gebhart/patrepeval huggingface dataset:
Skin biopsies predict acute graft-versus-host disease after small bowel transplantation in pigs (2007)

Intestinal transplantation is being increasingly performed to treat patients with irreversible intestinal failure. The major cause of intestinal graft failure is graft-versus-host disease (GVHD) that represents a life-threatening complication after small bowel transplantation (Itx). The purpose of this study was to assess the diagnostic and prognostic value of skin biopsy histological changes for acute GVHD after Itx in pigs. Thirty-four Large White pigs were divided into three groups: Group 1 with Itx only, Group 2 with Itx and donor bone marrow infusion (Itx BM) and Group 3 (control group - before the operation). Animals received tacrolimus-based immunosuppression from day 0 to day 30 postoperatively. Skin and small bowel biopsies were histologically assessed, analysed and classified from grade 1 to 4 on postoperative days 15, 30, 45 and 60. There was a strong correlation between the histological grading values of skin biopsy changes and the histological grading values of small bowel biopsy changes (Kendall's tau_b is 0.855 for the Itx group and 0.730 for the Itx BM group). The significant correlation found between skin and small bowel histological changes suggests the prognostic value of skin biopsies after Itx. In conclusion, our findings emphasise the diagnostic and prognostic value of skin biopsy analysis for acute GVHD after Itx.
Review: The structure and function of yeast xylose (aldose) reductases (1998)

Yeast xylose (aldose) reductases are members of the aldo-keto reductase family of enzymes which are widely distributed in a variety of other organisms. In yeasts, these enzymes catalyse the first step of xylose metabolism where xylose is converted to xylitol. In the past 16 years, xylose reductases from yeasts able to ferment or utilize xylose have been isolated and studied mainly because of their importance in xylose bioconversions. In recent years, genes encoding xylose reductases from several yeasts have been cloned and sequenced. A comparison of the primary sequences of yeast xylose reductases with the much better characterized human aldose reductase and human aldehyde reductase reveals that the yeast enzymes are hybrids between aldo-keto reductases and the short chain dehydrogenases/reductases families of enzymes. Why this is so and its evolutionary significance is presently not known. This short review will critically examine the structure and function information that can be gleaned from the sequence comparison. Several interesting questions arise from the sequence comparison and these can provide fruitful areas for further investigations.
Metal Complexes Derived from <i>cis</i> ‐1,2‐dicyano‐1,2‐ethylenedithiolate and Bis(Trifluoromethyl)‐1,2‐dithiete (1967)

This chapter contains sections titled: Sodium cis-1,2-dicyano-1,2-ethylenedithiolate Bis(cis-1,2-dicyano-1,2-ethylenedithiolato) metallate Complexes, [MS4C4(CN)4]2- Bis(cis-1,2-dicyano-1,2-ethylenedithiolato) metallate Complexes, [MS4C4(CN)4]1 Bis[cis-1,2-bis (trifluoromethyl)-1,2-ethylenedithiolato]metal Complexes Tris[cis-1,2-bis(trifluoromethyl)-1,2-ethylenedithiolato]metal Complexes
Software code base conversions (2007)

Current and future military avionic systems require real-time embedded software based on the latest technological advances in software tools, capabilities, and languages. However, the development time and lifecycle of avionic systems is so long, that the tools, processes, methodologies, and languages used by the system developers are often obsolete by the time the systems need significant upgrades or replacement. Hence, software obsolescence is a major issue faced by many avionic systems. Previously, avionics programs have tackled software obsolescence using different approaches. These approaches have included code conversions by hand, which are costly and time consuming, scripting tools/languages which have scalability problems, emulators which involve re-engineering of the peripheral code base and retention of the obsolete code engineering environment, and software wrappers which are not costly but hinder future modifications to the legacy software that is accessed by the software wrappers. Each of these approaches has its own liabilities. For our research and development effort we chose to upgrade our legacy code base with a specially developed code refactoring transformer, the Boeing migration tool (BMT). Specially developed code transformers based on new technologies and more powerful computers are scalable, capable of converting almost the entire code base, allow for future development on the updated code base with the latest tools, processes, methodologies, and languages, and are less costly than updating code by hand. This paper details the inputs, the code transformer itself, the outputs, and how well the code transformer performed its task for updating a software code base. This work was performed for the Defense Advanced Research Projects Agency (DARPA) program composition for embedded systems (PCES) program. The resulting code base generated by the code transformer could be updated with the most recent tools, processes, and languages. DARPA's objective was to find faster and easier software code base conversion processes that lead to new software code bases that were closer to the final product than previous mechanizations.
Ulcerative colitis and colon cancer: Biology and surveillance (1992)

The risk of colorectal carcinoma is increased among patients with longstanding ulcerative colitis and Crohn's disease. The development of cancer in inflammatory bowel disease is hypothesized to evolve by a multistep process involving genetic instability, clonal expansion and the development of a malignant phenotype. The contribution of nutritional factors such as folate deficiency is of great interest; molecular genetic mechanisms are under study. In contrast to sporadic colorectal carcinoma, carcinomas in ulcerative colitis are associated with a long prior history of chronic inflammation and the subsequent development of epithelial dysplasia. Dysplasia is defined as an unequivocal neoplastic alteration of the colonic mucosa. The object of surveillance is prevention of death from cancer by detection at a premalignant or early curable stage. Patients at greatest risk of cancer who customarily undergo endoscopic surveillance are those with extensive colitis of more than 8 years duration. Dysplastic epithelium may occur in flat mucosa, and may produce a plaque or a nodular/villiform appearance. Dysplasia is not present in all patients with cancer in colitis. It is important to develop more sensitive and specific markers for the presence of precancer or cancer in colitis. Under study are proliferation-associated markers detected by immunohistochemistry, lectin binding, flow cytometry and laser-induced fluorescence coupled with endoscopy.
Dynamic cerebral autoregulation in healthy adolescents (2002)

: The autoregulatory index is physiologically lower in normal adolescents 12-17 years of age than in adults.
Study on biodegradable aromatic/aliphatic copolyesters (2008)

Progress on biodegradable aromatic/aliphatic copolyesters based on aliphatic and aromatic diacids, diols and ester monomers was reviewed. The aromatic/aliphatic copolyesters combined excellent mechanical properties with biodegradability. Physical properties and biodegradability of copolyesters varied with chain length of the aliphatic polyester segment and atacticity of copolyesters. The processability of copolyesters could be improved significantly after incorporating a stiff chain segment through copolymerization of aliphatic polyesters with an aromatic liquid crystal element. The aromatic/aliphatic copolyesters as a new type of biodegradable materials could replace some general plastics in certain applications, namely biomedical and environmental friendly fields.
Neonatal and early life immune responses to various forms of vaccine antigens qualitatively differ from adult responses: predominance of a Th2‐biased pattern which persists after adult boosting (1996)

Induction of neonatal immune responses to vaccine antigens is believed to be of limited efficacy because of immune immaturity and particular susceptibility to tolerogenic signals during this period of life. To characterize particular features of neonatal immune responses to vaccine antigens, we assessed the capacity of BALB/c mice at different stages of immunological maturation to respond to a selection of vaccine antigens and presentation systems. Significant B and T cell responses to vaccine antigens (tetanus and measles virus peptides, tetanus toxoid, live viral attenuated measles virus, canarypox recombinant measles vector or bacillus Calmette-Guérin) were obtained as early as the first week of life. However, these neonatal responses differed qualitatively from adult responses by a decreased IgG2a/IgG1 ratio of vaccine-specific antibodies, the secretion of significantly higher interleukin-5 and lower interferon-gamma levels by vaccine-specific T cells and an impaired induction of cytotoxic T cell precursors. This pattern of biased Th2 versus Th1 responses induced upon early exposure to vaccines was not reversed by decreasing the doses of vaccine antigens. It did not disappear with aging and was still reflected in adult responses to booster immunization with the corresponding antigen. Thus, neonatal immunization can induce significant vaccine specific responses with a predominance of a Th2 pattern which can persist in boosted adult mice.
Glucocorticoid and Mineralocorticoid Receptors in Gut Mucosa<sup>1</sup> (1975)

Both glucocorticoid and mineralocorticoid hormones are known to be involved in the physiology and pathophysiology of the gastrointestinal tract. Studies on the mechanism of action of steroid hormones indicate an initial obligatory step of binding to stereospecific receptor proteins in the cytoplasm of target tissue cells. Mucosal cells from the gastrointestinal tract of adrenalectomized, gonadectomized rats contain cytoplasmic glucocorticoid receptors which bind tritiated dexamethasone with an affinity (Kdiss4C) of approximately 10(-8)M. The concentration of glucocorticoid receptors per unit cytoplasmic protein is in order duodenum greater than jejunum greater than ileum=stomach greater than colon, and their affinity for steroid hormones is in order dexamethasone greater than corticosterone greater than deoxycorticosterone=aldosterone. No glucocorticoid receptors could be demonstrated in esophageal mucosal cells. Binding sites for tritiated aldosterone, with affinity characteristics appropriate for physiological mineralocorticoid receptors, were demonstrated in duodenum, jejunum, ileum and colon. No similar sites could be shown in the mucosa of the gastric antrum.
On A Responsive Replenishment System: A Fuzzy Logic Approach (2006)

In today's competitive business environment, it is important that customers are able to obtain the preferred items in the shops they visit, particularly for the convenience store chains such as 7-Eleven where popular items are expected to be readily available on the shelves of the stores for buyers. To minimize the cost of running such store chains, it is essential that the stocks must be kept to a minimum and at the same time large varieties of popular items are also available for customers. This paper attempts to propose a responsive replenishment system which is able to respond to the fluctuating demands of customers and provide a timely supply of needed items in a cost-effective way. The proposed system embraces the principle of fuzzy logic which is able to deal with uncertainties by virtue of its fuzzy rules reasoning mechanism, thereby leveraging the responsiveness of the entire replenishment system for the chain stores.
Oil Spills Abatement: Factors Affecting Oil Uptake by Cellulosic Fibers (2012)

Wood-derived cellulosic fibers prepared in different ways were successfully employed to absorb simulated crude oil, demonstrating their possible use as absorbents in the case of oil spills. When dry fibers were used, the highest sorption capacity (six parts of oil per unit mass of fiber) was shown by bleached softwood kraft fibers, compared to hardwood bleached kraft and softwood chemithermomechanical pulp(CTMP) fibers. Increased refining of CTMP fibers decreased their oil uptake capacity. When the fibers were soaked in water before exposure to the oil, the ability of the unmodified kraft fibers to sorb oil was markedly reduced, whereas the wet CTMP fibers were generally more effective than the wet kraft fibers. Predeposition of lignin onto the surfaces of the bleached kraft fibers improved their ability to take up oil when wet. Superior ability to sorb oil in the wet state was achieved by pretreating the kraft fibers with a hydrophobic sizing agent, alkenylsuccinic anhydride (ASA). Contact angle tests on a model cellulose surface showed that some of the sorption results onto wetted fibers could be attributed to the more hydrophobic nature of the fibers after treatment with either lignin or ASA.
Clinical use of lentiviral vectors (2018)

Viral vectors provide an efficient means for modification of eukaryotic cells, and their use is now commonplace in academic laboratories and industry for both research and clinical gene therapy applications. Lentiviral vectors, derived from the human immunodeficiency virus, have been extensively investigated and optimized over the past two decades. Third-generation, self-inactivating lentiviral vectors have recently been used in multiple clinical trials to introduce genes into hematopoietic stem cells to correct primary immunodeficiencies and hemoglobinopathies. These vectors have also been used to introduce genes into mature T cells to generate immunity to cancer through the delivery of chimeric antigen receptors (CARs) or cloned T-cell receptors. CAR T-cell therapies engineered using lentiviral vectors have demonstrated noteworthy clinical success in patients with B-cell malignancies leading to regulatory approval of the first genetically engineered cellular therapy using lentiviral vectors. In this review, we discuss several aspects of lentiviral vectors that will be of interest to clinicians, including an overview of lentiviral vector development, the current uses of viral vectors as therapy for primary immunodeficiencies and cancers, large-scale manufacturing of lentiviral vectors, and long-term follow-up of patients treated with gene therapy products.
Multiplex Sequencing by Hybridization (2001)

One of the limitations of classical sequencing by hybridization (SBH) is the inefficient use of probes in the "all k-mers" array. This limitation occurs due to the relatively short length (roughly the square root of C) of target that may be reconstructed by an array with C probes. We propose a new strategy, multiplex sequencing by hybridization, that greatly increases the efficiency of target reconstruction. In the typical multiplex SBH method, many different target sequences are simultaneously reconstructed (as compared to a single sequence in classic SBH). This is accomplished by pooling the target sequences and performing several hybridization experiments. This procedure makes more efficient use of probes so that the combined length of sequence reconstructed per DNA array increases significantly as compared to classical SBH.
Tuning the properties of the bacterial membrane with aminoacylated phosphatidylglycerol (2009)

The bacterial envelope is a semi-permeable barrier that protects the cell from the hostilities of the environment. To survive the ever-changing conditions of their surroundings, bacteria need to rapidly adjust the biochemical properties of their cellular envelope. Amino acid (aa) addition to phosphatidylglycerol (PG) of the membrane is one of the mechanisms used by bacteria to lower the net negative charge of their cellular envelope, thereby decreasing its affinity for several antibacterial agents such as the cationic antimicrobial peptides (CAMPs) produced by the innate immune response during host infection. This process requires the activity of an integral membrane protein, called aa-PG synthase (aaPGS), to transfer the aa of aminoacyl-tRNA (aa-tRNA) onto the PG of the membrane. aaPGSs constitute a new family of virulence factors that are found in a wide range of microorganisms. aa-PGs not only provide resistance to CAMPs but also to other classes of antibacterial agents and to environmental stresses such as those encountered during extreme osmotic or acidic conditions. This review will describe the known biochemical properties of aa-PGSs, their specificity for aa-tRNAs and phospholipids, and the growing repertoire of aa used as substrates by these enzymes. Their prevalence in bacteria and the phenotypes and modulations of membrane properties associated with these molecules will be addressed, as well as their regulation as a component of the envelope stress response system in certain bacteria.
Cell entry strategy of clostridial neurotoxins (2009)

Tetanus neurotoxin and botulinum neurotoxins are the causative agents of tetanus and botulism. They block the release of neurotransmitters from synaptic vesicles in susceptible animals and man and act in nanogram quantities because of their ability to specifically attack motoneurons. They developed an ingenious strategy to enter neurons. This involves a concentration step via complex polysialo gangliosides at the plasma membrane and the uptake and ride in recycling synaptic vesicles initiated by binding to a specific protein receptor. Finally, the neurotoxins shut down the synaptic vesicle cycle, which they had misused before to enter their target cells, via specific cleavage of protein core components of the cellular membrane fusion machinery. The uptake of four out of seven known botulinum neurotoxins into synaptic vesicles has been demonstrated to rely on binding to intravesicular segments of the synaptic vesicle proteins synaptotagmin or synaptic vesicle protein 2. This review summarizes the present knowledge about the cell receptor molecules and the mode of toxin-receptor interaction that enables the toxins' sophisticated access to their site of action.
An adjustable focusing system for a 2 MeV H – ion beam line based on permanent magnet quadrupoles (2016)

ABSTRACT: A compact adjustable focusing system for a 2 MeV H – RFQ Linac is designed, con-structed and tested based on four permanent magnet quadrupoles (PMQ). A PMQ model is realised using finite element simulations, providing an integrated field gradient of 2.35 T with a maximal field gradient of 57 Tm−1. A prototype is constructed and the magnetic field is measured, demon-strating good agreement with the simulation. Particle track simulations provide initial values for the quadrupole positions. Accordingly, four PMQs are constructed and assembled on the beam line, their positions are then tuned to obtain a minimal beam spot size of (1.2×2.2)mm2 on target. This paper describes an adjustable PMQ beam line for an external ion beam. The novel compact design based on commercially available NdFeB magnets allows high flexibility for ion beam applications.
The Antagonists RU486 and ZK98299 Stimulate Progesterone Receptor Binding to Deoxyribonucleic Acid in Vitro and in Vivo, but Have Distinct Effects on Receptor Conformation* (1998)

Three types of transfection experiments were used to detect the abilities of different classes of antagonists to stimulate binding of progesterone receptor (PR) to progesterone response elements (PRE) in intact mammalian cells. These included a promoter interference assay, in which PR binding to PREs positioned between the TATA box and the start of transcription is detected as a reduction of expression of a constitutively active reporter gene, competition of PR antagonist and glucocorticoid receptor agonist for a common glucocorticoid response element/PRE-controlled reporter construct, and activation of a chimeric receptor (PR-VP16) containing the constitutive trans-activation domain derived from the VP16 protein of herpes simplex virus. By each approach, all antagonists tested were equally effective in stimulating PR binding to PREs in the cell. This included previously designated type I (ZK98299) and type II (RU486, ZK98734, and ZK112993) 11beta-aryl substituted steroid analogs. Stimulation of PR binding to PREs in the cell by ZK98299 was of interest because this antagonist has been reported to lack the ability to stimulate PR-DNA binding in vitro by electrophoretic gel mobility shift assay compared with RU486, which promotes efficient binding of PR to PREs. To clarify the apparent discrepancy between intact cell and in vitro results with ZK98299, we altered electrophoretic gel mobility shift assay conditions to allow detection of less stable DNA complexes. Under these conditions, ZK98299 induced the formation of specific PR-PRE complexes. Further analysis of the ZK98299-induced DNA complexes revealed that they exhibited an electrophoretic mobility different from that of the complexes induced by RU486, and the off-rate of PR from DNA was faster than that of the PR bound to agonist. This suggests that ZK98299 promotes a conformational change within PR distinct from that induced by RU486. The present results are consistent with the conclusions that ZK98299 stimulates PR binding to target DNA sequences and that ZK98299 and RU486 represent two mechanistic classes of antagonists based on inducing different conformational changes in PR.
Identification of a novel p53 functional domain that is necessary for efficient growth suppression (1996)

Activation of the p53 tumor suppressor protein has been demonstrated to block cell growth by inducing either a transient cell cycle arrest or programmed cell death (apoptosis). Although evidence exists linking p53's function as an activator of transcription to its ability to effect cell cycle arrest, the role of this activity in the induction of apoptosis remains unclear. To gain insight into the molecular mechanisms underlying p53-mediated antiproliferative pathways, a study was initiated to explore the functions of a putative p53 signaling domain. This region of the human p53 protein is localized between amino acids 61 and 94 (out of 393) and is noteworthy in that it contains five repeats of the sequence PXXP (where P represents proline and X any amino acid). This motif has been shown to play a role in signal transduction via its SH3 domain binding activity. A p53 cDNA deletion mutant (delta pro AE), which lacks this entire proline-rich domain (deleted for amino acids 62-91), was created and characterized for a variety of p53 functions. The entire domain has been shown to be completely dispensable for transcriptional activation. On the other hand, this deletion of the p53 proline-rich domain impairs p53's ability to suppress tumor cell growth in culture. Amino acid substitution mutations at residues 22 and 23 of p53 (eliminates transcriptional activity) also impair p53-mediated inhibition of cell growth in culture. Unlike wild-type p53, the delta proAE mutant cDNA can be stably expressed in tumor derived cell lines with few immediate detrimental effects. These cells express physiologic levels of p53 protein that are induced normally in response to DNA damage, indicating that removal of the proline-rich domain does not disrupt p53's upstream regulation by DNA damage. These data indicate that, in addition to the transcriptional activation domain, the p53 proline-rich domain plays a critical role in the transmission of antiproliferative signals down-stream of the p53 protein and may link p53 to a direct signal transduction pathway.