gebhart/patrepeval huggingface dataset:
The case for determinism in database systems (2010)

Replication is a widely used method for achieving high availability in database systems. Due to the nondeterminism inherent in traditional concurrency control schemes, however, special care must be taken to ensure that replicas don't diverge. Log shipping, eager commit protocols, and lazy synchronization protocols are well-understood methods for safely replicating databases, but each comes with its own cost in availability, performance, or consistency. In this paper, we propose a distributed database system which combines a simple deadlock avoidance technique with concurrency control schemes that guarantee equivalence to a predetermined serial ordering of transactions. This effectively removes all nondeterminism from typical OLTP workloads, allowing active replication with no synchronization overhead whatsoever. Further, our system eliminates the requirement for two-phase commit for any kind of distributed transaction, even across multiple nodes within the same replica. By eschewing deadlock detection and two-phase commit, our system under many workloads outperforms traditional systems that allow nondeterministic transaction reordering.
CD4+ T Cells Migrate into Inflamed Skin Only If They Express Ligands for E- and P-Selectin (1998)

Previous data suggested a role of endothelial selectins in skin homing of lymphocytes. In the current study, we have analyzed the expression and functional role of E-and P-selectin ligands on CD4+ T cells induced in vivo upon skin sensitization, using soluble selectin-Ig chimera and blocking Abs. Only low numbers of CD4+ cells expressing significant levels of E- or P-selectin ligands were present in s.c. lymph nodes of untreated mice (0.5-1.5% and 2-4%, respectively). Induction of a delayed-type hypersensitivity reaction increased the percentage of E-selectin-binding CD4+ cells in the draining lymph nodes up to 6 to 9% and that of P-selectin-binding cells up to 14%. The majority of E- and P-selectin-binding cells displayed an activated phenotype as judged by the increase in IL-2R, CD71, or cell size. The populations of E- and P-selectin-binding cells were largely overlapping; all E-selectin-binding cells also bound to P-selectin, whereas only a subfraction of P-selectin-binding cells reacted with E-selectin. Both E- and P-selectin-binding CD4+ cells, isolated by FACS, efficiently migrated into inflamed, but not normal skin, whereas P- or E-selectin ligand-negative CD4+ T cells did not. Abs against one of the two endothelial selectins partially inhibited the entry of isolated, ligand-positive cells, whereas a combination of Abs against both selectins almost completely abrogated skin homing. These data indicate that the expression of functional ligands for E- and for P-selectin is essential for homing of CD4+ T cells into the inflamed skin.
Genetic Analysis of a Chromosomal Region Containing Genes Required for Assimilation of Allantoin Nitrogen and Linked Glyoxylate Metabolism in Escherichia coli (1999)

Growth experiments with Escherichia coli have shown that this organism is able to use allantoin as a sole nitrogen source but not as a sole carbon source. Nitrogen assimilation from this compound was possible only under anaerobic conditions, in which all the enzyme activities involved in allantoin metabolism were detected. Of the nine genes encoding proteins required for allantoin degradation, only the one encoding glyoxylate carboligase (gcl), the first enzyme of the pathway leading to glycerate, had been identified and mapped at centisome 12 on the chromosome map. Phenotypic complementation of mutations in the other two genes of the glycerate pathway, encoding tartronic semialdehyde reductase (glxR) and glycerate kinase (glxK), allowed us to clone and map them closely linked to gcl. Complete sequencing of a 15.8-kb fragment encompassing these genes defined a regulon with 12 open reading frames (ORFs). Due to the high similarity of the products of two of these ORFs with yeast allantoinase and yeast allantoate amidohydrolase, a systematic analysis of the gene cluster was undertaken to identify genes involved in allantoin utilization. A BLASTP search predicted four of the genes that we sequenced to encode allantoinase (allB), allantoate amidohydrolase (allC), ureidoglycolate hydrolase (allA), and ureidoglycolate dehydrogenase (allD). The products of these genes were overexpressed and shown to have the predicted corresponding enzyme activities. Transcriptional fusions to lacZ permitted the identification of three functional promoters corresponding to three transcriptional units for the structural genes and another promoter for the regulatory gene allR. Deletion of this regulatory gene led to constitutive expression of the regulon, indicating a negatively acting function.
Donepezil Therapy in Clinical Practice (2000)

This independent confirmation of data from phase 3 trials suggests that donepezil therapy modestly improves cognition in patients with Alzheimer disease who are encountered in clinical practice.
Chronic myeloid leukemia patients with the e13a2 BCR-ABL fusion transcript have inferior responses to imatinib compared to patients with the e14a2 transcript (2009)

Patients expressing the e14a2 transcript type have a higher rate and more rapid complete cytogenetic responses than e13a2-expressing patients, which may be due to higher BCR-ABL tyrosine kinase activity. Knowledge of the transcript type may yield additional prognostic information, although this requires testing on larger datasets.
Curcumin suppresses growth of head and neck squamous cell carcinoma (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

1520 

The purpose of this study was to determine whether curcumin would trigger cell death in the head and neck squamous cell carcinoma (HNSCC) cell lines CCL 23 and CAL 27 in a dose-dependent fashion, both in vitro and in vivo . In vitro studies included MTT assay of the HNSCC cells after treatment with curcumin. Control cells were treated with dimethylsulfoxide (DMSO) or saline. CCL23 and CAL27 were plated into 96-well plates, serum starved for 24 hours to synchronize cell cycles, treated with curcumin or DMSO for eight hours, and allowed to incubate in regular growth media for 8 and 15 hours after treatment before analysis of cell viability. MTT results showed that at both eight and fifteen hours after treatment, CCL23 cell lines had the greatest reduction in cell viability at concentrations between 100-300uM, with nearly 100% cell survival at 100uM and less than 5% survival at 300uM. CAL27 cell lines showed an even greater sensitivity to curcumin treatment. Reduction of CAL27 cell viability began at 60uM, and 0% survived at concentrations of 300uM. Fifteen hours after treatment with 100 μM of curcumin, CAL27 cell lines showed continued cell death, with an 83% reduction in cell viability. In vivo studies were done on HNSCC xenograft tumors grown in female nude mice. Curcumin paste was applied topically to each mouse tumor on a daily basis for 4 weeks. Tumors were measured in 3 dimensions each week and growth curves plotted. Blood and organs were harvested from the mice for toxicity studies after completion of the experiment. The xenograft tumors exhibited more than 50% decrease in size with the curcumin/saline paste. Curcumin/DMSO paste had only a modest suppressive effect on tumor growth, while control tumors continued to grow rapidly. In conclusion, curcumin has a direct effect on CCL23 and CAL27, reducing viability in both cell lines in a dose-dependent fashion. Both cell lines showed continued cell death over a period of several hours, suggesting that curcumin triggers the apoptotic pathway in these head and neck cancer cell lines rather than producing a sudden cell necrosis. In addition, curcumin/saline paste had a significant suppressive effect on HNSCC xenograft tumors in female nude mice, confirming curcumin’s antitumor properties in vivo .
DEVELOPMENT OF UREA-BASED AND LATEX EMULSION SYSTEMS FOR DUST CONTROL IN SUPPORT OF MILITARY OPERATIONS (1967)

This report presents the results of a program directed towards the development of materials for use by the military for dust control in the theater of operations. Criteria for defining the desirable properties of such dust control agents have been established, and materials which possess these properties have been procured, formulated, tested, and evaluated. The low material usage rates required (3 lbs per square yard or less) plus the variety of soils and soil conditions over which such dust control agents must be used preclude such treatments from adding to the load bearing capacity of the soil to any appreciable extent. The materials developed, therefore, are designed to be sprayed as liquids on the soil surface and produce coherent, highly flexible and extensible surface layers which effectively seal off the soil surface, preventing generation of dust. The flexible layers formed can withstand considerable deformation without failure. Because of their nature, these dust control agents serve to waterproof the soil as well. Several latex formulations have been developed which passed the laboratory screening tests and which show potential for military dust control purposes. A device has been developed for the simple application of these materials. Urea resin formulations were examined initially and determined to be generally ineffective, due primarily to their inability to withstand deformations of great enough magnitude. Subsequently, emphasis was directed toward synthetic and natural latex systems which show a greater potential.
Animation for Visualization: Opportunities and Drawbacks. (2010)

The use of Java, Flash, Silverlight, and JavaScript on the Web has made it easier to distribute animated, interactive visualizations. Many visualizers are beginning to think about how to make their visualizations more compelling with animation. There are many good guides on how to make static visualizations more effective, and many applications support interactivity well. But animated visualization is still a new area; there is little consensus on what makes for a good animation.
Charge Detection Mass Spectrometry with Resolved Charge States (2012)

Charge detection mass spectrometry (CDMS) measurements have been performed for cytochrome c and alcohol dehydrogenase (ADH) monomer using a modified cone trap incorporating a cryogenically cooled JFET. Cooling the JFET increases its transconductance and lowers thermal noise, improving the signal to noise (S/N) ratio. Single ions with as few as 9 elementary charges (e) have been detected. According to simulations, the detection efficiency for ions with a charge of 13 e is 75%, and for charges above 13 e the detection efficiency rapidly approaches 95%. With the low limit of detection achieved here, adjacent charge states are easily resolved in the m/z spectrum, so the accuracy and precision of the image charge measurements can be directly evaluated by comparing the measured image charge to the charge deduced from the m/z spectrum. For ADH monomer ions with 32 to 43 charges, the root mean square deviation of the measured image charge is around 2.2 e. Ions were trapped for over 1500 cycles. The number of cycles detected appears to be limited mainly by collisions with the background gas.
A model of focal ischemic stroke in the rat: reproducible extensive cortical infarction. (1986)

In the search for a more reproducible focal ischemic stroke model in the rat, we systematically interrupted blood flow to the right middle cerebral artery territory by ligating the right middle cerebral artery, and the right and left common carotid arteries in succession. Using a laser-Doppler flowmeter, we found that the relative surface blood flow in cerebral cortex supplied by the right middle cerebral artery decreased to 62, 48, and 18% of baseline respectively after successive ligation of the right middle cerebral artery, and the right and left common carotid arteries. A focal infarct in the cerebral cortex supplied by the right middle cerebral artery was consistently noted after ligation of the right middle cerebral and the right common carotid arteries and temporary clip occlusion of the left common carotid artery for 60 min. The surface areas of infarction measured 100 +/- 6 mm2 and the maximal cross-sectional area of infarction was 10.4 +/- 1.1 mm2 (N = 10). The mortality rate was 7% (N = 70). The characteristic changes of ischemic necrosis were limited to the cortex with sparing of subcortical structures. No motor deficits occurred. Occlusion of the right middle cerebral artery alone or together with the right common carotid artery did not consistently cause gross infarction and the maximal cross-sectional area of infarction was smaller (the right middle cerebral artery, 1.7 +/- 0.8 mm2, N = 10; the right middle cerebral artery plus the right common carotid artery, 4.8 +/- 1.9 mm2, N = 10). Permanent ligation of the right middle cerebral artery and both common carotid arteries had a high mortality (60% in 3 days, N = 10).(ABSTRACT TRUNCATED AT 250 WORDS)
Understanding Bioinformatics (2007)

Suitable for advanced undergraduates and postgraduates, Understanding Bioinformatics provides a definitive guide to this vibrant and evolving discipline. The book takes a conceptual approach.&nbsp;It guides the reader from first principles through to an understanding of the computational techniques and the key algorithms.&nbsp;Understanding Bioinformatics is an invaluable companion for students from their first encounter with the subject through to more advanced studies.&nbsp; The book is divided into seven parts, with the opening&nbsp;part introducing the basics of nucleic acids, proteins and databases.&nbsp;Subsequent parts are divided into 'Applications' and 'Theory' Chapters, allowing readers to focus their attention effectively.&nbsp; In each section, the Applications Chapter provides a fast and straightforward route to understanding the main concepts and 'getting started'. Each of these is then followed by Theory Chapters which give greater detail and present the underlying mathematics. In Part 2, Sequence Alignments, the Applications Chapter shows the reader how to get started on producing and analyzing sequence alignments, and using sequences for database searching, while the next two chapters look closely at the more advanced techniques and the mathematical algorithms involved.&nbsp;Part 3&nbsp;covers evolutionary processes and shows how bioinformatics can be used to help build phylogenetic trees.&nbsp;Part 4&nbsp;looks at the characteristics of whole genomes. In&nbsp;Parts 5&nbsp;and&nbsp;6&nbsp;the focus turns to secondary and tertiary structure – predicting structural conformation and analysing structure-function relationships.&nbsp;The last&nbsp;part surveys methods of analyzing data from a set of genes or proteins of an organism and is rounded off with an overview of systems biology.
Small B cells as antigen-presenting cells in the induction of tolerance to soluble protein antigens. (1992)

We have investigated the ability of resting B cells, acting as antigen-presenting cells, to induce tolerance to soluble protein antigens in mice, using an antigen targeted specifically to B cells. We inject mice intravenously with ultracentrifuged Fab fragments of rabbit anti-mouse immunoglobulin D (IgD) (Fab anti-delta). Treatment with Fab anti-delta results in profound tolerance to challenge with 100 micrograms Fab nonimmune rabbit Ig (Fab NRG), precipitated in alum, as measured by antibody production. Tolerance to rabbit Fab is antigen specific, since the treated mice make normal antibody responses to a control antigen, chicken Ig. Tolerance is dependent on antigen presentation by B cells, since intravenous injection of soluble Fab NRG, which is not targeted to B cells, results in a much lower frequency and degree of tolerance, especially at lower doses. T cell help in this system is affected, since T cells from Fab anti-delta-treated mice fail to provide help for an adoptive primary antibody response to Fab NRG when transferred together with normal B cells into severe combined immunodeficient (SCID) mice. The antigen-specific B cell compartment is also affected during tolerance induction, since B cells from treated animals make less antibody than normal B cells when transferred into SCID mice with normal T cells. Although the mechanism of nonresponsiveness in the helper T cell compartment remains to be determined, we think it is likely that the precursors of helper T cells are inactivated or deleted by encountering antigen presented by small, resting B cells, which lack accessory signals necessary to induce helper T cell proliferation and differentiation to effector function.(ABSTRACT TRUNCATED AT 250 WORDS)
Immunity and Immunopathology to Respiratory Syncytial Virus: The Mouse Model (1995)

Infection with respiratory syncytial virus (RSV) is a major unsolved challenge for vaccine development. RSV is worldwide in distribution and infects almost all children during the first 2 yr of life. The mouse model of RSV lung disease has been very successful in reproducing many aspects of the human disease. In particular, the role of antiviral T cells in both eliminating virus and causing enhanced disease has been shown dramatically. This immunopathologic paradox is now more clearly understood than for any other common human infection, largely due to insights gained from the mouse model. This review focuses on the unique ability of different RSV proteins to prime for specific functional subsets in the mouse, and the association between sensitization to the major surface glycoprotein G, the induction of T helper 2 cells, and the subsequent appearance of lung eosinophilia during RSV infection.
Adjuvant Tamoxifen Reduces Subsequent Breast Cancer in Women With Estrogen Receptor–Positive Ductal Carcinoma in Situ: A Study Based on NSABP Protocol B-24 (2012)

Patients in NSABP B-24 with ER-positive DCIS receiving adjuvant tamoxifen after standard therapy showed significant reductions in subsequent breast cancer. The use of adjuvant tamoxifen should be considered for patients with DCIS.
Extrachromosomal recombination in mammalian cells as studied with single- and double-stranded DNA substrates. (1987)

We have previously proposed a model to account for the high levels of homologous recombination that can occur during the introduction of DNA into mammalian cells (F.-L. Lin, K. Sperle, and N. Sternberg, Mol. Cell. Biol. 4:1020-1034, 1984). An essential feature of that model is that linear molecules with ends appropriately located between homologous DNA segments are efficient substrates for an exonuclease that acts in a 5'----3' direction. That process generates complementary single strands that pair in homologous regions to produce an intermediate that is processed efficiently to a recombinant molecule. An alternative model, in which strand degradation occurs in the 3'----5' direction, is also possible. In this report, we describe experiments that tested several of the essential features of the model. We first confirmed and extended our previous results with double-stranded DNA substrates containing truncated herpesvirus thymidine kinase (tk) genes (tk delta 5' and tk delta 3'). The results illustrate the importance of the location of double-strand breaks in the successful reconstruction of the tk gene by recombination. We next transformed cells with pairs of single-stranded DNAs containing truncated tk genes which should anneal in cells to generate the recombination intermediates predicted by the two alternative models. One of the intermediates would be the favored substrate in our original 5'----3' degradative model and the other would be the favored substrate in the alternative 3'----5' degradative model. Our results indicate that the intermediate favored by the 3'----5' model is 10 to 20 times more efficient in generating recombinant tk genes than is the other intermediate.
Directed Self-Assembly of Two Kinds of Nanoparticles Utilizing Monolayer Films of Diblock Copolymer Micelles (2003)

We demonstrated a self-assembly of two different kinds of nanoparticles simultaneously directed on a monolayer film of diblock copolymer micelles via physical and chemical arrangements. We first incorporated gold nanoparticles physically around the micelles of a monolayer film of PS-PVP micelles having a short-range hexagonal order. Iron oxide nanoparticles were then synthesized chemically in the PVP core area of the ordered micelles, resulting in a mosaic nanopattern of magnetic iron oxide nanoparticles surrounded by metallic gold nanoparticles. Thus, we were able to direct two kinds of nanoparticles to self-assemble in the specific positions as an example of controlled fabrication of nanometer-sized building blocks.
A tripartite motif protein TRIM11 binds and destabilizes Humanin, a neuroprotective peptide against Alzheimer's disease‐relevant insults (2003)

Humanin (HN) is a newly identified neuroprotective peptide that specifically suppresses Alzheimer's disease (AD)-related neurotoxicity. HN peptide has been detected in the human AD brain as well as in mouse testis and colon by immunoblot and immunohistochemical analyses. By means of yeast two-hybrid screening, we identified TRIM11 as a novel HN-interacting protein. TRIM11, which is a member of protein family containing a tripartite motif (TRIM), is composed of a RING finger domain, which is a putative E3 ubiquitin ligase, a B-box domain, a coiled-coil domain and a B30.2 domain. Deletion of the B30.2 domain in TRIM11 abolished the interaction with HN, whereas the B30.2 domain alone did not interact with HN. For their interaction, at least the coiled-coil domain was indispensable together with the B30.2 domain. The intracellular level of glutathione S-transferase-fused or EGFP-fused HN peptides or plain HN was drastically reduced by the coexpression of TRIM11. Disruption of the RING finger domain by deleting the first consensus cysteine or proteasome inhibitor treatment significantly diminished the effect of TRIM11 on the intracellular level of HN. These results suggest that TRIM11 plays a role in the regulation of intracellular HN level through ubiquitin-mediated protein degradation pathways.