gebhart/patrepeval huggingface dataset:
Chromosomal and genetic analysis of the electrophoretic karyotype of Trichoderma reesei: mapping of the cellulase and xylanase genes (1992)

An electrophoretic karyotype has been established for Trichoderma reesei strain QM6a, and several of its derivatives, by pulsed-field gel electrophoresis. All strains examined appear to have seven chromosomes with a total genome size of approximately 33 megabases (Mb). The sizes of the chromosomal bands in strain QM6a are approximately 6.2, 6.0, 5.1, 4.2 (doublet), 3.6 and 3.2 Mb. Genes encoding the cellulase complex and xylanases of T. reesei have been mapped, as have several other genes.
Recovery stress enhancement in shape memory composites from silicon carbide whisker–filled benzoxazine-epoxy polymer alloy (2017)

In this research, the benzoxazine-epoxy shape memory polymers with outstanding recovery stress improvement were prepared by filling with highly adamantine silicon carbide whisker at 0–20 wt%. The results revealed that the storage modulus at room temperature increased with increasing silicon carbide whisker, that is, from 5.1 GPa (without silicon carbide whisker) to 8.8 GPa (at 20 wt%). Glass transition temperatures were increased with increasing silicon carbide whisker in the range of 154°C–170°C. Furthermore, all samples exhibited approximately 99% of shape fixity with recovery time ranging from 8 to 27 min. Interestingly, the incorporation of silicon carbide whisker could significantly increase recovery stress from 3.4 MPa (without silicon carbide whisker) to 11.2 MPa (at 20 wt%). Moreover, the addition of silicon carbide whisker provides microwave actuating ability to the sample. Recovery time under microwave heating was significantly shortened to be in a range of 3–5 min. These results suggest potential use of the composites as microwave-responsive sensors and other shape memory devices.
Small optical magnetic-field sensor that uses rare-earth iron garnet films based on the Faraday effect (1999)

Highly accurate optical magnetic-field probe sensors that use iron garnet films have been developed. New probe-type sensors were designed with a confocal optical system. A new garnet composition, Bi(0.98)Gd(0.92)La(0.03)Y(1.07)Fe(4.72)Ga(0.28)O(12), was found that shows high temperature stability for a sensitivity of less than 2.0% from -20 to +80 degrees C. The linearity error of the sensor output was within 1.0% for alternating magnetic fields from 0.3 to 42 mT. An optical current transformer that uses the proposed sensor has an ac linearity of 1.0% for input current up to nearly 300 A. The sensor realized high performance in actual use.
Synthesis and Transporter Binding Properties of 3β-[4‘-(Phenylalkyl, -phenylalkenyl, and -phenylalkynl)phenyl]tropane-2β-carboxylic Acid Methyl Esters:  Evidence of a Remote Phenyl Binding Domain on the Dopamine Transporter (2002)

A series of 4'-substituted 3beta-phenyltropane-2beta-carboxylic acid methyl esters were synthesized and evaluated for binding at the dopamine transporter (DAT) in order to better define the pharmacophore for the cocaine binding site on the DAT. Results from the study of 3beta-[(4'-phenylalkyl)phenyl]tropane-2beta-carboxylic acid methyl esters (5a-c and 6a,b) revealed strong evidence of a previously unknown remote binding domain. The 3beta-[(4'-phenylethyl)phenyl]tropane-2beta-carboxylic acid methyl ester (5a), which has a two methylene linker between the 3beta-phenyl group and the remote phenyl group, has an IC(50) value of 5.14 nM at the DAT. The 3beta-[4'-(benzyl)phenyl] and 3beta-[4'-(phenylpropyl)phenyl] analogues 6b and 5b, respectively, are 102- and 68-fold less potent than 5a at the DAT. Compound 5a also has good affinity for the serotonin and norepinephrine transporters (K(i) = 21 and 6.5 nM, respectively) and is thus a nonselective monoamine uptake inhibitor. Electrostatic effects make a significant contribution to the DAT binding affinity of the 3beta-[(4'-phenylalkenyl)phenyl]tropane-2beta-carboxylic methyl esters (6c, 7a,b, and 8) and 3beta-[(4'-phenylalkynl)phenyl]tropane-2beta-carboxylic acid methyl esters (4a-e). However, the results from the DAT binding on these compounds suggest that there may be another binding domain even further remote from the 4'-position on the 3beta-phenyl group. In both cases, steric barriers have to be overcome before potent binding to the DAT is observed. 3beta-(4'(3-Phenyl-1-propynyl)phenyl)tropane-2beta-carboxylic acid methyl ester (4b), with an IC(50) value of 1.82 nM, was the most potent compound studied. This compound possessed K(i) values of 1.19 and 16.5 nM for the serotonin and norepinephrine transporter and is thus a nonselective monoamine uptake inhibitor.
A unified data model for representing multimedia, timeline, and simulation data (1998)

This paper describes a unified data model that represents multimedia, timeline, and simulation data utilizing a single set of related data modeling constructs. A uniform model for multimedia types structures image, sound, video, and long text data in a consistent way, giving multimedia schemas and queries a degree of data independence even for these complex data types. Information that possesses an intrinsic temporal element can all be represented using a construct called a stream. Streams can be aggregated into parallel multistreams, thus providing a structure for viewing multiple sets of time-based information. The unified stream construct permits real-time measurements, numerical simulation data, and visualizations of that data to be aggregated and manipulated using the same set of operators. Prototypes based on the model have been implemented for two medical application domains: thoracic oncology and thermal ablation therapy of brain tumors. Sample schemas, queries, and screenshots from these domains are provided. Finally, a set of examples is included for an accompanying visual query language discussed in detail in another document.
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif (2001)

Analysis of the 2.4-A resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2' OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3' terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.
Increased Production of Functional Recombinant Human Clotting Factor IX by Baby Hamster Kidney Cells Engineered to Overexpress VKORC1, the Vitamin K 2,3-Epoxide-reducing Enzyme of the Vitamin K Cycle (2005)

Some recombinant vitamin K-dependent blood coagulation factors (factors VII, IX, and protein C) have become valuable pharmaceuticals in the treatment of bleeding complications and sepsis. Because of their vitamin K-dependent post-translational modification, their synthesis by eukaryotic cells is essential. The eukaryotic cell harbors a vitamin K-dependent gamma-carboxylation system that converts the proteins to gamma-carboxyglutamic acid-containing proteins. However, the system in eukaryotic cells has limited capacity, and cell lines overexpressing vitamin K-dependent clotting factors produce only a fraction of the recombinant proteins as fully gamma-carboxylated, physiologically competent proteins. In this work we have used recombinant human factor IX (r-hFIX)-producing baby hamster kidney (BHK) cells, engineered to stably overexpress various components of the gamma-carboxylation system of the cell, to determine whether increased production of functional r-hFIX can be accomplished. All BHK cell lines secreted r-hFIX into serum-free medium. Overexpression of gamma-carboxylase is shown to inhibit production of functional r-hFIX. On the other hand, cells overexpressing VKORC1, the reduced vitamin K cofactor-producing enzyme of the vitamin K-dependent gamma-carboxylation system, produced 2.9-fold more functional r-hFIX than control BHK cells. The data are consistent with the notion that VKORC1 is the rate-limiting step in the system and is a key regulatory protein in synthesis of active vitamin K-dependent proteins. The data suggest that overexpression of VKORC1 can be utilized for increased cellular production of recombinant vitamin K-dependent proteins.
Suppression of macho-1-directed muscle fate by FGF and BMP is required for formation of posterior endoderm in ascidian embryos (2003)

Specification of germ layers is a crucial event in early embryogenesis. In embryos of the ascidian, Halocynthia roretzi, endoderm cells originate from two distinct lineages in the vegetal hemisphere. Cell dissociation experiments suggest that cell interactions are required for posterior endoderm formation, which has hitherto been thought to be solely regulated by localized egg cytoplasmic factors. Without cell interaction, every descendant of posterior-vegetal blastomeres, including endoderm precursors, assumed muscle fate. Cell interactions are required for suppression of muscle fate and thereby promote endoderm differentiation in the posterior endoderm precursors. The cell interactions take place at the 16- to 32-cell stage. Inhibition of cell signaling by FGF receptor and MEK inhibitor also supported the requirement of cell interactions. Consistently, FGF was a potent signaling molecule, whose signaling is transduced by MEK-MAPK. By contrast, such cell interactions are not required for formation of the anterior endoderm. Our results suggest that another redundant signaling molecule is also involved in the posterior endoderm formation, which is likely to be mediated by BMP. Suppression of the function of macho-1, a muscle determinant in ascidian eggs, by antisense oligonucleotide was enough to allow autonomous endoderm specification. Therefore, the cell interactions induce endoderm formation by suppressing the function of macho-1, which is to promote muscle fate. These findings suggest the presence of novel mechanisms that suppress functions of inappropriately distributed maternal determinants via cell interactions after embryogenesis starts. Such cell interactions would restrict the regions where maternal determinants work, and play a key role in marking precise boundaries between precursor cells of different tissue types.
Parabacteroides faecis sp. nov., isolated from human faeces (2015)

A bacterial strain, designated 157(T), isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20% (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157(T) was closely related to Parabacteroides gordonii JCM 15724(T) (96% sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157(T) was different from P. gordonii JCM 15724(T), with a hsp60 gene sequence similarity of 96.1%. The major cellular fatty acids of strain 157(T) were anteiso-C(15 : 0), iso-C(17 : 0) 3-OH, C(18 : 1)ω9c and anteiso-C(17 : 0) 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157(T) was 41.8 mol%. On the basis of these data, strain 157(T) represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157(T) ( = JCM 18682(T) = CCUG 66681(T)).
Computer Applications in Applied Polymer Science II (1989)

The computer has become an accepted part of our daily lives. Computer applications in applied polymer science now are focussing on modelling, simulation, robotics, and expert systems rather than on the traditional subject of laboratory instrument automation and data reduction. The availability of inexpensive computing power and of package software for many applications has allowed the scientist to develop sophisticated applications in many areas without the need for extensive program development. The increasing availability of more powerful computers at a lower cost, and of easy-to-use and inexpensive technical software packages is expected to accelerate these trends.
Left ventricular function and energy metabolism in middle-aged men undergoing long-lasting sustained aerobic oxidative training (2008)

Trained middle-aged subjects showed a better pattern of LV energy metabolism and of diastolic function than their sedentary counterparts. At this age the exercise-related cardiac benefits were detectable when physical exercise was performed regularly and for a long period of time.
Design of potent protein kinases inhibitors using the bisubstrate approach (1991)

A new class of serine/threonine protein kinase inhibitors was designed by associating, in the same structure, mimics of both the ATP binding site and a protein substrate. Among the several potent antagonists which were obtained, the most active consists of isoquinoline-5-sulfonamide, as ATP mimic, and Ser-Arg6, as peptidic moiety, bound by a-NH(CH2)2NH(CH2)2CO-linker. This compound, with a Ki of 0.1 microM toward protein kinase C (PKC) and 0.004 microM toward cyclic AMP dependent protein kinase (PKA), is respectively 60- and 750-fold more active than the commercial inhibitor H-7.
mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer (2007)

This is the first report that indicates the existence of differences in miRNA expression between MSS versus MSI-H colorectal cancers. In addition, the work suggests that the combination of mRNA/miRNA expression signatures may represent a general approach for improving bio-molecular classification of human cancer.
Degradation of the epidermal-dermal junction by proteolytic enzymes from human skin and human polymorphonuclear leukocytes. (1984)

The degradation of normal human skin by the human polymorphonuclear leukocyte proteinases cathepsin G and elastase, and by a human skin chymotrypsin-like proteinase that appears to be a mast cell constituent, was examined. Enzymes were incubated with fresh, split-thickness skin for up to 8 h; the tissue was examined ultrastructurally and immunohistochemically using antibodies to known basement membrane constituents. In all cases, the primary damage observed was at the epidermal-dermal junction. Elastase degraded the lamina densa leaving scattered and disorganized anchoring fibrils, dermal microfibril bundles, and normal-appearing collagen fibers. Immunohistochemically, type IV collagen, laminin, KF1 antigen, and EBA antigen were absent. The bullous pemphigoid antigen was present and localized on the basal cells. Epidermal-dermal separation produced by the chymotrypsin-like proteinases, cathepsin G, and the human skin proteinase, was confined to the lamina lucida. The lamina densa and sub-lamina densa fibrillar network remained intact. The human skin chymotrypsin-like proteinase produced extensive epidermal-dermal separation, while cathepsin G, at comparable concentrations, produced only focal separations. Immunohistochemically, all antigens were present after incubation with enzyme. The bullous pemphigoid antigen, however, was found on the epidermal side of the split, while laminin was found on the dermal side. These results show that the epidermal-dermal junction is highly susceptible to neutral serine proteinases located in mast cells and polymorphonuclear leukocytes. Although all the proteinases produce epidermal-dermal separation, the patterns and extent of degradation are different. The distinctive patterns of degradation may provide a clue to the involvement of these proteinases in skin diseases.
Synthesis and Fungitoxicity of Some 5-Substituted-3-Polynitrophenyl Rhodanines (1978)

Department of Chemistry, D. N. College, Meerut <em>Manuscript received. 9 February 1977, revised 6 October 1971, accepted 1 February 1978</em> Forty-four 5-substituted-3-polynitrophenyl rhodanines have been prepared by the condensation of reactive halogenonitrobenzenes and 5-substituted rhodanine in the presence of an alkali. They have been characterised and tested for their antifungal activity against <em>\(Helminthosporium\) \(sativum\)</em>, <em>\(Alternaria\) \(tenuis\)</em>, <em>\(Aspergillus\) \(niger\)</em> and <em>\(Fusarium\) \(oxysporum\) </em>by spore germination method. A relation between fungitoxiticity and structure has also been established.
Interleukin 21 prevents antigen-induced IgE production by inhibiting germ line Cε transcription of IL-4–stimulated B cells (2002)

Interleukin 21 (IL-21) has recently been identified as a multifunctional cytokine that induces the proliferation of T cells and B cells and differentiation of natural killer cells. To determine whether IL-21 regulates IL-4-mediated immune responses, we examined the effect of IL-21 on antigen-specific IgE production in mice. We also examined the effect of IL-21 on IL-4-induced IgE production from B cells and antigen-induced T-helper 2 (T(h)2) cell differentiation. The in vivo injection of IL-21 prevented antigen-specific IgE but not IgG2a production on immunization. IL-21 did not affect T(h)2 cell differentiation or IL-4 production from CD4(+) T cells but directly inhibited IL-4-induced IgE production from B cells at single-cell levels. Moreover, IL-21 inhibited IL-4-induced germ line C(epsilon) transcription in B cells without the inhibition of signal transducer and activator of transcription 6 (Stat6) activation. Taken together, these results indicate that IL-21 down-regulates IgE production from IL-4-stimulated B cells through the inhibition of germ line C(epsilon) transcription and thus suggest that IL-21 may be useful for the treatment of IgE-dependent allergic diseases.
Extended screening by PCR for seven cry-group genes from field-collected strains of Bacillus thuringiensis (1997)

An extended multiplex PCR method was established to rapidly identify and classify Bacillus thuringiensis strains containing cry (crystal protein) genes toxic to species of Lepidoptera, Coleoptera, and Diptera. The technique enriches current strategies and simplifies the initial stages of large-scale screening of cry genes by pinpointing isolates that contain specific genes or unique combinations of interest with potential insecticidal activities, thus facilitating subsequent toxicity assays. Five pairs of universal primers were designed to probe the highly conserved sequences and classify most (34 of about 60) genes known in the following groups: 20 cry1, 3 cry2, 4 cry3, 2 cry4, 2 cry7, and 3 cry8 genes. The DNA of each positive strain was probed with a set of specific primers designed for 20 of these genes and for cry11A. Twenty-two distinct cry-type profiles were identified from 126 field-collected B. thuringiensis strains. Several of them were found to be different from all published profiles. Some of the field-collected strains, but none of the 16 standard strains, were positive for cry2Ac. Three standard and 38 field-collected strains were positive by universal primers but negative by specific primers for all five known genes of cry7 and cry8. These field-collected strains seem to contain a new gene or genes that seem promising for biological control of insects and management of resistance.
Fusion of EML4 and ALK is associated with development of lung adenocarcinomas lacking EGFR and KRAS mutations and is correlated with ALK expression (2010)

The EML4-ALK fusion gene was present at a high frequency in Chinese NSCLC patients, particularly in those with adenocarcinomas lacking EGFR/KRAS mutations. The EML4-ALK fusion appears to be tightly associated with ALK mRNA expression levels. RACE-coupled PCR sequencing is a highly sensitive method that could be used clinically for the identification of EML4-ALK-positive patients.
14-3-3 protein ? chain gene (YWHAH) polymorphism and its genetic association with schizophrenia (1999)

Recent genetic analyses have suggested a linkage between schizophrenia and the chromosomal region 22q12-q13. 14-3-3 protein, abundant in the brain, mediates interactions between diverse molecules of biological activities; its gene was recently mapped to chromosome 22q12.1-q13.1. We therefore investigated allele frequencies of a variable number of tandem repeat (VNTR) in the 5'-noncoding region of the 14-3-3 eta chain gene in controls and schizophrenics. The frequencies of the two-repeat allele were significantly higher (P < 0.05) in the schizophrenics, and particularly in those with onset before age 22 (early-onset schizophrenics, P < 0.02), than in the controls. The odds ratio was significantly increased in the early-onset schizophrenics homozygous for the two-repeat allele (OR = 3.3, 95% CI = 1.1-9.7). The 14-3-3 eta chain gene is a potential susceptibility gene for schizophrenia, and particularly for early-onset schizophrenia.
Selective CCR2-targeted macrophage depletion ameliorates experimental mesangioproliferative glomerulonephritis (2008)

The CCL2/CCR2 chemokine/receptor axis directs the chemotaxis of infiltrating monocytes/macrophages and T cells and plays a pivotal role in tissue damage and fibrosis in kidney diseases. The eradication of the activated leucocytes should diminish the production of inflammatory mediators, limit tissue damage and ameliorate disease. A recombinant fusion protein (OPL-CCL2-LPM) comprised of the human CCL2 (monocyte chemoattractant protein-1) chemokine fused to a truncated form of the enzymatically active A1 domain of Shigella dysenteriae holotoxin (SA1) has been developed. The CCL2 portion binds specifically to CCR2-bearing leucocytes and the fusion protein enters the cells, where the SA1 moiety inhibits protein synthesis resulting in cell death. The compound was tested in a model of anti-thymocyte serum (ATS)-induced mesangioproliferative glomerulonephritis (ATS-GN). Male rats were injected with ATS on day 0 and treated intravenously with vehicle, 50 or 100 microg/kg of OPL-CCL2-LPM Q2D from days 2, 4, 6 and 8. Urine and blood were collected on days 0, 5 and 9. Animals were sacrificed on day 9. No treatment-related effects on body weight or signs of clinical toxicity were observed. Urine protein levels were decreased in treated animals. At the highest dose, histopathological analyses of kidney sections revealed maximum reductions of 36, 31, 30 and 24% for macrophage count, glomerular lesions, alpha-smooth muscle actin and fibronectin respectively. These results indicate a significant protective effect of OPL-CCL2-LPM in this model of nephritis.