gebhart/patrepeval huggingface dataset:
Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power (1989)

Amino acid sequence patterns suggested to characterize specific recurrent turn conformation in protein are tested as to their predictive power in a database containing 75 proteins of known structure. Many of these patterns are found to be associated with local structures that differ from the motifs originally used to derive them. It is therefore concluded that, while they could be useful for improving predictions made by other methods, their stand-alone predictive power is poor. The issue of deriving and validating consensus sequence patterns for use in protein structure prediction is raised.
Power Generation By Organic Rankine Cycle From Low Temperature Waste Heat Of Metallurgical Industry (2016)

Organic Rankine Cycle (ORC) is an effective technology for low-grade waste heat power generation. In this paper, the thermal-dynamic performance of ORC system, in which low-temperature waste heat (from 40-140oC) is used as heat source, was evaluated with software RefProp 8.0. The result indicates that in the range of low temperature, the working fluids like R601, R601a, R600a, R141b, R245fa and R245ca have better thermal performance. Furthermore, pilot-scale experiment using R245fa as working fluid was conducted, which validated the operation of the system for low-grade waste heat recovery. Finally, the economic feasibility of ORC has been analyzed for an ORC system using the waste heat from quenching water of blast furnace slag (80oC). According to the analysis, the project is reasonable in economy because the recovery period of investment is less than 4.2 years and environment-friendly since the CO2 emissions can be reduced by almost 43650.68t annually.
Adenovector-mediated gene transfer of active transforming growth factor-beta1 induces prolonged severe fibrosis in rat lung. (1997)

Transforming growth factor (TGF)-beta1 has been implicated in the pathogenesis of fibrosis based upon its matrix-inducing effects on stromal cells in vitro, and studies demonstrating increased expression of total TGF-beta1 in fibrotic tissues from a variety of organs. The precise role in vivo of this cytokine in both its latent and active forms, however, remains unclear. Using replication-deficient adenovirus vectors to transfer the cDNA of porcine TGF-beta1 to rat lung, we have been able to study the effect of TGF-beta1 protein in the respiratory tract directly. We have demonstrated that transient overexpression of active, but not latent, TGF-beta1 resulted in prolonged and severe interstitial and pleural fibrosis characterized by extensive deposition of the extracellular matrix (ECM) proteins collagen, fibronectin, and elastin, and by emergence of cells with the myofibroblast phenotype. These results illustrate the role of TGF-beta1 and the importance of its activation in the pulmonary fibrotic process, and suggest that targeting active TGF-beta1 and steps involved in TGF-beta1 activation are likely to be valuable antifibrogenic therapeutic strategies. This new and versatile model of pulmonary fibrosis can be used to study such therapies.
Therapeutic Advances in the Treatment of Glioblastoma: Rationale and Potential Role of Targeted Agents (2006)

Despite advances in standard therapy, including surgical resection followed by radiation and chemotherapy, the prognosis for patients with glioblastoma multiforme (GBM) remains poor. Unfortunately, most patients die within 2 years of diagnosis of their disease. Molecular abnormalities vary among individual patients and also within each tumor. Indeed, one of the distinguishing features of GBM is its marked genetic heterogeneity. Nonetheless, recent developments in the field of tumor biology have elucidated signaling pathways and genes involved in the development of GBM, and several novel agents that target these signaling pathways are being developed. As new details on the genetic characteristics of this disease become available, innovative treatment regimens, including a variety of traditional treatment modalities such as surgery, radiation, and cytotoxic chemotherapy, will be combined with newer targeted therapies. This review introduces these new targeted therapies in the context of current treatment options for patients with GBM. It is hoped that this combined approach will overcome the current limitations in the treatment of patients with GBM and result in a better prognosis for these patients.
An assessment of serum leptin levels in patients with chronic viral hepatitis: a prospective study (2007)

Our data clearly suggest that cirrhosis due to CHB or CHC is associated with higher leptin levels. Increased serum leptin levels represent a negative prognostic factor for response to lamivudine monotherapy in patients with CHB. In CHC patients insulin resistance strongly influences the response to antiviral treatment in patients infected with genotype 1.
Theoretical and experimental study of the analysis and modeling of integrated optical components (1988)

Using a mode-matching technique, a modular microwave equivalent circuit incorporating both guided and continuum spectra has been developed to model open guided-wave integrated optical components accurately with limited computational effort. The accuracy of the analysis is verified by comparison with other methods of analysis, and by experiments performed on GaAs homojunction rib waveguides, directional couplers, and three-guide couplers. The limitations of approximate theories for the analysis of coupled structures are also identified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Role of the Transmembrane Domain of Marburg Virus Surface Protein GP in Assembly of the Viral Envelope (2007)

The major protein constituents of the filoviral envelope are the matrix protein VP40 and the surface transmembrane protein GP. While VP40 is recruited to the sites of budding via the late retrograde endosomal transport route, GP is suggested to be transported via the classical secretory pathway involving the endoplasmic reticulum, Golgi apparatus, and trans-Golgi network until it reaches the plasma membrane where most filoviral budding takes place. Since both transport routes target the plasma membrane, it was thought that GP and VP40 join there to form the viral envelope. However, it was recently shown that, upon coexpression of both proteins, GP is partially recruited into peripheral VP40-enriched multivesicular bodies, which contained markers of the late endosome. Accumulation of GP and VP40 in this compartment was presumed to play an important role in the formation of the filoviral envelope. Using a domain-swapping approach, we were able to show that the transmembrane domain of GP was essential and sufficient for (i) partial recruitment of chimeric glycoproteins into VP40-enriched multivesicular bodies and (ii) incorporation into virus-like particles (VLPs) that were released upon expression of VP40. Only those chimeric glycoproteins which were targeted to VP40-enriched endosomal multivesicular bodies were subsequently recruited into VLPs. These data show that the transmembrane domain of GP is critical for the mixing of VP40 and GP in multivesicular bodies and incorporation of GP into the viral envelope. Results further suggest that trapping of GP in the VP40-enriched late endosomal compartment is important for the formation of the viral envelope.
Parameters Influencing Stable Transformation of Rice Immature Embryos and Recovery of Transgenic Plants using Electric Discharge Particle Acceleration (1995)

Recovery of transgenic rice plants from elite varieties was reported from the author's laboratory. By using electric discharge particle acceleration, recombinant technology was extended to commercially important japonica and indica rice cultivars not amenable to conventional transformation methodologies. Critical parameters influencing the recovery of transformed embryogenic callus from which transgenic plants were recovered have been defined. Such parameters included the physiological condition of explants prior to bombardment, DNA and gold particle loading rates, accelerating voltage, and depth of particle penetration. Selection for recovery of stable transformants was not critical in this transformation/regeneration system; both selected and non-selected tissues yielded transformed embryogenic callus and plants at approximately similar frequencies.Copyright 1995, 1999 Academic Press
Cellular and humoral immune responses to a human pancreatic cancer antigen, coactosin-like protein, originally defined by the SEREX method (2002)

Among a number of human tumor antigens identified using the serological analysis of recombinant cDNA expression libraries (SEREX), only MAGE-1, tyrosinase, and NY-ESO-1 have been reported to be immunogenic tumor antigens that have the potential to elicit both humoral and cellular immunity. In this study, we determined whether our SEREX-defined pancreatic cancer antigens could be recognized by CTL, and report that one SEREX-defined antigen, coactosin-like protein (CLP), encoded cellular epitopes recognized by HLA-A2-restricted and tumor-reactive CTL. Three CLP peptides at positions 15-24, 57-65, and 10-113 possessed the ability to induce HLA-A2-restricted and tumor-reactive CTL from the PBMC of cancer patients. Subsequently, humoral responses to these peptides were investigated. IgG antibodies specific to the CLP 15-24, 57-65, and 104-113 peptides were detected in sera from 12, 0, and 12 of 12 cancer patients tested, and were also found in 5, 0, and 0 of 9 healthy donors, respectively. IgE antibodies specific to these peptides were also detected in sera from certain cancer patients and healthy donors. Since peptide-specific IgE was detected, type-I allergy to these peptides was tested. Unexpectedly the CLP 57-65 peptide, to which IgE was found in only 2 healthy donors, but not the other two peptides, was found to elicit an immediate-type hypersensitivity in all 10 healthy volunteers tested. These results indicate that identical antigenic peptides can be recognized by both cellular and humoral immune systems to a tumor-associated antigen. The CLP 15-24 and 104-113 peptides might be appropriate vaccine candidates for peptide-based immunotherapy of HLA-A2(+) cancer patients.
The Addition of Lipids Increases the Total Parenteral Nutrition-Associated Cholestasis in the Rat (1993)

Cholestasis is one of the most frequent complications of Total Parenteral Nutrition (TPN). Among the components of TPN, amino acids (AA) and dextrose are considered responsible in terms of quantity. The aim of this study was to determine whether IV lipids have a protective effect on the liver lesions induced by TPN, as well as on the bile flow in rats. Two groups of 6 animals, 6 receiving TPN containing AA and dextrose (Group A-D) and 6 receiving AA, dextrose and lipids (Group A-D-L) were studied. Both groups received the same amount of AA (3.4 g/day) and the same amount of energy (50 kcal/day). The TPN lasted 3 days, after which blood samples were obtained for liver function tests and the bile flow was determined gravimetrically, subsequently the liver was removed for histological analysis. A significant weight loss (p < 0.01) was observed in both groups (Group A-D: -13 +/- 4 g; Group A-D-L: -16 +/- 2g). The bile flow was significantly lowered in A-D-L at 10.14 +/- 1.27 microliters/minute when compared to Group A-D (15.61 +/- 1.31 microliters/minute). The Aspartate Amino Transferase (AST) plasma level was elevated at 188 +/- 20 UI in Group A-D and at 185 +/- 33 UI in Group A-D-L. Gamma-Glutamyl-Transferase (gamma-GT) plasma level was in the normal range in both groups. In conclusion, this study indicates that TPN-associated cholestasis is significantly increased by lipid addition. However, the hepatocellular necrosis seems unchanged.
Understanding and Using DICOM, the Data Interchange Standard for Biomedical Imaging (1997)

The Digital Imaging and Communications in Medicine (DICOM) Standard specifies a non-proprietary data interchange protocol, digital image format, and file structure for biomedical images and image-related information. The fundamental concepts of the DICOM message protocol, services, and information objects are reviewed as background for a detailed discussion of the functionality of DICOM; the innovations and limitations of the Standard; and the impact of various DICOM features on information system users. DICOM addresses five general application areas: (1) network image management, (2) network image interpretation management, (3) network print management, (4) imaging procedure management, (5) off-line storage media management. DICOM is a complete specification of the elements required to achieve a practical level of automatic interoperability between biomedical imaging computer systems--from application layer to bit-stream encoding. The Standard is being extended and expanded in modular fashion to support new applications and incorporate new technology. An interface to other Information Systems provides for shared management of patient, procedure, and results information related to images. A Conformance Statement template enables a knowledgeable user to determine if interoperability between two implementations is possible. Knowledge of DICOM's benefits and realistic understanding of its limitations enable one to use the Standard effectively as the basis for a long term implementation strategy for image management and communications systems.
An Efficient Zone Reconstruction Method on the Zone-Structured Disk (1999)

Many popularly used recent high-sped and high-capacity disks use the Zone-Structured in which a disk consists of multiple zones. A zone-structured disk has multiple zones, and the bandwidth and the number of sectors in each zone are different from each other. When the previous studies that modeled disks based on the assumption that the number of sectors in all tracks are same are applied to the zone-structured disk and the video data stored in a round-robin manner are read out with the SCAN technique, the transfer rate of the disk is fixed with that of the innermost zone. And excessive disk space is wasted either. To resolve the problem, this paper proposes a method for reconstructing the physical zones into logical zones by split and merge operations and develops a method for determining optimum transfer block size.
Transcranial Direct Current Stimulation Augments Perceptual Sensitivity and 24-Hour Retention in a Complex Threat Detection Task (2012)

We have previously shown that transcranial direct current stimulation (tDCS) improved performance of a complex visual perceptual learning task (Clark et al. 2012). However, it is not known whether tDCS can enhance perceptual sensitivity independently of non-specific, arousal-linked changes in response bias, nor whether any such sensitivity benefit can be retained over time. We examined the influence of stimulation of the right inferior frontal cortex using tDCS on perceptual learning and retention in 37 healthy participants, using signal detection theory to distinguish effects on perceptual sensitivity (d') from response bias (ß). Anodal stimulation with 2 mA increased d', compared to a 0.1 mA sham stimulation control, with no effect on ß. On completion of training, participants in the active stimulation group had more than double the perceptual sensitivity of the control group. Furthermore, the performance enhancement was maintained for 24 hours. The results show that tDCS augments both skill acquisition and retention in a complex detection task and that the benefits are rooted in an improvement in sensitivity (d'), rather than changes in response bias (ß). Stimulation-driven acceleration of learning and its retention over 24 hours may result from increased activation of prefrontal cortical regions that provide top-down attentional control signals to object recognition areas.
Geometric Methods for Modeling and Control of Free-Swimming Fin-Actuated Underwater Vehicles (2007)

In this paper, techniques from geometric mechanics and geometric nonlinear control theory are applied to modeling and construction of trajectory tracking algorithms for a free-swimming underwater vehicle that locomotes and maneuvers using a two-link actuated ldquotailrdquo and independently actuated ldquopectoral finrdquo bow planes. Restricting consideration of fluid forces to the simple effects of added mass and quasi-steady lift and drag, the resulting system model can be expressed in a control-affine structure. With particular choices of oscillatory actuation of the four system joints, maneuvers such as swimming forward, in and out of plane turning, surfacing, and diving can be constructed. Further, the vehicle and model can generate agile maneuvers such as snap turns. Trajectory tracking can then be produced using state error feedback. The methods are demonstrated both in simulation and in experiment using the University of Washington prototype fin-actuated underwater vehicle.
Evaluation of the Immunogenicity and Biological Activity of the Citrobacter freundii Vi-CRM 197 Conjugate as a Vaccine for Salmonella enterica Serovar Typhi (2011)

Typhoid fever remains a major health problem in developing countries. Young children are at high risk, and a vaccine effective for this age group is urgently needed. Purified capsular polysaccharide from Salmonella enterica serovar Typhi (Vi) is licensed as a vaccine, providing 50 to 70% protection in individuals older than 5 years. However, this vaccine is ineffective in infants. Vi conjugated to a carrier protein (i.e., an exoprotein A mutant from Pseudomonas aeruginosa [rEPA]) is highly immunogenic, provides long-term protection, and shows more than 90% protective efficacy in children 2 to 5 years old. Here, we describe an alternative glycoconjugate vaccine for S. Typhi, Vi-CRM(197), where Vi was obtained from Citrobacter freundii WR7011 and CRM(197), the mutant diphtheria toxin protein, was used as the carrier. We investigated the optimization of growth conditions for Vi production from C. freundii WR7011 and the immunogenicity of Vi-CRM(197) conjugates in mice. The optimal saccharide/protein ratio of the glycoconjugates was identified for the best antibody production. We also demonstrated the ability of this new vaccine to protect mice against challenge with Vi-positive Salmonella enterica serovar Typhimurium.
Efficient production of silicon-on-insulator films by co-implantation of He/sup +/ with H/sup +/ (2002)

The thin film separation process with H/sup +/ proceeds by both chemical interactions (bond breaking and internal surface passivation) and physical interaction (gas coalescence, pressure, fracture) of implanted H/sup +/ with the Si substrate. It is difficult to isolate the contribution of each component to the overall process using implantation of H only. In this work, we have combined H/sup +/ and He/sup +/ gas implantation to decouple the physical and chemical contributions to the blistering and thin film separation processes. We have observed that combination of H and He gas implants results in a synergistic effect that allows the threshold dose for both processes to be significantly reduced.
The Art of Power (2007)

Turning our conventional understanding of power on its head, world-renowned Zen master, spiritual leader, and national bestselling author Thich Nhat Hanh reveals how true power comes from within. What we seek, we already have. Whether we want it or not, power remains one of the central issues in all of our lives. Every day, each of us exercises power in many ways, and our every act subtly affects the world we live in. This struggle for control and authority permeates every aspect of our private and public lives, preventing us from attaining true happiness. me-first mentality in our culture seeps unnoticed into our decisions and choices. Our bottom-line approach to getting ahead may be most visible in the business world, but the stress, fear, and anxiety it causes are being felt by people in all walks of life. Thich Nhat Hanh illustrates how the current understanding of power leads us on a never-ending search for external markers like job title or salary. The Art of Power boldly challenges our assumptions and teaches each of us how to access the true power that is within our grasp.
Mycobacterium tuberculosisPathogenesis and Molecular Determinants of Virulence (2003)

Tuberculosis (TB), one of the oldest known human diseases. is still is one of the major causes of mortality, since two million people die each year from this malady. TB has many manifestations, affecting bone, the central nervous system, and many other organ systems, but it is primarily a pulmonary disease that is initiated by the deposition of Mycobacterium tuberculosis, contained in aerosol droplets, onto lung alveolar surfaces. From this point, the progression of the disease can have several outcomes, determined largely by the response of the host immune system. The efficacy of this response is affected by intrinsic factors such as the genetics of the immune system as well as extrinsic factors, e.g., insults to the immune system and the nutritional and physiological state of the host. In addition, the pathogen may play a role in disease progression since some M. tuberculosis strains are reportedly more virulent than others, as defined by increased transmissibility as well as being associated with higher morbidity and mortality in infected individuals. Despite the widespread use of an attenuated live vaccine and several antibiotics, there is more TB than ever before, requiring new vaccines and drugs and more specific and rapid diagnostics. Researchers are utilizing information obtained from the complete sequence of the M. tuberculosis genome and from new genetic and physiological methods to identify targets in M. tuberculosis that will aid in the development of these sorely needed antitubercular agents.
The second extracellular loop of the dopamine D2receptor lines the binding-site crevice (2004)

The binding site of the dopamine D(2) receptor (D2R), like those of homologous rhodopsin-like G protein-coupled receptors (GPCRs) that bind small molecules, is contained within a water-accessible crevice formed among its seven transmembrane segments (TMs). The high-resolution structure of bovine rhodopsin, however, revealed that the second extracellular loop (E2), which connects TM4 and TM5, folds down into the transmembrane domain and forms part of the ligand-binding surface for retinal. Whether E2 plays a related role in other rhodopsin-like GPCRs is unclear. To address this issue, we have now mutated to cysteine, one at a time, 10 consecutive residues in E2 of D2R. The reaction of five of these mutants with sulfhydryl reagents inhibited antagonist binding, and bound antagonist protected two, I184C and N186C, from reaction. The pattern of accessibility in E2 is consistent with a structure similar to that of bovine rhodopsin, in which the region C-terminal to the conserved disulfide bond is deeper in the binding-site crevice than is the N-terminal part of E2. Thus, E2 likely contributes to the binding site in the D2R and probably in other aminergic GPCRs as well. Knowledge of its detailed positioning and interactions with ligand would benefit GPCR molecular modeling and facilitate the design of novel drugs.