate ECs from pluripotent stem cells and nonvascular cells, the minimum number of transcription factors that specialize in directly inducing vascular ECs remains undefined. Here, by screening 18 transcription factors that are important for both endothelial and hematopoietic development, we demonstrate that ets variant 2 (ETV2) alone directly converts primary human adult skin fibroblasts into functional vascular endothelial cells (ETVECs). In coordination with endogenous FOXC2 in fibroblasts, transduced ETV2 elicits expression of multiple key endothelial development factors, including FLI1, ERG, and TAL1, and induces expression of endothelial functional molecules, including EGFL7 and von Willebrand factor. Consequently, ETVECs exhibits EC characteristics in vitro and forms mature functional vasculature in Matrigel plugs transplanted in NOD SCID mice. Furthermore, ETVECs significantly improve blood flow recovery in a hind limb ischemic model using BALB/c-nu mice. Our study indicates that the creation of ETVECs provides further understanding of human EC development induced by ETV2.
Use of Self-Sustained Sequence Replication Amplification Reaction to Analyze and Detect Mutations in Zidovudine-Resistant Human Immunodeficiency Virus (1991)

Mutations at amino acid positions 67, 70, 215, and 219 in the human immunodeficiency virus type 1 (HIV-1) pol gene correlate with the emergence of resistance to zidovudine (AZT). These four positions were monitored in viral RNA extracted from infected peripheral blood mononuclear cells (PBMC) and viral stocks obtained after coculture with uninfected lymphocytes. Genotype determinations were made using the self-sustained sequence replication (3SR) and differential bead-based sandwich hybridization (BBSH) assay. The hybridization results obtained by 3SR and BBSH analyses were verified by dideoxynucleotide sequencing of the 3SR products. Correlation of 3SR and BBSH with polymerase chain reaction and Southern hybridization analyses of the PBMC and corresponding viral isolates indicated that PBMC and corresponding HIV-1 isolates may differ in their genotypes at the monitored amino acid positions, variations from the wild-type nucleotide sequence may occur proximal to the codons being monitored, and viral isolates possessing the same genotypes at the four monitored amino acid positions showed a threefold variation in their ID50 measurements.
Experiments in domain adaptation for statistical machine translation (2007)

The special challenge of the WMT 2007 shared task was domain adaptation. We took this opportunity to experiment with various ways of adapting a statistical machine translation systems to a special domain (here: news commentary), when most of the training data is from a different domain (here: European Parliament speeches). This paper also gives a description of the submission of the University of Edinburgh to the shared task.
Genetics of Psychiatric Disease (2000)

Genetic epidemiologic studies reveal that relatives of bipolar (BIP) probands are at increased risk for recurrent unipolar (RUP), BIP, and schizoaffective (SA) disorders, while relatives of schizophrenia (SZ) probands are at increased risk for SZ, SA, and RUP disorders. The overlap in familial risk may reflect shared genetic susceptibility. Recent genetic linkage studies have defined confirmed susceptibility loci for BIP disorder for multiple regions of the human genome, including 4p16, 12q24, 18p11.2, 18q22, 21q21, 22q11-13, and Xq26. Studies of SZ kindreds have yielded robust evidence for susceptibility at 18p11.2 and 22q11-13, both of which are implicated in susceptibility to BIP disorder. Similarly, confirmed SZ vulnerability loci have been mapped for 6p24, 8p and 13q32. Strong statistical evidence for a 13q32 BIP susceptibility locus has been reported. Thus, both family and molecular studies of these disorders suggest shared genetic susceptibility. These two group of disorders may not be so distinct as current nosology suggests.
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake (2007)

Our new fast and accurate method for detecting transcription terminators has allowed us to identify and analyze terminators in many new genomes and to identify DNA uptake signal sequences in several species where they have not been previously reported. Our software and predictions are freely available.
Liarozole and 13-cis-retinoic acid anti-prostatic tumor activity. (1993)

Liarozole fumarate (R85,246), a novel benzimidazole derivative, reduced s.c. and bone metastasis tumor growth by the androgen-independent PC-3ML-B2 human prostatic carcinoma clone in SCID mice. The drug inhibited cell invasion of Matrigel in Boyden chamber chemotactic assays and the secretion of type IV collagenase. In vitro, liarozole failed to inhibit cell proliferation and cell attachment to various substrates (Matrigel, laminin, type IV collagen, and fibronectin). In vivo, the drug also blocked type IV collagenase production in established s.c. tumors. Liarozole has been postulated by others (R. De Coster, W. Wouters, R. Van Ginckel, D. End, et al. J. Steroid Biochem. Mol. Biol., 43: 197-201, 1992) to inhibit retinoic acid catabolism. Our data indicate that liarozole treatment can increase the tumor retinoic acid levels in vivo. Studies of retinoic acid revealed that the drug independently reduced tumor growth in vivo and inhibited cell invasion of Matrigel and the secretion of collagenase IV. Surprisingly, liarozole and retinoic acid failed to exhibit measurable synergistic activity both in vitro and in vivo. Taken together these data suggest that liarozole might inhibit retinoic acid catabolism in vivo and consequently have significant therapeutic value as an anti-prostatic tumor agent.
The Analgesic Effect of a Metered-Dose 8% Lidocaine Pump Spray In Posttraumatic Peripheral Neuropathy: A Pilot Study (2009)

The present study suggests that XPS provides a significant improvement in PTPN due to its prompt analgesia, lack of systemic side effects and convenience.
Lymphocytes' cytotoxicity towards cells of human lymphoblastoid lines in patients with rheumatoid arthritis and systemic lupus erythematosus. (1977)

A research study and discussion of antiinterferon immunoglobulin in the treatment of rheumatoid arthritis and systemic lupus erythematosus, and its possible value in the treatment of allergic diseases, autoimmune diseases and other diseases where it is presumed there may be an autoimmune genesis.
Crystallographic Evidence for Substrate-assisted Catalysis in a Bacterial β-Hexosaminidase (2001)

beta-Hexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of beta-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. Heritable deficiency of this enzyme results in various forms of GalNAc-beta(1,4)-[N-acetylneuraminic acid (2,3)]-Gal-beta(1,4)-Glc-ceramide gangliosidosis, including Tay-Sachs disease. We have determined the x-ray crystal structure of a beta-hexosaminidase from Streptomyces plicatus to 2.2 A resolution (Protein Data Bank code ). beta-Hexosaminidases are believed to use a substrate-assisted catalytic mechanism that generates a cyclic oxazolinium ion intermediate. We have solved and refined a complex between the cyclic intermediate analogue N-acetylglucosamine-thiazoline and beta-hexosaminidase from S. plicatus to 2.1 A resolution (Protein Data Bank code ). Difference Fourier analysis revealed the pyranose ring of N-acetylglucosamine-thiazoline bound in the enzyme active site with a conformation close to that of a (4)C(1) chair. A tryptophan-lined hydrophobic pocket envelopes the thiazoline ring, protecting it from solvolysis at the iminium ion carbon. Within this pocket, Tyr(393) and Asp(313) appear important for positioning the 2-acetamido group of the substrate for nucleophilic attack at the anomeric center and for dispersing the positive charge distributed into the oxazolinium ring upon cyclization. This complex provides decisive structural evidence for substrate-assisted catalysis and the formation of a covalent, cyclic intermediate in family 20 beta-hexosaminidases.
Effect of Hatching Cabinet Sanitation Treatments on Salmonella Cross-Contamination and Hatchability of Broiler Eggs (1996)

Four trials were conducted to evaluate the efficacy of hatcher air sanitation utilizing ultraviolet light (UV), ozone, or hydrogen peroxide on bacterial populations, the spread of Salmonella, and hatchability of broiler eggs. The UV light (254 nm, 146 mu W/s) and ozone (0.2 or 0.4 ppm) treatments were continuously applied through the last 3 d of hatch, the hydrogen peroxide treatment (2.5%) was administered 1 or 2 min of each 10 min at rates of 500 or 100 mL/h. Hatchability was not significantly reduced by sanitizing treatments when compared with the untreated control (94 vs 95.6%). As compared to controls, all sanitizing treatments reduced 75 to 99% of the total bacteria, Enterobacteriaceae, and Salmonella in the hatching cabinet air samples. The use of hydrogen peroxide resulted in greater reduction of bacteria than ozone or UV light. Only hydrogen peroxide significantly reduced Salmonella levels on eggshell fragments. Significant reductions in the number of Salmonella-positive chicks occurred using the ozone and hydrogen peroxide treatments. Hydrogen peroxide significantly reduced the magnitude of Salmonella colonization in chicken ceca. These trials demonstrated that the spread of bacteria can be effectively reduced in the hatching cabinet by air sanitization using UV light, ozone, and hydrogen peroxide. The potential to reduce bacterial cross contamination in the hatcher is achievable without depressing hatchability.
Differentiation of Human Liver-Derived, Insulin-Producing Cells Toward the β-Cell Phenotype (2005)

beta-Cell transplantation is viewed as a cure for type 1 diabetes; however, it is limited by the number of pancreas donors. Human stem cells offer the promise of an abundant source of insulin-producing cells, given the existence of methods for manipulating their differentiation. We have previously demonstrated that the expression of the beta-cell transcription factor pancreatic duodenal homeobox 1 (PDX-1) in human fetal liver cells activates multiple aspects of the beta-cell phenotype. These cells, termed FH-B-TPN cells, produce insulin, release insulin in response to physiological glucose levels, and replace beta-cell function in diabetic immunodeficient mice. However, they deviate from the normal beta-cell phenotype by the lack of expression of a number of beta-cell genes, the expression of non-beta-cell genes, and a lower insulin content. Here we aimed to promote differentiation of FH-B-TPN cells toward the beta-cell phenotype using soluble factors. Cells cultured with activin A in serum-free medium upregulated expression of NeuroD and Nkx2.2 and downregulated paired box homeotic gene 6 (PAX-6). Glucokinase and prohormone convertase 1/3 were also upregulated, whereas pancreatic polypeptide and glucagon as well as liver markers were downregulated. Insulin content was increased by up to 33-fold, to approximately 60% of the insulin content of normal beta-cells. The cells were shown to contain human C-peptide and release insulin in response to physiological glucose levels. Cell transplantation into immunodeficient diabetic mice resulted in the restoration of stable euglycemia. The cells continued to express insulin in vivo, and no cell replication was detected. Thus, the manipulation of culture conditions induced a significant and stable differentiation of FH-B-TPN cells toward the beta-cell phenotype, making them excellent candidates for beta-cell replacement in type 1 diabetes.
Establishing project management guidelines for successfully managing resettlement projects (2013)

Although millions of people globally are displaced annually, resettlement has a poor history for achieving the objective of leaving people who are resettled 'no worse off after project implementation than before'. While excellent guidelines and policies for resettlement have been established, resettlement/displacement projects still do not succeed in resettling affected peoples in a way that they are eventually better off. Consensus was reached by a Delphi panel of experts on a set of guidelines for resettlement projects. It is proposed that, supplementing the existing frameworks and guidelines for resettlement with well-established project management principles - including a phased project management approach - the chances of executing a resettlement project successfully are much higher. This paper proposes an improved framework and valuable guidelines for future resettlement projects