gebhart/patrepeval huggingface dataset:
Isothermal amplification method for next-generation sequencing (2013)

We report an approach for generating immobilized monoclonal templates for next- generation sequencing applications. Our isothermal amplification method is based on a template walking mechanism using a pair of low-melting temperature (Tm) solid-surface homopolymer primers and a low-Tm solution phase primer. The method can generate more than one billion submicrometer-sized colonies in a single lane of a next-generation sequencing flowchip. An alternative paired-end sequencing method using interstrand DNA photo cross-linking to covalently link the complementary strands of the original templates to the solid surface is also demonstrated.
Experimental Autoimmune Encephalomyelitis Is Exacerbated in Mice Lacking the NOS2 Gene (1998)

Nitric oxide is believed to be a prominent mediator of inflammation based in part on the correlative expression of the inducible nitric oxide synthase (iNOS) gene in various pathologies. The resulting high output of the highly reactive molecule nitric oxide is then believed to play an important role in the evolving inflammatory response. Studies have shown that iNOS and nitric oxide are present in the tissues of patients with multiple sclerosis (MS). In rodent models of MS, experimental autoimmune encephalomyelitis (EAE), it has been shown that nonspecific NOS inhibitors partially ameliorate the disease. To determine the importance of iNOS in this model of MS, we induced EAE in mice containing a disrupted iNOS (NOS2) gene. Surprisingly, by day 24, the NOS2 knockout mice had a greater incidence of EAE than wild-type control mice (75 vs 12%), and had a higher average severity score (2.42 vs 0.44). These differences appear to result largely from the failure of the disease to remit in NOS2 KO mice. Wild-type mice have a profound ability to reverse EAE (82%) compared with the knockout mice (19%). This result implies that iNOS may in some instances play a protective role in autoimmune-mediated tissue destruction.
Construction of recombinant Bacillus subtilis strains for efficient pimelic acid synthesis (2011)

As a precursor, pimelic acid plays an important role in biotin biosynthesis pathway of Bacillus subtilis . Fermentations supplemented with pimelic acid could improve the production of biotin, however, with a disadvantage-high cost. So it is necessary to improve the biosynthesis of pimelic acid via genetic engineering in B. subtilis . In this study, we constructed a recombinant B. subtilis strain for improving the synthesis of pimelic acid, in which a maltose-inducible P glv promoter was inserted into the upstream of the cistron bioI-orf2-orf3 and, meanwhile, flanked by the tandem cistrons via a single crossover event. The copy number of the integrant was amplified by high-concentration resistance screen and increased to 4-5 copies. The production of pimelic acid from multiple copies integrant was about 4 times higher than that from single copy (1017.13 μg/ml VS. 198.89 μg/ml). And when induced by maltose the production of pimelic acid was about 2 times of that under non-induction conditions (2360.73 μg/ml VS. 991.59 μg/ml). Thus, these results demonstrated that the production of pimelic acid was improved obviously through reconstructed B. subtilis . It also suggested that our expression system provided a convenient source of pimelic acid that would potentially lower the cost of production of biotin from engineered B. subtilis .
Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig (2018)

There is increasing evidence that induction of local immune responses is a key component of effective vaccines. For respiratory pathogens, for example tuberculosis and influenza, aerosol delivery is being actively explored as a method to administer vaccine antigens. Current animal models used to study respiratory pathogens suffer from anatomical disparity with humans. The pig is a natural and important host of influenza viruses and is physiologically more comparable to humans than other animal models in terms of size, respiratory tract biology and volume. It may also be an important vector in the birds to human infection cycle. A major drawback of the current pig model is the inability to analyze antigen-specific CD8+ T-cell responses, which are critical to respiratory immunity. Here we address this knowledge gap using an established in-bred pig model with a high degree of genetic identity between individuals, including the MHC (Swine Leukocyte Antigen (SLA)) locus. We developed a toolset that included long-term in vitro pig T-cell culture and cloning and identification of novel immunodominant influenza-derived T-cell epitopes. We also generated structures of the two SLA class I molecules found in these animals presenting the immunodominant epitopes. These structures allowed definition of the primary anchor points for epitopes in the SLA binding groove and established SLA binding motifs that were used to successfully predict other influenza-derived peptide sequences capable of stimulating T-cells. Peptide-SLA tetramers were constructed and used to track influenza-specific T-cells ex vivo in blood, the lungs and draining lymph nodes. Aerosol immunization with attenuated single cycle influenza viruses (S-FLU) induced large numbers of CD8+ T-cells specific for conserved NP peptides in the respiratory tract. Collectively, these data substantially increase the utility of pigs as an effective model for studying protective local cellular immunity against respiratory pathogens.
Protein Kinase C (PKC ): Activation Mechanisms and Functions (2002)

Protein kinase C (PKC)delta was the first new/novel PKC isoform to be identified by the screening of mammalian cDNA libraries, based on the structural homology of its nucleotide sequences with those of classical/conventional PKC isoforms. PKC delta is expressed ubiquitously among cells and tissues. It is activated by diacylglycerol produced by receptor-mediated hydrolysis of membrane inositol phospholipids as well as by tumor-promoting phorbol ester through the binding of these compounds to the C1 region in its regulatory domain. It is also cleaved by caspase to generate a catalytically active fragment, and it is converted to an active form without proteolysis through the tyrosine phosphorylation reaction. Various lines of evidence indicate that PKC delta activated in distinct ways plays critical roles in cellular functions such as the control of growth, differentiation, and apoptosis. This article briefly summarizes the regulatory mechanisms of PKC delta activity and its functions in cell signaling.
Plasma etching endpoint detection using multiple wavelengths for small open-area wafers (2001)

This article proposes a new approach for etch endpoint detection of small open area wafers. The traditional endpoint detection technique uses a few manually selected wavelengths, which are adequate for large open areas. As the integrated circuit devices continue to shrink in geometry and increase in device density, detecting the endpoint for small open areas presents a serious challenge to process engineers. In this work, a high-resolution optical emission spectroscopy (OES) system is used to provide the necessary sensitivity for detecting subtle endpoint signals. Principal component analysis is used to analyze the OES data and extract key components that capture the endpoint signal. Data analysis from many wafers shows that the endpoint pattern in the principal components is repeatable. Two methods are used to select wavelengths so as to improve reliability and reduce susceptibility to noise. The first method is to remove those spectrum windows that contain no endpoint information. The second method is to use a “sphere” criterion to select the most relevant wavelengths. The final endpoint algorithm using a much-reduced number of wavelengths shows more distinguishable and reliable endpoint features.
The CED-3/ICE-like Protease Mch2 Is Activated during Apoptosis and Cleaves the Death Substrate Lamin A (1996)

Phylogenetic analysis of the CED-3/ICE family of cysteine proteases suggests the existence of a subfamily most related to the Caenorhabditis elegans death gene ced-3 and includes Yama (CPP32, apopain), LAP3 (Mch3, CMH1), and Mch2. Here, we show that Mch2 is processed from its zymogen form to a proteolytically active dimeric species during execution of the apoptotic program and by the cytotoxic T cell death protease granzyme B. Additionally, like Yama and LAP3, Mch2 functions downstream of the death inhibitors Bcl-2, Bcl-xL, and CrmA. Importantly, Mch2, but not Yama or LAP3, is capable of cleaving lamin A to its signature apoptotic fragment, indicating that Mch2 is an apoptotic laminase.
Recent insights into stearoyl-CoA desaturase-1 (2003)

SCD1, therefore, appears to be an important metabolic control point, and inhibition of its expression could be of benefit for the treatment of obesity, diabetes and other metabolic diseases.
Chemistry of sulfoxides and related compounds. X. Ylides from salts of sulfoximines (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of sulfoxides and related compounds. X. Ylides from salts of sulfoximinesCarl R. Johnson, Eugene R. Janiga, and Manfred HaakeCite this: J. Am. Chem. Soc. 1968, 90, 14, 3890–3891Publication Date (Print):July 1, 1968Publication History Published online1 May 2002Published inissue 1 July 1968https://pubs.acs.org/doi/10.1021/ja01016a068https://doi.org/10.1021/ja01016a068research-articleACS PublicationsRequest reuse permissionsArticle Views444Altmetric-Citations39LEARN 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
Late onset X‐linked hydrocephalus with normal cerebrospinal fluid pressure (2000)

A family with X-linked hydrocephalus with normal cerebrospinal fluid (CSF) pressure and in which three brothers and a grandson of case 1, a proband, were affected is reported. The symptoms at onset were epileptic attacks that started in adulthood in the three brothers and at the age of 6 years in the grandson. In the three brothers, from 10 to 27 years after the onset of epileptic episodes, disorganization of intelligence and psychiatric deterioration were gradually noticed by their families. At the same time, they showed occasional urinary incontinence. Brain computed tomography (CT) scans revealed dilatation of the ventricular systems. Based on the results of the measurement of CSF pressure and radioactive-iodinated human serum albumin (RISA)-cysternography, two of the brothers were diagnosed as having normal pressure hydrocephalus (NPH), and they were treated neurosurgically. However, no obvious improvement in clinical symptoms was observed. Although the grandson had shown normal psychomotor development during his early childhood, temporal epilepsy and temper tantrums started at the age of 6 years. Computed tomography-scanning revealed dilatation of the ventricular system similar to the other three cases at the age of 8 years. With the diagnosis of NPH, the patient underwent a shunt operation, which resulted in no obvious effects. As it is reasonable to surmise that the pathological gene would have been transferred via the daughter of the proband to the grandson, it is suggested that the inheritance manner might be X-linked recessive. The cases presented here are different from the cases of hydrocephalus due to stenosis of the aqueduct Sylvius (HSAS) and other types of X-linked hydrocephalus reported previously in terms of the age of onset, course, symptoms, and CT findings. Thus, it is suggested that the present cases might be a new type of X-linked hydrocephalus.
Rodent nutritional model of non‐alcoholic steatohepatitis: Species, strain and sex difference studies (2003)

The Wistar strain and the male sex are associated with the greatest degree of steatosis in rats subjected to the MCD diet. Of the groups studied, male C57/BL6 mice develop the most inflammation and necrosis, lipid peroxidation, and ultrastructural injury, and best approximate the histological features of NASH.
The role of p53 in spontaneous and radiation-induced apoptosis in the gastrointestinal tract of normal and p53-deficient mice. (1994)

Three h after whole-body irradiation (8 Gy) of C57BL x DBA/2 F1 mice, p53 protein was expressed strongly in the stem cell compartment of the small intestine but at lower levels in the colon. At this time, apoptotic cells were also observed in the stem cell position of the small intestine, with fewer in the colon. In mice without copies of the p53 gene (nulls), the levels of spontaneous apoptosis, in both the small intestine and the colon, were not different from wild-type. Irradiation of the nulls with 8 Gy of gamma-rays failed to induce any further apoptosis: the loss of p53 essentially rendered the epithelial cells, from both the small intestine and the colon, radioresistant. The response of the epithelial stem cells of the small intestine suggests that p53 may play a role in the deletion of damaged cells with carcinogenic potential, whereas this process is limited in the colon.
Material Properties and Composition of Soft‐Tissue Fixation (2010)

Surgical interference screws and suture anchors for attaching soft tissue, such as ligaments and tendons, to bone are routinely used in arthroscopic surgery and sports medicine. Interference screw fixation provides a press fit between bone, graft/tendon, and screw and is frequently used to attach replacement ligaments in tunnels drilled for anterior and posterior cruciate ligament reconstruction. Suture anchors are used in surgical procedures wherein it is necessary for a surgeon to attach (tie) tissue to the surface of the bone, for example, during joint reconstruction and ligament repair or replacement. The composition of these implants ranges from metals to polymers and composites. Typically, because of the relatively large amount of torque that must be applied during insertion, these screws are constructed from metal. However, interference screws and suture anchors have also been constructed from bioabsorbable polymers and composites. The ideal material would (1) provide adequate mechanical fixation, (2) completely degrade once no longer needed, and (3) be completely replaced by bone. Because no material has been shown to be superior for all applications, the surgeon must weigh the advantages and disadvantages of each to evaluate the optimum material for a given application and patient. The purpose of this article is to present a comprehensive review of the commercially available interference screws and suture anchors, with an emphasis on implant composition, interaction, and design. This article provides the orthopaedic surgeon with a background on biomaterials, specifically those used in interference screws and suture anchors. Because there is no material that is perfect for all surgical situations, this review can be used to make educated decisions on a case-by-case basis.
Synthesis and Biological Activity of NK-1 Selective, N-Backbone Cyclic Analogs of the C-Terminal Hexapeptide of Substance P (1996)

The application of the concept of backbone cyclization to linear substance P (SP) analogs is presented. We describe the synthesis, characterization, and biological activity of a series of backbone-to-amino-terminus cyclic analogs of the C-terminal hexapeptide of SP. These analogs were designed on the basis of NMR data and molecular modeling of the selective NK-1 analog WS-septide (Ac[Arg6,Pro9]SP6-11). A series of peptides with the general formula: cyclo[-CH2)m-NH-CO-(CH2)n-CO-Arg-Phe-Phe-N-]-CH2-CO-Leu-Met-NH2 (n = 2, 3, 6 and m = 2, 3, 4) was synthesized by solid phase methodology using Fmoc chemistry for the main chain and Boc chemistry for the building units [Na-(omega-aminoalkyl)Gly] side chains. Cyclization was performed on the resin after removal of the Boc protecting group from the omega-aminoalkyl chain. Cyclic and precyclic analogs were compared. They were purified by HPLC and characterized by mass spectroscopy and NMR. Biological activity and selectivity to the NK-1 neurokinin receptor were found to depend on cyclization and the ring size: The most active and selective analog had a ring of 20 atoms. This analog was found to have enhanced metabolic stability in various tissue preparation compared to WS-septide.
Multimeric vitronectin. Identification and characterization of conformation-dependent self-association of the adhesive protein. (1993)

The adhesive glycoprotein vitronectin (VN) shows a high degree of conformational flexibility implicating that different molecular forms of the molecular may exist. Conformation-dependent monoclonal antibodies 13H1 or 16A7 that, per se, did not react with plasma VN bound to VN treated with heparin, chaotropes, detergents, pH below 6, or by heating at 56 degrees C. Dependent on the stimulus, recognition of VN by these antibodies varied and preceded heparin binding and self-association of VN resulting in the formation of noncovalently linked multimeric species of the protein. Both monoclonal antibodies also reacted with VN in serum or in platelet releasates as well as with VN in extracellular matrices of endothelial cells and inhibited cell adhesion on immobilized VN. Critical VN levels were needed for concentration-dependent multimerization indicating a nonlinear type of polymerization process. The nature of VN multimers was judged by nondenaturing gel electrophoresis, gel filtration, and sucrose gradient ultracentrifugation and revealed the formation of 3- to 16-mer multimeric species within an M(r) range of 200-1200 kDa representing a mean sedimentation coefficient of 9.6 S. In electron microscopy, multimeric VN occurred as globular specimens with an average diameter of 15-28 nm (monomeric plasma VN, 6-8 nm). In contrast to plasma VN, VN multimers were efficiently stabilized by covalent inter-molecular bonds following chemical or transglutaminase-induced cross-linking. A synthetic peptide comprising the central heparin binding region of VN (residues 348-361) not only bound to plasma VN but induced its multimerization also in plasma. During plasmin proteolysis of VN, fragments were generated that lacked the heparin binding region and that lost the ability to multimerize following urea or detergent treatment, implicating that the highly basic region is essential for multimer formation. These data suggest that non-plasma forms of VN, which are abundant in platelets and subendothelium, represent the prototype conformer of the reactive heparin binding form of VN. Our findings implicate that conformationally altered forms of VN enable the adhesive protein to multimerize in a characteristic fashion and thereby endow extracellular matrix sites with unique multivalent properties.
Automated in-camera detection of flash-eye defects (2005)

This paper examines the problem of performing automated real-time detection of flash eye dejects (redeye) in the firmware of a digital camera. Several different algorithms are compared, timing and memory requirements on several embedded architectures are presented. A discussion on advanced in-camera techniques to improve on standard algorithms is also presented.
Washing our hands of the congenital cytomegalovirus disease epidemic (2005)

Perhaps no single cause of birth defects and developmental disabilities in the United States currently provides greater opportunity for improved outcomes in more children than congenital CMV. Given the present state of knowledge, women deserve to be informed about how they can reduce their risk of CMV infection during pregnancy, and trials are needed to identify effective educational interventions.
Drug Targeting to the Brain (2006)

The central nervous system (CNS) is a sanctuary site and is protected by various barriers. These regulate brain homeostasis and the transport of endogenous and exogenous compounds by controlling their selective and specific uptake, efflux, and metabolism in the brain. Unfortunately, potential drugs for the treatment of most brain diseases are therefore often not able to cross these barriers. As a result, various drug delivery and targeting strategies are currently being developed to enhance the transport and distribution of drugs into the brain. Here we discuss briefly the biology and physiology of the blood-brain barrier (BBB) and the blood-cerebro-spinal-fluid barrier (BCSFB), and, in more detail, the possibilities for delivering large-molecular-weight drugs by local and global delivery and by viral and receptor-mediated nonviral drug delivery to the (human) brain.
Addressing Semantic Drift in Question Generation for Semi-Supervised Question Answering (2019)

Shiyue Zhang, Mohit Bansal. Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP). 2019.
Real-Time PCR Targeting the penA Mosaic XXXIV Type for Prediction of Extended-Spectrum-Cephalosporin Susceptibility in Clinical Neisseria gonorrhoeae Isolates (2017)

<i>Neisseria gonorrhoeae</i> isolates with decreased susceptibility to extended-spectrum cephalosporins (ESCs) are increasing. We developed an assay to predict <i>N. gonorrhoeae</i> susceptibility to ESCs by targeting <i>penA</i> mosaic XXXIV, an allele prevalent among U.S. isolates with elevated ESC MICs. The assay was 97% sensitive and 100% specific for predicting at least one ESC MIC above the CDC alert value among clinical isolates, and it could be multiplexed with a previously validated <i>gyrA</i> PCR to predict ciprofloxacin susceptibility.
La reforma de la Organización Común de Mercados del azúcar: el mínimo necesario (2007)

El 20 de febrero de 2006 se aprobo el Reglamento n.o 318/2006 del Consejo que reforma la OCM del azucar. Este articulo defiende que se trata de una reforma de minimos en base a un analisis en clave internacional del regimen europeo del azucar antes y despues de la reforma. Por un lado, se pone de manifiesto que la anterior OCM del azucar no podia cumplir ni con la reciente resolucion del Organo de Solucion de Diferencias de la Organizacion Mundial del Comercio, ni con las demandas de liberalizacion planteadas en el marco de la Ronda de Doha. Por otro lado, queda evidenciado que los cambios introducidos en la OCM son el minimo necesario para hacer frente a dichos retos.
A Kinetic Analysis of the Thermal Degradation of Pyrolytic Heavy Oils obtained from Kiln Pyrolysis Process (2011)

The kinetic analysis of the thermal degradation of pyrolytic heavy oils obtained from mixed waste
plastics by kiln pyrolysis process has been studied by conventional thermogravimetric technique with
various heating rates in nitrogen atmosphere. Results of kinetic analysis show that the activation
energies are 24.4~26.5 kJ/mol and the reaction orders are 1.0~1.25, respectively. To verify the
effectiveness of the kinetic analysis method used in this work, the experimental values were
compared with those of the numerical integration results using kinetic parameters obtained in this
work. It was found that the kinetic analysis method used in this work gave the reliable kinetic
parameters of the thermal degradation of pyrolytic heavy oils.