gebhart/patrepeval huggingface dataset:
Genetically recombinant antibodies: new therapeutics against candidiasis (2004)

Historically, the therapy of serious fungal infection has been dominated by monotherapy with the polyene antibiotic amphotericin B. Clinical failures, side effects, the lack of alternatives and the toxicity of this drug have heightened the need to produce alternative therapies, which have included fluconazole, voriconazole and caspofungin. The observation that recovery from disseminated candidiasis was associated with an antibody response to the 47 kDa Candida heat-shock protein (HSP)90 homologue, coupled with the ability to sequence all the antibodies from patients who have recovered from the infection and to re-express the dominant ones as fragments in Escherichia coli, has opened the possibility of immunotherapy. The first recombinant antibody fragment, Mycograb® (NeuTec Pharma plc), against Candida HSP90 is now in clinical trials in patients with disseminated candidiasis in Europe and the US. Laboratory and early clinical data support the concept of synergy between Mycograb and amphotericin B. This should improve outcome and diminish the risk of resistance occurring to either drug, without an increase in toxicity, as this should be minimal in a human antibody fragment representing the natural antibody that a patient produces on recovery.
Evaluation of a Microplate Latex Agglutination Method (Verotox-F Assay) for Detecting and Characterizing Verotoxins (Shiga Toxins) in Escherichia coli (1999)

ABSTRACT The performance of a commercial microplate latex agglutination assay, the Verotox-F assay, was compared with that of the Vero cell assay for the detection and characterization of Escherichia coli verocytotoxins (VTs). Culture filtrates of 68 VT-positive E. coli strains (65 human isolates [33 of serotype O157:H7/H−, 32 of non-O157 serotypes] and 3 reference strains) and 104 VT-negative strains (100 human isolates and 4 reference strains) were investigated. The toxin phenotypes and genotypes of the 68 VT-positive isolates were VT1 only (18 strains), VT2 and/or VT2c (33 strains), and VT1 plus VT2 (17 strains). The Verotox-F assay involved incubation of serial dilutions of culture filtrates with equal volumes of latex particles sensitized with anti-VT1 antibody or anti-VT2 antibody in 96-well microtiter plates with appropriate controls and examination for latex agglutination after 20 to 24 h. Compared to the results of the Vero cell assay, the Verotox-F assay was 100% sensitive and 100% specific for the detection of VTs in culture filtrates and correctly identified the toxin types of all 68 VT producers. By checkerboard titration with purified toxins, the sensitivity of the Verotox-F assay was found to be 14 pg (0.7 ng/ml) for VT1, 12 pg (0.6 ng/ml) for VT2, and 350 pg (17.5 ng/ml) for VT2c; this sensitivity is comparable to that of the bioassay. The anti-VT2 latex reagent detected both VT2 and VT2c and did not cross-react with VT1. The anti-VT1 reagent showed a low-level cross-reaction with VT2c only at levels (≥4.5 μg/ml) that were about 1,000-fold higher than those found in culture filtrates. We conclude that the Verotox-F assay is highly sensitive and specific for the detection and characterization of VTs in culture filtrates of human E. coli isolates. The test is rapid, reliable, and easy to perform; its results are easy to interpret; and it should allow testing for VT to become more widely performed.
Liver‐specific protein 2: a Plasmodium protein exported to the hepatocyte cytoplasm and required for merozoite formation (2012)

The liver stage is the first stage of the malaria parasite that replicates in the vertebrate host. However, little is known about the interplay between the parasite liver stage and its host cell, the hepatocyte. In this study, we identified an exported protein that has a critical role in parasite development in host hepatocytes. Expressed sequence tag analysis of Plasmodium berghei liver-stage parasites indicated that transcripts encoding a protein with an N-terminal signal peptide, designated liver-specific protein 2 (LISP2), are highly expressed in this stage. Expression of LISP2 was first observed 24 h after infection and rapidly increased during the liver-stage schizogony. Immunofluorescent staining with anti-LSP2 antibodies showed that LISP2 was carried to the parasitophorous vacuole and subsequently transported to the cytoplasm and nucleus of host hepatocytes. Gene targeting experiments demonstrated that majority of the LISP2-mutant liver-stage parasites arrested their development during formation of merozoites. These results indicate that exported LISP2 is involved in parasite-host interactions required for the development of liver-stage parasites inside hepatocytes. This study demonstrated that mid-to-late liver-stage malarial parasites have a system for exporting proteins to the host cell as intraerythrocytic stages do and presumably to use the proteins to modify the host cell and improve the environment.
Identification and Topology of Variant Sequences within Individual Repeat Domains of the Human Epithelial Tumor Mucin MUC1 (2001)

This study shows for the first time that the tandemly repeated icosapeptide of human MUC1 underlies a genetic sequence polymorphism at three positions (underlined): PDTRPAPGSTAPPAHGVTSA. The concerted replacement DT-->ES (sequence variation 1) and the single replacements P-->Q (sequence variation 2), P-->A (sequence variation 3), and P-->T (sequence variation 4) were identified by sequencing of polymerase chain reaction products and studied by minisatellite variant repeat analysis for their incidence and topology in the 5' and 3' peripheral regions of the variable number of tandem repeats domain. Minisatellite variant repeat analyses were performed with 27 individual samples of genomic DNA from human cells and tissues covering 30-60% of the domain. Within the peripheral regions, sequence variations 1-4 occur at high incidence and show a nearly constant repeat topology in all individual normal and tumor samples. Also, individuals who were non-Caucasian or of different ethnic background were found to have the same set of replacements with identical topology. The repeat variant 1 replacing the established tumor target motif DTR with ESR was found in all individuals and appears predominantly in repeat clusters (diads and triads). The largely constant topology of variant repeats is interpreted by the assumption that the variable number of tandem repeats domain has evolved as a recent expansion of sequence variable super-repeats.
Tear Film Changes Associated with Normal Aging (1996)

We examined a group of normal subjects to evaluate the tear film function by measuring reflex tear capacity using the Schirmer test without anesthetic, steady state tear flow using fluorophotometry, meibomian gland function based on gland drop-out, expressible lipid volume and viscosity, tear loss from evaporation, and tear osmolarity. We found the average tear flow to be 0.19 +/- 0.19 microliters/min, lower than previously measured. The average tear volume was also correspondingly less, 2.74 +/- 2.0 microliters. We found there was a decline associated with advancing age for all parameters except the decay constant and lipid volume. The highest correlations with aging were tear volume (-0.64), Schirmer test (-0.63), and tear osmolarity (0.59). Our results indicate that there is a decline in tear film function throughout life and that tear flow is considerably less than previously estimated.
Delayed hypersensitivity in mice infected with reovirus. I. Identification of host and viral gene products responsible for the immune response. (1980)

Delayed-type hypersensitivity (DTH) can be demonstrated in mice infected with reovirus by challenging primed animals in the footpad with virus. Maximal responses occur 7 days after immunization with as little as 10(5) viral particles. DTH to reovirus is transferable by lymph node cells and is mediated by T cells as the transfer of reactivity can be abrogated by treatment of cells with anti-Thy 1.2 plus complement. DTH to reovirus is serotype specific, animals infected with reovirus type 1 or 3 only develop DTH responses when challenged with the same serotype with which they were infected. Using recombinant viral clones containing genes from both parental serotypes, we have demonstrated that the S1 gene, the gene encoding the viral hemagglutinin, determines serotype specificity. Furthermore, in adoptive transfer experiments between mice of varying histocompatibility backgrounds, it was found that D or K, IA-IB region identity was required for the transfer of reactivity. These studies demonstrate that specific host and viral genes determine the in vivo cellular immune response to reovirus and should allow a more precise definition of the host cellular immune response to viral antigens.
Development of a biological process for livestock wastewater treatment using a technique for predominant outgrowth of Bacillus species (2002)

The investigation has been carried out by treating 1 m3/day of livestock wastewater for 9 months. The biological process is composed of two reactors connected in series. Each reactor has been designed to stimulate the growth of Bacillus sp., spore-forming aerobic or facultatively anaerobic bacteria. As a consequence, the population of Bacillus sp. is aptly increased via the cycle of sporulation, germination and proliferation. With a predominant growth of Bacillus sp., the microbial activity has been increased comparing to activated sludge based on the result of measuring specific oxygen uptake rate (SOUR). This process was able to remove nitrogen and phosphorus as well as organic matter efficiently. More than 98% of biochemical oxygen demand (BOD) and chemical oxygen demand (COD) were removed. In term of removing the total nitrogen (T-N), about 98% of this was reduced. On average, the T-N concentration in the feed was 3,270 mg/l but 74 mg/l in the effluent including 30 mg/l of nitrite and nitrate nitrogen. The total phosphorus (T-P) reduction averaged 87.5%. As a result, it would be advantageous to load this process in order to deal with high-strength wastewater.
Proton extrusion is an essential signalling component in the HR of epidermal single cells in the barley–powdery mildew interaction (2000)

We propose a model for activation of the epidermal cell hypersensitive response (HR) in the barley/powdery mildew interaction. The model suggests that the plasma membrane proton pump (H+-ATPase) of epidermal cells is activated following penetration by an avirulent powdery mildew fungus. This will cause an acidification of the apoplast towards the mesophyll cells, thereby activating generation of H2O2 from the mesophyll, which subsequently triggers the epidermal cell to undergo HR. The model is supported by the following data: (1) the earliest HR-related H2O2 is found in the attachment zones between the epidermal cell and underlying mesophyll cells; (2) scavenger treatment reduces HR; (3) treatment of leaves with low-pH (3.5) citrate and succinate buffers causes more cells to undergo HR in the compatible interaction, while treatment with the same buffers at pH 5.5 reduces the number of HR-cells in the incompatible interaction; (4) race-specific proton extrusion is observed underneath epidermal tissue detached from leaves inoculated 15 h earlier; and (5) treatment of leaves with fusicoccin, an activator of the plasma membrane H+-ATPase, increases the number of HR-cells in the compatible interaction.
Contrast‐enhanced high resolution MRI for atherosclerotic carotid artery tissue characterization (2002)

The ability of contrast-enhanced MRI to identify neovascularization and potentially improve differentiation of necrotic core from fibrous tissue further establishes MRI as a viable tool for in vivo study of atherosclerotic plaque.
The effects of tissue‐non‐specific alkaline phosphatase gene therapy on craniosynostosis and craniofacial morphology in the FGFR2C342Y/+ mouse model of Crouzon craniosynostosis (2015)

These results suggest that TNAP deficiency may mediate FGFR2-associated craniosynostosis. Future studies should incorporate injection of recombinant TNAP protein, to avoid potential side effects and variable efficacy of lentiviral gene delivery.
Improved Binding Affinity for Cyclophilin A by a Cyclosporin Derivative Singly Modified at Its Effector Domain (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImproved Binding Affinity for Cyclophilin A by a Cyclosporin Derivative Singly Modified at Its Effector DomainChristos Papageorgiou, Andrea Florineth, and Vincent MikolCite this: J. Med. Chem. 1994, 37, 22, 3674–3676Publication Date (Print):October 1, 1994Publication History Published online1 May 2002Published inissue 1 October 1994https://pubs.acs.org/doi/10.1021/jm00048a002https://doi.org/10.1021/jm00048a002research-articleACS PublicationsRequest reuse permissionsArticle Views417Altmetric-Citations27LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Phosphorylation of CDC25B by Aurora-A at the centrosome contributes to the G2–M transition (2004)

Aurora-A protein kinase, which is the product of an oncogene, is required for the assembly of a functional mitotic apparatus and the regulation of cell ploidy. Overexpression of Aurora-A in tumour cells has been correlated with cancer susceptibility and poor prognosis. Aurora-A activity is required for the recruitment of CDK1-cyclin B1 to the centrosome prior to its activation and the commitment of the cell to mitosis. In this report, we demonstrate that the CDC25B phosphatase, an activator of cyclin dependent kinases at mitosis, is phosphorylated both in vitro and in vivo by Aurora-A on serine 353 and that this phosphorylated form of CDC25B is located at the centrosome during mitosis. Knockdown experiments by RNAi confirm that the centrosome phosphorylation of CDC25B on S353 depends on Aurora-A kinase. Microinjection of antibodies against phosphorylated S353 results in a mitotic delay whilst overexpression of a S353 phosphomimetic mutant enhances the mitotic inducing effect of CDC25B. Our results demonstrate that Aurora-A phosphorylates CDC25B in vivo at the centrosome during mitosis. This phosphorylation might locally participate in the control of the onset of mitosis. These findings re-emphasise the role of the centrosome as a functional integrator of the pathways contributing to the triggering of mitosis.
Pig Islet Xenotransplantation Into Non-human Primate Model (2008)

Allogeneic islet transplantation faces difficulties because (1) organ shortage is recurrent; (2) several pancreas donors are often needed to treat one diabetic recipient; and (3) the intrahepatic site of islet implantation may not be the most appropriate site. Another source of insulin-producing cells, therefore, would be of major interest, and pigs represent a possible and serious source for obtaining such cells. Pig islet grafts may seem difficult because of the species barrier, but recent reports demonstrate that pig islets may function in primates for at least 6 months. Pig islet xenotransplantation, however, must still overcome several hurdles before becoming clinically applicable. The actual consensus is to produce more preclinical data in the pig-to-primate model as a necessary requirement to envisage any pig-to-human transplantation of islets; therefore, a summary of the actual acquired knowledge of pig islet transplantation in primates seemed useful and is summarized in this overview.
Supplementation of a bovine milk formula with an oligosaccharide mixture increases counts of faecal bifidobacteria in preterm infants (2002)

Supplementing preterm formula with a mixture of galacto- and fructo-oligosaccharides at a concentration of 10 g/l stimulates the growth of bifidobacteria in the intestine and results in stool characteristics similar to those found in preterm infants fed human milk. Therefore prebiotic mixtures such as the one studied may help to improve intestinal tolerance to enteral feeding in preterm infants.
An Hispanic-American Research-based In-service (2006)

The majority of regular classroom teachers (i.e. those with no experience teaching gifted and talented students) have had little or no exposure to gifted education in college courses or in-service training. With this in mind, a thirty-clock hour, community-based ethnic in-service was developed to teach research-based theory and practices skills in five gifted student needs areas. The teacher skill areas were: (a) nature and needs of gifted and talented students, (b) identification and assessment of gifted and talented students, (c) social and emotional needs, (d) differentiated curriculum, and (e) creativity and instructional strategies for gifted and talented students. A pre/post teacher self-evaluation was used to identify skills needed and skills achieved. The reading for this in-service focused on twenty research articles advocating the above skills for gifted and talented students. Two literature searches were completed. Ten articles focused on the research participants who were students in the general population and ten of the research participants were Hispanic-American students. Ethnic group identity was an important factor to this in-service process…..because the authors felt that teachers and students in the school felt a closer relationship to research when research participants were of the same ethnic group as the in-service participants. Another identify factor to this in-service was that one of the three presenters spoke their language. A verbal pre-post self evaluation helped each teacher identify skills needed and skills achieved. A paper/pencil pre-post picture of each teacher’s classroom helped teachers see how they accommodated for different learning rates differences before and after the in-service. Each six-hour, working-lunch, day teachers discussed one of the skill areas and constantly referred to their research for answers to their questions. The in-service facilitators served as guides-on-the-side. Teachers discussed their pre-post feeling and cited pre-post classroom examples for each of the five skill areas as they happened in their classroom and compared what they did with in the research.
Predictive Properties of Impaired Glucose Tolerance for Cardiovascular Risk Are Not Explained by the Development of Overt Diabetes During Follow-Up (2003)

Baseline IGT was an independent risk predictor for cardiovascular morbidity and mortality and for total mortality, which was not confounded by the subsequent development of overt diabetes.
Library and Information Science (LIS) Education and Training in Kenya: Emergence, Evolution, Challenges and Opportunities (2016)

The purpose of this study is to examine the reasons for the development of Library and Information Science (LIS) education in Kenya, challenges that LIS education has been facing and suggestions for solutions to these challenges are given. The methodology used was literature survey, questionnaires to founding members of staff of the oldest schools of LIS education, authors’ experiences with and exposures of LIS education. Analysis of the data on the questionnaire was done using content analysis. The findings revealed that there were challenges in LIS education in Kenya: inadequate teaching staff, shortage of teaching materials and infrastructure among others. The solutions to these challenges were suggested.  These  findings  are  of  importance  to  LIS  educators  and  students  in  Kenya  since  LIS education is hardly three decades in Kenya and therefore it is still evolving.

	Key words: Library, information science, education, training curriculum, challenges in information science education, universities, college and information science education.
Structure of Severe Acute Respiratory Syndrome Coronavirus Receptor-binding Domain Complexed with Neutralizing Antibody (2006)

The severe acute respiratory syndrome coronavirus (SARS-CoV, or SCV), which caused a world-wide epidemic in 2002 and 2003, binds to a receptor, angiotensin-converting enzyme 2 (ACE2), through the receptor-binding domain (RBD) of its envelope (spike, S) glycoprotein. The RBD is very immunogenic; it is a major SCV neutralization determinant and can elicit potent neutralizing antibodies capable of out-competing ACE2. However, the structural basis of RBD immunogenicity, RBD-mediated neutralization, and the role of RBD in entry steps following its binding to ACE2 have not been elucidated. By mimicking immune responses with the use of RBD as an antigen to screen a large human antibody library derived from healthy volunteers, we identified a novel potent cross-reactive SCV-neutralizing monoclonal antibody, m396, which competes with ACE2 for binding to RBD, and determined the crystal structure of the RBD-antibody complex at 2.3-A resolution. The antibody-bound RBD structure is completely defined, revealing two previously unresolved segments (residues 376-381 and 503-512) and a new disulfide bond (between residues 378 and 511). Interestingly, the overall structure of the m396-bound RBD is not significantly different from that of the ACE2-bound RBD. The antibody epitope is dominated by a 10-residue-long protruding beta6-beta7 loop with two putative ACE2-binding hotspot residues (Ile-489 and Tyr-491). These results provide a structural rationale for the function of a major determinant of SCV immunogenicity and neutralization, the development of SCV therapeutics based on the antibody paratope and epitope, and a retrovaccinology approach for the design of anti-SCV vaccines. The available structural information indicates that the SCV entry may not be mediated by ACE2-induced conformational changes in the RBD but may involve other conformational changes or/and yet to be identified coreceptors.
Flexible Piezotronic Strain Sensor (2008)

Strain sensors based on individual ZnO piezoelectric fine-wires (PFWs; nanowires, microwires) have been fabricated by a simple, reliable, and cost-effective technique. The electromechanical sensor device consists of a single electrically connected PFW that is placed on the outer surface of a flexible polystyrene (PS) substrate and bonded at its two ends. The entire device is fully packaged by a polydimethylsiloxane (PDMS) thin layer. The PFW has Schottky contacts at its two ends but with distinctly different barrier heights. The I- V characteristic is highly sensitive to strain mainly due to the change in Schottky barrier height (SBH), which scales linear with strain. The change in SBH is suggested owing to the strain induced band structure change and piezoelectric effect. The experimental data can be well-described by the thermionic emission-diffusion model. A gauge factor of as high as 1250 has been demonstrated, which is 25% higher than the best gauge factor demonstrated for carbon nanotubes. The strain sensor developed here has applications in strain and stress measurements in cell biology, biomedical sciences, MEMS devices, structure monitoring, and more.
Prevention of autoimmune diabetes by FTY720 in nonobese diabetic mice (2002)

FTY720 is a safe and benign therapeutic agent that may be used chronically in prediabetic individuals.