gebhart/patrepeval huggingface dataset:
The ecology of anthrax spores: tough but not invincible. (1995)

Bacillus anthracis is the causative agent of anthrax, a serious and often fatal disease of wild and domestic animals. Central to the persistence of anthrax in an area is the ability of B. anthracis to form long-lasting, highly resistant spores. Understanding the ecology of anthrax spores is essential if one hopes to control epidemics. Studies on the ecology of anthrax have found a correlation between the disease and specific soil factors, such as alkaline pH, high moisture, and high organic content. Researchers initially suggested that these factors influenced vegetative anthrax bacilli. However, subsequent research has shown that vegetative cells of B. anthracis have very specific nutrient and physiological requirements and are unlikely to survive outside a host. Review of the properties of spores of B. anthracis and other Bacillus species suggests that the specific soil factors linked to epidemic areas reflect important environmental conditions that aid the anthrax spores in causing epidemics. Specifically, high levels of calcium in the soil may help to maintain spore vitality for prolonged periods, thereby increasing the chance of spores encountering and infecting a new host. Cycles of runoff and evaporation may collect spores dispersed from previous epidemics into storage areas, thereby concentrating them. Uptake of large doses of viable spores from storage areas by susceptible animals, via altered feeding or breeding behavior, may then allow the bacterium to establish infection and cause a new epidemic. Literature search for this review was done by scanning the Life Sciences Collection 1982-1994 using the keywords "anthrax" and "calcium and spore."
Studies on Glass. II. The Transition between the Glassy and Liquid States in the Case of Glucose (1928)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on Glass. II. The Transition between the Glassy and Liquid States in the Case of GlucoseG. S. ParksG. S. ParksMore by G. S. Parks, H. M. HuffmanH. M. HuffmanMore by H. M. Huffman, and F. R. CattoirF. R. CattoirMore by F. R. CattoirCite this: J. Phys. Chem. 1928, 32, 9, 1366–1379Publication Date (Print):September 1, 1928Publication History Published online1 May 2002Published inissue 1 September 1928https://doi.org/10.1021/j150291a008Request reuse permissionsArticle Views321Altmetric-Citations69LEARN 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 InReddit PDF (638 KB) Get e-Alerts
Direct reprogramming of fibroblasts into endothelial cells capable of angiogenesis and reendothelialization in tissue-engineered vessels (2012)

The generation of induced pluripotent stem (iPS) cells is an important tool for regenerative medicine. However, the main restriction is the risk of tumor development. In this study we found that during the early stages of somatic cell reprogramming toward a pluripotent state, specific gene expression patterns are altered. Therefore, we developed a method to generate partial-iPS (PiPS) cells by transferring four reprogramming factors (OCT4, SOX2, KLF4, and c-MYC) to human fibroblasts for 4 d. PiPS cells did not form tumors in vivo and clearly displayed the potential to differentiate into endothelial cells (ECs) in response to defined media and culture conditions. To clarify the mechanism of PiPS cell differentiation into ECs, SET translocation (myeloid leukemia-associated) (SET) similar protein (SETSIP) was indentified to be induced during somatic cell reprogramming. Importantly, when PiPS cells were treated with VEGF, SETSIP was translocated to the cell nucleus, directly bound to the VE-cadherin promoter, increasing vascular endothelial-cadherin (VE-cadherin) expression levels and EC differentiation. Functionally, PiPS-ECs improved neovascularization and blood flow recovery in a hindlimb ischemic model. Furthermore, PiPS-ECs displayed good attachment, stabilization, patency, and typical vascular structure when seeded on decellularized vessel scaffolds. These findings indicate that reprogramming of fibroblasts into ECs via SETSIP and VEGF has a potential clinical application.
The Immunological Synapse: A Molecular Machine Controlling T Cell Activation (1999)

The specialized junction between a T lymphocyte and an antigen-presenting cell, the immunological synapse, consists of a central cluster of T cell receptors surrounded by a ring of adhesion molecules. Immunological synapse formation is now shown to be an active and dynamic mechanism that allows T cells to distinguish potential antigenic ligands. Initially, T cell receptor ligands were engaged in an outermost ring of the nascent synapse. Transport of these complexes into the central cluster was dependent on T cell receptor-ligand interaction kinetics. Finally, formation of a stable central cluster at the heart of the synapse was a determinative event for T cell proliferation.
Targeting enteric bacteria in treatment of inflammatory bowel diseases (2003)

Normal, nonpathogenic enteric bacteria induce and perpetuate chronic intestinal inflammation in genetically susceptible hosts with defective immunoregulation, bacterial clearance, or mucosal barrier function. Altering the composition and decreasing mucosal adherence/invasion of commensal bacteria with antibiotics, probiotics, and prebiotics can potentially prevent and treat Crohn disease, pouchitis, and possibly ulcerative colitis, but optimal treatments have not yet been identified.
Decomposition and release of elements from zooplankton debris (1992)

In experiments examining the retention of trace elements in decomposing zooplankton debris, the rates of C degradation and metal release from radiolabeled copepod fecal pellets and carcasses were measured for up to 1 mo using radlotracers. Fecal pellets incubated at 18 and 2 "C retained 35 to 40 % and 80 % of their I4C, respectively, after 30 d. Carcasses retained only 13 to 18 % and 28 to 38 % of their 14C after 18 d at 18 and 2 "C, respectively. Leaching of 14C from fecal pellets and carcasses as D0I4C accounted for about half of the 14C loss, even in the absence of microbial activity. Proportionately more of the 14C from carcasses was mlcrobially oxidized to I4CO2 than "C from fecal pellets Release of the particle-reactlve transuranic element 2 4 1 ~n 1 from fecal pellets was unaffected by microbial activity while release of 75Se and 6 5 ~n from both fecal pellets and carcasses increased with microbial activity and closely followed I4C loss. Release rates of all elements decreased exponentially over time, wlth the most pronounced decreases occurnng wlthin the first 6 d Retention half-times (t,,,,'~) of 2 4 1 ~m were 248 d in fecal pellets. By contrast, the t,,12's for "Zn ranged from 2.1 to 13.5 d in fecal pellets and both and had t,,,?'s of only about 1 d in carcasses. The results help explain oceanographic observations that C. Se and Zn are recycled in surface waters while scavenged elements like Am are enriched in fecal pellets and have short residence times in surface waters.
Shape-and-solder-directed self-assembly to package semiconductor device segments (2004)

The self-assembly and packaging of integrated semiconductor device segments have been accomplished by combining geometrical shape recognition with site specific wetting and binding involving liquid solder. Components with complementary shapes were fabricated to recognize and encapsulate functional semiconductor devices. The components were suspended in water and agitated using a pulsating liquid flow. Two hundred AlGaN∕GaN light-emitting diodes with a chip size of 380×330 micrometers were assembled and packaged with a yield of 95% in 2min. The self-assembly procedure forms electrical interconnects between three-dimensionally shaped objects and provides a route to parallel assembly of hybrid microsystems.
Distinct expression and shared activities of members of the hedgehog gene family of Xenopus laevis (1995)

The hedgehog family of signaling proteins is associated with a variety of spatial patterning activities in insects and vertebrates. Here we show that new members of this family isolated from Xenopus laevis are expressed embryonically in patterns suggestive of roles in patterning in the ectoderm, nervous system and somites. Banded hedgehog is expressed throughout the neural plate and subsequently in both the nervous system and in the dermatome of somites. Cephalic hedgehog is expressed in anterior ectoderm and endodermal structures, and sonic hedgehog is expressed in patterns which parallel those in other species. Injection of RNAs encoding Xenopus hedgehogs induces ectopic cement gland formation in embryos. Similar to reported activities of noggin and follistatin, Xenopus hedgehogs share a common ability to induce cement glands in animal cap explants. However, hedgehog activities in naive ectoderm appear capable of acting independently of noggin and follistatin since, although all three are induced by activin in animal cap explants, X-hh expression does not induce noggin or follistatin.
Developing an instrument to assess the endoscopic severity of ulcerative colitis: the Ulcerative Colitis Endoscopic Index of Severity (UCEIS) (2011)

The Ulcerative Colitis Endoscopic Index of Severity accurately predicts overall assessment of endoscopic severity of UC. Validity and responsiveness need further testing before it can be applied as an outcome measure in clinical trials or clinical practice.
Interleukin-21 is increased in active systemic lupus erythematosus patients and contributes to the generation of plasma B cells. (2013)

Increased IL-21 may synergise with TLR-9 signalling and contributes to generation of plasma cells in active SLE patients.
Outcome of specific COX-2 inhibition in rheumatoid arthritis. (1997)

We reviewed data suggesting the hypothesis that specific inhibition of the inducible isoform of cyclooxygenase, COX-2, would provide therapeutic benefit in patients with rheumatoid arthritis (RA) with less gastrointestinal toxicity and presented the results of a therapeutic trial to test this hypothesis. Various doses of the selective COX-2 inhibitor, celecoxib, or placebo were used to treat patients with RA in a 4 week, double blind, placebo controlled trial. Celecoxib provided significant improvement in patient global assessment, morning stiffness, and the number of painful and tender joints compared with placebo. In addition, the number of withdrawals in celecoxib treated patients was significantly less than in the placebo group. No significant adverse events and no difference in the total number of adverse events were noted between the placebo and celecoxib groups. At the doses employed, celecoxib inhibited only COX-2 and not COX-1. Specific COX-2 inhibition with celecoxib causes significant improvement in the signs and symptoms of RA.
<title>Evaluation of motion compensation and coding strategies for compression of depth map sequences</title> (2004)

Current investigations in the area of 3D video systems are based on depth map sequences. They are used to obtain the compatibility to conventional 2D video systems. Instead of transmitting or storing two video sequences for each eye, 2D video and the appropriate depth information is delivered. If the viewer owns a standard TV set only the 2D video is displayed. In the case of using a stereoscopic display or shutter glasses a second virtual view is synthesized based on depth information. Because of limited storage and bandwidth, data compression has to be used. In this paper several approaches for compression of depth sequences, applicable for 3D video systems, are investigated and evaluated. For temporal prediction established video compression standards perform a block based motion compensation and encode the prediction residuals for every block separately. Alternatively, motion compensation methods using control grid interpolation and coding algorithms based on wavelet transform are applicable. Another possible approach is given by a mesh-based interpolation of the depth scene content. In that case the temporal prediction can be obtained by node tracking. We demonstrate the coding performance of these alternative methods for compressing depth map sequences in comparison with the video compression standards MPEG-2, MPEG-4 and H.264.
Correlation of omega-3 levels in serum phospholipid from 2053 human blood samples with key fatty acid ratios (2009)

Strong inverse correlations between the levels of omega-3 fatty acids in serum (or plasma) phospholipid and omega-6: omega-3 ratios are apparent based on this large database of 2053 samples. Certain fatty acid ratios may aid in cardiovascular disease-related risk assessment if/when complete profiles are not available.
Biochemical and molecular identification of distinct forms of alkaline phosphodiesterase I expressed on the apical and basolateral plasma membrane surfaces of rat hepatocytes (1997)

We have identified B10, a plasma membrane protein previously defined by a monoclonal antibody, as an alkaline phosphodiesterase I (APDE) expressed in the plasma membrane of rat hepatocytes and enterocytes, with a restricted apical distribution. B10 complementary DNA (cDNA) was cloned from a rat intestinal library screened with a polyclonal antibody directed to the hepatic protein. Two distinct B10 clones with an open reading frame of 2,625 bp were obtained that differed only by 12 bases in the coding region. One B10 clone had a single base difference with gp130RB13-6 cDNA, which was recently cloned in rat fetal brain. B10/gp130RB13-6 had 50% identity at the amino acid level with the plasma cell antigen PC-1, an APDE cloned in the mouse and in human. Anti-B10 antibodies immunoprecipitated 34% of the APDE activity in liver plasma membranes and over 95% of the APDE activity in intestinal cells. Most of the remaining activity in hepatocytes (44%) could be immunoprecipitated by antibodies directed to PC-1. APDE activity immunoprecipitated with anti-B10 antibodies was found in the apical rat liver plasma membrane fractions on a sucrose gradient whereas most of the remaining APDE activity was associated with the basolateral fractions, which contained PC-1. By immunofluorescence, B10 was localized to the apical surfaces of hepatocytes and enterocytes whereas PC-1 was present on the basolateral surfaces of hepatocytes. B10/gp130RB13-6 and rat PC-1 are a unique example of distinct molecules having similar enzymatic activity but different apical/basolateral location, and possibly different functions.
Characterization of Salivary Immunoglobulin A Responses in Children Heavily Exposed to the Oral Bacterium Streptococcus mutans : Influence of Specific Antigen Recognition in Infection (2005)

The initial infection of children by Streptococcus mutans, the main pathogen of dental caries, depends on the ability of S. mutans to adhere and accumulate on tooth surfaces. These processes involve the adhesin antigen I/II (AgI/II), glucosyltransferases (GTF) and glucan-binding protein B (GbpB), each a target for anticaries vaccines. The salivary immunoglobulin A (IgA) antibody responses to S. mutans antigens (Ags) were characterized in 21 pairs of 5- to 13-month-old children. Pairs were constructed with one early S. mutans-infected and one noninfected child matched by age, racial background, number of teeth, and salivary levels of IgA. Specific salivary IgA antibody response and S. mutans infection levels were then measured during a 1-year follow-up. Robust responses to S. mutans were detected from 6 months of age. Salivary IgA antibody to AgI/II and GTF was commonly detected in salivas of all 42 children. However, GbpB-specific IgA antibody was seldom detected in the subset of infected children (38.1% at baseline). In contrast, most of the subset of noninfected children (76.2%) showed GbpB-reactive IgA antibody during the same period. Frequencies of GbpB responses increased with age, but differences in intensities of GbpB-IgA antibody reactions were sustained between the subsets. At baseline, GbpB-reactive IgA antibody accounted for at least half of the total salivary IgA S. mutans-reactive antibody in 33.3 and 9.5% of noninfected and infected children, respectively. This study provides evidence that a robust natural response to S. mutans Ags can be achieved by 1 year of age and that IgA antibody specificities may be critical in modulating initial S. mutans infection.
<title>GMPLS-based control plane for optical networks: early implementation experience</title> (2002)

Generalized Multi-Protocol Label Switching (GMPLS) extends MPLS signaling and Internet routing protocols to provide a scalable, interoperable, distributed control plane, which is applicable to multiple network technologies such as optical cross connects (OXCs), photonic switches, IP routers, ATM switches, SONET and DWDM systems. It is intended to facilitate automatic service provisioning and dynamic neighbor and topology discovery across multi-vendor intelligent transport networks, as well as their clients. Efforts to standardize such a distributed common control plane have reached various stages in several bodies such as the IETF, ITU and OIF. This paper describes the design considerations and architecture of a GMPLS-based control plane that we have prototyped for core optical networks. Functional components of GMPLS signaling and routing are integrated in this architecture with an application layer controller module. Various requirements including bandwidth, network protection and survivability, traffic engineering, optimal utilization of network resources, and etc. are taken into consideration during path computation and provisioning. Initial experiments with our prototype demonstrate the feasibility and main benefits of GMPLS as a distributed control plane for core optical networks. In addition to such feasibility results, actual adoption and deployment of GMPLS as a common control plane for intelligent transport networks will depend on the successful completion of relevant standardization activities, extensive interoperability testing as well as the strengthening of appropriate business drivers.
The Difficulty of Targeting Cancer Stem Cell Niches (2010)

Normal stem cell niches typically are identified by their distinctive anatomical features and by association with tissue-specific stem cells. Identifying cancer stem cell (CSC) niches presents a special problem because there are few if any common anatomical features among tumors, and the physical phenotypes that reportedly describe the CSCs as entities may be subject to the host's microenvironment, sex, and tumor stage. Irrespective of a niche's location, the occupant's phenotype, or the precise molecular composition, all niches must do basically the same thing: maintain the activities in a stem cell that define it as such. Therefore, a potentially successful strategy, both for elaborating a molecular and cellular portrait of a CSC niche, and for therapeutically targeting them, is to identify components in the tumor microenvironment that are required for maintaining the functions of self-renewal, differentiation, and quiescence in the face of cytotoxic therapeutic regimens.
Inflammatory Bowel Disease and Pregnancy (2001)

Most women with inflammatory bowel disease who desire to become pregnant can expect to conceive successfully, carry to term, and deliver a healthy infant. However, the management of inflammatory bowel disease during pregnancy remains challenging, and some women with ulcerative colitis or Crohn's disease will have difficulty becoming pregnant or have increased disease symptoms while pregnant. Control of disease activity before conception and during pregnancy is critical to optimize both maternal and fetal health. The natural history of inflammatory bowel disease during pregnancy will be reviewed and the medical and surgical therapy discussed.
Bacterial Pneumonia in the Elderly (1983)

Bacterial pneumonia in the elderly is common, and causes more morbidity and mortality than in the younger adult. As patients live longer with more underlying disease and more iatrogenic disease, the incidence of nosocomial pneumonia will probably rise. Adequate sterilization of inhalation therapy equipment can reduce the risk of gram-negative nosocomial pneumonia. Methods to prevent colonization and microaspiration need to be investigated. The development of a gram-negative vaccine using Salmonella RE or E. coli J5 mutant would augur well for the future. Most important, the elderly patient with pneumonia should be managed promptly and aggressively in an attempt to determine the specific etiology of the pneumonia. The practice of antibiotic "shotgunning" of the elderly patient is to be avoided. Transtracheal aspiration or sheathed bronchoscopy can be performed if the patient is not able to produce sputum, or Gram stain is difficult to interpret. Morbidity and mortality can be reduced by early appropriate antibiotic therapy directed by Gram stain.
A Therapeutic Uricase with Reduced Immunogenicity Risk and Improved Development Properties (2016)

Humans and higher primates are unique in that they lack uricase, the enzyme capable of oxidizing uric acid. As a consequence of this enzyme deficiency, humans have high serum uric acid levels. In some people, uric acid levels rise above the solubility limit resulting in crystallization in joints, acute inflammation in response to those crystals causes severe pain; a condition known as gout. Treatment for severe gout includes injection of non-human uricase to reduce serum uric acid levels. Krystexxa® is a hyper-PEGylated pig-baboon chimeric uricase indicated for chronic refractory gout that induces an immunogenic response in 91% of treated patients, including infusion reactions (26%) and anaphylaxis (6.5%). These properties limit its use and effectiveness. An innovative approach has been used to develop a therapeutic uricase with improved properties such as: soluble expression, neutral pH solubility, high E. coli expression level, thermal stability, and excellent activity. More than 200 diverse uricase sequences were aligned to guide protein engineering and reduce putative sequence liabilities. A single uricase lead candidate was identified, which showed low potential for immunogenicity in >200 human donor samples selected to represent diverse HLA haplotypes. Cysteines were engineered into the lead sequence for site specific PEGylation and studies demonstrated >95% PEGylation efficiency. PEGylated uricase retains enzymatic activity in vitro at neutral pH, in human serum and in vivo (rats and canines) and has an extended half-life. In canines, an 85% reduction in serum uric acid levels was observed with a single subcutaneous injection. This PEGylated, non-immunogenic uricase has the potential to provide meaningful benefits to patients with gout.