gebhart/patrepeval huggingface dataset:
Effect of Megasphaera elsdenii NCIMB 41125 dosing on rumen development, volatile fatty acid production and blood β‐hydroxybutyrate in neonatal dairy calves (2015)

Thirty calves were randomly assigned to two treatments and fed until weaning [42 days (d) of age]. Treatments were a control group (n = 15), which did not receive Megasphaera elsdenii (Me0) and a M. elsdenii group, which received a 50-ml oral dose of M. elsdenii NCIMB 41125 (10(8) CFU/ml) at day 14 day of age (Me14). Calves were given colostrum for the first 3 day followed by limited whole milk feeding. A commercial calf starter was offered ad libitum starting at day 4 until the end of the study. Fresh water was available throughout the study. Feed intake and growth were measured. Blood samples were collected via jugular venipuncture to determine β-hydroxybutyrate (BHBA) concentrations. Fourteen male calves (seven per group) were euthanised on day 42 and digestive tracts harvested. Reticulo-rumen weight was determined and rumen tissue samples collected from the cranial and caudal sacs of the ventral and dorsal portions of the rumen for measurements of papillae length, papillae width and rumen wall thickness. Dosing with M. elsdenii NCIMB 41125 improved starter dry matter intake (DMI), weaning body weight (BW) and tended to improve average daily gain. Calves in Me14 group had greater plasma BHBA concentration than Me0-calves during the last 3 weeks of the trial and had at day 42 greater reticulo-rumen weight, papillae width and papillae density compared to Me0. No differences in rumen wall thickness or papillae length were observed between the two groups. Total volatile fatty acids, acetate and propionate production did not differ between treatments, but butyrate production was greater in Me14 than Me0. Dosing M. elsdenii NCIMB 41125 showed benefit for calves with improved feed intake and rumen development suggesting increased epithelium metabolism and improved absorption of digestive end products.
Homeostatic Effects of TLR9 Signaling in Experimental Colitis (2006)

The commensal microflora of the intestinal tract confer multiple health benefits to the host, including amelioration of inflammatory bowel disease (IBD). Yet, the exact mechanisms by which it ameliorates experimental colitis in animals and human IBD are largely unknown. We tested whether the attenuation of experimental colitis by probiotic bacteria is mediated by toll-like receptor (TLR) signaling. The severity of colitis was attenuated by delivery of nonviable, gamma-irradiated, or by viable probiotics, but not by heat-killed probiotics, in wild-type mice in mice deficient in TLR2 or TLR4. In contrast we did not observe any inhibition of experimental colitis by probiotics, in mice deficient in MyD88 or TLR9. Furthermore, administration of probiotic DNA ameliorated the severity of experimental colitis, whereas methylated probiotic DNA, calf thymus DNA, and Dnase-treated probiotics had no effect. In subsequent studies, we identified that TLR9-induced type 1 IFN mediates the anti-inflammatory effects in experimental colitis. The addition of neutralization antibodies to type 1 IFN abolished the anti-inflammatory effects, whereas the administration of recombinant IFN-beta mimicked the anti-inflammatory effects induced by TLR9 agonists. Taken together, these results indicate that the protective effects of probiotics are mainly mediated by their own DNA rather than by their metabolites or their ability to colonize the colon. These findings underscore the diverse effects of indigenous microbial TLR ligands in intestinal homeostasis and intestinal inflammation and suggest that strategies, that modulate type 1 IFN may be of therapeutic value for intestinal inflammatory conditions.
Selection of Guide Sequences That Direct Efficient Cleavage of mRNA by Human Ribonuclease P (1994)

Any RNA, when in a complex with another oligoribonucleotide known as an external guide sequence (EGS), can become a substrate for ribonuclease P. Simulation of evolution in vitro was used to select EGSs that bind tightly to a target substrate messenger RNA and that increase the efficiency of cleavage of the target by human ribonuclease P to a level equal to that achieved with natural substrates. The most efficient EGSs form transfer RNA precursor-like structures with the target RNA, in which the analog of the anticodon stem has been disrupted, an indication that selection for the optimal substrate for ribonuclease P yields an RNA structure different from that of present-day transfer RNA precursors.
Duplicated NHP6 genes of Saccharomyces cerevisiae encode proteins homologous to bovine high mobility group protein 1. (1990)

The nonhistone chromosomal protein NHP6 from Saccharomyces cerevisiae has been previously isolated and its amino-terminal sequence determined. In this report, synthetic oligonucleotides, designed from the limited NHP6 amino acid sequence, were used as hybridization probes to clone the NHP6A gene from a yeast genomic library. Low stringency Southern blot analysis showed that there was a second gene homologous to NHP6A. This gene, NHP6B, was also cloned and sequenced. Nucleotide sequence analysis revealed that NHP6B has six extra amino acids at its amino terminus, but that NHP6A and NHP6B match at 87% of the rest of their sequences. S1 nuclease analysis was used to show that both genes are transcribed; the major transcription start sites lie 30 bases before the first ATG codon. Interestingly, the approximately 11-kDa NHP6A and NHP6B proteins are homologous to the middle segment of the 27-kDa chromatin-associated high mobility group protein 1 from calf; NHP6A and NHP6B each have over 40% identity with this part of high mobility group protein 1. Possible functions for the NHP6 proteins are discussed in light of this homology.
Compact Sources of Ultrashort Pulses (1995)

This comprehensive volume provides a survey of the many innovations in the field of ultrashort pulse generation, and reviews the state of the art in compact, modelocked laser systems, discussing both their operational principles and potential applications. The theory of short optical pulse generation by modelocking is covered in the first chapter. Thereafter, modelocking techniques in different types of lasers are discussed: solid state lasers; diode-pumped lasers; fiber lasers; surface emitting semiconductor lasers; external cavity semiconductor lasers; hybrid soliton pulse sources; and monolithic colliding pulse modelocked diode lasers. Presenting both theoretical and experimental aspects throughout, this book will be invaluable to anyone interested in short pulse laser systems, and particularly to researchers involved in high-speed communications or the investigation of ultrafast phenomena.
Molecular Orientation Affects Localization Accuracy in Superresolution Far-Field Fluorescence Microscopy (2010)

We investigate the cooperative effect of molecular tilt and defocus on fluorophore localization by centroid calculation in far-field superresolution microscopy based on stochastic single molecule switching. If tilt angle and defocus are unknown, the localization contains systematic errors up to about ±125 nm. When imaging rotation-impaired fluorophores of unknown random orientation, the average localization accuracy in three-dimensional samples is typically limited to about ±32 nm, restricting the attainable resolution accordingly.
Identification of a Src SH3 domain binding motif by screening a random phage display library. (1994)

A phage display library was constructed in the filamentous bacteriophage fuse5. The library was made by inserting a degenerate oligonucleotide which encodes 15 variable amino acids into the NH2-terminal region of the phage gene III protein. This library, containing over 10(7) different phage, was screened with a glutathione S-transferase (GST) fusion protein containing the Src homology 3 (Src SH3) domain and a protein kinase A phosphorylation site (GST/PKA/Src SH3). A family of proline-rich sequences was isolated following four cycles of enrichment and amplification. Phage containing these sequences were shown to specifically bind to the GST/PKA/Src SH3 protein but not to GST/PKA only. A comparison of the inferred amino acid sequence of the different phage clones revealed a consensus sequence, RPLPXXP, which conforms to a Src SH3 domain binding motif identified independently during an affinity screen of a lambda-lox mouse embryo cDNA library using a 32P-labeled Src SH3 protein fragment as the probe (Y. Ivashchenko, manuscript in preparation). Peptides based upon the 7-amino acid SH3 binding domain core motif displayed strong binding to both the Src and to the Fyn SH3 domains, but failed to bind to the SH3 domain of p21 Ras-GTPase-activating protein (Ras-GAP) and other proteins. We anticipate that further screening of the phage display library will be a useful tool for the rapid identification of additional SH3 domain binding sequences and will also help to establish the essential core motifs that define the specificity of interactions among the diverse proteins containing SH3 domains and those containing SH3 binding motifs.
Induction of dormant HIV-1 by sodium butyrate (1991)

Reactivation of latent HIV-1 is believed to play a major role in the pathogenesis of AIDS. Here we show that sodium butyrate (NaB), which can cause gene induction or cell differentiation, reactivates dormant HIV-1 in vitro in chronically infected cells of T-lymphoid and monocytoid origin. The effect of NaB on HIV-1 expression in T-lymphoid cells was apparent 3 h after addition of drug and peaked at 24 h. During this time the proportion of HIV-1 antigen expressing cells increased from less than 0.5 to greater than 90%, and virus production increased by three orders of magnitude. The virus released by the NaB-induced cells was infectious. The extent and kinetics of NaB effects were similar to effects of phorbol 12-myristate 13-acetate in T cells, but not monocytes. Transient expression assays using an indicator gene under the control of the HIV-1 long terminal repeat revealed that mutations which altered the nucleotide sequence in the TATA box significantly reduced the NaB effect. These data show that NaB is a potent inducer of dormant HIV-1 and suggest that the TATA motif is required for this activity.
Antitumor Effects of a Monoclonal Antibody that Binds Anionic Phospholipids on the Surface of Tumor Blood Vessels in Mice (2005)

3G4 localizes specifically to complexes of anionic phospholipids and serum proteins on the surface of vascular endothelial cells in tumors in mice. This results in damage to tumor vasculature and suppression of tumor growth.
Array CGH profiling of favourable histology Wilms tumours reveals novel gains and losses associated with relapse (2006)

Despite the excellent survival of Wilms tumour patients treated with multimodality therapy, approximately 15% will suffer from tumour relapse, where response rates are markedly reduced. We have carried out microarray-based comparative genomic hybridisation on a series of 76 Wilms tumour samples, enriched for cases which recurred, to identify changes in DNA copy number associated with clinical outcome. Using 1Mb-spaced genome-wide BAC arrays, the most significantly different genomic changes between favourable histology tumours that did (n = 37), and did not (n = 39), subsequently relapse were gains on 1q, and novel deletions at 12q24 and 18q21. Further relapse-associated loci included losses at 1q32.1, 2q36.3-2q37.1, and gain at 13q31. 1q gains correlated strongly with loss of 1p and/or 16q. In 3 of 11 cases with concurrent 1p(-)/1q(+), a breakpoint was identified at 1p13. Multiple low-level sub-megabase gains along the length of 1q were identified using chromosome 1 tiling-path arrays. One such recurrent region at 1q22-q23.1 included candidate genes RAB25, NES, CRABP2, HDGF and NTRK1, which were screened for mRNA expression using quantitative RT-PCR. These data provide a high-resolution catalogue of genomic copy number changes in relapsing favourable histology Wilms tumours.
Blog credibility ranking by exploiting verified content (2009)

People use weblogs to express thoughts, present ideas and share knowledge. However, weblogs can also be misused to influence and manipulate the readers. Therefore the credibility of a blog has to be validated before the available information is used for analysis. The credibility of a blogentry is derived from the content, the credibility of the author or blog itself, respectively, and the external references or trackbacks. In this work we introduce an additional dimension to assess the credibility, namely the quantity structure. For our blog analysis system we derive the credibility therefore from two dimensions. Firstly, the quantity structure of a set of blogs and a reference corpus is compared and secondly, we analyse each separate blog content and examine the similarity with a verified news corpus. From the content similarity values we derive a ranking function. Our evaluation showed that one can sort out incredible blogs by quantity structure without deeper analysis. Besides, the content based ranking function sorts the blogs by credibility with high accuracy. Our blog analysis system is therefore capable of providing credibility levels per blog.
In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen (2008)

The growing resistance to current first-line antimalarial drugs represents a major health challenge. To facilitate the discovery of new antimalarials, we have implemented an efficient and robust high-throughput cell-based screen (1,536-well format) based on proliferation of Plasmodium falciparum (Pf) in erythrocytes. From a screen of approximately 1.7 million compounds, we identified a diverse collection of approximately 6,000 small molecules comprised of >530 distinct scaffolds, all of which show potent antimalarial activity (<1.25 microM). Most known antimalarials were identified in this screen, thus validating our approach. In addition, we identified many novel chemical scaffolds, which likely act through both known and novel pathways. We further show that in some cases the mechanism of action of these antimalarials can be determined by in silico compound activity profiling. This method uses large datasets from unrelated cellular and biochemical screens and the guilt-by-association principle to predict which cellular pathway and/or protein target is being inhibited by select compounds. In addition, the screening method has the potential to provide the malaria community with many new starting points for the development of biological probes and drugs with novel antiparasitic activities.
RB status as a determinant of response to UCN-01 in non-small cell lung carcinoma. (1999)

7-Hydroxystaurosporine (UCN-01), a protein kinase inhibitor in clinical development, demonstrates potent antineoplastic activity. To determine whether specific genetic abnormalities would modulate the response to UCN-01, a model of human non-small cell lung carcinoma (NSCLC) cell lines with differential abnormalities of p16CDKN2, RB, and p53 was used for these studies. Cell growth was measured by the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay, and cell cycling was studied using flow cytometric analysis of DNA content. Changes in protein levels and phosphorylation were assessed by Western blotting. In cell lines expressing wild-type RB (A549 and Calul), UCN-01 treatment resulted in dose-dependent growth inhibition, arrest of cells in G1, and a reduction of cells in S phase. p16CDKN2-null cells showed similar growth inhibition to normal fetal lung fibroblasts. UCN-01-induced growth arrest was accompanied by induction of p21CDKN1 and a shift of Rb to the hypophosphorylated state in both p53 wild-type and mutant cell lines. In contrast, UCN-01 treatment of the RB-null cell line H596 resulted in less growth inhibition. To test the role of RB in response to UCN-01, effects of treatment were examined in two human isogenic models of RB expression: the bladder cancer cell line 5637 (RB-null) and the prostate cancer cell line DU-145 (RB-mutant). In the Rb-expressing 5637 subline (RB5), UCN-01 treatment resulted in Rb hypophosphorylation and an accumulation in G1 in contrast to the parent line. Similarly, the wild-type Rb-expressing DU-145 sublines (DU1.1 and B5) showed increased G1 arrest compared with the parent cells. We conclude that UCN-01-induced G1 arrest can occur in cells null for p53 and p16CDKN2, and that RB status influences the ability of UCN-01 to induce a G1 arrest. These data suggest that the molecular profile of cell cycle regulating genes in individual tumors may predict responsiveness and provide insight into optimal therapeutic application of this new antineoplastic agent.
Positively selected FimH residues enhance virulence during urinary tract infection by altering FimH conformation (2013)

Chaperone-usher pathway pili are a widespread family of extracellular, Gram-negative bacterial fibers with important roles in bacterial pathogenesis. Type 1 pili are important virulence factors in uropathogenic Escherichia coli (UPEC), which cause the majority of urinary tract infections (UTI). FimH, the type 1 adhesin, binds mannosylated glycoproteins on the surface of human and murine bladder cells, facilitating bacterial colonization, invasion, and formation of biofilm-like intracellular bacterial communities. The mannose-binding pocket of FimH is invariant among UPEC. We discovered that pathoadaptive alleles of FimH with variant residues outside the binding pocket affect FimH-mediated acute and chronic pathogenesis of two commonly studied UPEC strains, UTI89 and CFT073. In vitro binding studies revealed that, whereas all pathoadaptive variants tested displayed the same high affinity for mannose when bound by the chaperone FimC, affinities varied when FimH was incorporated into pilus tip-like, FimCGH complexes. Structural studies have shown that FimH adopts an elongated conformation when complexed with FimC, but, when incorporated into the pilus tip, FimH can adopt a compact conformation. We hypothesize that the propensity of FimH to adopt the elongated conformation in the tip corresponds to its mannose binding affinity. Interestingly, FimH variants, which maintain a high-affinity conformation in the FimCGH tip-like structure, were attenuated during chronic bladder infection, implying that FimH's ability to switch between conformations is important in pathogenesis. Our studies argue that positively selected residues modulate fitness during UTI by affecting FimH conformation and function, providing an example of evolutionary tuning of structural dynamics impacting in vivo survival.
TRANSCRIPTIONAL REGULATION BY CYCLIC AMP (1997)

A number of hormones and growth factors have been shown to stimulate target cells via second messenger pathways that in turn regulate the phosphorylation of specific nuclear factors. The second messenger cyclic AMP, for example, regulates a striking number of physiologic processes, including intermediary metabolism, cellular proliferation, and neuronal signaling, by altering basic patterns of gene expression. Our understanding of cyclic AMP signaling in the nucleus has expanded considerably over the past decade, owing in large part to the characterization of cyclic AMP-responsive promoter elements, transcription factors that bind them, and signal-dependent coactivators that mediate target gene induction. More importantly, these studies have revealed new insights into biological problems as diverse as biological clocks and long-term memory. The purpose of this review is to describe the components of the cyclic AMP response unit and to analyze how these components cooperate to induce target gene expression in response to hormonal stimulation.
An Analysis of UNIX System Configuration (1997)

Management of operating system configuration files files is an essential part of UNIX systems administration. It is particularly difficult in environments with a large number of computers.

This paper presents a study of UNIX configuration file management. It compares existing systems and tools from the literature, presents several case studies of configuration file management in practice, examines one site in depth, and makes numerous observations on the configuration process.
WDR20 Regulates Activity of the USP12·UAF1 Deubiquitinating Enzyme Complex (2010)

The UAF1 (Usp1-associated factor 1) protein binds and stimulates three deubiquitinating enzymes: USP1, USP12, and USP46. Although the USP1 x UAF1 complex is required for regulation of the Fanconi anemia (FA) DNA repair pathway, less is known about the USP12 x UAF1 and the USP46 x UAF1 complexes. To understand further the nature of the USP12 and USP46 complexes, we attempted to identify proteins that interact with the USP12 and USP46 deubiquitinating enzyme complexes. We identified WDR20, a WD40-repeat containing protein, as a common binding partner of UAF1, USP12, and USP46. Further analysis showed that WDR20 associates exclusively with USP12 and USP46, not with USP1. Furthermore, we demonstrate the purification of a ternary USP12 x UAF1 x WDR20 complex. Interestingly, and consistent with the binding assays, WDR20 stimulated the enzymatic activity of USP12 x UAF1, but not of USP1 x UAF1. Consistent with our previous report that USP12 and USP46 do not regulate the FA pathway, small interference RNA-mediated depletion of WDR20 protein did not affect the FA pathway or DNA damage responses. We provide a model in which WDR20 serves as a stimulatory subunit for preserving and regulating the activity of the subset of the UAF1 x USP complexes.
Production of high-concentration n-caproic acid from lactate through fermentation using a newly isolated Ruminococcaceae bacterium CPB6 (2017)

This study demonstrated that high concentration of CA production can be obtained by a newly isolated pure culture CPB6. This strain can be employed as a powerful workhorse for high-efficient CA recovery from lactate-containing waste streams. Our preliminary investigation suggested that the CA production from lactate in strain CPB6 might be via the chain elongation pathway of the reverse β-oxidation; the detailed mechanism, however, warrants further investigation using various molecular microbiology techniques.
Self Assembling and Crosslinking of Polyelectrolyte Multilayer Films of Chitosan and Alginate Studied by QCM and IR Spectroscopy (2009)

The formation of novel biocompatible multilayer films based on the alternate deposition of CHI and ALG was investigated for the first time by QCM-D and FTIR-ATR. A linear increase of the thickness was found during the film build-up. GLUT was used to crosslink the films terminated with either CHI or ALG. A change in the QCM-D signal was observed just in the first case, indicating that crosslinking only takes place in the top CHI layer. The evolution of the dissipation factor during crosslinking was modelled with a first-order kinetics; this reaction was found to be faster for chitosan terminated films with a lower number of multilayers. It was also found that more robust films could be produced by crosslinking the intermediate CHI layers during the build-up.
Reductive Cleavage of Aliphatic Nitro Groups in Organic Synthesis (1986)

This article reviews the methods of reductive cleavage of aliphatic nitro groups using tri-n-butyltin hydride (TBTH) and their applications in organic synthesis. 1. Introduction 2. Denitration Reactions 3. Synthetic Applications of Denitration Reactions 4. Aliphatic Nitro Compounds as Radical Precursors 5. Olefin Formation via Reductive Cleavage of Nitro Groups
Advances in UV-inscribed fiber grating optic sensor technologies (2003)

In this paper, we describe the recent advances in fiber grating sensing devices and applications with emphasis on multi-parameter measurement and realization of high-sensitivity sensors utilizing novel gratings of the Bragg and long-period structures.