gebhart/patrepeval huggingface dataset:
Improving microstructural quality of semipolar (1122) GaN on m-plane sapphire by a two-step growth process (2009)

This letter reports a two-step growth process for improving microstructural quality of semipolar (112̱2) GaN on nitridized m-plane sapphire. The two-step growth of (112̱2) GaN, islanding growth under high pressure followed by islands coalescence under low pressure, went through a roughening-recovery process, which was found very effective in reducing the density of stacking faults and dislocations in (112̱2) GaN. The x-ray rocking curves of both on-axis and off-axis planes were narrowed down by more than 50%. The improvement of GaN quality was confirmed by a boost in blue and green optical output of semipolar (112̱2) InGaN/GaN quantum wells.
Structure of the A Site of Escherichia coli 16 S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic (1996)

Aminoglycoside antibiotics that bind to 30S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation. The aminoglycoside antibiotic paromomycin binds specifically to an RNA oligonucleotide that contains the 30S subunit A site, and the solution structure of the RNA-paromomycin complex was determined by nuclear magnetic resonance spectroscopy. The antibiotic binds in the major groove of the model A-site RNA within a pocket created by an A-A base pair and a single bulged adenine. Specific interactions occur between aminoglycoside chemical groups important for antibiotic activity and conserved nucleotides in the RNA. The structure explains binding of diverse aminoglycosides to the ribosome, their specific activity against prokaryotic organisms, and various resistance mechanisms, and provides insight into ribosome function.
Exon skipping-mediated dystrophin reading frame restoration for small mutations (2009)

Exon skipping using antisense oligonucleotides (AONs) has successfully been used to reframe the mRNA in various Duchenne muscular dystrophy patients carrying deletions in the DMD gene. In this study we tested the feasibility of the exon skipping approach for patients with small mutations in in-frame exons. We first identified 54 disease-causing point mutations. We selected five patients with nonsense or frameshifting mutations in exons 10, 16, 26, 33, and 34. Wild-type and mutation specific 2'OMePS AONs were tested in cell-free splicing assays and in cultured cells derived from the selected patients. The obtained results confirm cell-free splicing assay as an alternative system to test exon skipping propensity when patients' cells are unavailable. In myogenic cells, similar levels of exon skipping were observed for wild-type and mutation specific AONs for exons 16, 26, and 33, whereas for exon 10 and exon 34 the efficacy of the AONs was significantly different. Interestingly, in some cases skipping efficiencies for mutated exons were quite dissimilar when compared with previous reports on the respective wild-type exons. This behavior may be related to the effect of the mutations on exon skipping propensity, and highlights the complexity of identifying optimal AONs for skipping exons with small mutations.
Silicidation-induced band gap shrinkage in Ge epitaxial films on Si (2004)

Ge epitaxial films on Si grown at high temperatures show a shrinkage in the direct band gap EgΓ as a result of the tensile strain accumulated during the cooling process after growth, making it a promising candidate for effective photon detection in L-band telecommunications. However, because of strain relaxation at temperatures &amp;gt;750 °C, only about 0.20% tensile strain can be accumulated at most. This leads to a direct band gap of 0.773 eV, corresponding to 1605 nm and is not enough to cover the whole L band (1561–1620 nm). In this letter, we report the strain enhancement in epitaxial Ge films induced by the formation of C54TiSi2 on the backside of the Si wafers. The backside C54-TiSi2 layer not only forms a good electric contact, but also increases the tensile strain of the Ge film on the front side from 0.20% to 0.24% and a further direct band gap shrinkage from 0.773 to 0.765 eV, corresponding to 1620 nm, which covers the whole L band. Since the silicidation process is compatible with Si complementary metal-oxide-semiconductor technology, this technique is promising to achieve low cost L-band photon detection completely with tensile strained Ge on Si.
The incidence of metastasis from cutaneous squamous cell carcinoma and the impact of its risk factors (2012)

We show a 1.9-2.6% metastatic rate for cSCC with MCD, histologic differentiation, PNI, and certain anatomical sub-sites being independent risk factors for metastasis. A prospective study on our proposed risk stratification scheme based on these parameters may lead to identification of high-risk lesions that would benefit from more intensive treatment and/or routine post-operative follow-up.Inc.
BCG and Cancer (1974)

Clinical StudiesPrevention of Acute Leukemia by Neonatal Vaccination with BCGReports that BCG inhibits the development of experimental neoplasms, including spontaneous murine leukemia, have prompted several groups to consider the possibility of lowering the incidence of leukemia in a human population by means of BCG vaccination. By comparing records of leukemia deaths with records of children receiving BCG vaccination at less than 15 years of age in the Province of Quebec, Davignon et al.131 132 133 found that death from leukemia was approximately half as common among children who had been vaccinated against BCG as among those who had not. The . . .
IL-32, a proinflammatory cytokine in rheumatoid arthritis (2006)

IL-32 is a recently discovered cytokine that induces TNFalpha, IL-1beta, IL-6, and chemokines. We investigated whether IL-32 is expressed in the synovia of patients with rheumatoid arthritis (RA) and studied associations with disease severity and the presence of other cytokines. Immunohistochemistry revealed that IL-32 is highly expressed in RA synovial tissue biopsies, whereas IL-32 was not observed in synovial tissues from patients with osteoarthritis. Moreover, in synovial biopsies from 29 RA patients with active disease, the level of IL-32 staining correlated with erythrocyte sedimentation rate, a marker of systemic inflammation (R = 0.63 and P < 0.0003). Synovial staining of IL-32 also correlated with indices of synovial inflammation (R = 0.80 and P < 0.0001) as well as synovial presence of TNFalpha (R = 0.68 and P < 0.004), IL-1beta (R = 0.79 and P < 0.0001), and IL-18 (R = 0.82 and P < 0.001). IL-32 was a potent inducer of prostaglandin E(2) release in mouse macrophages and human blood monocytes, an important property for inflammation. After the injection of human IL-32gamma into the knee joints of naïve mice, joint swelling, with pronounced influx of inflammatory cells and cartilage damage, was observed. In TNFalpha-deficient mice, IL-32-driven joint swelling was absent and cell influx was markedly reduced, but loss of proteoglycan was unaffected, suggesting that IL-32 activity is, in part, TNFalpha-dependent. IL-32, strongly associated with TNFalpha, IL-1beta, and IL-18, appears to play a role in human RA and may be a novel target in autoimmune diseases.
Remdesivir for pregnancy: A systematic review of antiviral therapy for COVID-19 (2022)

In pregnancy, the use of Remdesivir in combination with other COVID-19 treatments is inconclusive but its use should be followed with careful monitoring of adverse reactions and transaminase enzyme levels. Further studies are required to confirm its finding.
The gene structure of tetranectin, a plasminogen binding protein (1992)

The gene for human tetranectin was isolated from a genomic library with a mixture of degenerate oligonucleotide probes. The gene is about 12 kbp and contains two intervening sequences. The gene encodes a protein of 202 amino acid residues, with a signal peptide of 21 amino acid residues, followed by the tetranectin sequence of 181 amino acid residues. Northern blot analysis revealed that tetranectin mRNA was present in all eight tissues tested with the highest concentration in lung. Southern blot analysis showed hybridization to two genes. Further investigations are needed to determine whether the genes are allelic or non-allelic.
A Newly Developed Chemically Crosslinked Dextran–Poly(Ethylene Glycol) Hydrogel for Cartilage Tissue Engineering (2009)

Cartilage tissue engineering, in which chondrogenic cells are combined with a scaffold, is a cell-based approach to regenerate damaged cartilage. Various scaffold materials have been investigated, among which are hydrogels. Previously, we have developed dextran-based hydrogels that form under physiological conditions via a Michael-type addition reaction. Hydrogels can be formed in situ by mixing a thiol-functionalized dextran with a tetra-acrylated star poly(ethylene glycol) solution. In this article we describe how the degradation time of dextran-poly(ethylene glycol) hydrogels can be varied from 3 to 7 weeks by changing the degree of substitution of thiol groups on dextran. The degradation times increased slightly after encapsulation of chondrocytes in the gels. The effect of the gelation reaction on cell viability and cartilage formation in the hydrogels was investigated. Chondrocytes or embryonic stem cells were mixed in the aqueous dextran solution, and we confirmed that the cells survived gelation. After a 3-week culturing period, chondrocytes and embryonic stem cell-derived embryoid bodies were still viable and both cell types produced cartilaginous tissue. Our data demonstrate the potential of dextran hydrogels for cartilage tissue engineering strategies.
Applications of DNA microarray in disease diagnostics. (2009)

Rapid and accurate diagnosis of diseases is very important for appropriate treatment of patients. Recent advances in molecular-level interaction and detection technologies are upgrading the clinical diagnostics by providing new ways of diagnosis, with higher speed and accuracy. In particular, DNA microarrays can be efficiently used in clinical diagnostics which span from discovery of diseaserelevant genes to diagnosis using its biomarkers. Diagnostic DNA microarrays have been used for genotyping and determination of disease-relevant genes or agents causing diseases, mutation analysis, screening of single nucleotide polymorphisms (SNPs), detection of chromosome abnormalities, and global determination of posttranslational modification. The performance of DNA-microarray-based diagnosis is continuously improving by the integration of other tools. Thus, DNA microarrays will play a central role in clinical diagnostics and will become a gold standard method for disease diagnosis. In this paper, various applications of DNA microarrays in disease diagnosis are reviewed. Special effort was made to cover the information disclosed in the patents so that recent trends and missing applications can be revealed.
Electrospinning of nanofibers with core-sheath, hollow, or porous structures (2004)

Recently there has been a great deal of progress in the production of one-dimensional nanostructures with core-sheath structures from a rich variety of materials. Here we highlight the use of electrospinning in the fabrication of polymeric, ceramic, and composite nanofibers with core-sheath, hollow, or porous structures, as well as the efforts made to improve their morphological homogeneity, functionality, and device performance.
Methane and Trichloroethylene Degradation by Methylosinus trichosporium OB3b Expressing Particulate Methane Monooxygenase (1998)

Whole-cell assays of methane and trichloroethylene (TCE) consumption have been performed on Methylosinus trichosporium OB3b expressing particulate methane monooxygenase (pMMO). From these assays it is apparent that varying the growth concentration of copper causes a change in the kinetics of methane and TCE degradation. For M. trichosporium OB3b, increasing the copper growth concentration from 2.5 to 20 muM caused the maximal degradation rate of methane (V(max)) to decrease from 300 to 82 nmol of methane/min/mg of protein. The methane concentration at half the maximal degradation rate (K(s)) also decreased from 62 to 8.3 muM. The pseudo-first-order rate constant for methane, V(max)/K(s), doubled from 4.9 x 10 to 9.9 x 10 liters/min/mg of protein, however, as the growth concentration of copper increased from 2.5 to 20 muM. TCE degradation by M. trichosporium OB3b was also examined with varying copper and formate concentrations. M. trichosporium OB3b grown with 2.5 muM copper was unable to degrade TCE in both the absence and presence of an exogenous source of reducing equivalents in the form of formate. Cells grown with 20 muM copper, however, were able to degrade TCE regardless of whether formate was provided. Without formate the V(max) for TCE was 2.5 nmol/min/mg of protein, while providing formate increased the V(max) to 4.1 nmol/min/mg of protein. The affinity for TCE also increased with increasing copper, as seen by a change in K(s) from 36 to 7.9 muM. V(max)/K(s) for TCE degradation by pMMO also increased from 6.9 x 10 to 5.2 x 10 liters/min/mg of protein with the addition of formate. From these whole-cell studies it is apparent that the amount of copper available is critical in determining the oxidation of substrates in methanotrophs that are expressing only pMMO.
Actor-Critic based Training Framework for Abstractive Summarization (2018)

We present a training framework for neural abstractive summarization based on actor-critic approaches from reinforcement learning. In the traditional neural network based methods, the objective is only to maximize the likelihood of the predicted summaries, no other assessment constraints are considered, which may generate low-quality summaries or even incorrect sentences. To alleviate this problem, we employ an actor-critic framework to enhance the training procedure. For the actor, we employ the typical attention based sequence-to-sequence (seq2seq) framework as the policy network for summary generation. For the critic, we combine the maximum likelihood estimator with a well designed global summary quality estimator which is a neural network based binary classifier aiming to make the generated summaries indistinguishable from the human-written ones. Policy gradient method is used to conduct the parameter learning. An alternating training strategy is proposed to conduct the joint training of the actor and critic models. Extensive experiments on some benchmark datasets in different languages show that our framework achieves improvements over the state-of-the-art methods.
Signaling through Adenylyl Cyclase Is Essential for Hyphal Growth and Virulence in the Pathogenic FungusCandida albicans (2001)

The human fungal pathogen Candida albicans switches from a budding yeast form to a polarized hyphal form in response to various external signals. This morphogenetic switching has been implicated in the development of pathogenicity. We have cloned the CaCDC35 gene encoding C. albicans adenylyl cyclase by functional complementation of the conditional growth defect of Saccharomyces cerevisiae cells with mutations in Ras1p and Ras2p. It has previously been shown that these Ras homologues regulate adenylyl cyclase in yeast. The C. albicans adenylyl cyclase is highly homologous to other fungal adenylyl cyclases but has less sequence similarity with the mammalian enzymes. C. albicans cells deleted for both alleles of CaCDC35 had no detectable cAMP levels, suggesting that this gene encodes the only adenylyl cyclase in C. albicans. The homozygous mutant cells were viable but grew more slowly than wild-type cells and were unable to switch from the yeast to the hyphal form under all environmental conditions that we analyzed in vitro. Moreover, this morphogenetic switch was completely blocked in mutant cells undergoing phagocytosis by macrophages. However, morphogenetic switching was restored by exogenous cAMP. On the basis of epistasis experiments, we propose that CaCdc35p acts downstream of the Ras homologue CaRas1p. These epistasis experiments also suggest that the putative transcription factor Efg1p and components of the hyphal-inducing MAP kinase pathway depend on the function of CaCdc35p in their ability to induce morphogenetic switching. Homozygous cacdc35 Delta cells were unable to establish vaginal infection in a mucosal membrane mouse model and were avirulent in a mouse model for systemic infections. These findings suggest that fungal adenylyl cyclases and other regulators of the cAMP signaling pathway may be useful targets for antifungal drugs.
Oncolytic Activity of Vesicular Stomatitis Virus Is Effective against Tumors Exhibiting Aberrant p53, Ras, or Myc Function and Involves the Induction of Apoptosis (2001)

We have recently shown that vesicular stomatitis virus (VSV) exhibits potent oncolytic activity both in vitro and in vivo (S. Balachandran and G. N. Barber, IUBMB Life 50:135-138, 2000). In this study, we further demonstrated, in vivo, the efficacy of VSV antitumor action by showing that tumors that are defective in p53 function or transformed with myc or activated ras are also susceptible to viral cytolysis. The mechanism of viral oncolytic activity involved the induction of multiple caspase-dependent apoptotic pathways was effective in the absence of any significant cytotoxic T-lymphocyte response, and occurred despite normal PKR activity and eIF2alpha phosphorylation. In addition, VSV caused significant inhibition of tumor growth when administered intravenously in immunocompetent hosts. Our data indicate that VSV shows significant promise as an effective oncolytic agent against a wide variety of malignant diseases that harbor a diversity of genetic defects.
Microtiter format gene quantification by covalent capture of competitive PCR products: application to HIV-1 detection (1993)

We have developed a simple gene quantification system using the competitive polymerase chain reaction (CPCR) followed by microtiter format analysis. CPCR is carried out using a mutant competitor with the same size as the target DNA product, and a minimal base exchange to insure the same amplification kinetics. One primer is aminated at the 5' end to produce PCR products that are captured onto carboxylated wells of microtiter plates through peptide bond formation. The non-aminated DNA strands are stripped off from the wells by alkali washing, and the remaining aminated strands are hybridized with either a digoxigenin-labeled wild type-specific oligonucleotide probe or a competitor-specific probe. To standardize the hybridization conditions of the probes, a DNA construct containing wild type and mutant competitor sequences in tandem is captured at different concentrations, hybridized with the probes, and used to generate a standard curve. Bound probes are detected by anti-digoxigenin antibody conjugated with peroxidase and chromogen. Optical densities are recorded with a conventional microtiter plate reader and converted to concentrations according to the standard curves. The ratios of wild type DNA to mutant competitor are used to determine the initial amounts of wild type DNA in the samples. This method was used successfully to quantify human immunodeficiency virus type 1 (HIV-1) env gene in human lymphocytes. It only requires a thermal cycler and a conventional microtiter plate reader, and can be readily done on a large scale. Potential applications include detection of other pathogens, diagnosis of genetic disorders and studies of gene expression.
Use of an intensity threshold to improve the visibility of ghost images produced by incoherent light (2007)

In thermal light ghost imaging, the transparent mask, located in the object arm of the optical setup, is numerically reconstructed by correlating the speckle patterns acquired by the video camera with the output of a bucket detector placed behind the mask. We show that the visibility of images can be significantly improved by discarding every speckle pattern whose bucket output falls below a certain threshold. We also demonstrate that the efficiency of the conventional method strongly decreases when the speckle statistics deviate from the negative exponential, whereas the threshold method is more robust against changes in the statistical distribution of the speckle intensity. We also provide reasonable statistical explanations for these results.
Solving the Data Inter-operability Problem Using a Universal Data Access Broker (2008)

other. However like translation of human languages this solution falls short of the ultimate. We want the translator to be dynamically available. We want the translator not just to literally transpose but to deduce or infer semantics. We want the translator to understand all representations, including new variants or dialects as they are added. We want the translator to operate in real time (on the fly). Last but of course not least, we want to inter-operate with the translator in the representation of our choice, not one that the translator imposes on us because it will only support certain combinations of representations. Another human tendency is to continually attempt to solve a problem by inventing the ultimate representation for persistent data. For the problem of data inter-operability this tendency manifests as a series of generations of database technology with corresponding persistent representations for stored data. In theory translating all required data int
Side Chain Orientation in the Selectivity Filter of a Voltage-gated Ca2+ Channel (2000)

Four glutamate residues (EEEE locus) are essential for ion selectivity in voltage-gated Ca(2+) channels, with ion-specific differences in binding to the locus providing the basis of selectivity. Whether side chain carboxylates or alternatively main chain carbonyls of these glutamates project into the pore to form the ion-binding locus has been uncertain. We have addressed this question by examining effects of sulfhydryl-modifying agents (methanethiosulfonates) on 20 cysteine-substituted mutant forms of an L-type Ca(2+) channel. Sulfhydryl modifiers partially blocked whole oocyte Ba(2+) currents carried by wild type channels, but this block was largely reversed with washout. In contrast, each of the four EEEE locus glutamate --> cysteine mutants (0 position) was persistently blocked by sulfhydryl modifiers, indicating covalent attachment of a modifying group to the side chain of the substituted cysteine. Cysteine substitutions at positions immediately adjacent to the EEEE locus glutamates (+/-1 positions) were also generally susceptible to sulfhydryl modification. Sulfhydryl modifiers had lesser effects on channels substituted one position further from the EEEE locus (+/-2 positions). These results indicate that the carboxylate-bearing side chains of the EEEE locus glutamates and their immediate neighbors project into the water-filled lumen of the pore to form an ion-binding locus. Thus the structure of the Ca(2+) channel selectivity filter differs substantially from that of ancestral K(+) channels.
A Pd complex of a tridentate pincer CNC bis-carbene ligand as a robust homogenous Heck catalyst (2001)

The bis-carbene precursor, 1, gives a thermally very robust Pd(II) catalyst for Heck coupling that maintains activity even in boiling diethylacetamide (bp 184 °C) in air.
Control of gene expression by CRISPR-Cas systems (2013)

Clustered regularly interspaced short palindromic repeats (CRISPR) loci and their associated cas (CRISPR-associated) genes provide adaptive immunity against viruses (phages) and other mobile genetic elements in bacteria and archaea. While most of the early work has largely been dominated by examples of CRISPR-Cas systems directing the cleavage of phage or plasmid DNA, recent studies have revealed a more complex landscape where CRISPR-Cas loci might be involved in gene regulation. In this review, we summarize the role of these loci in the regulation of gene expression as well as the recent development of synthetic gene regulation using engineered CRISPR-Cas systems.