gebhart/patrepeval huggingface dataset:
Induction of actinorhodin production by rpsL (encoding ribosomal protein S12) mutations that confer streptomycin resistance in Streptomyces lividans and Streptomyces coelicolor A3(2) (1996)

A strain of Streptomyces lividans, TK24, was found to produce a pigmented antibiotic, actinorhodin, although S. lividans normally does not produce this antibiotic. Genetic analyses revealed that a streptomycin-resistant mutation str-6 in strain TK24 is responsible for induction of antibiotic synthesis. DNA sequencing showed that str-6 is a point mutation in the rpsL gene encoding ribosomal protein S12, changing Lys-88 to Glu. Gene replacement experiments with the Lys88-->Glu str allele demonstrated unambiguously that the str mutation is alone responsible for the activation of actinorhodin production observed. In contrast, the strA1 mutation, a genetic marker frequently used for crosses, did not restore actinorhodin production and was found to result in an amino acid alteration of Lys-43 to Asn. Induction of actinorhodin production was also detected in strain TK21, which does not harbor the str-6 mutation, when cells were incubated with sufficient streptomycin or tetracycline to reduce the cell's growth rate, and 40 and 3% of streptomycin- or tetracycline-resistant mutants, respectively, derived from strain TK21 produced actinorhodin. Streptomycin-resistant mutations also blocked the inhibitory effects of relA and brgA mutations on antibiotic production, aerial mycelium formation or both. These str mutations changed Lys-88 to Glu or Arg and Arg-86 to His in ribosomal protein S12. The decrease in streptomycin production in relC mutants in Streptomyces griseus could also be abolished completely by introducing streptomycin-resistant mutations, although the impairment in antibiotic production due to bldA (in Streptomyces coelicolor) or afs mutations (in S. griseus) was not eliminated. These results indicate that the onset and extent of secondary metabolism in Streptomyces spp. is significantly controlled by the translational machinery.
Analysis of Quantitative Trait Loci for Blood Pressure on Rat Chromosomes 2 and 13 (1996)

Previous studies have suggested the presence of quantitative trait loci (QTLs) influencing blood pressure on rat chromosomes 2 and 13. In this study, we mapped the QTLs in F2 rats derived from a cross of the spontaneously hypertensive rat and the Wistar-Kyoto rat and analyzed the effect of the QTLs on blood pressures measured longitudinally between 12 and 25 weeks of age. We analyzed 16 polymorphic markers spanning 147.3 cM on chromosome 2 and 13 markers spanning 91.6 cM on chromosome 13. Both chromosomes contained QTLs with highly significant effects on blood pressure (peak logarithm of the odds [LOD] scores, 5.64 and 5.75, respectively). On chromosome 2, the peak was localized to a position at anonymous marker D2Wox7, 2.9 cM away from the gene for the sodium-potassium ATPase alpha 1-subunit. On chromosome 13, the major peak coincided with the marker D13Mit2, 21.7 cM away from the renin gene, but there was a suggestion of multiple peaks. The effect of the QTL on chromosome 2 was seen throughout from 12 to 25 weeks of age, whereas interestingly, the effect for the QTL on chromosome 13 was maximal at 20 weeks of age but disappeared at 25 weeks of age, presumably because of the effect of either epistatic factors or environmental influences. The findings provide important information on QTLs influencing blood pressure on rat chromosomes 2 and 13 that will be useful in localizing and identifying the causative genes and emphasize the importance of age being taken into account when the effects of individual QTLs on a trait that shows significant age-related changes are being analyzed.
A survey of the optimal power flow literature (1991)

A survey is presented of publications in the fields of optimal power flow and dispatching. It suggests a classification of methods based on the choice of optimization techniques. The survey is summarized in a single flow-chart-type figure, which indicates the relationship between methods, their chronology, and their popularity. This figure is based on a compilation of over three hundred publications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Influence of Sn Migration on phase transition in GeTe and Ge2Se3 thin films (2010)

Phase transitions in GeTe/SnSe and Ge2Se3/SnTe are investigated using time resolved x-ray diffraction. GeTe exhibits a structural transition from rhombohedral to the cubic phase at 300 °C, which is ∼100 °C lower than that of pure GeTe. This is facilitated by incorporation of Sn from SnSe. Sn migration is observed explicitly in Ge2Se3/SnTe by separation of SnSe phase. Amorphous Ge2Se3 is also found to crystallize at a lower temperature of 300 °C resulting in orthorhombic GeSe and monoclinic GeSe2. Thus, inclusion of a Sn containing layer may offer a means to tailor phase transition in Ge-chalcogenide thin films for phase change memory applications.
Incorporating image degeneration modeling with multitask learning for image super-resolution (2015)

Learning the non-linear image upscaling process has previously been considered as a simple regression process, where various models have been utilized to describe the correlations between high-resolution (HR) and low-resolution (LR) images/patches. In this paper, we present a multitask learning framework based on deep neural network for image super-resolution, where we jointly consider the image super-resolution process and the image degeneration process. By sharing parameters between the two highly relevant tasks, the proposed framework could effectively improve the obtained neural network based mapping model between HR and LR image patches. Experimental results have demonstrated clear visual improvement and high computational efficiency, especially with large magnification factors.
Knowledge Authoring and Question Answering via Controlled Natural Language (2017)

Knowledge acquisition from text is the process of automatically acquiring, organizing and structuring knowledge from text which can be used to perform question answering or complex reasoning. However, current state-of-the-art systems are limited by the fact that they are not able to construct the knowledge base with high quality as knowledge representation and reasoning (KRR) has a keen requirement for the accuracy of data. Controlled Natural Languages (CNLs) emerged as a technology to author knowledge using a restricted subset of English. However, they still fail to do so as sentences that express the same information may be represented by different forms. Current CNL systems have limited power to standardize sentences that express the same meaning into the same logical form. We solved this problem by building the Knowledge Authoring Logic Machine (KALM), which is a technology for domain experts who are not familiar with logic to author knowledge using CNL. The system performs semantic analysis of English sentences and achieves superior accuracy of standardizing sentences that express the same meaning to the same logical representation. Besides, we developed the query part of KALM to perform question answering, which also achieves very high accuracy in query understanding.
Photochemistry of metal coordination complexes: metal to ligand charge transfer excited states (1986)

Abstract
CCR5 Gene Disruption via Lentiviral Vectors Expressing Cas9 and Single Guided RNA Renders Cells Resistant to HIV-1 Infection (2014)

CCR5, a coreceptor for HIV-1 entry, is a major target for drug and genetic intervention against HIV-1. Genetic intervention strategies have knocked down CCR5 expression levels by shRNA or disrupted the CCR5 gene using zinc finger nucleases (ZFN) or Transcription activator-like effector nuclease (TALEN). In the present study, we silenced CCR5 via CRISPR associated protein 9 (Cas9) and single guided RNAs (sgRNAs). We constructed lentiviral vectors expressing Cas9 and CCR5 sgRNAs. We show that a single round transduction of lentiviral vectors expressing Cas9 and CCR5 sgRNAs into HIV-1 susceptible human CD4+ cells yields high frequencies of CCR5 gene disruption. CCR5 gene-disrupted cells are not only resistant to R5-tropic HIV-1, including transmitted/founder (T/F) HIV-1 isolates, but also have selective advantage over CCR5 gene-undisrupted cells during R5-tropic HIV-1 infection. Importantly, using T7 endonuclease I assay we did not detect genome mutations at potential off-target sites that are highly homologous to these CCR5 sgRNAs in stably transduced cells even at 84 days post transduction. Thus we conclude that silencing of CCR5 via Cas9 and CCR5-specific sgRNAs could be a viable alternative strategy for engineering resistance against HIV-1.
Global perspectives on clinical adoption of NIPT (2015)

This study provides a snapshot of current use and experiences with NIPT globally. It also highlights differences in service provision that exists both across and within countries, emphasizing the need for developing national and international implementation guidelines for NIPT.
Treatment of ovarian cancer: current status. (1994)

Cytoreductive surgery followed by platinum-based combination chemotherapy has been standard therapy for patients with advanced epithelial ovarian cancer. Despite advances in surgery and in the development of a less toxic platinum compound (carboplatin), most patients with advanced ovarian cancer are not cured. Current clinical trials focus on dose-intense chemotherapy, routes and schedules of administration, and the role of paclitaxel (Taxol; Bristol-Myers Squibb Co, Princeton, NJ). This novel agent has been shown to be highly active in patients with platinum-resistant ovarian cancer. Paclitaxel together with platinum (ie, cisplatin or carboplatin) combinations are now being tested in prospective randomized trials and in pilot studies in previously untreated patients with advanced disease.
The DMAP interaction domain of UDP-GlcNAc:lysosomal enzyme N -acetylglucosamine-1-phosphotransferase is a substrate recognition module (2013)

UDP-GlcNAc:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-1-phosphotransferase) is an α2β2γ2 heterohexamer that mediates the initial step in the formation of the mannose 6-phosphate recognition signal on lysosomal acid hydrolases. We previously reported that the specificity of the reaction is determined by the ability of the α/β subunits to recognize a conformation-dependent protein determinant present on the acid hydrolases. We now present evidence that the DNA methyltransferase-associated protein (DMAP) interaction domain of the α subunit functions in this recognition process. First, GST-DMAP pulled down several acid hydrolases, but not nonlysosomal glycoproteins. Second, recombinant GlcNAc-1-phosphotransferase containing a missense mutation in the DMAP interaction domain (Lys732Asn) identified in a patient with mucolipidosis II exhibited full activity toward the simple sugar α-methyl d-mannoside but impaired phosphorylation of acid hydrolases. Finally, unlike the WT enzyme, expression of the K732N mutant in a zebrafish model of mucolipidosis II failed to correct the phenotypic abnormalities. These results indicate that the DMAP interaction domain of the α subunit functions in the selective recognition of acid hydrolase substrates and provides an explanation for the impaired phosphorylation of acid hydrolases in a patient with mucolipidosis II.
Current source density analysis of the potential evoked in hippocampus by perirhinal cortex stimulation (1997)

Previous anatomical research has demonstrated that the perirhinal cortex (PRC) projects to the dorsal hippocampal CA1 field. We have recently presented data (Liu and Bilkey, Hippocampus 1996; 6:125-135) which suggests that this pathway courses via the lateral perforant path (LPP). In the present study, laminar profiles of the average evoked potentials and current source density (CSD) analysis were used to study the input from the perirhinal cortex to the dorsal hippocampus in the urethane-anaesthetized rat. Stimulation of the lateral perforant path activated a current sink in the stratum lacunosum-moleculare of CA1 and the outer molecular layer of the dentate gyrus with an onset latency of 3.5 ms. Stimulation of the perirhinal cortex produced a very similar sink-source pattern with an onset latency of 4.0 ms. Higher-intensity stimulation of lateral entorhinal cortex also produced a similar pattern with an onset latency of 4.5 ms. Electrolytic lesions of PRC conducted 4-5 days prior to testing resulted in a major decrease (58%) in the amplitude of the LPP-elicited potentials and a corresponding reduction across the whole source-sink pattern. A similar result was observed following ibotenic acid lesions of PRC. In contrast, similar-sized electrolytic lesions of lateral entorhinal cortex produced a much smaller (16%) decrease in potential amplitude and little change in the source-sink pattern. These data provide further support for the hypothesis that perirhinal cortex projects to both the dentate gyrus and CA1 regions of the hippocampus via the lateral perforant path.
Alu-primed polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: identification of clones associated with a disease locus. (1991)

Over 400 yeast artificial chromosome (YAC) clones were isolated from the human X chromosome, and 110 of these were assigned to regions defined by chromosome translocation and deletion breakpoints. Polymerase chain reaction using Alu primers was applied to YAC clones in order to generate probes, to identify overlapping clones, and to derive "fingerprints" and sequence data directly from total yeast DNA. Several clones were identified in regions of medical interest. One set of three overlapping clones was found to cross a chromosomal translocation implicated in Lowe syndrome. The regional assignment of groups of YAC clones provides initiation points for further attempts to develop large cloned contiguous sequences, as well as material for investigation of regions involved in genetic diseases.
Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations (2001)

We report the genetic organisation of six prophages present in the genome of Lactococcus lactis IL1403. The three larger prophages (36-42 kb), belong to the already described P335 group of temperate phages, whereas the three smaller ones (13-15 kb) are most probably satellites relying on helper phage(s) for multiplication. These data give a new insight into the genetic structure of lactococcal phage populations. P335 temperate phages have variable genomes, sharing homology over only 10-33% of their length. In contrast, virulent phages have highly similar genomes sharing homology over >90% of their length. Further analysis of genetic structure in all known groups of phages active on other bacterial hosts such as Escherichia coli, Bacillus subtilis, MYCOBACTERIUM: and Streptococcus thermophilus confirmed the existence of two types of genetic structure related to the phage way of life. This might reflect different intensities of horizontal DNA exchange: low among purely virulent phages and high among temperate phages and their lytic homologues. We suggest that the constraints on genetic exchange among purely virulent phages reflect their optimal genetic organisation, adapted to a more specialised and extreme form of parasitism than temperate/lytic phages.
Probable Inference, the Law of Succession, and Statistical Inference (1927)

(1927). Probable Inference, the Law of Succession, and Statistical Inference. Journal of the American Statistical Association: Vol. 22, No. 158, pp. 209-212.
Magnetite Nanoparticles for the Preparation of Ultrapure RAFT Polymers (2008)

Magnetic nanoparticles (MNP) and the application of a strong external magnetic fields were used to separate living chains from dead chains prepared by the reversible addition-fragmentation chain transfer (RAFT) process, by using Z-functional RAFT agents that are strongly attracted to the MNP surface. The MNP dispersion was mixed with a 32% HCL solution and the organic phase containing the oleic acid and the polymer was extracted and dried to give the extracted polymer. The RAFT functional chains in the unextracted polymer result from the ligand exchange process in the extraction step, which does not attach all RAFT functional chains to the MNP surface. The results also show that the extension data for the unextracted polymer show a significant fraction of high M polymer that apparently contains some RAFT groups.
Violacein Extracted from Chromobacterium violaceum Inhibits Plasmodium Growth In Vitro and In Vivo (2009)

Violacein is a violet pigment extracted from the gram-negative bacterium Chromobacterium violaceum. It presents bactericidal, tumoricidal, trypanocidal, and antileishmanial activities. We show that micromolar concentrations efficiently killed chloroquine-sensitive and -resistant Plasmodium falciparum strains in vitro; inhibited parasitemia in vivo, even after parasite establishment; and protected Plasmodium chabaudi chabaudi-infected mice from a lethal challenge.
Polyphenol Supplementation as a Complementary Medicinal Approach to Treating Inflammatory Bowel Disease (2011)

Inflammatory bowel disease (IBD) comprises a group of idiopathic chronic intestinal inflammation syndromes that are very common in developed countries. It is characterized by intermittent episodes of clinical remission and relapse, with recurrent inflammatory injury that can lead to structural damage of the intestine. The uncontrolled intestinal immune response to bacterial antigens leads to the production of abundant cytokines and chemokines, by activated leukocytes and epithelial cells, which trigger inflammatory and oxidative reactions. The current treatment of IBD consists in long-term anti-inflammatory therapy that, however, does not exclude relapses and side effects, frequently resulting in surgical intervention. Polyphenols have been acknowledged to be anti-oxidant and anti-inflammatory and therefore, have been proposed as an alternative natural approach to prevent or treat chronic inflammatory diseases. Most studies have been in animal models of colitis, using chemical inducers or mice defective in anti-inflammatory mediators and in intestinal cell lines treated with pro-inflammatory cytokines or lipid oxidation products. These studies provide evidence that polyphenols can effectively modulate intestinal inflammation. They exert their effects by modulating cell signaling pathways, mainly activated in response to oxidative and inflammatory stimuli, and NF-kB is the principal downstream effector. Polyphenols may thus be considered able to prevent or delay the progression of IBD, especially because they reach higher concentrations in the gut than in other tissues. However, knowledge of the use of polyphenols in managing human IBD is still scanty, and further clinical studies should afford more solid evidence of their beneficial effects.
The binding site for the liver-specific transcription factor Tf-LF1 and the TATA box of the human transferrin gene promoter are the only elements necessary to direct liver-specific transcriptionin vitro (1990)

We have studied the liver-specific transcriptional activity of the human transferrin gene promoter. Results of competition experiments, site-directed mutagenesis, and 5' deletion analysis have demonstrated that a TATA box and a binding site for the liver-specific protein Tf-LF1 are the only elements needed to direct hepatic-specific transcription in vitro. Thus, Tf-LF1 behaves as other previously described proteins, HNF-1, DBP and LF-A1, in that it is sufficient to confer liver-specific transcriptional activity to a promoter in vitro. This results contrast with observations made in transient expression experiments, in which Tf-LF1 binding alone cannot direct hepatic-specific expression, and the binding of at least one more protein, similar to C/EBP, is needed. Thus, as described for other hepatic genes, the number of elements necessary to confer tissue specificity is different in vivo and in vitro.
Papillary carcinoma of the thyroid: can operative management be based solely on fine-needle aspiration? (1997)

When papillary carcinoma of the thyroid or follicular-variant of papillary carcinoma of the thyroid is definitively diagnosed on fine-needle aspiration, the surgeon can perform definitive thyroidectomy without frozen section because of the high specificity for cancer. If the fine-needle aspiration is suspicious for papillary carcinoma of the thyroid, the incidence of cancer is 54 percent, and patients with these conditions should undergo surgery with frozen section. When either gross findings or frozen sections suggest malignancy, definitive thyroidectomy can be performed because 90 percent of such cases will be cancer. If frozen section is not diagnostic of malignancy, a thyroid lobectomy/isthmusectomy is recommended because 71 percent have a benign lesion. This systematic approach to papillary carcinoma of the thyroid will obviate unnecessary frozen sections while maintaining excellent diagnostic specificity.
Integrated Physiological Mechanisms of Exercise Performance, Adaptation, and Maladaptation to Heat Stress (2011)

This article emphasizes significant recent advances regarding heat stress and its impact on exercise performance, adaptations, fluid electrolyte imbalances, and pathophysiology. During exercise-heat stress, the physiological burden of supporting high skin blood flow and high sweating rates can impose considerable cardiovascular strain and initiate a cascade of pathophysiological events leading to heat stroke. We examine the association between heat stress, particularly high skin temperature, on diminishing cardiovascular/aerobic reserves as well as increasing relative intensity and perceptual cues that degrade aerobic exercise performance. We discuss novel systemic (heat acclimation) and cellular (acquired thermal tolerance) adaptations that improve performance in hot and temperate environments and protect organs from heat stroke as well as other dissimilar stresses. We delineate how heat stroke evolves from gut underperfusion/ischemia causing endotoxin release or the release of mitochondrial DNA fragments in response to cell necrosis, to mediate a systemic inflammatory syndrome inducing coagulopathies, immune dysfunction, cytokine modulation, and multiorgan damage and failure. We discuss how an inflammatory response that induces simultaneous fever and/or prior exposure to a pathogen (e.g., viral infection) that deactivates molecular protective mechanisms interacts synergistically with the hyperthermia of exercise to perhaps explain heat stroke cases reported in low-risk populations performing routine activities. Importantly, we question the "traditional" notion that high core temperature is the critical mediator of exercise performance degradation and heat stroke. Published 2011. This article is a U.S. Government work and is in the public domain in the USA.