gebhart/patrepeval huggingface dataset:
High-Throughput Functional Analysis of the Synechococcus elongatus PCC 7942 Genome (2005)

Synechococcus elongatus PCC 7942 was the first cyanobacterial strain to be reliably transformed by exogenously added DNA and has become the model organism for cyanobacterial circadian rhythms. With a small genome (2.7 Mb) and well-developed genetic tools, PCC 7942 provides an exceptional opportunity to elucidate the circadian mechanism through genetics. We describe a project to create mutations in every locus of the genome, both to assay each locus for its potential contribution to the circadian clock and to archive data for the cyanobacterial community. Cosmid clones that carry inserts of PCC 7942 DNA are saturated with transposon insertions in vitro to provide sequencing templates and substrates for mutagenesis of the PCC 7942 genome via homologous recombination. We have mutagenized 53% of the chromosome from 50 chromosome-bearing cosmids and identified the positions of insertions in 31 of those cosmids and the 46 kb plasmid, pANL. PCC 7942 mutants defective for 490 different genes have been screened for circadian phenotypes. Mutagenesis of three apparently essential loci, including clpPIIclpX, resulted in circadian phenotypes. We developed an effective antisense suppression method to further the analysis of essential genes. When completed, the set of comprehensive mutations will provide the community with a unique resource whose impact will extend beyond circadian research.
The mood stabilizer valproic acid stimulates GABA neurogenesis from rat forebrain stem cells (2004)

Valproate, an anticonvulsant drug used to treat bipolar disorder, was studied for its ability to promote neurogenesis from embryonic rat cortical or striatal primordial stem cells. Six days of valproate exposure increased by up to fivefold the number and percentage of tubulin beta III-immunopositive neurons, increased neurite outgrowth, and decreased by fivefold the number of astrocytes without changing the number of cells. Valproate also promoted neuronal differentiation in human fetal forebrain stem cell cultures. The neurogenic effects of valproate on rat stem cells exceeded those obtained with the neurotrophins brain-derived growth factor (BDNF) or NT-3, and slightly exceeded the effects obtained with another mood stabilizer, lithium. No effect was observed with carbamazepine. Most of the newly formed neurons were GABAergic, as shown by 10-fold increases in neurons that immunostained for GABA and the GABA-synthesizing enzyme GAD65/67. Double immunostaining for bromodeoxyuridine and tubulin beta III showed that valproate increased by four- to fivefold the proliferation of neuronal progenitors derived from rat stem cells and increased cyclin D2 expression. Valproate also regulated the expression of survival genes, Bad and Bcl-2, at different times of treatment. The expression of prostaglandin E synthase, analyzed by quantitative RT-PCR, was increased by ninefold as early as 6 h into treatment by valproate. The enhancement of GABAergic neuron numbers, neurite outgrowth, and phenotypic expression via increases in the neuronal differentiation of neural stem cell may contribute to the therapeutic effects of valproate in the treatment of bipolar disorder.
[Angiomyolipoma of the kidney: report of three cases and a statistical study of 194 cases in Japan]. (1984)

Three cases of renal angiomyolipoma are reported. The first case was a 53-year-old female with the complaint of left flank pain. In both cases selective angiography revealed a renal tumor, and computerized tomography disclosed a renal mass with low density corresponding to the fat tissue. From several examinations these two cases were preoperatively diagnosed as renal angiomyolipoma and nephrectomy was performed. Histopathological diagnosis was renal angiomyolipoma. The third case was a 64-year-old female with the complaints of left flank pain and macrohematuria. In this case computerized tomography revealed a renal mass which did not have a low density area. The possibility of renal cell carcinoma was considered and nephrectomy was performed. Histological diagnosis was renal angiomyolipoma which was primarily composed of smooth muscle cells. The first case had a calcified lesion in the brain. But there was no evidence of tuberous sclerosis in the following two cases. Some problems in diagnosis and treatment of renal angiomyolipoma are presented, and a statistical study is made on 194 reported cases of renal angiomyolipoma in Japan.
An Architecture for Web-Based E-Learning Promoting Re-Usable Adaptive Educational E-Content (2002)

advantage and that copies bear the full citation on the first page. Copyrights for components of this work owned by others than IFETS must be honoured. Abstracting with credit is permitted. To copy otherwise, to republish, to post on servers, or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from the authors of the articles you wish to copy or kinshuk@massey.ac.nz.
Neuroanatomical Circuitry Associated with Exploratory Eye Movement in Schizophrenia: A Voxel-Based Morphometric Study (2011)

Schizophrenic patients present abnormalities in a variety of eye movement tasks. Exploratory eye movement (EEM) dysfunction appears to be particularly specific to schizophrenia. However, the underlying mechanisms of EEM dysfunction in schizophrenia are not clearly understood. To assess the potential neuroanatomical substrates of EEM, we recorded EEM performance and conducted a voxel-based morphometric analysis of gray matter in 33 schizophrenic patients and 29 well matched healthy controls. In schizophrenic patients, decreased responsive search score (RSS) and widespread gray matter density (GMD) reductions were observed. Moreover, the RSS was positively correlated with GMD in distributed brain regions in schizophrenic patients. Furthermore, in schizophrenic patients, some brain regions with neuroanatomical deficits overlapped with some ones associated with RSS. These brain regions constituted an occipito-tempro-frontal circuitry involved in visual information processing and eye movement control, including the left calcarine cortex [Brodmann area (BA) 17], the left cuneus (BA 18), the left superior occipital cortex (BA 18/19), the left superior frontal gyrus (BA 6), the left cerebellum, the right lingual cortex (BA 17/18), the right middle occipital cortex (BA19), the right inferior temporal cortex (BA 37), the right dorsolateral prefrontal cortex (BA 46) and bilateral precentral gyri (BA 6) extending to the frontal eye fields (FEF, BA 8). To our knowledge, we firstly reported empirical evidence that gray matter loss in the occipito-tempro-frontal neuroanatomical circuitry of visual processing system was associated with EEM performance in schizophrenia, which may be helpful for the future effort to reveal the underlying neural mechanisms for EEM disturbances in schizophrenia.
Photoluminescence from silicon nano-particles synthesized by laser-induced decomposition of silane (2000)

This work deals with photoluminescence study of silicon nanoparticles produced by CO2-laser-induced decomposition of SiH4 mixed to helium in a controlled atmosphere reactor. By adjusting the pressure of both reactor and precursor gas and its dilution rate in helium, we were able to control, to a certain extent, the silicon growth rate and hence the particle diameter. This latter was determined by both small angle neutron scattering techniques and high resolution transmission electron microscopy observations. Particles with mean diameter ranging between 3 and 10 nm were submitted to photoluminescence and infrared absorption spectroscopy measurements. The photoluminescence spectra revealed two main peaks at about 1.7 and 2.1 eV. The peak position of the former was insensitive to the change of particle size, while its intensity increased after oxidation. The latter showed, however, a slight size dependence but had undergone a drastic decrease after oxidation. These features enabled us to ascribe the red peak (1.7 eV) to some radiative surface defect, while the yellow peak (2.1 eV) appeared consistent with an emission from an oxygen-related defect such as the nonbridging oxygen hole center.
InfoGather (2012)

The Web contains a vast corpus of HTML tables, specifically entity attribute tables. We present three core operations, namely entity augmentation by attribute name, entity augmentation by example and attribute discovery, that are useful for "information gathering" tasks (e.g., researching for products or stocks). We propose to use web table corpus to perform them automatically. We require the operations to have high precision and coverage, have fast (ideally interactive) response times and be applicable to any arbitrary domain of entities. The naive approach that attempts to directly match the user input with the web tables suffers from poor precision and coverage.
Misacylated Transfer RNAs Having a Chemically Removable Protecting Group (1998)

The 4-pentenoyl group and a number of derivatives have been studied as protecting groups for N(alpha) of the aminoacyl moiety in misacylated tRNAs. The unsubstituted 4-pentenoyl group itself was found to function as efficiently as any of the derivatives studied. Four different N-(4-pentenoyl)aminoacyl-tRNA(CUA)s were prepared and shown to undergo deprotection readily upon admixture of aqueous iodine; the derived misacylated tRNAs all functioned well as suppressors of a nonsense codon in an in vitro protein biosynthesizing system. Also prepared were four N(alpha)-(4-pentenoyl)aspartyl-tRNA(CUA)s that were protected on the side chain carboxylate as the nitroveratryl ester. Following treatment with aqueous iodine, the misacylated suppressor tRNAs incorporated the aspartate derivatives into position 27 of dihydrofolate reductase by suppression of a UAG codon in the mRNA. The suppression yields were significantly better than those obtained when side chain protection was absent. The resulting "caged proteins" were inactive, but full catalytic potential was restored by irradiation under conditions sufficient to effect deprotection of the side chain carboxylate moiety.
Immunohistochemical analysis of NY-ESO-1 antigen expression in normal and malignant human tissues (2001)

NY-ESO-1, a member of the CT (cancer/testis) family of antigens, is expressed in normal testis and in a range of human tumor types. Knowledge of NY-ESO-1 expression has depended on RT-PCR detection of mRNA and there is a need for detecting NY-ESO-1 at the protein level. In the present study, a method for the immunochemical detection of NY-ESO-1 in paraffin-embedded tissues has been developed and used to define the expression pattern of NY-ESO-1 in normal tissues and in a panel of human tumors. No normal tissue other than testis showed NY-ESO-1 reactivity, and expression in testis was restricted to germ cells particularly spermatogonia. In human tumors, the frequency of NY-ESO-1 antigen expression corresponds with past analysis of NY-ESO-1 mRNA expression e.g., 20-30% of lung cancers, bladder cancers and melanoma, and no expression in colon and renal cancer. Co-typing of NY-ESO-1 antigen and mRNA expression in a large panel of lung cancers showed a good correlation. There is great variability in NY-ESO-1 expression in individual tumors, ranging from an infrequent homogeneous pattern of staining to highly heterogeneous antigen expression.
Folic acid-induced renal injury and repair. Correlation of structural and functional abnormalities. (1980)

Folic acid administered to rats in doses of 100, 200, 300, and 400 mg/kg of body weight resulted in alterations in renal tubular morphologic features and renal function, with the severity of the changes proportional to the dose. Renal cell incorporation of tritiated thymidine varied according to cell type and increased with the dose of folic acid. The results demonstrate (1) a spectrum of renal injury and subsequent repair; (2) a reduction in concentrating ability and creatinine clearance proportional to the dose of folic acid in the range of 100 to 300 mg/kg; and (3) increased mitotic activity at high doses of folic acid (300 and 400 mg/kg) of all renal tubular cell types examined, with collecting ducts demonstrating the greatest degree of regeneration. From these observations, we conclude that there is a predictable relationship between the dosage of folic acid and the abnormalities of morphologic features and function in this model of kidney injury.
Dengue viruses and mononuclear phagocytes. I. Infection enhancement by non-neutralizing antibody (1977)

Cultured mononuclear peripheral blood leukocytes (PBL) from nonimmune human beings and monkeys are nonpermissive to dengue 2 virus (D2V) infection at multiplicities of infection of 0.001-0.1, but become permissive when non-neutralizing dengue antibody is added to medium. D2V infection occurred in PBL prepared from anti-coagulated but not from defibrinated plasma. Infection enhancement was produced by multiple lots of heterotypic anti-dengue raised in several mammalian species. Homotypic anti-dengue neutralized D2V at high concentrations but enhanced at low concentrations; enhancement end point in one serum was 1:320,000. The infection-enhancing factor was a noncytophilic antibody of the IgG class. D2V infection occurred in the absence of heat-labile complement components but did not occur when complexes were prepared with anti- dengue F(ab)(2). Treatment of PBL with several proteases increased permissiveness to D2V infection by immune complexes but not by virus alone. Two rhesus monkey serums collected 14 days after D2V infection contained an IgG antibody with high-titered enhancing activity but with no hemagglutination-inhibition or neutralizing activity. Virus-antibody complexes are irreversibly attached to PBL within 15 min and completely internalized in 60 min. There was considerable variation in cellular infection in different experiments, however, maximum virus yields usually exceeded 1,000 plaque-forming units per 1 x 10(6) PBL occurring between 2 and 4 days in culture. In vitro antibody-dependent infection of PBL provides a possible model for study of pathogenetic mechanisms in infants with dengue shock syndrome who passively acquire maternal anti-dengue IgG.
Metabolic Engineering of a 1,2-Propanediol Pathway in Escherichia coli (1999)

1,2-Propanediol (1,2-PD) is a major commodity chemical that is currently derived from propylene, a nonrenewable resource. A goal of our research is to develop fermentation routes to 1,2-PD from renewable resources. Here we report the production of enantiomerically pure R-1,2-PD from glucose in Escherichia coli expressing NADH-linked glycerol dehydrogenase genes (E. coli gldA or Klebsiella pneumoniae dhaD). We also show that E. coli overexpressing the E. coli methylglyoxal synthase gene (mgs) produced 1,2-PD. The expression of either glycerol dehydrogenase or methylglyoxal synthase resulted in the anaerobic production of approximately 0.25 g of 1,2-PD per liter. R-1,2-PD production was further improved to 0.7 g of 1,2-PD per liter when methylglyoxal synthase and glycerol dehydrogenase (gldA) were coexpressed. In vitro studies indicated that the route to R-1,2-PD involved the reduction of methylglyoxal to R-lactaldehyde by the recombinant glycerol dehydrogenase and the reduction of R-lactaldehyde to R-1, 2-PD by a native E. coli activity. We expect that R-1,2-PD production can be significantly improved through further metabolic and bioprocess engineering.
简评《国家的贫困:关于饥饿与人口的政治经济学》 (1983)

本书作者为美国社会学家威廉·默多克,1981年由约翰·霍普金斯大学出版社出版,共382页。作者认为,人口的迅速增长是造成贫困的基本原因。贫困并不是由于资源有限,而是由于穷国与富国之间,穷国内部精萃人物与广大群众之间财富与权力分配的不均。因此,要解决人口增长与生产(尤其是粮食)不足的问题,必须在国与国之间以及各国内部进行财富与权力的再分配。光靠计划生育放慢人口增长速度是不够的。
A Pilot Open Label Study of Cystoprotek® in Interstitial Cystitis (2005)

Interstitial cystitis (IC) is a disorder of the urinary bladder characterized by urgency, frequency, nocturia and suprapubic pain. IC occurs primarily in women and symptoms are exacerbated by stress, ovulatory hormones and certain foods. IC pathogenesis is unknown, but the most consistent findings involve some dysfunction of the bladder glycosaminoglycan (GAG) protective layer and a high number of activated bladder mast cells. There is no effective therapy even through intravesical administration of dimethylsulfoxide (DMSO) or oral pentosanpolysulfate (PPS) have had variable success. A dietary supplement, CystoProtek, was formulated with the natural GAG components chondroitin sulfate and sodium hyaluronate to provide urothelial cytoprotection, together with the flavonoid quercetin that has anti-inflammatory properties and inhibits activation of mast cells. Thirty-seven female patients diagnosed by the NIDDK criteria who had failed all forms of therapy took six softgel CystoProtek capsules per day for 6 months. Global assessment scale was reduced from 9.0 +/- 2.9 to 4.3 +/- 2.1 (p < 0.05); moreover, the O'Leary/Sant Symptom Index decreased from 15.3 +/- 3.1 to 6.9 +/- 4.2 (p < 0.05) and the Problem Index from 13.1 +/- 3.7 to 5.4 +/- 4.0 (p <0.05). These results are very promising and warrant a larger study that may permit further analyses with respect to other, especially atopic, comorbid diseases.
Insulin-like growth factor 1 receptor enhances invasion and induces resistance to apoptosis of colon cancer cells through the Akt/Bcl-x(L) pathway. (2003)

Colon cancer overexpresses insulin-like growth factor 1 (IGF1) and insulin-like growth factor 1 receptor (IGF1-R), as compared with normal or adenomatous mucosa, and it has been postulated that colorectal cancer cells depend on the IGF1/IGF1-R pathway for their growth and progression. In this study, using the human colon cancer cell line HCT116, we find that established HCT116/IGF1-R transfectants exhibit a more aggressive transformed phenotype than the parental cell line, as demonstrated by their higher proliferation rate in response to IGF1, higher degree of anchorage-independent growth, resistance to serum deprivation-induced apoptosis, and higher migratory capability in a monolayer "wounding assay." When injected into nude mice, HCT116/IGF1-R transfectants were highly invasive and produced distant metastases, whereas the parental cell did not. Moreover, the overexpression of IGF1-R in these cells was associated with IGF1-R-induced activation of Akt and up-regulation of the antiapoptotic protein Bcl-x(L). We also show that Akt pathway mediates IGF1-R-induced Bcl-x(L) expression at transcriptional level. Our data demonstrate, for the first time, that IGF1-R/Akt/Bcl-x(L) pathway may contribute to a more aggressive malignant phenotype, in a subset of colorectal cancers.
Asymmetric epoxidation of allyl alcohol: efficient routes to homochiral .beta.-adrenergic blocking agents (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric epoxidation of allyl alcohol: efficient routes to homochiral .beta.-adrenergic blocking agentsJanice M. Klunder, Soo Y. Ko, and K. Barry SharplessCite this: J. Org. Chem. 1986, 51, 19, 3710–3712Publication Date (Print):September 1, 1986Publication History Published online1 May 2002Published inissue 1 September 1986https://pubs.acs.org/doi/10.1021/jo00369a032https://doi.org/10.1021/jo00369a032research-articleACS PublicationsRequest reuse permissionsArticle Views2243Altmetric-Citations164LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
FRAME: femtosecond videography for atomic and molecular dynamics (2017)

Many important scientific questions in physics, chemistry and biology require effective methodologies to spectroscopically probe ultrafast intra- and inter-atomic/molecular dynamics. However, current methods that extend into the femtosecond regime are capable of only point measurements or single-snapshot visualizations and thus lack the capability to perform ultrafast spectroscopic videography of dynamic single events. Here we present a laser-probe-based method that enables two-dimensional videography at ultrafast timescales (femtosecond and shorter) of single, non-repetitive events. The method is based on superimposing a structural code onto the illumination to encrypt a single event, which is then deciphered in a post-processing step. This coding strategy enables laser probing with arbitrary wavelengths/bandwidths to collect signals with indiscriminate spectral information, thus allowing for ultrafast videography with full spectroscopic capability. To demonstrate the high temporal resolution of our method, we present videography of light propagation with record high 200 femtosecond temporal resolution. The method is widely applicable for studying a multitude of dynamical processes in physics, chemistry and biology over a wide range of time scales. Because the minimum frame separation (temporal resolution) is dictated by only the laser pulse duration, attosecond-laser technology may further increase video rates by several orders of magnitude.
The immunological properties of haptens coupled to thymus‐independent carrier molecules. III. The role of the immunogenicity and mitogenicity of the carrier in the induction of primary IgM anti‐hapten responses (1975)

Abstract Hapten (DNP‐lys) conjugates of two putatively nonimmunogenic polymers, hyaluronic acid and poly‐γ‐D‐glutamic acid, induce significant primary IgM anti‐DNP responses in C3H mice. Preparations of various immunogenic (Type 3 pneumococcal polysaccharide (SIII), levan, E. coli lipopolysaccharide) and nonimmunogenic (hyaluronic acid and poly‐glutamic acid) polymers were tested for their ability to act as polyclonal mitogens in vitro . In serum‐containing spleen cell cultures, only lipopolysaccharide stimulated substantial cell proliferation. In serum‐free medium, and using high specific activity [ 3 H]thymidine, lipopolysaccharide, levan, SIII and to a lesser degree hyaluronic acid induced significant thymidine incorporation. However, under the latter conditions cell survival and proliferation were much less impressive. There was no apparent correlation between the capacity of various polymers to induce lymphocyte proliferation and their „potency”︁ as carriers for the generation of a primary IgM anti‐DNP response. Furthermore while low doses of lipopolysaccharide elicited „polyclonal”︁ antibody formation in vivo , high doses of SIII, levan and hyaluronic acid did not. These results indicate that T cell‐independent B cell triggering is dependent on the polymeric nature of the antigen, and that polymers need not be immunogenic or mitogenic to act as carriers for the induction of primary IgM anti‐hapten antibody responses.