gebhart/patrepeval huggingface dataset:
Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation. (1988)

A theoretical description of aqueous hydration in the minor groove of a B-form DNA is presented on the basis of a liquid-state Monte Carlo computer simulation on a system consisting of the oligonucleotide duplex d(CGCGAATTCGCG).d(GCGCTTAAGCGC) in a canonical B-form together with 1777 water molecules contained in a hexagonal prism cell and treated under periodic boundary conditions. The results are analyzed in terms of solvent density distributions. The calculated minor-groove solvent density shows considerable localization, indicative of discrete solvation sites and providing theoretical evidence for a well-defined ordered water structure. In the AATT sequence, this corresponds to the "spine of hydration" described by H. R. Drew and R. E. Dickerson [(1981) J. Mol. Biol. 151, 535-556] based on the x-ray crystal structure of the dodecamer hydrate. We find, however, that the calculated ordered water structure also extends into the CGCG flanking sequences, supported by the N2 hydrogen bond donors of the guanine residues and indicating that the spine of hydration could thus extend throughout the minor groove of a B-form DNA. This provides a possible explanation of the positive binding entropies observed by L. A. Marky and K. J. Breslauer [(1984) Proc. Natl. Acad. Sci. USA 84, 4359-4363] for both A.T and C.G sequences on the complexation of netropsin to the minor groove of DNAs. Implications of these results with regard to the thermodynamic stability of DNA in water and the sequence specificity of the minor groove hydration are discussed.
EZ-sketching (2014)

We present a new image-guided drawing interface called EZ-Sketching , which uses a tracing paradigm and automatically corrects sketch lines roughly traced over an image by analyzing and utilizing the image features being traced. While previous edge snapping methods aim at optimizing individual strokes, we show that a co-analysis of multiple roughly placed nearby strokes better captures the user's intent. We formulate automatic sketch improvement as a three-level optimization problem and present an efficient solution to it. EZ-Sketching can tolerate errors from various sources such as indirect control and inherently inaccurate input, and works well for sketching on touch devices with small screens using fingers. Our user study confirms that the drawings our approach helped generate show closer resemblance to the traced images, and are often aesthetically more pleasing.
Protein-tyrosine-phosphatase SHPTP2 is a required positive effector for insulin downstream signaling. (1995)

SHPTP2 is a ubiquitously expressed tyrosine-specific protein phosphatase that contains two amino-terminal Src homology 2 (SH2) domains responsible for its association with tyrosine-phosphorylated proteins. In this study, expression of dominant interfering mutants of SHPTP2 was found to inhibit insulin stimulation of c-fos reporter gene expression and activation of the 42-kDa (Erk2) and 44-kDa (Erk1) mitogen-activated protein kinases. Cotransfection of dominant interfering SHPTP2 mutants with v-Ras or Grb2 indicated that SHPTP2 regulated insulin signaling either upstream of or in parallel to Ras function. Furthermore, phosphotyrosine blotting and immunoprecipitation identified the 125-kDa focal adhesion kinase (pp125FAK) as a substrate for insulin-dependent tyrosine dephosphorylation. These data demonstrate that SHPTP2 functions as a positive regulator of insulin action and that insulin signaling results in the dephosphorylation of tyrosine-phosphorylated pp125FAK.
A Self‐Replicating Hexadeoxynucleotide (1986)

Autocatalysis in a nonenzymatic, templete-directed condensation has been demonstrated in a system consisting of three oligonucleotides. A simple form of self-replication occurs, albeit only to a small extent: the template T organizes the building blocks Å and B in such a way that condensation can occur, leading to a second template molecule. Such a nonenzymatic process has long been sought, because it is postulated as a sine qua non for prebiotic evolution in theories on the origin of life.
Type 5 and 8 capsular polysaccharides are expressed by Staphylococcus aureus isolates from rabbits, poultry, pigs, and horses (1993)

A total of 103 Staphylococcus aureus isolates from rabbits (n = 37), poultry (n = 33), pigs (n = 27), and horses (n = 6) and 14 Staphylococcus intermedius isolates from wild animals were serotyped for capsular polysaccharide types 5 and 8 by an enzyme-linked immunosorbent assay using polyclonal rabbit antibodies. About 98% of the S. aureus isolates were typeable. Type 5 was predominant in the poultry (75.8%) and pig (66.7%) isolates, whereas type 8 was more frequent among the isolates from rabbits (59.5%) and horses (83.3%). By contrast, none of the 14 S. intermedius isolates was typeable.
Immunosuppression Derived from Human B-Lymphoblastoid and Melanoma Cell Lines (1992)

Previous work conducted by the authors, using a murine model, suggested that soluble factors secreted by tumor cells suppress lymphocyte responses. To apply this premise to human tumors, the effects of UC729-6 (lymphoblastoid B-cell) and M21-HPB (malignant melanoma) conditioned media (CM) on normal lymphocyte proliferation, as well as on tumor cell growth in autologous CM was studied. The CM was collected at 2-5 day intervals from cultures of UC729-6 and M21-HPB cells in serum-free media. Phytohemagglutinin- and concanavalin A-stimulated mononuclear peripheral blood cells from healthy human donors showed decreased [3H]thymidine ([3H]Tdr) uptake in the presence of each CM when compared with controls. In assays using 100% CM, mitogen stimulation was 68-85% less than that of controls and 40-50% less using 50% CM. The suppression was more pronounced with UC729-6 CM than with M21-HPB CM. In mixed lymphocyte cultures (MLC), addition of 50% CM from either tumor cell line resulted in 40-50% reduction in [3H]Tdr uptake by lymphocytes. Incubation of UC729-6 cells in 5% to 100% of UC729-6 fCM (filter-concentrated) produced a decrease in [3H]Tdr uptake which was directly proportional to the amount of fCM present. In contrast, M21-HPB cell growth in autologous fCM was dependent on cell number, as well as on the amount of fCM used. Treatment of the UC729-6 fCM using acid (pH 4.5), trypsin (100 micrograms/ml), and heat (56 degrees C) did not restore mitogen-stimulated lymphoproliferation. However, the inhibition observed with UC729-6 fCM was partially reversed after dialysis with membranes having M(r) limits of 2.5 x 10(4), 1.5 x 10(4), or 1 x 10(4).
In vitro and in vivo characterization of porous poly‐L‐lactic acid coatings for subcutaneously implanted glucose sensors (2008)

The purpose of this study was to test the hypothesis that porous poly-L-lactic acid (PLLA) sensor coatings reduce fibrosis and promote blood microvessel formation in tissue adjacent to the sensor surface. Porous PLLA coatings were produced using ammonium bicarbonate as the gas foaming/salt leaching agent, and deployed on functional and nonfunctional sensors. The porous coatings minimally affected sensor accuracy and response rate in vitro. Three-week subcutaneous rat studies of nonfunctional glucose sensors showed the anticipated effect of porous coatings enhancing vascularity and decreasing collagen deposition. In contrast, percutaneous functional sensors with and without porous coatings showed no significant difference in terms of histology or sensor response. In spite of the observation that texturing increases the vascularity of the tissue that surrounds implanted sensors, other factors such as the additional mechanical stresses imposed by percutaneous tethering may override the beneficial effects of the porous coatings.
Large Signal Stability Analysis and Stabilization of Converters Connected to Grid Through <inline-formula> <tex-math notation="TeX">$LCL$</tex-math></inline-formula> Filters (2014)

This paper develops a robust tool for handling ac side stability issues occurring in LCL-filter-based grid-connected converters.LCL filters give advantages in cost and dynamic as smaller inductors employed compared with L filters for the same required damping of the switching harmonics. Nevertheless, the additional poles introduced by the LC part induce resonance in the system leading to stability problems. To deal with this stability issue, a new damping method based on the generalized circle criterion is proposed in this paper. The large signal nature of the applied theory allows obtaining high damping efficiency and robustness under large variations of the grid impedance. A theoretical analysis and the experimental results are presented to show the effectiveness of the proposed compensating method.
Activin-Binding Protein from Rat Ovary Is Follistatin (1990)

Activin, a member of the transforming growth factor beta protein family, was originally isolated from gonadal fluids and stimulates the release of pituitary follicle-stimulating hormone (FSH). Activin has numerous functions in both normal and neoplastic cells. Various cells synthesize activin and have a specific binding site for this peptide. However, the molecular basis for its actions is unknown. A binding protein for activin was purified from rat ovary and was identical to follistatin, a specific inhibitor of FSH release. It is likely that the binding protein participates in the diverse regulatory actions of activin.
Ectodomain Shedding of Epidermal Growth Factor Receptor Ligands Is Required for Keratinocyte Migration in Cutaneous Wound Healing (2000)

Keratinocyte proliferation and migration are essential to cutaneous wound healing and are, in part, mediated in an autocrine fashion by epidermal growth factor receptor (EGFR)-ligand interactions. EGFR ligands are initially synthesized as membrane-anchored forms, but can be processed and shed as soluble forms. We provide evidence here that wound stimuli induce keratinocyte shedding of EGFR ligands in vitro, particularly the ligand heparin-binding EGF-like growth factor (HB-EGF). The resulting soluble ligands stimulated transient activation of EGFR. OSU8-1, an inhibitor of EGFR ligand shedding, abrogated the wound-induced activation of EGFR and caused suppression of keratinocyte migration in vitro. Soluble EGFR-immunoglobulin G-Fcgamma fusion protein, which is able to neutralize all EGFR ligands, also suppressed keratinocyte migration in vitro. The application of OSU8-1 to wound sites in mice greatly retarded reepithelialization as the result of a failure in keratinocyte migration, but this effect could be overcome if recombinant soluble HB-EGF was added along with OSU8-1. These findings indicate that the shedding of EGFR ligands represents a critical event in keratinocyte migration, and suggest their possible use as an effective clinical treatment in the early phases of wound healing.
Temporal dynamics in the ruminal microbiome of dairy cows during the transition period (2014)

The transition period in dairy cows refers to the period from 3 wk before calving to 3 wk post-calving and is a critical time for influencing milk production and cow health. We hypothesize that the ruminal microbiome shifts as dairy cows transition from a non-lactation period into lactation due to changes in dietary regimen. The purpose of this study was to identify differences in the ruminal microbiome of primiparous and multiparous (study group) cows during the transition period. Five primiparous and 5 multiparous cows were randomly selected from a herd, and ruminal contents were sampled, via stomach tube, 4 times (study day) at 3 wk before calving date (S1), 1 to 3 d post-calving (S2), and 4 (S3) and 8 wk (S4) into lactation and were evaluated for bacterial diversity using 16S pyrotags. Both groups received the same pre-fresh diet (14.6% CP, 44.0% NDF, 21.9% starch) and 3 different lactation diets (L1, L2, and L3) varying in forage base but not amount and formulated to have similar nutrient specifications (16.8% to 17.7% CP; 32.5% to 33.6% NDF; 26.2% to 29.1% starch) post-calving. Forty bacterial communities were analyzed on the basis of annotations of 100,000 reads, resulting in 15,861 operational taxonomic units grouped into 17 bacterial phyla. The UniFrac distance metric revealed that both study group and study day had an effect on the community compositions (P < 0.05; permutational multivariate ANOVA test). The most abundant phyla observed were Bacteroidetes and Firmicutes across all the communities. As the cows transitioned into lactation, the ratio of Bacteroidetes to Firmicutes increased from 6:1 to 12:1 (P < 0.05; Mann-Whitney U test), and this ratio was greater in primiparous cows than in multiparous cows (P < 0.05). This report is the first to explore the effect of parity on dynamics in the ruminal microbiome of cows during the transition period.
Synthesis of disubstituted tetrahydrocarbazoles with potential antidepressive activity. (1989)

A new series of disubstituted tetrahydrocarbazoles were synthesized. They are tested for antidepressive activity by the Porsolt's forced swimming test (one of the acute stress methods) and by the prevention of reserpine induced hypothermia and ptosis in mice. 3-Morpholino-1-[N-(6-methoxy-1,2,3,4- tetrahydrocarbozolyl)2-propanol, fumarate (XI) was demonstrated to be the most promising compound of this series. Besides, this series did not present the most common adverse effects of the conventional tricyclic-antidepressants (loss of locomotor coordination, ataxia and anticholinergic activity).
Cytochrome P-450 mediates tissue-damaging hydroxyl radical formation during reoxygenation of the kidney. (1994)

Renal reperfusion injury results from oxygen radical generation. During reoxygenation of hypoxic kidney cells, xanthine oxidase produces superoxide radical, which eventuates in hydroxyl radical formation by the Fenton reaction. This reaction, catalyzed by transition metals such as iron, is particularly important because hydroxyl radical is highly reactive with a wide variety of biomolecules. We tested the hypothesis that this catalytic function is fostered by iron released from the heme moiety of cytochrome P-450. Primary cultures of rat proximal tubule epithelial cells studied in a subconfluent stage were subjected to 60 min of hypoxia and 30 min of reoxygenation. When cells were pretreated with one of three cytochrome P-450 inhibitors (piperonyl butoxide, cimetidine, or ketoconazole), lethal cell injury was attenuated. There was the expected increase in O2-. production during hypoxia/reoxygenation that cytochrome P-450 inhibitors did not prevent; on the other hand, inhibitors did prevent reoxygenation-induced hydroxyl radical formation. Analogously, the increase in catalytic iron (bleomycin-detectable iron) that accompanies hypoxia/reoxygenation did not occur in the presence of cytochrome P-450 inhibitors. In vivo studies confirmed a protective effect of cytochrome P-450 inhibition because glomerular filtration rate was better preserved in rats pretreated with cimetidine and then subjected to renal artery occlusion. In summary, several chemically distinct cytochrome P-450 inhibitors reduced iron release, and thereby, hydroxyl radical formation and reoxygenation-induced lethal cell injury, without inhibiting superoxide radical formation. We conclude that highly labile P-450 may act as an Fe-donating catalyst for Fenton reaction production of HO.-mediated reperfusion injury.
Diagnosis, treatment, and outcomes of coccidioidomycosis in allogeneic stem cell transplantation (2015)

Coccidioidomycosis is associated with high morbidity and mortality in allo-HSCT recipients in an area endemic for Coccidioides. Diagnosis of this infection can be difficult and often requires multiple and frequently invasive tests. Antifungal prophylaxis should be considered for patients at highest risk.
Automatic detection of cross-browser incompatibilities using machine learning and screenshot similarity (2017)

Cross Browser Incompatibilities (XBIs) stands for compatibility issues which can be observed while rendering the same Web application in different browsers. The increasing number of browser implementations and the continuous evolving characteristic of Web technologies, lead to differences in how browsers behave and render Web applications. Every element of a Web application should be correctly rendered and present the same behavior, despite the Web browser implementation, version, or OS which is used by users [1]. In order to overcome this issue during the Web Engineering process, developers must detect and fix XBIs before deploying Web applications, regardless of the effort and cost required to conduct these inspections. This research has the goal of elaborating an approach for automatically detecting XBIs in Web applications, using machine learning (supervised learning algorithms) and screenshot similarity to detect XBIs. Next section presents the related work of this research.
A Deficiency of the Small GTPase rab8 Inhibits Membrane Traffic in Developing Neurons (1995)

One of the major activities of developing neurons is the transport of new membrane to the growing axon. Candidates for playing a key role in the regulation of this intense traffic are the small GTP-binding proteins of the rab family. We have used hippocampal neurons in culture and analyzed membrane traffic activity after suppressing the expression of the small GTP-binding protein rab8. Inhibition of protein expression was accomplished by using sequence-specific antisense oligonucleotides. While rab8 depletion resulted in the blockage of morphological maturation in 95% of the neurons, suppression of expression of another rab protein, rab3a, had no effect, and all neurons developed normal axons and dendrites. The impairment of neuronal maturation by rab8 antisense treatment was due to inhibition of membrane traffic. Thus, by using video-enhanced differential interference contrast microscopy, we observed in the rab8-depleted cells a dramatic reduction in the number of vesicles undergoing anterograde transport. Moreover, by incubating antisense-treated neurons with Bodipy-labeled ceramide, a fluorescent marker for newly formed exocytic vesicles, we observed fluorescence labeling restricted to the Golgi apparatus, whereas in control cells labeling was found also in the neurites. These results show the role of the small GTPase rab8 in membrane traffic during neuronal process outgrowth.
Chlamydia trachomatisPolymorphic Membrane Protein D Is an Oligomeric Autotransporter with a Higher-Order Structure (2008)

Chlamydia trachomatis is a globally important obligate intracellular bacterial pathogen that is a leading cause of sexually transmitted disease and blinding trachoma. Effective control of these diseases will likely require a preventative vaccine. C. trachomatis polymorphic membrane protein D (PmpD) is an attractive vaccine candidate as it is conserved among C. trachomatis strains and is a target of broadly cross-reactive neutralizing antibodies. We show here that immunoaffinity-purified native PmpD exists as an oligomer with a distinct 23-nm flower-like structure. Two-dimensional blue native-sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses showed that the oligomers were composed of full-length PmpD (p155) and two proteolytically processed fragments, the p73 passenger domain (PD) and the p82 translocator domain. We also show that PmpD undergoes an infection-dependent proteolytic processing step late in the growth cycle that yields a soluble extended PD (p111) that was processed into a p73 PD and a novel p30 fragment. Interestingly, soluble PmpD peptides possess putative eukaryote-interacting functional motifs, implying potential secondary functions within or distal to infected cells. Collectively, our findings show that PmpD exists as two distinct forms, a surface-associated oligomer exhibiting a higher-order flower-like structure and a soluble form restricted to infected cells. We hypothesize that PmpD is a multifunctional virulence factor important in chlamydial pathogenesis and could represent novel vaccine or drug targets for the control of human chlamydial infections.
A Decade of Step and Flash Imprint Lithography (2009)

Step and Flash Imprint Lithography (SFIL) was first reported ten years ago. The technology has advanced in many ways during the last decade. There are sophisticated, imprint tools available from commercial suppliers and high resolution templates can be purchased from several vendors. The materials and the process have evolved and matured to enable printing of sub 10nm structures, inverse tone printing, printing on both sides of disk drive substrates, printing in three dimensions to enable efficient production of CMOS wiring levels and printing of functional materials tailored to enable production of photonic crystals, insulators, etc. While great progress has been made in many areas, there remain concerns among some about defectivity and the throughput of the process.
Quasi-holographic techniques in the microwave region (1971)

Various microwave processes, including synthetic-aperture radar and linearly frequency-modulated pulse compression, are described as analogs of holography. The holographic viewpoint often leads to a new understanding and to new methods of signal processing.
Transcriptional Activation by NF-κB Requires Multiple Coactivators (1999)

Nuclear factor-kappaB (NF-kappaB) plays a role in the transcriptional regulation of genes involved in inflammation and cell survival. In this report we demonstrate that NF-kappaB recruits a coactivator complex that has striking similarities to that recruited by nuclear receptors. Inactivation of either cyclic AMP response element binding protein (CREB)-binding protein (CBP), members of the p160 family of coactivators, or the CBP-associated factor (p/CAF) by nuclear antibody microinjection prevents NF-kappaB-dependent transactivation. Like nuclear receptor-dependent gene expression, NF-kappaB-dependent gene expression requires specific LXXLL motifs in one of the p160 family members, and enhancement of NF-kappaB activity requires the histone acetyltransferase (HAT) activity of p/CAF but not that of CBP. This coactivator complex is differentially recruited by members of the Rel family. The p50 homodimer fails to recruit coactivators, although the p50-p65 heterodimeric form of the transcription factor assembles the integrator complex. These findings provide new mechanistic insights into how this family of dimeric transcription factors has a differential effect on gene expression.
PLA nonwovens modified with poly(dimethylaminoethyl methacrylate) as antimicrobial filter materials for workplaces (2014)

The objective of the present study was to assess the antimicrobial effectiveness of silver- and copper-modified polylactide (PLA)–poly(dimethylaminoethyl methacrylate) (PDMAEMA) nonwovens used as materials for the production of air purifying respirators. The antimicrobial activity of six types of PLA nonwovens, with different PDMAEMA, Ag, and Cu contents, were tested using the ATCC 100 method. Microorganisms were isolated from the air in 12 workplaces within composting plants, tanneries, and museums. Dominant bacterial and fungal species were identified using 16S RNA and ITS1/2 molecular analysis, respectively. Air samples collected from the composting plant and tannery were highly contaminated with bacteria, while those from museums with fungi (10 3 –10 4 CFU/m 3 ). We identified potentially pathogenic microorganisms from the following genera: Bacillus, Corynebacterium, Pseudomonas, Candida, Aspergillus, Penicillium, Scopulariopsis, and Paecilomyces. PLA nonwovens containing 5.1% poly(dimethylaminoethyl methacrylate) and 2.7% Ag or 3.8% Cu exhibited good antimicrobial properties ( R &gt; 99.9%) against the pathogenic strains found in the above workplaces. These nonwovens also have good inspiratory resistance parameters.