gebhart/patrepeval huggingface dataset:
Teduglutide ([Gly2]GLP‐2) protects small intestinal stem cells from radiation damage (2004)

Glucagon-like peptide-2 and its dipeptidyl peptidase (DP-IV) resistant analogue teduglutide are trophic for the gastrointestinal epithelium. Exposure increases villus height and crypt size and results in increased overall intestinal weight. As these effects may be mediated through stimulation of the stem cell compartment, they may promote intestinal healing and act as potential anti-mucositis agents in patients undergoing cancer chemotherapy. A study was initiated to investigate the protective effects of teduglutide on the murine small intestinal epithelium following gamma-irradiation using the crypt microcolony assay as a measure of stem cell survival and functional competence. Teduglutide demonstrated intestinotrophic effects in both CD1 and BDF1 mouse strains. In BDF1 mice, subcutaneous injection of GLP-2 or teduglutide (0.2 mg/kg/day, b.i.d.) for 14 days increased intestinal weight by 28% and resulted in comparable increases in crypt size, villus height and area. Teduglutide given daily for 6 or 14 days prior to whole body, gamma-irradiation significantly increased crypt stem cell survival when compared with vehicle-treated controls. The mean levels of protection over a range of doses provided protection factors from 1.3 to 1.5. A protective effect was only observed when teduglutide was given before irradiation. These results suggest that teduglutide has the ability to modulate clonogenic stem cell survival in the small intestine and this may have a useful clinical application in the prevention of cancer therapy-induced mucositis.
Studies on the Proteolytic Enzyme of Aspergilli (1954)

(1) A procedure for studying 542 strains of Aspergilli is described in this paper. Two types of proteolytic enzyme systems are obtained. (2) Five hundred strains of Asp. orysae type are tested. Thirty-three strains produce, sufficient proteinase activity to warrant further study. (3) Individual mold strains varied in their ability to attack various substrates, and these dissimilarities suggest differences in the specificity and composition of the proteolytic enzyme systems elaborated by the various strains.
A Maximum Likelihood Approach to Continuous Speech Recognition (1983)

Speech recognition is formulated as a problem of maximum likelihood decoding. This formulation requires statistical models of the speech production process. In this paper, we describe a number of statistical models for use in speech recognition. We give special attention to determining the parameters for such models from sparse data. We also describe two decoding methods, one appropriate for constrained artificial languages and one appropriate for more realistic decoding tasks. To illustrate the usefulness of the methods described, we review a number of decoding results that have been obtained with them.
Effect of PDE4 inhibitors on zymosan‐induced IL‐8 release from human neutrophils: synergism with prostanoids and salbutamol (1998)

1. The activation of neutrophils with particulate stimuli such as zymosan induces the generation of the C-X-C chemokine interleukin (IL)-8. There is evidence that neutrophil derived IL-8 plays an important role in human diseases such as the adult respiratory distress syndrome. In the present study, we examined the effects of cyclic AMP elevating agents on the ability of human neutrophils to generate IL-8 in response to zymosan particles. 2. The PDE4 inhibitor rolipram had limited effect on zymosan-induced IL-8 generation. In contrast, the PDE4 inhibitors RP 73401 and SB 207499 concentration-dependently suppressed IL-8 generation. The potency of these inhibitors was RP 73401 > SB 207499 > rolipram which is correlated with their rank order of potency at inhibiting the catalytic site of purified neutrophil PDE4. Pretreatment of neutrophils with the PDE3 inhibitor ORG 9935 or the PDE5 inhibitor zaprinast had no effect on IL-8 generation. 3. The prostanoids prostaglandin E1 (PGE1) and PGE2 inhibited zymosan-induced IL-8 release from neutrophils in a dose-dependent manner, in response to 10(-5) M PGE1 and PGE2 inhibiting IL-8 generation by 89% and 75%, respectively. Similarly, the beta2-adrenoceptor agonist salbutamol also inhibited IL-8 generation, but it was less effective than the prostanoids. 4. Significant synergism between prostanoids or salbutamol and the PDE4 inhibitors to inhibit IL-8 generation was observed. In contrast, there was no significant synergism between PGE2 and the PDE3 inhibitor ORG 9935 or the PDE5 inhibitor zaprinast. 5. In order to evaluate the potential role of protein kinase A in mediating the inhibitory effects of cyclic AMP-elevating agents, we used the protein kinase A inhibitors, H 89 and KT 5720. Pretreatment of neutrophils with these drugs completely reversed the inhibitory effects of a combination treatment with rolipram and PGE2 on zymosan-induced IL-8 release. 6. Microscopic examination revealed that most neutrophils contained one or more zymosan particles and that combination treatment with rolipram and PGE2 noticeably reduced the number of ingested particles. Moreover, there was a significant reduction in the percentage of neutrophils which ingested three or more zymosan particles. 7. Thus, our results demonstrate that cyclic AMP-elevating agents modulate the ability of neutrophils to generate IL-8 in response to a particulate stimulus. However, these agents also modulate the ability of neutrophils to phagocytose zymosan particles. Whether this effect will translate into inhibition of the ability of neutrophils to deal with infectious agents needs to be investigated further.
A PROCEDURE FOR MAP UPDATING USING DIGITAL MONO-PLOTTING AND DTMs (1998)

The production and updating of maps of the terrain surface is a procedure that can be done easily by using aerial photographs. In general this procedure needs to use expensive equipment that are not at reach of most offices requiring such maps. The advances in the computer science and the availability of low cost equipment for the digitizing and digital processing of the aerial photographs, open a wide range of applications for the production of cartographic information of the terrain surface by digital means, being one of them the Digital Monoplotting. Digital monoplotting consists in the production of planimetric information of the terrain surface through the direct vectorization on a digital aerial photograph, by using an image display for the digitizing of all the significant features of the terrain, and afterwards performing a analytical transformation on those vectors in order to correct the deformations intrinsic to the aerial photographs. In the case of non flat terrain, a rigorous transformation has to be performed to the digitized lines (vectors), by using the colinearity equations based on control points of known coordinates and the Digital Terrain Model (DTM) of the terrain. In such a way, deformations due to relief displacement and photograph tilt are corrected, obtaining a map free of deformations, at a known scale and referenced to a terrain coordinate system. In order to know the planimetric position of an image point on the terrain surface, it is necessary to determine the intersection point of the corresponding projective ray with the DTM of the terrain. In general this is an iterative and time-consuming procedure. In this paper an alternative direct solution to this problem is presented, and the requirements of the DTM density and accuracy applied to digital monoplotting are analyzed, with an application example.
Fine tuning of peptide binding to HLA-B*3501 molecules by nonanchor residues. (1995)

The prerequisites of peptide HLA-B*3501 interactions have been revisited by quantitative peptide binding assays with 190 chemically synthesized peptide possessing two anchor residues corresponding to the HLA-B*3501 peptide motif and a statistical residue-position analysis of binding and nonbinding peptides. According to the peptide motif of HLA-B*3501, aliphatic hydrophobic (Leu, Ile, and Met) or aromatic residues (Tyr and Phe) specify the main anchor at the C terminus, and position 2 renders an auxiliary anchor for proline. The importance of these residues was confirmed as a minimum requirement for peptide binding. Moreover, we demonstrated that high affinity peptide binding requires more than one favorable position of positions 3, 4, and 7. Aliphatic hydrophobic residues and residues that contain -OH or -SH side chains in position 3, 7, and 4 significantly enhance binding. Positions 1 and 5, or 7 may deteriorate peptide binding if these positions are held by proline and small residues (Ala and Gly) or basic residues carrying positively charged side chains (Arg and Lys), respectively. Positions 6 and 8 were statistically free of constrains. Yet, bulky aromatic residues and basic residues with a positively charged side chain at position 8 decreased the binding affinity. These findings were used to assess the predictability of binding and nonbinding peptides. Our binding predictions of 28 nonamers were verified by experimental data. Taking into account the importance of anchor and nonanchor positions in peptide binding and their practical value in peptide binding prediction, the search for peptide epitopes becomes more efficient.
Polymethyl methacrylate microspheres in collagen (2004)

Artecoll was developed about 20 years ago and underwent a number of production changes until it recently became FDA approved under the new name of Artefill. This product contains 20% polymethyl methacrylate (PMMA) microspheres with a diameter of 30 to 40 microm, which are suspended in a 3.5% atelo-collagen solution. The PMMA microspheres are now purified and no longer have an electrostatic charge, which in part was the cause for the early granulomatous reactions. Further, PMMA has long been known as bone cement and has been used in cosmetic surgery with a very good safety record. PMMA microspheres are biologically inert and nondegradable. The treatment results are therefore permanent and technical errors as well as incorrect injections will last. Due to the early record of granuloma formation, there is still a debate as to whether this product-as well as all other permanent fillers-should be injected for cosmetic reasons or not. With proper indications, excellent injection techniques, and realistic expectations as to what can be expected, this product has now proved to be one of the superior permanent filler substances.
In situ measurement of the remanence curve of magnetic recording media (1988)

A measurement technique is described that yields a normalized remanence curve of the recording medium under the actual conditions of the write process directly as a function of the write-head current. This could be a more useful result than the standard representation as a function of the applied field. The result, however, could be represented in the standard form if the head field function and the flying height were known. The measurement consists of writing a low-frequency, saturated all-ones pattern and subsequently overwriting an all-ones pattern, at the same frequency but displaced in phase, using the head-current value for which the remanence is to be measured. The head field has the same direction as the original field for the part of the bit cell unaffected. It has the position direction for the remaining part, reducing or partially reversing the magnetization of this part of the bit cell to the corresponding remanence value. On reading this record with a inductive read head, the area under each voltage pulse yields the remanent magnetization for the overwrite current used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modulation of Phosphoenolpyruvate Synthase Expression Increases Shikimate Pathway Product Yields in E. coli (2002)

Product yields in microbial synthesis are ultimately limited by the mechanism utilized for glucose transport. Altered expression of phosphoenolpyruvate synthase was examined as a method for circumventing these limits. Escherichia coli KL3/pJY1.216A was cultured under fed-batch fermentor conditions where glucose was the only source of carbon for the formation of microbial biomass and the synthesis of product 3-dehydroshikimic acid. Shikimate pathway byproducts 3-deoxy-D-arabino-heptulosonic acid, 3-dehydroquinic acid, and gallic acid were also generated. An optimal expression level of phosphoenolpyruvate synthase was identified, which did not correspond to the highest expression levels of this enzyme, where the total yield of 3-dehydroshikimic acid and shikimate pathway byproducts synthesized from glucose was 51% (mol/mol). For comparison, the theoretical maximum yield is 43% (mol/mol) for synthesis of 3-dehydroshikimic acid and shikimate pathway byproducts from glucose in lieu of amplified expression of phosphoenolpyruvate synthase.
A system for extracting and representing feature information driven by the application context (2002)

The system described works in two steps. The first step starts from a boundary model of an object and identifies the generic shape features by considering only geometric and topological aspects. These features are divided into two general classes, protrusions and depressions, extracted as solid volumes, and arranged in a multilevel structure. This representation, called shape-feature object graph (SFOG), is capable of representing the recursive decomposition of an object in its main shape and the set of its form features (possibly compound). The SFOG is a hierarchical and relational boundary model represented by a graph in which the root component nodes correspond to the boundary representation of the main shape, while the other nodes correspond to the boundary representations of features; arcs between nodes define parent-child relations between components. In the second step, the identified features are classified according to the functional meaning in the application context. Thus, the hierarchical representation is reorganized by gluing and/or grouping sets of shape features which are functionally related in the context considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ku70 Corrupts DNA Repair in the Absence of the Fanconi Anemia Pathway (2010)

A conserved DNA repair response is defective in the human genetic illness Fanconi anemia (FA). Mutation of some FA genes impairs homologous recombination and error-prone DNA repair, rendering FA cells sensitive to DNA cross-linking agents. We found a genetic interaction between the FA gene FANCC and the nonhomologous end joining (NHEJ) factor Ku70. Disruption of both FANCC and Ku70 suppresses sensitivity to cross-linking agents, diminishes chromosome breaks, and reverses defective homologous recombination. Ku70 binds directly to free DNA ends, committing them to NHEJ repair. We show that purified FANCD2, a downstream effector of the FA pathway, might antagonize Ku70 activity by modifying such DNA substrates. These results reveal a function for the FA pathway in processing DNA ends, thereby diverting double-strand break repair away from abortive NHEJ and toward homologous recombination.
A Transcription-dependent Micrococcal Nuclease-resistant Fragment of the Urokinase-type Plasminogen Activator Promoter Interacts with the Enhancer (2007)

We show the interaction between the enhancer and the minimal promoter of urokinase-type plasminogen activator gene during active transcription by coupling micrococcal nuclease digestion of cross-linked, sonicated chromatin, and chromatin immunoprecipitation. This approach allowed the precise identification of the interacting genomic fragments, one of which is resistant to micrococcal nuclease cleavage. The interacting fragments form a single transcriptional control unit, as indicated by their common protein content. Furthermore, we show that the enhancer-MP interaction persists during the early stages of transcription and is lost upon alpha-amanitin treatment, indicating the requirement for active transcription. Our results support a looping model of interaction between the enhancer and the MP of the urokinase-type plasminogen activator gene.
Intradermal administration of viral vaccines (1998)

Intradermal administration maybe useful in lowering the cost of vaccination against hepatitis B significantly, and may also be helpful for the rapid induction of antibodies, reversing non-responsiveness, improving postexposure prophylaxis and immunising immunocompromised people. In addition, delayed type hypersensitivity skin reaction to the vaccine could serve as a useful marker for the acquisition of T helper type 1 immunoreactivity in vivo. However, there are some disadvantages when using intradermal vaccinations, including the requirement for skilful administration, the absence of approval from licensing authorities, the development of local skin reactions and a lower antibody response when 1/10 of the standard vaccine dose is used. This requires that appropriate vaccination regimens, including the correct vaccine dosage, and vaccination schedule are followed. In the future, a similar vaccination strategy might also be applied for the prevention and control of other infectious diseases. Copyright 1998 John Wiley & Sons, Ltd.
Pathophysiology of Gene-Targeted Mouse Models for Cystic Fibrosis (1999)

Grubb, Barbara R., and Richard C. Boucher. Pathophysiology of Gene-Targeted Mouse Models for Cystic Fibrosis. Physiol. Rev. 79, Suppl.: S193–S214, 1999. — Mutations in the gene causing the fatal disease cystic fibrosis (CF) result in abnormal transport of several ions across a number of epithelial tissues. In just 3 years after this gene was cloned, the first CF mouse models were generated. The CF mouse models generated to date have provided a wealth of information on the pathophysiology of the disease in a variety of organs. Heterogeneity of disease in the mouse models is due to the variety of gene-targeting strategies used in the generation of the CF mouse models as well as the diversity of the murine genetic background. This paper reviews the pathophysiology in the tissues and organs (gastrointestinal, airway, hepatobiliary, pancreas, reproductive, and salivary tissue) involved in the disease in the various CF mouse models. Marked similarities to and differences from the human disease have been observed in the various murine models. Some of the CF mouse models accurately reflect the ion-transport abnormalities and disease phenotype seen in human CF patients, especially in gastrointestinal tissue. However, alterations in airway ion transport, which lead to the devastating lung disease in CF patients, appear to be largely absent in the CF mouse models. Reasons for these unexpected findings are discussed. This paper also reviews pharmacotherapeutic and gene therapeutic studies in the various mouse models.
HUMAN AUTOIMMUNE NEUROPATHIES (1998)

Peripheral nerve diseases are among the most prevalent disorders of the nervous system. Because of the accessibility of the peripheral nervous system (PNS) to direct physiological and pathological study, neuropathies have traditionally played a unique role in developing our understanding of basic mechanism of nervous system injury and repair. At present they are providing new insight into the mechanisms of immune injury to the nervous system. A rapidly growing catalogue of PNS disorders are now suspected to be immune-mediated, and in the best understood of these disorders, the molecular and cellular targets of immune attack are known, and the pathophysiology follows directly from the specific immune injury. This review summarizes the immunologically relevant features of the PNS, then considers selected immune-mediated neuropathies, focusing on pathogenetic mechanisms. Finally, the PNS is providing a testing ground for new immunotherapies and approaches to protection and regeneration, including the use of trophic factors. The current status of treatment and implications for future approaches is reviewed.
DCT-Based Iris Recognition (2007)

This paper presents a novel iris coding method based on differences of discrete cosine transform (DCT) coefficients of overlapped angular patches from normalized iris images. The feature extraction capabilities of the DCT are optimized on the two largest publicly available iris image data sets, 2,156 images of 308 eyes from the CASIA database and 2,955 images of 150 eyes from the Bath database. On this data, we achieve 100 percent Correct Recognition Rate (CRR) and perfect Receiver-Operating Characteristic (ROC) Curves with no registered false accepts or rejects. Individual feature bit and patch position parameters are optimized for matching through a product-of-sum approach to Hamming distance calculation. For verification, a variable threshold is applied to the distance metric and the False Acceptance Rate (FAR) and False Rejection Rate (FRR) are recorded. A new worst-case metric is proposed for predicting practical system performance in the absence of matching failures, and the worst case theoretical Equal Error Rate (EER) is predicted to be as low as 2.59 x 10(-4) on the available data sets.
Preliminary observation with dronabinol in patients with intractable pruritus secondary to cholestatic liver disease (2002)

Pruritus due to cholestatic liver disease can be particularly difficult to manage and frequently is intractable to a variety of medical therapies. The aim of our study is to evaluate the efficacy of delta-9-tetrahydrocannabinol (delta-9-THC) for intractable cholestatic related pruritus (ICRP) that has failed conventional (and unconventional) remedies. Three patients were evaluated for plasmapheresis because of ICRP. All 3 patients had previously been extensively treated with standard therapies for ICRP including: diphenhydramine, chlorpheniramine, cholestyramine, rifampicin, phenobarbital, doxepin, naltrexone, UV therapy, and topical lotions. Even multiple courses of plasmapheresis were performed without any benefit for the intractable pruritus. All patients reported significant decreases in their quality of life, including lack of sleep, depression, inability to work, and suicidal ideations. All patients were started on 5 mg of delta-9-THC (Marinol) at bedtime. All 3 patients reported a decrease in pruritus, marked improvement in sleep, and eventually were able to return to work. Resolution of depression occurred in two of three. Side effects related to the drug include one patient experiencing a disturbance in coordination. Marinol dosage was decreased to 2.5 mg in this patient with resolution of symptoms. The duration of antipruritic effect is approximately 4-6 hrs in all three patients suggesting the need for more frequent dosing. Delta-9-tetrahydrocannabinol may be an effective alternative in patients with intractable cholestatic pruritus.
Clonal analysis using recombinant DNA probes from the X-chromosome. (1987)

It has been demonstrated that restriction fragment length polymorphisms of X-chromosome genes can be used in conjunction with methylation patterns to determine the clonal composition of human tumors. In this report, we show that several X-chromosome probes can be used for such analyses. In particular, probes derived from the hypoxanthine phosphoribosyltransferase gene and the phosphoglycerate kinase gene could be used for clonal analysis in over 50% of American females. The X-inactivation patterns observed with these probes were found to accurately reflect clonality in more than 95% of 92 tumors tested.
CD40 and its ligand in cell-mediated immunity (1998)

CD40 and its ligand (gp39, CD40L, TBAM) is central to the control of thymus-dependent humoral immunity. However, in recent years it has become evident that CD40 signaling also is critical in the development of cell-mediated immune responses. How CD40 regulates cell-mediated immunity is discussed.