gebhart/patrepeval huggingface dataset:
Potential Role of the Microbiome in Acne: A Comprehensive Review (2019)

Acne is a highly prevalent inflammatory skin condition involving sebaceous sties. Although it clearly develops from an interplay of multiple factors, the exact cause of acne remains elusive. It is increasingly believed that the interaction between skin microbes and host immunity plays an important role in this disease, with perturbed microbial composition and activity found in acne patients. Cutibacterium acnes (C. acnes; formerly called Propionibacterium acnes) is commonly found in sebum-rich areas and its over-proliferation has long been thought to contribute to the disease. However, information provided by advanced metagenomic sequencing has indicated that the cutaneous microbiota in acne patients and acne-free individuals differ at the virulent-specific lineage level. Acne also has close connections with the gastrointestinal tract, and many argue that the gut microbiota could be involved in the pathogenic process of acne. The emotions of stress (e.g., depression and anxiety), for instance, have been hypothesized to aggravate acne by altering the gut microbiota and increasing intestinal permeability, potentially contributing to skin inflammation. Over the years, an expanding body of research has highlighted the presence of a gut-brain-skin axis that connects gut microbes, oral probiotics, and diet, currently an area of intense scrutiny, to acne severity. This review concentrates on the skin and gut microbes in acne, the role that the gut-brain-skin axis plays in the immunobiology of acne, and newly emerging microbiome-based therapies that can be applied to treat acne.
Combining behavior and data modeling in automated test case generation (2003)

Software testing plays a critical role in the process of creating and delivering high-quality software products. Manual software testing can be an expensive, tedious and error-prone process, therefore testing is often automated in an attempt to reduce its cost and improve its defect detection capability. Model-based testing, a technique used in automated test case generation, is an important topic because it addresses the need for test suites that are of high-quality and yet, maintainable. Current model-based techniques often use a single model to represent system behavior. Using a single model may restrict the number and type of test cases that may be generated. In this paper, system-level test case generation is accomplished using two models to represent system behavior. The results of case studies used to evaluate this technique indicate that for the systems studied a larger percentage of the required test cases can be generated using the combined modeling approach.
Effects of Sequential Calcium Phosphate- Fluoride Rinses on Fluoride Uptake in Rats (1979)

This study measured the effects of a calcium phosphate rinse followed by various fluoride rinses on fluoride uptake by enamel in rats. Calcium phosphate rinses promoted fluoride uptake by the enamel.
Capacity maximizing linear space-time codes (2002)

Spatial multiplexingt or BLASTt is a signal- ing technique for multiple-input multiple-output (MIMe) channels in which multiple independent data streams are transmitted in parallel in space. The independence between streamst unfortunatelyt limits the diversity advantage. In this paper we present a space-time code designt using the linear dispersion code framework [1It for MIMe Rayleigh fading channels. Our design provides codes that have the same ergodic capacity performance as spatial multiplexing but allows for improved diversity advantage. We present a technique for finding good codes based on successive projection. Monte Carlo simulations illustrate performance improvements over spatial multiplexing in terms of bit error probability.
Endocytosis and Signal Transduction: Basic Science Update (2003)

Endocytosis can be separated into the categories of phagocytosis and pinocytosis. Phagocytosis can be distinguished from pinocytosis primarily by the size of particle ingested and by its dependence on actin polymerization as a key step in particle ingestion. Several specific forms of pinocytosis have been identified that can be distinguished based on their dependence on clathrin or caveolin. Both clathrin- and caveolin-dependent pinocytosis appear to require the participation of dynamin to internalize the plasma membrane. Other, less well-characterized forms of pinocytosis have also been described. Although endocytosis has long been known to affect receptor density, recent studies have demonstrated that endocytosis through clathrin- and caveolin-dependent processes plays a key role in receptor-mediated signal transduction. In some cases, blockade of these processes attenuates, or even prevents, signal transduction from taking place. This information, coupled with a better understanding of endocytosis mechanisms, will help advance the field of cell biology as well as present new targets for drug development and disease treatment.
Packing and hydrophobicity effects on protein folding and stability: Effects of <i>β</i>‐branched amino acids, valine and isoleucine, on the formation and stability of two‐stranded <i>α</i>‐helical coiled coils/leucine zippers (1993)

The aim of this study was to examine the differences between hydrophobicity and packing effects in specifying the three-dimensional structure and stability of proteins when mutating hydrophobes in the hydrophobic core. In DNA-binding proteins (leucine zippers), Leu residues are conserved at positions "d," and beta-branched amino acids, Ile and Val, often occur at positions "a" in the hydrophobic core. In order to discern what effect this selective distribution of hydrophobes has on the formation and stability of two-stranded alpha-helical coiled coils/leucine zippers, three Val or three Ile residues were simultaneously substituted for Leu at either positions "a" (9, 16, and 23) or "d" (12, 19, and 26) in both chains of a model coiled coil. The stability of the resulting coiled coils was monitored by CD in the presence of Gdn.HCl. The results of the mutations of Ile to Val at either positions "a" or "d" in the reduced or oxidized coiled coils showed a significant hydrophobic effect with the additional methylene group in Ile stabilizing the coiled coil (delta delta G values range from 0.45 to 0.88 kcal/mol/mutation). The results of mutations of Leu to Ile or Val at positions "a" in the reduced or oxidized coiled coils showed a significant packing effect in stabilizing the coiled coil (delta delta G values range from 0.59 to 1.03 kcal/mol/mutation). Our results also indicate the subtle control hydrophobic packing can have not only on protein stability but on the conformation adopted by the amphipathic alpha-helices. These structural findings correlate with the observation that in DNA-binding proteins, the conserved Leu residues at positions "d" are generally less tolerant of amino acid substitutions than the hydrophobic residues at positions "a."
High power microwave discharge as an excitation source for spectroscopic experiments (1971)

In order to obtain high radiation intensity per steradian per square centimetre, the axial radiant flux of a long capillary discharge tube (50 cm length, 4 mm i.d.) was investigated which served as the 'inner conductor' of the coaxial line in one microwave circuit. The maximum input power of 800 W was supplied without an isolator to the capillary discharge tube, filled with Xe at pressures below 400 torr; the voltage standing wave ratio was about 1.5. In the near ultraviolet region, this xenon discharge had as intense a continuum as the Hitachi type 4141 hydrogen discharge lamp.
Multiple fault diagnosis on a synchronous 2 pole generator using shaft and flux probe signals (2013)

A method for diagnosis of multiple incipient faults on a 2-pole synchronous generator is presented. Simulation of the generator on a finite element analysis (FEA) software package is used to predict the effects of these faults. Experimental analysis of the generator under fault conditions is then conducted and confirms the predicted behaviour. The investigation utilises shaft brushes as a non-invasive condition monitoring tool and search coils are used to validate findings from the shaft signal analysis. Results of the investigation indicate definitive relationships between the faults and specific harmonics of the output signals from the condition monitoring tools.
Ire1p: A Kinase and Site-Specific Endoribonuclease (2003)

The lumen of the endoplasmic reticulum (ER) is a highly specialized compartment in eukaryotic cells. Here, secretory and most membrane proteins are folded, covalently modified, and oligomerized with the assistance of specialized ER resident proteins (1). Perturbation of the ER lumen interferes with the production of many essential cellular components and can thus be highly deleterious. Indeed, in humans, defects in protein folding in the ER can lead to devastating diseases, such as cystic fibrosis, alpha1-antitrypsin deficiency, and osteogenesis imperfecta (2). One way in which cells cope with the accumulation of unfolded proteins in the ER is by activating the unfolded protein response (UPR), an ER-to-nucleus signal transduction pathway (3–5). In the yeast Saccharomyces cerevisiae, Ire1p is an essential component of this pathway.
A Hierarchical Scheme for Rapid Video Copy Detection (2008)

Today with the rapid increasing popularity of web video sharing, digital copyright protection encounters many troubles. Video copy detection schemes are emerging to cope with the digital video piracy and illegal distribution problems. But the large amount of video data and diversity of copy attacks pose difficulties on copy detection. This paper presents a hierarchical scheme to detect video copies, especially the temporal attacked and re-encoded ones. Our algorithm which is based on the ordinal signature of intra frames and effective R*-tree indexing structure archives real time performance. Comparison experiments are conducted on the benchmarked database of CIVR 2007 copy detection showcase and demonstrate the promising results of the proposed approach.
Predictors of Delayed Gastric Emptying in Diabetes (2001)

We conclude that the presence of abdominal bloating/fullness but not any other upper gastrointestinal symptom is associated with diabetic gastroparesis and that gastric emptying is slower in diabetic women than in diabetic men.
Elastase of U-937 Monocytelike Cells (1982)

As an approach to facilitating the understanding of proteinases associated with monocytes we have studied U-937 monocytelike cells. Elastase activity was identified in U-937 cell extracts and compared to monocyte elastase activity, neutrophil elastase, and the elastase activity from a continuous line of murine macrophagelike cells (P388D1). Serine proteinase activity which solubilized (14)C-labeled elastin accounted for >90% of the neutral proteinase activity of both U-937 cells and monocyte extracts. U-937 cell and monocyte elastase activities were similar catalytically, resembling neutrophil elastase. U-937 cells and monocytes showed other similarities: (a) both had activities reacting with [(3)H]diisopropylfluorophosphate that migrated in sodium dodecyl sulfate (SDS) polyacrylamide gels at approximately 30,000 and 60,000 daltons and (b) both contained material that cross-reacted with antiserum raised to neutrophil elastase. Preliminary characterization of U-937 cell elastase activity by affinity chromatography and ion-exchange chromatography suggested the presence of at least two distinct elastases. Minimal elastase activity was found in U-937 cell-conditioned medium, indicating that the activity is not spontaneously released by the cells. In contrast to the elastase activity associated with U-937 cells and monocytes, the elastase activity associated with P388D1 cells was a metalloproteinase and was found principally in the culture medium. These results indicate (a) U-937 cells will be useful for further investigation of proteinases associated with normal monocytes; (b) monocytes and U-937 cells contain material with catalytic and immunologic similarities to neutrophil elastase; (c) monocyte elastase activity differs from elastase activity secreted by murine macrophages and murine macrophagelike cells of the P388D1 line.
Rapid Solid-State Photopolymerization of Cyclic Acetal-Containing Acrylates (2009)

A cyclic acetal-functionalized urethane acrylate monomer is synthesized here and polymerized in a crystalline state without the polymerization kinetics being deleteriously affected by the solid state. Depending on the processing conditions, the cyclic acetal urethane acrylate monomer exists in either a metastable liquid state or a crystalline state at ambient conditions. Due to mobility restrictions, extremely poor polymerization kinetics and functional group conversions are typically achieved in solid state polymerizations. However, the solid-state photopolymerization of a cyclic acetal urethane acrylate results in nearly identical polymerization rates and ultimately higher conversion in the crystalline state than in the liquid state under otherwise identical conditions. We conclude that the crystallization process occurs in such a manner as to template the acrylic double bonds in a structure that facilitates rapid, minimally activated propagation.
Systematic design of flat band slow light in photonic crystal waveguides (2008)

We present a systematic procedure for designing "flat bands" of photonic crystal waveguides for slow light propagation. The procedure aims to maximize the group index - bandwidth product by changing the position of the first two rows of holes of W1 line defect photonic crystal waveguides. A nearly constant group index - bandwidth product is achieved for group indices of 30-90 and as an example, we experimentally demonstrate flat band slow light with nearly constant group indices of 32.5, 44 and 49 over 14 nm, 11 nm and 9.5 nm bandwidth around 1550 nm, respectively.
Phage Display Libraries as a Source of Tumour-Targeting Agents (2001)

One way to improve the therapeutic index of anti-cancer agents would be to target them to the tumour site, thereby sparing normal tissues. Tumour targeting approaches heavily rely on the availability of specific binding molecules, recognising markers which are selectively expressed in the tumour environment. The display of antibody repertoires on the surface of filamentous phage, together with efficient selection-amplification schemes, allows the isolation of good-quality human antibodies against virtually any molecular target. This article illustrates how antibody phage technology has been used in our laboratory for the isolation of tumour targeting agents. Furthermore, we present recent developments in the display of repertoires of small globular proteins on filamentous phage, aimed at the isolation of specific binding molecules with molecular weight < 10000 Dalton.
Enzymatic Resolution of Aminocyclopentenols as Precursors to <scp>d</scp>- and <scp>l</scp>-Carbocyclic Nucleosides (1998)

Racemic cis-4-aminocyclopent-2-en-1-ols were synthesized in three steps utilizing hetero Diels−Alder chemistry. Starting from suitably protected hydroxylamines, oxidization with sodium periodate and trapping with cyclopentadiene afforded cycloadducts (±)-5a−d. The N−O bond of the cycloadducts was reduced with Mo(CO)6 to afford (±)-cis-4-aminocyclopent-2-en-1-ols (±)-6a−d. These compounds, or their corresponding acetates, were kinetically resolved by enzymatic acetylation or hydrolysis, respectively. Enzymatic acetylation of cis-N-(benzylcarbamoyl)-4-aminocyclopent-2-enol [(±)-6a] with Candida antarctica B lipase and Pseudomonas species lipase gave the corresponding acetate (−)-7a in 90% and 92% ee, respectively, after 40% conversion. Enzymatic hydrolysis of cis-N-acetyl-4-aminocyclopent-2-enol 1-O-acetate (±)-7d with electric eel acetylcholine esterase was successful in providing both cis-N-acetyl-4-aminocyclopent-2-enols (+)-6d and (+)-7d in 92% ee (99% ee after a single recrystallization) after 40% conversion. Further synthetic transformations of these resolved synthetic building blocks and derivatives are also reported.
Absence of lymph nodes in lymphotoxin-alpha(LT alpha)-deficient mice is due to abnormal organ development, not defective lymphocyte migration. (1995)

Mice homozygous for a targeted null mutation of lymphotoxin-alpha (LT alpha) are born without lymph nodes (LN) or Peyer's patches (PP) and with altered splenic architecture. To investigate the mechanism of failed LN organogenesis, we transferred bone marrow (BM) from Thy 1.2 LT alpha-deficient or Thy 1.2 wild type mice to lethally irradiated 8-12-week-old Thy 1.1 wild type recipients. Six to 10 weeks later, reconstitution of LN and spleen with Thy 1.2 cells was similar whether the BM was derived from LT alpha-deficient or wild type donors. In contrast, reconstitution of irradiated LT alpha-deficient mice with wild type BM did not induce the development of detectable LN, although reconstitution of the spleen occurred appropriately. The expression and regulation of the lymphocyte adhesion molecule L-selectin from the LT alpha-deficient mice appeared normal. These data indicate that LT alpha-dependent interactions must occur during development in order for LN genesis to take place; however, lymphocyte expression of LT alpha is not required for these cells to home to existing LN structures.
Encoding Dublin Core Metadata in HTML (1999)

The Dublin Core [DC1] is a small set of metadata elements for describing information resources. This document explains how these elements are expressed using the META and LINK tags of HTML [HTML4.0]. A sequence of metadata elements embedded in an HTML file is taken to be a description of that file. Examples illustrate conventions allowing interoperation with current software that indexes, displays, and manipulates metadata, such as [SWISH-E], [freeWAIS-sf2.0], [GLIMPSE], [HARVEST], [ISEARCH], etc., and the Perl [PERL] scripts in the appendix.
The Dynamics of Chromosome Organization and Gene Regulation (2003)

With the sequence of the human genome now complete, studies must focus on how the genome is functionally organized within the confines of the cell nucleus and the dynamic interplay between the genome and its regulatory factors to effectively control gene expression and silencing. In this review I describe our current state of knowledge with regard to the organization of chromosomes within the nucleus and the positioning of active versus inactive genes. In addition, I discuss studies on the dynamics of chromosomes and specific genetic loci within living cells and its relationship to gene activity and the cell cycle. Furthermore, our current understanding of the distribution and dynamics of RNA polymerase II transcription factors is discussed in relation to chromosomal loci and other nuclear domains.
A New Peptide Conjugate as a Highly Specific Substrate for MAP Kinase (1997)

A synthetic peptide (APRTPGGRC) cross-linked to poly-L-lysine through a carboxy-terminal cysteinyl residue was found to be a highly specific substrate for mitogen-activated protein (MAP) kinases. This peptide conjugate exhibited a much lower Km value (74 microM) than the free peptide substrate (APRTPGGRR, Km > 1 mM) previously used as a specific substrate for MAP kinases. Unlike myelin basic protein, which has been often used as a substrate for MAP kinases, this conjugate did not serve as substrate for cAMP-dependent protein kinase, protein kinase C, or multifunctional calmodulin-dependent protein kinases. Using the peptide conjugate as a substrate, MAP kinase activities in crude cell extracts were directly determined by in vitro assay and specifically detected by in-gel assay.
Characterization of the agarase system of a multiple carbohydrate degrading marine bacterium. (2001)

A marine bacterium strain 2-40 (2-40) degraded numerous complex carbohydrates, such as agar, chitin and alginate. It may play an important role in altering carbon fluxes in marine environments. End-product analyses revealed that 2-40 synthesized an agarase system that consisted of at least three enzymes, beta-agarase I, beta-agarase II and alpha-agarase, which acted in concert to degrade polymeric agar to D-galactose and 3,6-anhydro-L-galactose. The agarase system was shown to be both cell envelope-associated and extracellular, with the relative concentrations depending on the growth phase. The principal depolymerase, a beta-agarase I, hydrolysed agar to both neoagarotetrose and neoagarobiose, as identified by thin layer chromatography. This agarase had a mass of 98 kD and a Pi of 4.3. The agarase system was repressed by D-glucose and D-galactose and induced by agar, agarose, neoagarobiose, neoagarotetrose and neoagarohexose.
Myeloid Derived Suppressor Cells Are Present at High Frequency in Neonates and Suppress In Vitro T Cell Responses (2014)

Over 4 million infants die each year from infections, many of which are vaccine-preventable. Young infants respond relatively poorly to many infections and vaccines, but the basis of reduced immunity in infants is ill defined. We sought to investigate whether myeloid-derived suppressor cells (MDSC) represent one potential impediment to protective immunity in early life, which may help inform strategies for effective vaccination prior to pathogen exposure. We enrolled healthy neonates and children in the first 2 years of life along with healthy adult controls to examine the frequency and function of MDSC, a cell population able to potently suppress T cell responses. We found that MDSC, which are rarely seen in healthy adults, are present in high numbers in neonates and their frequency rapidly decreases during the first months of life. We determined that these neonatal MDSC are of granulocytic origin (G-MDSC), and suppress both CD4+ and CD8+ T cell proliferative responses in a contact-dependent manner and gamma interferon production. Understanding the role G-MDSC play in infant immunity could improve vaccine responsiveness in newborns and reduce mortality due to early-life infections.
Effect of the diaminocyclohexane carrier ligand on platinum adduct formation, repair, and lethality (1990)

Platinum compounds with the diaminocyclohexane (dach) carrier ligand are of particular interest because cell lines that have developed resistance to platinum compounds in general often retain sensitivity to dach-platinum compounds, suggesting that the dach carrier ligand affects the formation, repair, or lethality of platinum-DNA adducts. The effect of the dach ligand on platinum adduct formation was assessed by using the (HaeIII-HindIII)146 fragment of pBR322 treated to give equal amounts of dach- or ethylene-diamine-platinum adducts. The sites of adduct formation were mapped by digestion with Escherichia coli ABC excinuclease. There were no significant effects of the dach carrier ligand on the types or sites of platinum adduct formation. The effect of the dach ligand on platinum adduct repair was determined by using synthetic oligomers designed to have single, specific platinum adducts (G monoadduct; GG, AG, or GNG diadduct) with either the dach or ethylenediamine (en) carrier ligand. These adducts differed significantly in their ability to serve as substrates for ABC excinuclease with GNG greater than or equal to G greater than AG greater than GG. The dach carrier ligand had little effect on the recognition of AG and GG adducts by ABC excinuclease, but significantly improved the ability of ABC excinuclease to excise G monoadducts and GNG diadducts. These data suggest that if the carrier ligand has any effect on the repair of platinum adducts, it is more likely to exert that effect on the repair of platinum monoadducts or GNG diadducts rather than on the more abundant AG or GG diadducts. [14C]Thiourea incorporation was used to quantitate the rate of monoadduct to diadduct conversion.(ABSTRACT TRUNCATED AT 250 WORDS)