gebhart/patrepeval huggingface dataset:
Integrating Containers into Workflows (2015)

Workflows are a widely used abstraction for representing large scientific applications and executing them on distributed systems such as clusters, clouds, and grids. However, workflow systems have been largely silent on the question of precisely what environment each task in the workflow is expected to run in. As a result, a workflow may run correctly in the environment in which it was designed, but when moved to another machine, is highly likely to fail due to differences in the operating system, installed applications, available data, and so forth. Lightweight container technology has recently arisen as a potential solution to this problem, by providing a well-defined execution environments at the operating system level. In this paper, we consider how to best integrate container technology into an existing workflow system, using Makeflow, Work Queue, and Docker as examples of current technology. A brief performance study of Docker shows very little overhead in CPU and I/O performance, but significant costs in creating and deleting containers. Taking this into account, we describe four different methods of connecting containers to different points of the infrastructure, and explain several methods of managing the container images that must be distributed to executing tasks. We explore the performance of a large bioinformatics workload on a Docker-enabled cluster, and observe the best configuration to be locally-managed containers that are shared between multiple tasks.
Highly potent, orally active diester macrocyclic human renin inhibitors (1992)

Replacing one amide bond in macrocyclic renin inhibitors of the general structure 1 and 2 with an ester linkage gave glutamate-derived inhibitors 3 and serine-derived inhibitors 4. While this oxygen-for-nitrogen exchange had little effect on potency in the glutamate series, potency was dramatically increased in the serine series. In this series, the 14-membered ring compounds proved to be more potent than the corresponding 13-membered ring derivatives. Substitution of the ring at the position corresponding to P2' generally increased potency. The absolute configuration at this center was shown to be R for the 4-morpholinomethyl derivative (4o), both by asymmetric synthesis and X-ray crystallography. Replacing the "Boc-Phe" moiety of inhibitor 4o with a variety of substituents led to subnanomolar inhibitors, one of which (the "3(S)-quinuclidinyl-Phe" derivative 33) lowered blood pressure 20 mmHg and completely inhibited plasma renin activity for 6 h in sodium-depleted rhesus monkeys. This compound proved to have limited bioavailability (1% in rats) due to cleavage of the serine ester bond and rapid hepatic extraction.
The epidemiology of breast cancer (1991)

Table 5 presents risk factors for breast cancer generally regarded as established, together with their approximate relative risks. With the exception of age, country of birth, and a history of breast cancer in both a mother and a sister, all of the relative risks reported to date are of a relatively modest magnitude. Thus, new risk factors need to be identified and knowledge of existing risk factors refined. Factors for which the evidence of an etiologic role has mounted over the past several years, but which are not yet considered to be established, include the protective effects of parity and lactation in certain age groups and the increased risks associated with alcohol consumption and with DES exposure during pregnancy. In addition, physical activity has emerged as a factor worthy of further study. Some evidence suggests that use of oral contraceptives for several years at an early age modestly increases the risk for breast cancer diagnosed before age 35 and perhaps age 45. Use of estrogen-replacement therapy for 20 years or more has been found by a few studies to increase the risk for breast cancer in the postmenopausal years; further studies of very long-term users are needed. Also, other risks and benefits of these hormones need to be taken into account when women decide whether to use them. Surprisingly elusive has been the etiologic role of endogenous hormones, especially in view of the large number of studies that have been concerned with them. A better understanding of the role of endogenous hormones should help explain the mechanisms of action of known and suspected risk factors. Areas of high priority for further research thus include establishing with more certainty whether the risk for breast cancer is increased in any subgroups of women who use oral contraceptives and estrogen-replacement therapy and determining the etiologic roles of specific endogenous hormones. The possible risks associated with alcohol consumption and lack of physical activity need to be studied more thoroughly, and ideas about new potential risk factors are needed. Although epidemiologic studies will continue to be concerned with diet, enthusiasm for its etiologic role in women has been considerably dampened by the lack of association in many of the studies reported to date. The studies in women exposed to radiation, DES, and oral contraceptives suggest that the timing of some exposures may be critical, since the effects of these agents may mostly be limited to specific time periods of rapid breast development.(ABSTRACT TRUNCATED AT 400 WORDS)
Learning to Track and Identify Players from Broadcast Sports Videos (2013)

Tracking and identifying players in sports videos filmed with a single pan-tilt-zoom camera has many applications, but it is also a challenging problem. This paper introduces a system that tackles this difficult task. The system possesses the ability to detect and track multiple players, estimates the homography between video frames and the court, and identifies the players. The identification system combines three weak visual cues, and exploits both temporal and mutual exclusion constraints in a Conditional Random Field (CRF). In addition, we propose a novel Linear Programming (LP) Relaxation algorithm for predicting the best player identification in a video clip. In order to reduce the number of labeled training data required to learn the identification system, we make use of weakly supervised learning with the assistance of play-by-play texts. Experiments show promising results in tracking, homography estimation, and identification. Moreover, weakly supervised learning with play-by-play texts greatly reduces the number of labeled training examples required. The identification system can achieve similar accuracies by using merely 200 labels in weakly supervised learning, while a strongly supervised approach needs a least 20,000 labels.
Molecular and Cytogenetic Analyses of Stably and Unstably Expressed Transgene Loci in Tobacco (1997)

Victor A. Iglesias, Eduardo A. Moscone, , Franz Neuhuber, Susan Michalowski, Thomas Phelan, Steven Spiker, Marjori Matzke, Antonius J. M. Matzke, Molecular and Cytogenetic Analyses of Stably and Unstably Expressed Transgene Loci in Tobacco, The Plant Cell, Vol. 9, No. 8 (Aug., 1997), pp. 1251-1264
Both DNA strands of antibody genes are hypermutation targets (1998)

During the maturation of the immune response, antibody genes are subjected to localized hypermutation. Mutations are not evenly distributed along the V gene; intrinsic hot spots exist that are correlated with primary sequence motifs. Although the mechanism of hypermutation remains unknown, it has been proposed to exhibit DNA strand polarity because purine residues on the coding strand are more frequently targeted for mutation than pyrimidines. However, this polarity may not be an intrinsic property of the hypermutation mechanism but a consequence of evolutionary-selected peculiarities of V gene sequences. Furthermore, the possibility that both strands are hypermutation targets has received little attention. To discriminate between these possibilities, we have analyzed the average frequency of mutations of each of the three bases of all nucleotide triplets by using large databases taken from both V and non-V mutation targets. We also have reassessed the sequence motifs associated with hot spots. We find that even in non-Ig sequences, A mutates more than T, consistent with a strand-dependent component to targeting. However, the mutation biases of triplets and of their inverted complements are correlated, demonstrating that there is a sequence-specific but strand-independent component to mutational targeting. Thus, there are two aspects of the hypermutation process that are sensitive to local DNA sequences, one that is DNA strand-dependent and the other that is not.
The magnetic immuno-polymerase chain reaction assay for the detection of Campylobacter in milk and poultry (1996)

A rapid and sensitive technique, based on the magnetic immuno-polymerase chain reaction assay (MIPA), was developed for the detection of Campylobacter jejuni in milk and chicken products. Target bacteria are captured from the food sample by magnetic particles coated with a specific antibody and the bound bacteria then lysed and subjected to PCR. The MIPA could detect 420 cfu g-1 of chicken after 18 h, 42 cfu g-1 after 24 h, and 4.2 cfu g-1 after 36 h enrichment. For artificially contaminated milk 63 cfu ml-1 could be detected after 18 and 24 h and 6.3 cfu ml-1 after 36 h enrichment.
NGF gene expression and secretion in white adipose tissue: regulation in 3T3-L1 adipocytes by hormones and inflammatory cytokines (2004)

The sympathetic nervous system plays a central role in lipolysis and the production of leptin in white adipose tissue (WAT). In this study, we have examined whether nerve growth factor (NGF), a target-derived neurotropin that is a key signal in the development and survival of sympathetic neurons, is expressed and secreted by white adipocytes. NGF mRNA was detected by RT-PCR in the major WAT depots of mice (epididymal, perirenal, omental, mesenteric, subcutaneous) and in human fat (subcutaneous, omental). In mouse WAT, NGF expression was observed in mature adipocytes and in stromal vascular cells. NGF expression was also evident in 3T3-L1 cells before and after differentiation into adipocytes. NGF protein, measured by ELISA, was secreted from 3T3-L1 cells, release being higher before differentiation. Addition of the sympathetic agonists norepinephrine, isoprenaline, or BRL-37344 (beta(3)-agonist) led to falls in NGF gene expression and secretion by 3T3-L1 adipocytes, as did IL-6 and the PPARgamma agonist rosiglitazone. A substantial decrease in NGF expression and secretion occurred with dexamethasone. In contrast, LPS increased NGF mRNA levels and NGF secretion. A major increase in NGF mRNA level (9-fold) and NGF secretion (<or=40-fold) in 3T3-L1 adipocytes occurred with TNF-alpha. RT-PCR showed that the genes encoding the p75 and trkA NGF receptors were expressed in mouse WAT. These results demonstrate that white adipocytes secrete NGF (an adipokine), NGF synthesis being influenced by several factors with TNF-alpha having a major stimulatory effect. We suggest that NGF is a target-derived neurotropin and an inflammatory response protein in white adipocytes.
Phosphorylation of Vif and Its Role in HIV-1 Replication (1996)

Vif is a 23-kDa protein encoded by human immunodeficiency virus, type 1 (HIV-1) which is important for virion infectivity. Here, we describe the phosphorylation of HIV-1 Vif and its role in HIV-1 replication. In vivo studies demonstrated that Vif is highly phosphorylated on serine and threonine residues. To identify phosphorylation sites and characterize the Vif kinase(s), Vif was expressed in Escherichia coli and purified for use as a substrate in in vitro kinase assays. The purified Vif protein was phosphorylated in vitro on serine and threonine residues by a kinase(s) present in both cytosol and membrane fractions. Phosphorylation of Vif was stimulated by phorbol 12-myristate 13-acetate and inhibited by staurosporine and hypericin, a drug with potent anti-HIV activity. The Vif kinase(s) was resistant to inhibitors of protein kinase C, cAMP-dependent kinase, and cGMP-dependent kinase, suggesting that it is distinct from these enzymes. To identify the phosphorylation sites, 32P-labeled Vif was digested by V8 protease and the peptides were resolved by reverse-phase high performance liquid chromatography. Radioactive peptide sequencing identified three phosphorylation sites within the C terminus, Ser144, Thr155, and Thr188. Two-dimensional tryptic phosphopeptide mapping indicated that these sites are also phosphorylated in vivo. Both Ser144 and Thr188 are contained in the recognition motifs (R/KXXS*/T* and R/KXXXS*/T*) used by serine/threonine protein kinases such as cGMP-dependent kinase and PKC. Ser144 is present in the motif SLQXLA, which is the most highly conserved sequence among all lentivirus Vif proteins. Mutation of Ser144 to alanine resulted in loss of Vif activity and >90% inhibition of HIV-1 replication. These studies suggest that phosphorylation of Vif by a serine/threonine protein kinase(s) plays an important role in regulating HIV-1 replication and infectivity.
Multimedia management and query processing issues in distributed digital libraries: a HERMES perspective (2002)

Multimedia applications accessing large amounts of data require efficient browsing and searching mechanisms to extract relevant information. The system has to preselect items of interest from the database. Additionally, it has to support continuous presentation of time-dependent media. Browsing system components for multimedia data management are proposed that are developed within the HERMES project. They offer conceptual, content based access to videos. Our retrieval engine calculates relevance values for the results of a conceptual query by feature aggregation on video shot granularity. An intelligent client buffer strategy uses the relevance values from retrieval as presentation support. It prefers to keep those shots in the cache which have a high relevance value.
Antisense and/or Immunostimulatory Oligonucleotide Therapeutics (2001)

Antisense technology, which is based on a simple and rational principle of Watson-Crick complementary base pairing of a short oligonucleotide with the targeted mRNA to downregulate the disease-causing gene product, has progressed tremendously in the last two decades. Antisense oligonucleotides targeted to a number of cancer-causing genes are being evaluated in human clinical trials. While the first-generation phosphorothioate antisense oligonucleotides are in clinical trials, a number of factors, including sequence motifs that could lead to unwanted mechanisms of action and side effects, have been identified. The severity of the side effects of first-generation antisense oligonucleotides is mostly dependent on the presence of certain sequence motifs, such as CpG dinucleotides. A number of second-generation chemical modifications have been proposed to overcome the limitations of the first-generation antisense oligonucleotides. The safety and efficacy of several second-generation mixed-backbone antisense oligonucleotides are being evaluated in clinical trials. The immune stimulation affects observed with CpG-containing antisense oligonucleotides are being exploited as a novel therapeutic modality, with several CpG oligonucleotides being evaluated in clinical trials. A number of medicinal chemistry studies performed to date suggest that the immunomodulatory activity of CpG oligonucleotides can be fine-tuned by site-specific incorporation of chemical modifications in order to design disease-specific oligonucleotide therapeutics.
Tumor characterization with dynamic contrast–enhanced MRI using mr contrast agents of various molecular weights (1998)

Dynamic contrast-enhanced MR imaging was used to measure the kinetics of enhancement in three different animal tumor models (Walker 256, R3230 AC, MCF7) using three different Gd complexes (Gd-DTPA, Gd-DTPA-24-cascade-polymer 30 kD, and polylysine-Gd-DTPA 50 kD). The three tumor models varied in growth rate, with the most rapid growth demonstrated by Walker 256 cells and the slowest growth occurring in the MCF7 cells. For each tumor, the kinetics of enhancement using polylysine-Gd-DTPA was analyzed using a pharmacokinetic model to estimate the vascular volume of the tumor. The rate of entry of the contrast agent into the interstitial space served as the measure of vascular permeability. The smallest molecular-weight agent, Gd-DTPA, could not provide information about vascular permeability. The intermediate and the largest agents both demonstrated that the faster-growing Walker 256 tumor had greater vascular permeability than did the slower-growing R3230 AC tumor. The degree of vascular permeability in the MCF7 tumor could not be assessed fairly due to insufficient statistics. The current study provides evidence supporting the hypothesis that more rapidly growing tumors have higher vascular permeability than do tumors that grow more slowly.
First epidemiological data for venotonics in pregnancy from the EFEMERIS database (2015)

We found no increased risk of adverse pregnancy outcome among women exposed to veinotonics compared with unexposed pregnant women.
Assessment and optimisation of normalisation methods for dual-colour antibody microarrays (2010)

The simulation study and the data application demonstrate the superior performance of the improved invariant selection algorithms in comparison to other normalisation methods, especially in situations where the assumptions of the usual global loess normalisation are violated.
Death-associated protein 3 (Dap-3) is overexpressed in invasive glioblastoma cells in vivo and in glioma cell lines with induced motility phenotype in vitro. (2001)

Dap-3 is up-regulated in invasive glioblastoma multiforme cells in vivo and in glioma cells with an induced motility phenotype in vitro. When migration is activated, Dap-3 is up-regulated and cells become resistant to apoptosis. These findings suggest that Dap-3 confers apoptosis-resistance when migration behavior is engaged.
Lane Geometry Estimation in Urban Environments Using a Stereovision System (2007)

This paper presents a lane detection system that combines stereovision-specific techniques with grayscale image processing for maximizing the robustness and applicability against the difficult conditions of the urban environment. The lane marking features are extracted using a fast and robust dark-light-dark transition detector that's aware of the perspective effect. The clothoid lane model is matched to the extracted features using line segment fitting for two distance intervals, under special constraints that ensure correctness. Freeform lane border detection, independent on the geometry constraints, driven by lane marking features only, is used to solve the situations not suited for clothoid representation. The results of each detection method are fused together in a Kalman filter based framework.
Gender, work orientations and job satisfaction (2015)

This article studies the gender gap in job satisfaction and argues that the observed gender difference is a consequence of the heterogeneity in work orientations between men and women. Using data from the 2006 Skills Survey, the analysis yields three major findings. The first shows that women, either in full-time or part-time employment, report significantly higher levels of job satisfaction than men. Secondly, work orientations are closely associated with one’s job satisfaction and their relationships vary significantly across men, women full-time and part-time workers. Finally and most importantly, the observed gender satisfaction differential is eliminated once work orientations are taken into consideration.
Cytokine therapies in HIV-1 infection: present and future (2003)

Since the introduction of highly active antiretroviral therapy (HAART), HIV-related deaths have declined dramatically in the developed world. However, HAART is neither able to eradicate the virus nor are its immunomodulatory effects sufficient to effect complete control of the virus. In addition, the long-term use of HAART is complicated by drug-related toxicities and compliance issues, both of which impact upon the development of viral resistance. The failure of structured treatment interruption strategies in those with chronic HIV-infection combined with the above limitations, has prompted renewed interest in immunotherapy. Cytokines and therapeutic vaccination have been proposed as HAART-adjunctive and HAART-sparing treatments in HIV-infection, and the current and future role of cytokine therapy in this disease will be the subject of this review.
Multifrequency zero-jitter delay-locked loop (1994)

The approach of an all-digital phase locked loop is used in this delay-locked loop circuit. This design is designated to a system with two processing units, a master CPU and a slave system chip, that share the same bus. It allows maximum utilization of the bus, as the minimal skew between the clocks of the two components significantly reduces idle periods, and also set-up and hold times. Changes in the operating frequency are possible, without falling out of synchronization. Due to the special lead-lag phase detector, the jitter of the clock is zero, when the loop is locked, under any working conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sliding-Window Digital Fountain Codes for Streaming of Multimedia Contents (2007)

Digital fountain codes are becoming increasingly important for multimedia communications over networks subject to packet erasures. These codes have significantly lower complexity than Reed-Solomon ones, exhibit high erasure correction performance, and are very well suited to generating multiple equally important descriptions of a source. In this paper we propose an innovative scheme for streaming multimedia contents by using digital fountain codes applied over sliding windows, along with a suitably modified belief-propagation decoder. The use of overlapped windows allows one to have a virtually extended block, which yields superior performance in terms of packet recovery. Simulation results using LT codes show that the proposed algorithm has better performance in terms of efficiency, reliability and memory with respect to fixed-window encoding.