gebhart/patrepeval huggingface dataset:
Regulation of Hematopoietic Stem Cell Self-Renewal (2003)

Every day, billions of new blood cells are produced in the body, each one derived from a hematopoietic stem cell (HSC). Because most mature blood stem cells have a limited life span, the ability of HSCs to perpetuate themselves through self-renewal and generate new blood cells for the lifetime of an organism is critical to sustaining life. A key problem in hematopoietic stem cell biology is how HSC self-renewal is regulated. Recent evidence suggests that signaling pathways classically involved in embryonic development--such as the Wnt signaling pathway--play an important role in regulating stem cell self-renewal. The Wnt signaling pathway has been shown to regulate stem cell fate choice in a variety of organs, including the skin, the nervous system, and the hematopoietic system. In the hematopoietic system, stimulation of hematopoietic progenitors and stem cells with soluble Wnt proteins or downstream activators of the Wnt signaling pathway leads to their expansion. Future studies focusing on the mechanism of action of the Wnt signaling pathway and its interaction with other pathways are needed to gain further insight into the regulation of stem cell self-renewal, not only in the hematopoietic system but also in a variety of other tissues.
SWISS-MODEL: an automated protein homology-modeling server (2003)

SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated modeling facility today. In 2002 the server computed 120 000 user requests for 3D protein models. SWISS-MODEL provides several levels of user interaction through its World Wide Web interface: in the 'first approach mode' only an amino acid sequence of a protein is submitted to build a 3D model. Template selection, alignment and model building are done completely automated by the server. In the 'alignment mode', the modeling process is based on a user-defined target-template alignment. Complex modeling tasks can be handled with the 'project mode' using DeepView (Swiss-PdbViewer), an integrated sequence-to-structure workbench. All models are sent back via email with a detailed modeling report. WhatCheck analyses and ANOLEA evaluations are provided optionally. The reliability of SWISS-MODEL is continuously evaluated in the EVA-CM project. The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server.
An embedded real-time vision system for 24-hour indoor/outdoor car-counting applications (2004)

We describe an embedded vision system, which integrates a Web-cam quality CMOS imaging chip with a RISC processor, to perform real-time car-counting functions in the indoor and outdoor environment. The challenge of this application, especially for the outdoor environment, is to develop vision algorithms for day and night, and during the light-transition periods (i.e., dawn and dusk). The vision system also needs to accommodate a tremendous range of illumination change (from sunny summer to snowy winter). Finally, we report briefly the result of an outdoor system we deployed in Germany since June 2003. The entire system consists of a network of 13 embedded vision systems covering a parking facility over 1 square kilometer. The vision-network has been in daily use for the employee parking guidance.
Diversity of cutinases from plant pathogenic fungi: Purification and characterization of two cutinases from Alternaria brassicicola (1993)

Previous evidence indicated a relationship between the pH optima of fungal cutinases and the tissue specificities of respective pathogens. Cutinases with slightly acidic pH optima were associated with leaf pathogens, whereas stem base pathogens produced cutinases most active under alkaline conditions. Alternaria brassicicola secreted both types of cutinases and caused disease on all above-ground host tissues. Two cutinases, Ac and Ba, which were expressed after growth of the pathogen on polymer cutin and in the presence of cutin monomers as cutinase inducers, were purified to apparent homogeneity. Cutinase Ac had a cutinolytic pH optimum of 6·5 and cutinase Ba had a cutinolytic pH optimum of 8·5. Their molecular weights were 23·0 kDa and 21·0 kDa, respectively. Other enzymatic and structural parameters were similar for both enzymes. The V- and Km-values for p-nitrophenyl esters with acyl chains ranging from C4 to C16 decreased for both enzymes with increasing chain length. The esterase inhibitors ebelactones A and B were equally active competitive inhibitors of both cutinases. Amino acid compositions were similar but not identical, and the separation pattern of tryptic peptides indicated structural differences between the two isozymes. Although both cutinases could be distinguished by their pH dependency of cutinolytic activities and their size, the similarities indicate a close evolutionary relationship.
Small RNAs Guide Hematopoietic Cell Differentiation and Function (2010)

MicroRNAs (miRNAs) are key regulators of gene expression that help direct normal differentiation and malignant transformation of hematopoietic cells. This review summarizes our current knowledge of how miRNAs function in normal and malignant hematopoiesis and how miRNAs might be applied for disease treatment.
Dexamethasone Effects on Myoblast Proliferation and Differentiation* (1980)

Effects of glucocorticoids on myoblast proliferation and differentiation were determined in cell culture. Dexamethasone (1 X 10(-7) M) decreased myoblast doubling time by 7 h and increased cell densities as much as 800% after 8 days of exposure of the cells to dexamethasone. Stimulation of myoblast proliferation by glucocorticoids was dose dependent, with half-maximal activity exhibited at concentrations of 3 X 10(-9) M dexamethasone or 2.3 X 10(-8) M corticosterone. In differentiating cultures, the rate of accumulation and final levels of DNA and creatine phosphokinase were highly stimulated by dexamethasone. However, normalization of creatine phosphokinase levels (a marker for myoblast differentiation) per microgram DNA demonstrated a small (30%) decrease in differentiation in cultures exposed to glucocorticoids. These results indicate that glucocorticoids stimulate early myogenesis by increasing the number of myoblasts but do not stimulate the differentiation of these cells.
PPARs in atherosclerosis: the clot thickens (2004)

Cardiovascular disease is the leading cause of morbidity and mortality in Western countries. Previous studies have highlighted the beneficial effects of PPARgamma activators on cardiovascular disease; however, the role of other PPAR family members in atherosclerosis is less clear. A report in this issue of the JCI expands our understanding of PPARs in vascular biology and highlights the potential use of multiple PPAR agonists to limit lipid accumulation in macrophages.
Influence of carrier-specific, thymus-derived cells on the immunologlobulin M antibody response to staphylococcal lipoteichoic acid (1980)

The immunoglobulin M antibody response to the lipoteichoic acid (LTA) of Staphylococcus aureus ATCC 6538P was examined by a procedure in which erythrocytes sensitized with periodate-activated LTA were used for the detection of immunoglobulin M-producing plaque-forming cells LTA-specific plaque-forming cells were first detected 2 days after immunization with heat-killed bacterial cells, and maximal numbers of plaque-forming cells, mostly of the immunoglobulin M class rather than the immunoblogulin G or immunoglobulin A class, were attained by day 4; specificity for LTA was affirmed by plaque inhibition tests. No plaque-forming cells were found in mice given isolated LTA over a 10,000-fold range of immunizing doses. Mice pretreated with a carrier known to activate thymus-derived helper lymphocytes produced a plaque-forming cell response to LTA only when immunized with LTA bound to the same carrier. This suggests that carrier-specific thymus-derived cells are needed to initiate an antibody response to poorly immunogenic LTA. Since an antibody response can be elicited in mice given heat-killed cells, other cell wall and/or cell membrane constituents may play an important role as immunologically active carriers for this antigen.
Medicinal Foodstuffs. VIII. Fenugreek Seed.(2) : Structures of Six New Furostanol Saponins, Trigoneosides IVa, Va, Vb, VI, VIIb, and VIIIb, from the Seeds of Indian Trigonella foenum-graecum L. (1998)

Following the characterization of trigoneosides la, Ib, Ila, IIb, IIIa, and IIIb, seven new steroidal saponins called Vigoneosides IVa, Va, Vb, VI, VIIb.VIIIb, and IX were isolated from a medicinal foodstuff fenugreek seed, the seeds of Trigonello foenum-graecum L.(Leguminosae) originating from India.The structures of trigoneosides N a , Va, Vb, VI.VIIb, and VlIlb were elucidated on the basis of chemical and physicochemical evidence.
A Single Amino Acid Substitution in the Antimicrobial Defense Protein Cecropin B Is Associated with Diminished Degradation by Leaf Intercellular Fluid (1997)

Degradation is one of several factors that may affect the level of accumulation of transgene products in plants. In plants engineered to secrete antimicrobial proteins to the intercellular compartment of leaves, the degenerative activity of proteases residing in leaf intercellular fluid (IF) could be critical to achieving the expected transgene function. We synthesized a structural analogue (MB39) of the antibacterial protein cecropin B and compared the susceptibility of both proteins to degradation in vitro by IF extracted from leaves of various crops. The half-life of the two proteins in the various IF extracts ranged from 3 min to 25.5 h, with the analogue MB39 displaying the longer half-life in IF from nine of 10 species. Overall, the half-life of MB39 averaged 2.9 times greater than that of cecropin B. Analysis of the peptides produced by endopeptidase activity in potato iF indicated that the 5.7-fold lower degradation rate of MB39 was associated with the substitution of valine for methionine at residue 11 of cecropin B. These findings point to the possibility of tailoring antimicrobial protein genes to reduce the rate of protein degradation in a particular target crop.
Fast pyrolysis of pretreated wood (1995)

During the 1980`s, several research groups reported the fact that pyrolysis in a non-oxidizing atmosphere of wood that had been prehydrolyzed with dilute acid allowed a substantial depolymerization of the cellulose to occur to give anhydrosugars. More recent work has shown that only deionization of the wood is necessary, and not necessarily a partial hydrolysis. The indigineous alkaline inorganic cations contained in the wood (principally calcium and potassium) have a profound effect on the mechanism of thermal decomposition of the cellulose and hemicellulose fractions. Also, it has been known for many years that alkaline cations are efficient oxidation catalysts for biomass. We have explored the possibility that oxidation reactions in fast pyrolysis of prehydrolyzed, or of deionized, biomass may be altered much more for carbohydrates than for lignins. Results obtained show that fast pyrolysis of pretreated biomass with controlled levels of oxygen will selectively oxidize lignins with relatively little effect on anhydrosugar yields. This partial oxidation approach generated needed heat in situ. As well, by removing a substantial fraction of the lignin-derived material from the pyrolysis liquid, the recovery of anhydrosugars for use as fermentable sugars or as chemicals is simplified.
Vertical Transmission of Neospora caninum in Mice (1995)

Herein we report a murine model to examine transplacental transmission, transmammary transmission, or both, of Neospora caninum. Prevalence of transplacental transmission in outbred Swiss-Webster mouse pups was 85%, with 11 of 13 litters containing at least 1 transplacentally infected pup. Sixty-two percent of litters born to experimentally infected dams contained 85% or more transplacentally infected pups. Numbers of pups congenitally infected per litter was higher if dams were inoculated during the first half of pregnancy. Transplacental transmission decreased to 25% when a singly infected dam delivered a second litter. Transmammary transmission was observed in 1 of 51 pups suckling dams experimentally infected 5, 10, or 15 days postparturition. No pups were infected when cross-fostered onto chronically infected dams.
Narrow-band imaging endoscopy for diagnosis of malignant and premalignant gastrointestinal lesions. (2006)

Narrow-band imaging (NBI) is a novel endoscopic technique that may enhance the accuracy of diagnosis by using narrow-bandwidth filters in a red-green-blue (R/G/B) sequential illumination system. Magnifying endoscopy by using NBI has two distinct applications: the analysis of the surface architecture of the epithelium (pit pattern) and the analysis of the vascular network. This new technique allows a better characterization of distinct types of gastrointestinal epithelia (e.g. intestinal metaplasia in Barret's esophagus), as well as the disorganization of the vascular pattern in inflammatory disorders and the irregular pit pattern in early neoplastic lesions of the esophagus, stomach and large bowel.
Microstrip couplers with improved directivity (1978)

Backward wave microstrip couplers with weak coupling reach small values for the directivity. This is caused by the unequal phase constants of the even and odd modes of the line waves. A very simple compensation method is shown by loading the coupler with additional coupled lines.
Botulinum toxin in movement disorders (1994)

The most potent biologic toxin, botulinum toxin (BTX), has become a powerful therapeutic tool in the treatment of a variety of neurologic, ophthalmic, and other disorders manifested by abnormal, excessive, or inappropriate muscle contractions. This review focuses on the use of BTX in the treatment of dystonia and other movement disorders. The therapeutic application of BTX, however, extends beyond movement disorders; chemodenervation with BTX has been found to ameliorate spasticity, rigidity, spastic bladder, achalasia, and even some cosmetic conditions. In addition to describing its therapeutic effects, this article also reviews recent advances in the understanding of the molecular and cellular mechanisms of BTX. Few therapeutic agents have been better understood in terms of their mechanism of action or have had greater impact on patients' functioning than BTX. BTX-A has been used in nearly all clinical trials. Blocking anti-BTX-A antibodies have been detected in about 5% of patients chronically treated with this type of BTX. Patients who develop immunoresistance to BTX-A may benefit from other serotypes of BTX, such as BTX-B and -F, currently undergoing clinical trials.
CW Singly-resonant Optical Parametric Oscillators Based on 1.064-μm-pumped Periodically Poled LiNbO3 (1996)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text L. E. Myers, W. R. Bosenberg, J. I. Alexander, M. A. Arbore, M. M. Fejer, and R. L. Byer, "CW Singly-resonant Optical Parametric Oscillators Based on 1.064-μm-pumped Periodically Poled LiNbO3," in Advanced Solid State Lasers, S. Payne and C. Pollack, eds., Vol. 1 of OSA Trends in Optics and Photonics Series (Optica Publishing Group, 1996), paper QM2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation (1987)

Homopyrimidine oligodeoxyribonucleotides with EDTA-Fe attached at a single position bind the corresponding homopyrimidine-homopurine tracts within large double-stranded DNA by triple helix formation and cleave at that site. Oligonucleotides with EDTA.Fe at the 5' end cause a sequence specific double strand break. The location and asymmetry of the cleavage pattern reveal that the homopyrimidine-EDTA probes bind in the major groove parallel to the homopurine strand of Watson-Crick double helical DNA. The sequence-specific recognition of double helical DNA by homopyrimidine probes is sensitive to single base mismatches. Homopyrimidine probes equipped with DNA cleaving moieties could be useful tools for mapping chromosomes.
Methanogen genomics to discover targets for methane mitigation technologies and options for alternative H2 utilisation in the rumen (2008)

Reducing ruminant methane emissions is an important objective for ensuring the sustainability of ruminant-based agriculture. Methane is formed in the rumen by methanogens (part of the domain Archaea), mainly from H2 and CO2. Methanogens from a wide range of habitats are being genome-sequenced to gain a better understanding of their biology and, in particular, to identify targets for inhibition technologies for gut-associated methanogens. Genome comparisons are identifying common genes that define a methanogen, while gene differences are providing an insight into adaptations that allow methanogen survival and persistence under different environmental conditions. Within the rumen microbial food web, methanogens perform the beneficial task of removing H2, which allows reduced cofactors to be reoxidised and recycled, thereby enhancing the breakdown and fermentation of plant material. Therefore, rumen methane mitigation strategies need to consider alternative routes of H2 utilisation in the absence (or decreased levels) of methanogenesis to maintain rumen function. Two main alternatives are possible: enhancing rumen microorganisms that carry out reductive acetogenesis (combining CO2 and H2 to form acetate) or promotion of organisms that consume reducing equivalents during the conversion of metabolic intermediates (malate, fumarate and crotonate) into propionate and butyrate. A better understanding of the role and scale of methane oxidation in the rumen may also lead to future options for methane mitigation.
Safety and Tolerability of Oral BG-12 (Dimethyl Fumarate) in Relapsing–Remitting Multiple Sclerosis (RRMS): Interim Results from ENDORSE Extension Study (P01.162) (2013)

OBJECTIVE: To report interim safety results (as of 30 March 2012) from ENDORSE, an ongoing 5-year extension of DEFINE and CONFIRM.
Late bone metastasis from an encapsulated follicular carcinoma of the thyroid withoutcapsular and vascular invasion (1996)

A unique case of encapsulated follicular carcinoma of the thyroid, which lacked histologic evidence of capsular and vascular invasion but developed a late bone metastasis, is described. The thyroid tumor was found in a 42-year-old man. It was relatively small (2.5 cm) and totally encapsulated. Histologically, the thyroid tumor showed a microfollicular growth pattern of follicular cells and revealed no histologic evidence of nuclear atypia, mitotic figures or capsular and vascular invasion. The diagnosis of microfollicular adenoma was made and partial thyroidectomy was performed. Bone (rlb) metastasis of the thyroid tumor developed 22 years after the thyroidectomy. The present case suggested that capsular and/or vascular invasion is not always sufficient for the diagnosis of encapsulated follicular carcinoma of the thyroid.
High Energy Density Simulations for Inertial Fusion Energy Reactor Design (2005)

The so-called “threat spectra” of an inertial fusion energy (IFE) high gain target (neutron, x-ray, and ion energy fraction and particle spectra) are the usual starting point for IFE reactor conceptual design. The threat spectra are typically computed using the same radiation hydrodynamics and thermonuclear burn computer simulation codes used to compute implosion, ignition and burn. We analyze the validity of this model for simulating the expansion of the direct drive IFE target plasma and for computing threat spectra. Particular attention is paid to the collisionality of the expanding plasma.
In Situ Polymerization of a Conductive Polymer in Acellular Muscle Tissue Constructs (2008)

We present a method to chemically deposit a conductive polymer, poly(3,4-ethylenedioxythiophene) (PEDOT), on acellularized muscle tissue constructs. Morphology and structure of the deposition was characterized using optical and scanning electron microscopies (SEM). The micrographs showed elongated, smooth, tubular PEDOT structures completely penetrating and surrounding the tissue fibers. The chemical polymerization was performed using iron chloride, a mild oxidizer. Remaining iron and chlorine in the tissue constructs were reduced to acceptable metabolic levels, while preserving the structural integrity of the tissue. We expect that these acellular, polymerized tissue implants will remain essentially unmodified in cellular environments in vitro and in vivo because of the chemical and thermal stability of the PEDOT polymer depositions. Our results indicate that in situ polymerization occurs throughout the tissue, converting it into an extensive acellular, non-antigenic substrate of interest for in vivo experiments related to nerve repair and bioartificial prosthesis. We expect these conducting polymer scaffolds to be useful for direct integration with electronically and ionically active tissues.
Development of a Versatile Procedure Based on Natural Transformation for Marker-Free Targeted Genetic Modification in Streptococcus thermophilus (2010)

A versatile natural transformation protocol was established for and successfully applied to 18 of the 19 Streptococcus thermophilus strains tested. The efficiency of the protocol enables the use of in vitro-amplified mutagenesis fragments to perform deletion or insertion of large genetic fragments. Depending on the phenotype linked to the mutation, markerless mutants can be selected either in two steps, i.e., resistance marker insertion and excision using an adapted Cre-loxP system, or in one step using a powerful positive screening procedure as illustrated here for histidine prototrophy.
The enantiomers of tramadol and its major metabolite inhibit peristalsis in the guinea pig small intestine via differential mechanisms (2007)

The results show that the metabolite O-desmethyltramadol is more potent in inhibiting peristalsis than its parent compound. The action of all tramadol forms depends on opioid receptors, and that of (+)- and (-)-tramadol also involves adrenoceptors.
Cellular vaccine therapy for cancer (2002)

Observations that cells of the immune system are able to kill tumor cells both in vitro and in animal models have provided a compelling rationale for pursuit of a strategy whereby immune cells are administered as a therapeutic vaccine to patients with cancer. The successful outcome of this approach depends upon the ability to deliver this therapy in a manner in which a potent immune response is elicited. By harnessing the capacity of dendritic cells that are pivotal in priming the immune response and using gene therapy approaches to optimise the immune response, this may ultimately prove efficacious in the management of human cancer. Promising reports from recent clinical trials suggest that this may well be a realistic goal.
In Vitro JAK Kinase Activity and Inhibition Assays (2012)

The discovery that a range of myeloproliferative diseases and leukemias are associated with Janus Kinase (JAK) mutations has highlighted the importance of JAK/STAT signalling in disease and sparked a renewed interest in developing JAK inhibitors. In vitro kinase assays are the most direct and quantitative method to assess mutant forms of JAK for altered enzymatic properties as well as verifying and quantifying the affinity and efficacy of potential inhibitors. Here, we describe protocols for heterologous expression and purification of JAK kinases from insect cells, assays to determine the activity of these purified kinases, and finally inhibition assays to determine the effectiveness of potential inhibitors.