gebhart/patrepeval huggingface dataset:
Effect of perioperative management on prognosis of bile duct injury (2009)

Objective To investigate the important auxiliary effect of perioperative management on bile duct injury. Methods The clinical and follow-up data of 66 patients with bile duct injury trea-ted in our hospital during 1987-2006 were analyzed to explore the effect of perioperative management on the prognosis of the bile duet injury. Results The bile duct injury in 48 cases was proved by Bus, CT, MRCP, ERCP or other imaging methods. The injury in 44 cases was found during operation by imaging methods and were timely anastomosed or repaired. Nine cases obtained the opportunity for the second-stage bile duct reconstruction after treatments of effective external drainage, general support and anti-infection treatment for 3-6 months. Two patients died of diffuse biliary peritonitis or systemic failure, 1 died of pancreatojejunal or eholedochojejunal anastomotie syndrome because the major duode-nal papilla and minor duodenal papilla was located in diverticulum after the diverticulum was excised. Bile duct stenosis happened after cholangiojejunostomy and the syndrome was obviously alleviated re-cently by ballon dilatation therapy. One post-cholangiojejunostomy patient died of systemic failure af-ter repeated attack cholangitis and reiterative operations. Conclusion In addition to operative treat-ment, perioperative management is a very important factor to affect the prognosis of the bile duct inju-ry. Bile duet injury should be found and disposed in time. Intraoperative cholangiography could in-crease the diagnostic accuracy and play an important guiding role in selecting treatment methods. For the cases with eritical abdominal infection, it should be operated in proper time after effective drain-age, general support and infection control. Proper plaeing of the support tube and the application of bile duct dilator are crucial for decreasing the ratio of biliary duct stricture.

Key words: 
Bile duct injury; Perioperative management; Prognosis
Phylogenetic Placement of a New, Diminutive Nyctitheriid (Mammalia, Eulipotyphla) with Arboreal Characteristics (2014)

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Characterization of T-cell response to woodchuck hepatitis virus core protein and protection of woodchucks from infection by immunization with peptides containing a T-cell epitope (1997)

Specific activation of T cells appears to be a prerequisite for viral clearance during hepatitis B virus (HBV) infection. The T-cell response to HBV core protein is essential in determining an acute or chronic outcome of HBV infection, but how this immune response contributes to the course of infection remains unclear. This is due to results obtained from humans, which are restricted to phenomenological observations occurring during the clinical onset after HBV infection. Thus, a useful animal model is needed. Characterization of the T-cell response to the core protein (WHcAg) of woodchuck hepatitis virus (WHV) in woodchucks contributes to the understanding of these mechanisms. Therefore, we investigated the response of woodchuck peripheral blood mononuclear cells (PBMCs) to WHcAg and WHcAg-derived peptides, using our 5-bromo-2'-deoxyuridine assay. We demonstrated WHcAg-specific proliferation of PBMCs and nylon wool-nonadherent cells from acutely WHV-infected woodchucks. Using a cross-reacting anti-human T-cell (CD3) antiserum, we identified nonadherent cells as woodchuck T cells. T-cell epitope mapping with overlapping peptides, covering the entire WHcAg, revealed T-cell responses of acutely WHV-infected woodchucks to peptide1-20, peptide100-119, and peptide112-131. Detailed epitope analysis in the WHcAg region from amino acids 97 to 140 showed that T cells especially recognized peptide97-110. Establishment of polyclonal T-cell lines with WHcAg or peptide97-110 revealed reciprocal stimulation by peptide97-110 or WHcAg, respectively. We vaccinated woodchucks with peptide97-110 or WHcAg to prove the importance of this immunodominant T-cell epitope. All woodchucks immunized with peptide97-110 or WHcAg were protected. Our results show that the cellular immune response to WHcAg or to one T-cell epitope protects woodchucks from WHV infection.
Graphene as a Long-Term Metal Oxidation Barrier: Worse Than Nothing (2013)

Anticorrosion and antioxidation surface treatments such as paint or anodization are a foundational component in nearly all industries. Graphene, a single-atom-thick sheet of carbon with impressive impermeability to gases, seems to hold promise as an effective anticorrosion barrier, and recent work supports this hope. We perform a complete study of the short- and long-term performance of graphene coatings for Cu and Si substrates. Our work reveals that although graphene indeed offers effective short-term oxidation protection, over long time scales it promotes more extensive wet corrosion than that seen for an initially bare, unprotected Cu surface. This surprising result has important implications for future scientific studies and industrial applications. In addition to informing any future work on graphene as a protective coating, the results presented here have implications for graphene's performance in a wide range of applications.
Birt–Hogg–Dubé syndrome: Clinical and molecular aspects of recently identified kidney cancer syndrome (2015)

Birt-Hogg-Dubé syndrome is an autosomal dominantly inherited disease that predisposes patients to develop fibrofolliculoma, lung cysts and bilateral multifocal renal tumors, histologically hybrid oncocytic/chromophobe tumors, chromophobe renal cell carcinoma, oncocytoma, papillary renal cell carcinoma and clear cell renal cell carcinoma. The predominant forms of Birt-Hogg-Dubé syndrome-associated renal tumors, hybrid oncocytic/chromophobe tumors and chromophobe renal cell carcinoma are typically less aggressive, and a therapeutic principle for these tumors is a surgical removal with nephron-sparing. The timing of surgery is the most critical element for postoperative renal function, which is one of the important prognostic factors for Birt-Hogg-Dubé syndrome patients. The folliculin gene (FLCN) that is responsible for Birt-Hogg-Dubé syndrome was isolated as a novel tumor suppressor for kidney cancer. Recent studies using murine models for FLCN, a protein encoded by the FLCN gene, and its two binding partners, folliculin-interacting protein 1 (FNIP1) and folliculin-interacting protein 2 (FNIP2), have uncovered important roles for FLCN, FNIP1 and FNIP2 in cell metabolism, which include AMP-activated protein kinase-mediated energy sensing, Ppargc1a-driven mitochondrial oxidative phosphorylation and mTORC1-dependent cell proliferation. Birt-Hogg-Dubé syndrome is a hereditary hamartoma syndrome, which is triggered by metabolic alterations under a functional loss of FLCN/FNIP1/FNIP2 complex, a critical regulator of kidney cell proliferation rate; a mechanistic insight into the FLCN/FNIP1/FNIP2 pathway could provide us a basis for developing new therapeutics for kidney cancer.
The discovery of dystrophin, the protein product of the Duchenne muscular dystrophy gene (2020)

Duchenne muscular dystrophy was a well-established medical and genetic enigma by the 1970s. Why was the new mutation rate so high in all world populations? Why were affected boys doing well in early childhood, but then showed relentless progression of muscle wasting? What was wrong with the muscle? The identification of the first fragments of DMD gene cDNA in 1986, prediction of the entire 3685 amino acid protein sequence, and production of antibodies to dystrophin, both in 1987, provided key tools to understand DMD genetics and molecular pathology. The identification of dystrophin nucleated extensive research on myofiber membrane cytoskeleton, membrane repair, muscle regeneration, and failure of regeneration. This in turn led to molecular therapeutics based on understanding of dystrophin structure and function. This historical perspective describes the events surrounding the initial identification of the dystrophin protein.
The biology of animal stress: basic principles and implications for animal welfare. (2000)

1: Biological Response to Stress: Implications for Animal Welfare, G P Moberg, University of California, USA 2: Some Issues in the Interpretation of Behavioural Responses to Stress, J Rushen, Dairy and Swine Research and Development Centre, Agriculture and Agri-food Canada, Canada 3: Neoroendocrine Responses to Stress, R L Matteri, J A Carroll and C J Dyer, University of Missouri, USA 4: The Metabolic Consequences of Stress: Targets for Stress and Priority of Nutrient Use, T H Elsasser et al., USDA, Agricultural Research Service, USA 5: Immune System Response to Stress, F Blecha, Kansas State University, USA 6: Hands-on and Hands-off Measurement of Stress, C J Cook et al., Horticultural and Food Research Institute of New Zealand, New Zealand 7: Accumulation and Long-Term Effects of Stress in Fish, C B Schreck, Oregon State University, USA 8: Chronic Intermittent Stress: A Model for the Study of Long Term Stressors, J Ladewig, The Royal Veterinary and Agricultural University, Denmark 9: Quantifying Some Responses to Pain as a Stressor, D J Mellor, Massey University, New Zealand, C J Cook and K J Stafford, Horticultural and Food Research Institute of New Zealand, New Zealand 10: Multiple Factors Controlling Behaviour: Implications for Stress and Welfare, F Toates, The Open University, Milton Keynes, UK 11: Chronic Social Stress: Studies in Nonhuman Primates, S P Mendoza, J P Capitanio and W A Mason, University of California, USA 12: Consequences of Stress During Development, D C Lay Jr., Iowa State University, USA 13: Early Developmental Influences of Experience on Behaviour, Temperament, and Stress, W A Mason, University of California, USA 14: Genetic Selection to Reduce Stress in Animals, T G Pottinger, NERC Institute of Freshwater Ecology, Windermere Laboratory, Cumbria, UK 15: Human-Animal Interactions and Animal Stress, P H Hemsworth and J L Barnett, Agriculture Victoria, Australia 16: Alleviating Stress in Zoo Animals with Environmental Enrichment, K Carlstead, National Zoological Park, Washington, USA and D Shepherdson, Oregon Zoo, USA 17: Understanding the Role of Stress in Animal Welfare: Practical Considerations, T L Wolfle, formerly of the Institute for Laboratory Animal Research, National Research Council, National Academy of Sciences, USA
P element mediated germ line transformation of Drosophila melanogaster with the Tc1 transposable DNA element from Caenorhabditis elegans (1994)

Questions relating to the origin and regulation of mobile genetic elements are currently of considerable interest. Since it is now possible to address more precisely issues concerning the entry, dispersion, and regulation of elements within a virgin genome, one approach that may afford a better understanding of transposable elements in general could be provided by interspecific DNA transformation. Therefore, the Tc1 transposable DNA element from Caenorhabditis elegans was chosen as a proposed invading element of the Drosophila melanogaster genome. The basis for this selection resided in the inherent structural and functional similarities, as well as sequence identities, between the Caenorhabditis element and elements innate to Drosophila (e.g., P, HB1, and Uhu). Initial investigations were carried out to define a clone carrying an intact Tc1 element. This Tc1 element was inserted into a P transposon vector and two P-Tc1-ry+ constructs, differing only in insert orientation, were identified. P element mediated germ line transfer was then used to generate a transformant that was genetically and molecularly identified as containing a single, structurally intact Tc1 element at cytological location 64C4-5 on the third chromosome. The single P[(Tc1,ry+)]SAS-B insertion was thereafter mobilized by using a P[ry+ delta 2-3] element as a transposase source, and the genetic and molecular data suggested that the insertion had been successfully reintegrated to a variety of genomic locations. On the basis of genetic and molecular analyses, the Tc1 element in the P[Tc1,ry+)] transformed stock is not highly unstable in germ line and somatic tissues.
The zebrafish diwanka gene controls an early step of motor growth cone migration (1999)

During vertebrate embryogenesis different classes of motor axons exit the spinal cord and migrate on common axonal paths into the periphery. Surprisingly little is known about how this initial migration of spinal motor axons is controlled by external cues. Here, we show that the diwanka gene is required for growth cone migration of three identified subtypes of zebrafish primary motoneurons. In diwanka mutant embryos, motor growth cone migration within the spinal cord is unaffected but it is strongly impaired as motor axons enter their common path to the somites. Chimera analysis shows that diwanka gene activity is required in a small set of myotomal cells, called adaxial cells. We identified a subset of the adaxial cells to be sufficient to rescue the diwanka motor axon defect. Moreover, we show that this subset of adaxial cells delineates the common axonal path prior to axonogenesis, and we show that interactions between these adaxial cells and motor growth cones are likely to be transient. The studies demonstrate that a distinct population of myotomal cells plays a pivotal role in the early migration of zebrafish motor axons and identify the diwanka gene as a somite-derived cue required to establish an axonal path from the spinal cord to the somites.
Repair of a Mismatch Is Influenced by the Base Composition of the Surrounding Nucleotide Sequence (1987)

Heteroduplexes with single base pair mismatches of known sequence were prepared by annealing separated strands of bacteriophage lambda DNA and used to transfect Escherichia coli. A series of transition (G:T and A:C) and transversion (G:A and C:T) mismatches located throughout most of the bacteriophage lambda cI gene has been examined. The results suggest that the transition mismatches are generally better repaired than the transversion mismatches and that, at least for the transversion mismatches studied, repair efficiency increases with increasing G:C content in the neighboring nucleotide sequence. This specificity of the E. coli mismatch repair system can account, in part, for the similar frequencies of base substitution mutations throughout the E. coli genome.
Expressed Protein Ligation, a Novel Method for Studying Protein-Protein Interactions in Transcription (1998)

Expressed protein ligation is a novel protein semi-synthesis method that permits the in vitro ligation of a chemically synthesized C-terminal segment of a protein to a recombinant N-terminal segment fused through its C terminus to an intein protein splicing element. In principle, the practical convenience of this method, combined with the expanded opportunities in protein engineering that it provides, makes it well suited for probing the molecular basis of complex processes such as transcription. Here we describe the successful application of expressed protein ligation to the approximately 600 amino acid sigma70 subunit of Escherichia coli RNA polymerase. The resulting semi-synthetic sigma70 constructs are shown to be fully functional and have been used to map the binding region of the bacteriophage T4 anti-sigma protein, AsiA, to within amino acids 567-600 of sigma70. The success of these semi-synthesis studies sets the stage for the future generation of semi-synthetic sigma70 molecules in which unnatural amino acids and biophysical probes are site-specifically incorporated in the RNA polymerase complex.
High-resolution optical spectroscopy using multimode interference in a compact tapered fibre (2015)

Optical spectroscopy is a fundamental tool in numerous areas of science and technology. Much effort has focused on miniaturizing spectrometers, but thus far at the cost of spectral resolution and broad operating range. Here we describe a compact spectrometer that achieves both high spectral resolution and broad bandwidth. The device relies on imaging multimode interference from leaky modes along a multimode tapered optical fibre, resulting in spectrally distinguishable spatial patterns over a wide range of wavelengths from 500 to 1,600 nm. This tapered fibre multimode interference spectrometer achieves a spectral resolution down to 40 pm in the visible spectrum and 10 pm in the near-infrared spectrum (corresponding to resolving powers of 10(4)-10(5)). Multimode interference spectroscopy is suitable in a variety of device geometries, including planar waveguides in a broad range of transparent materials.
Functional and structural interactions between measles virus hemagglutinin and CD46 (1995)

We analyzed the roles of the individual measles virus (MV) surface glycoproteins in mediating functional and structural interactions with human CD46, the primary MV receptor. On one cell population, recombinant vaccinia virus vectors were used to produce the MV hemagglutinin (H) and fusion (F) glycoproteins. As fusion partner cells, various cell types were examined, without or with human CD46 (endogenous or recombinant vaccinia virus encoded). Fusion between the two cell populations was monitored by a quantitative reporter gene activation assay and by syncytium formation. MV glycoproteins promoted fusion with primate cells but not with nonprimate cells; recombinant CD46 rendered nonprimate cells competent for MV glycoprotein-mediated fusion. Markedly different fusion specificity was observed for another morbillivirus, canine distemper virus (CDV): recombinant CDV glycoproteins promoted fusion with primate and nonprimate cells independently of CD46. Fusion by the recombinant MV and CDV glycoproteins required coexpression of H plus F in either homologous or heterologous combinations. To assess the role of H versus F in determining the CD46 dependence of MV fusion, we examined the fusion specificities of cells producing heterologous glycoprotein combinations. The specificity of HMV plus FCDV paralleled that observed for the homologous MV glycoproteins: fusion occurred with primate cells but not with nonprimate cells unless they produced recombinant CD46. By contrast, the specificity of HCDV plus FMV paralleled that for the homologous CDV glycoproteins: fusion occurred with either primate or nonprimate cells with no dependence on CD46. Thus, for both MV and CDV, fusion specificity was determined by H. In particular, the results demonstrate a functional interaction between HMV and CD46. Flow cytometry and antibody coprecipitation studies provided a structural correlate to this functional interaction: CD46 formed a molecular complex with HMV but not with FMV or with either CDV glycoprotein. These results highlight the critical role of the H glycoprotein in determining MV specificity for CD46-positive cells.
Effect of simultaneous vaccination with H1N1 and GAD-alum on GAD65-induced immune response (2017)

ClinicalTrials.gov NCT00723411.
Characterization of the human 5-lipoxygenase gene. (1989)

The gene for human 5-lipoxygenase has been isolated from three different bacteriophage genomic libraries and a genomic cosmid library. The gene spans greater than 82 kilobases and consists of 14 exons. The size range for the exons is 82-613 base pairs, whereas that for the introns is approximately 200 bp to greater than 26 kb. A major site of transcription initiation in leukocytes was mapped to a thymidine residue 65 base pairs upstream of the ATG initiation codon by nuclease S1 protection and primer extension experiments. Other potential minor initiation sites were found. The putative promoter region contains no TATA and CCAAT sequences in the expected positions upstream of the major transcription initiation site but contains multiple GC boxes within a (G + C)-rich region, as does the immediate 5' region of the first intron. Characteristics common to the 5' end of the human 5-lipoxygenase gene and the promoter regions of the housekeeping genes raise important questions concerning the regulation of 5-lipoxygenase gene expression.
Noncathartic CT Colonography with Stool Tagging: Performance With and Without Electronic Stool Subtraction (2008)

In this increased-risk referral population, CT colonography in the non-cathartic-tagged colon without dietary restrictions compared favorably with optical colonoscopy.
Automatic capsule preparation for lecture video (2009)

In this paper, we propose a visual quality and content based approach for creating a lecture video capsule which essentially contains the highlights of the original lecture video. We first segment and recognize the activities in the instructional video using a hidden Markov model(HMM). The activities are classified into three categories : talking head, writing hand and slide show. Then a no-reference objective quality assessment of the non-content frames, i.e., talking head frames, are performed to detect a few high quality frames for highlight creation. A new method of defining the visual quality of content frames, i.e., writing hand and slide show frames which are very crucial in a lecture video, is proposed in this paper. Statistical parameters of the intensity histogram along with the horizontal projection profile(HPP) of the the content frames are used to derive an objective quality measure of these frames. This allows us to extract the high quality content frames, which are `well-written'. Finally on media re-creation to produce the video capsule, we select the video segments of a few seconds duration around these good quality frames along with the audio and merge with suitable proportion of the detected classes of instructional activity. This technique accounts for a very compact representation of the whole lecture video which finds a very potential application of video previews.
Immune responses to Cryptosporidium muris and Cryptosporidium parvum in adult immunocompetent or immunocompromised (nude and SCID) mice (1992)

Adult murine models of Cryptosporidium infection involving Cryptosporidium muris and C. parvum were used to study immunity to cryptosporidiosis in the mammalian host. Immunocompetent BALB/c or C57BL/6 mice developed a highly patent infection with the RN 66 strain of C. muris but overcame the infection and were immune to reinfection. In contrast, severe combined immunodeficiency (SCID) mice or nude mice had a chronic infection lasting at least 109 days. The development of the C. muris infection appeared to be confined to the gastric epithelium in immunocompetent and immunocompromised mice. SCID mice injected intraperitoneally with histocompatible spleen or mesenteric lymph node cells from uninfected BALB/c mice were able to recover from the C. muris infection. The protective effect of donor spleen cells was not reduced by depletion of the B cell population but was significantly reduced by depletion of Thy.1 cells. Treatment of C57BL/6 or BALB/c mice during infection with a gamma interferon-neutralizing monoclonal antibody, but not a tumor necrosis factor-neutralizing monoclonal antibody, resulted in a significant increase in oocyst production. In the C. parvum model, a severe and eventually fatal chronic infection with a cervine isolate was established in SCID mice, with parasitization occurring in the ileum, cecum, and colon. SCID mice injected with unprimed BALB/c spleen cells prior to inoculation of C. parvum oocysts were resistant to infection. These results suggested that the two animal models should be valuable in the study of immunity to cryptosporidial infection.