gebhart/patrepeval huggingface dataset:
Receptor Binding, Fusion Inhibition, and Induction of Cross-Reactive Neutralizing Antibodies by a Soluble G Glycoprotein ofHendra Virus (2005)

Hendra virus (HeV) and Nipah virus (NiV) are closely related emerging viruses comprising the Henipavirus genus of the Paramyxovirinae, which are distinguished by their ability to cause fatal disease in both animal and human hosts. These viruses infect cells by a pH-independent membrane fusion event mediated by their attachment (G) and fusion (F) glycoproteins. Previously, we reported on HeV- and NiV-mediated fusion activities and detailed their host-cell tropism characteristics. These studies also suggested that a common cell surface receptor, which could be destroyed by protease, was utilized by both viruses. To further characterize the G glycoprotein and its unknown receptor, soluble forms of HeV G (sG) were constructed by replacing its cytoplasmic tail and transmembrane domains with an immunoglobulin kappa leader sequence coupled to either an S-peptide tag (sG(S-tag)) or myc-epitope tag (sG(myc-tag)) to facilitate purification and detection. Expression of sG was verified in cell lysates and culture supernatants by specific affinity precipitation. Analysis of sG by size exclusion chromatography and sucrose gradient centrifugation demonstrated tetrameric, dimeric, and monomeric species, with the majority of the sG released as a disulfide-linked dimer. Immunofluorescence staining revealed that sG specifically bound to HeV and NiV infection-permissive cells but not to a nonpermissive HeLa cell line clone, suggesting that it binds to virus receptor on host cells. Preincubation of host cells with sG resulted in dose-dependent inhibition of both HeV and NiV cell fusion as well as infection by live virus. Taken together, these data indicate that sG retains important native structural features, and we further demonstrate that administration of sG to rabbits can elicit a potent cross-reactive neutralizing antibody response against infectious HeV and NiV. This HeV sG glycoprotein will be exceedingly useful for structural studies, receptor identification strategies, and vaccine development goals for these important emerging viral agents.
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data (2005)

We compare 11 different algorithms for analyzing array CGH data. These include both segment detection methods and smoothing methods, based on diverse techniques such as mixture models, Hidden Markov Models, maximum likelihood, regression, wavelets and genetic algorithms. We compute the Receiver Operating Characteristic (ROC) curves using simulated data to quantify sensitivity and specificity for various levels of signal-to-noise ratio and different sizes of abnormalities. We also characterize their performance on chromosomal regions of interest in a real dataset obtained from patients with Glioblastoma Multiforme. While comparisons of this type are difficult due to possibly sub-optimal choice of parameters in the methods, they nevertheless reveal general characteristics that are helpful to the biological investigator.
Recognizing Multi-talker Speech with Permutation Invariant Training (2017)

In this paper, we propose a novel technique for direct recognition of multiple speech streams given the single channel of mixed speech, without first separating them. Our technique is based on permutation invariant training (PIT) for automatic speech recognition (ASR). In PIT-ASR, we compute the average cross entropy (CE) over all frames in the whole utterance for each possible output-target assignment, pick the one with the minimum CE, and optimize for that assignment. PIT-ASR forces all the frames of the same speaker to be aligned with the same output layer. This strategy elegantly solves the label permutation problem and speaker tracing problem in one shot. Our experiments on artificially mixed AMI data showed that the proposed approach is very promising.
Visualizing Gene Expression in Living Mammals Using a Bioluminescent Reporter (1997)

Control of gene expression often involves an interwoven set of regulatory processes. As information regarding regulatory pathways may be lost in ex vivo analyses, we used bioluminescence to monitor gene expression in living mammals. Viral promoters fused to firefly luciferase as transgenes in mice allowed external monitoring of gene expression both superficially and in deep tissues. In vivo bioluminescence was detectable using either intensified or cooled charge-coupled device cameras, and could be detected following both topical and systemic delivery of substrate. In vivo control of the promoter from the human immunodeficiency virus was demonstrated. As a model for DNA-based therapies and vaccines, in vivo transfection of a luciferase expression vector (SV-40 promoter and enhancer controlling expression) was detected. We conclude that gene regulation, DNA delivery and expression can now be noninvasively monitored in living mammals using a luciferase reporter. Thus, real-time, noninvasive study of gene expression in living animal models for human development and disease is possible.
Swelling and sorption in polymer–CO2 mixtures at elevated pressures (1987)

Abstract Experimental data on gas sorption and polymer swelling in glassy polymer—gas systems at elevated pressures are presented for CO 2 with polycarbonate, poly(methyl methacrylate), and polystyrene over a range of temperatures from 33 to 65°C and pressures up to 100 atm. The swelling and sorption behavior were found to depend on the occurrence of a glass transition for the polymer induced by the sorption of CO 2 . Two distinct types of swelling and sorption isotherms were measured. One isotherm is characterized by swelling and sorption that reach limiting values at elevated pressures. The other isotherm is characterized by swelling and sorption that continue to increase with pressure and a pressure effect on swelling that is somewhat greater than the effect of pressure on sorption. Glass transition pressures estimated from the experimental results for polystyrene with CO 2 are used to obtain the relationship between CO 2 solubility and the glass transition temperature for the polymer. This relationship is in very good agreement with a theoretical corresponding‐states correlation for glass transition temperatures of polystyrene‐liquid diluent mixtures.
FOXD1 expression is associated with poor prognosis in non-small cell lung cancer. (2015)

The expression status of FOXD1 is a novel prognostic factor and may lead to new treatment strategies for NSCLC.
Analysis of the interaction of the human immunodeficiency virus type 1 gp120 envelope glycoprotein with the gp41 transmembrane glycoprotein (1997)

The human immunodeficiency virus type 1 (HIV-1) gp120 exterior envelope glycoprotein interacts with the viral receptor (CD4) and with the gp41 transmembrane envelope glycoprotein. To study the interaction of the gp120 and gp41 envelope glycoproteins, we compared the abilities of anti-gp120 monoclonal antibodies to bind soluble gp120 and a soluble glycoprotein, sgp140, that contains gp120 and gp41 exterior domains. The occlusion or alteration of a subset of gp120 epitopes on the latter molecule allowed the definition of a gp41 "footprint" on the gp120 antibody competition map. The occlusion of these epitopes on the sgp140 glycoprotein was decreased by the binding of soluble CD4. The gp120 epitopes implicated in the interaction with the gp41 ectodomain were disrupted by deletions of the first (C1) and fifth (C5) conserved gp120 regions. These deletions did not affect the integrity of the discontinuous binding sites for CD4 and neutralizing monoclonal antibodies. Thus, the gp41 interface on the HIV-1 gp120 glycoprotein, which elicits nonneutralizing antibodies, can be removed while retaining immunologically desirable gp120 structures.
Synthesis of Novel N‐Pyridylcantharidinimides by Using High Pressure (2001)

Abstract The recently described pressure reaction in the presence of trithylamine with subsequent thermal (200°C) cyclization provided 13N‐pyridylcantharidinimides 4a‐4m from aminopyridines and cantharidin in yields of 15–83%. 2‐Amino‐3,5‐dichloropyridine failed to yield 4n .
Structure of a Complex of the Human α/β T Cell Receptor (TCR) HA1.7, Influenza Hemagglutinin Peptide, and Major Histocompatibility Complex Class II Molecule, HLA-DR4 (DRA0101 and DRB10401) (2002)

The alpha/beta T cell receptor (TCR) HA1.7 specific for the hemagglutinin (HA) antigen peptide from influenza A virus is HLA-DR1 restricted but cross-reactive for the HA peptide presented by the allo-major histocompatibility complex (MHC) class II molecule HLA-DR4. We report here the structure of the HA1.7/DR4/HA complex, determined by X-ray crystallography at a resolution of 2.4 A. The overall structure of this complex is very similar to the previously reported structure of the HA1.7/DR1/HA complex. Amino acid sequence differences between DR1 and DR4, which are located deep in the peptide binding groove and out of reach for direct contact by the TCR, are able to indirectly influence the antigenicity of the pMHC surface by changing the conformation of HA peptide residues at position P5 and P6. Although TCR HA1.7 is cross-reactive for HA presented by DR1 and DR4 and tolerates these conformational differences, other HA-specific TCRs are sensitive to these changes. We also find a dependence of the width of the MHC class II peptide-binding groove on the sequence of the bound peptide by comparing the HA1.7/DR4/HA complex with the structure of DR4 presenting a collagen peptide. This structural study of TCR cross-reactivity emphasizes how MHC sequence differences can affect TCR binding indirectly by moving peptide atoms.
BLyS and APRIL Form Biologically Active Heterotrimers That Are Expressed in Patients with Systemic Immune-Based Rheumatic Diseases (2002)

BLyS and APRIL are two members of the TNF superfamily that are secreted by activated myeloid cells and have costimulatory activity on B cells. BLyS and APRIL share two receptors, TACI and BCMA, whereas a third receptor, BAFF-R, specifically binds BLyS. Both BLyS and APRIL have been described as homotrimeric molecules, a feature common to members of the TNF superfamily. In this study, we show that APRIL and BLyS can form active heterotrimeric molecules when coexpressed and that circulating heterotrimers are present in serum samples from patients with systemic immune-based rheumatic diseases. These findings raise the possibility that active BLyS/APRIL heterotrimers may play a role in rheumatic and other autoimmune diseases and that other members of the TNF ligand superfamily may also form active soluble heterotrimers.
A gigahertz silicon-on-insulator Mach-Zehnder modulator (2004)

We report a modulator in which a polysilicon-oxide-silicon capacitor forms a ridge waveguide to achieve unprecedented performance in silicon: 2.5 GHz small-signal bandwidth and a driver-limited extinction ratio of 5 dB at 1 gigabit per second.
Real Time Diagnostics For Space Shuttle Auxiliary Power System (APU) (1995)

&lt;div class="htmlview paragraph"&gt;The lack of visibility into high rate (100 Hz.) Improved Auxiliary Power Unit (IAPU) Shuttle data can potentially cause unnecessary launch delays. Current Shuttle day of launch procedures require strip chart identification of IAPU performance issues just prior to liftoff and during on-orbit operations. The current methods are outdated, require a high level of operator attention, and don't support continuous on-line analysis of the data. Depending on fatigue and training level, an operator might miss a significant feature or misinterpret a signature reading. The issue of how to accurately detect and predict space component performance in a streamlined operations environment through automated diagnostics is one of many issues that face the Shuttle Program and the designers of the next generation launch vehicles. A technical approach to automated diagnostics is to develop fast, efficient signature recognition and event detection algorithms that can automate the capture of anomalies, off-nominal, and nominal events and free up the operator to concentrate on the verification and resolution of the event. A generic neural network-based monitoring and analysis prototype system has been developed by the authors and demonstrated for the Shuttle IAPU application. This prototype has run in parallel during IAPU pre-launch operations since STS-66 (late 1994) in the Kennedy Space Center Launch Control Center. The major features of the system include high speed event detection, neural network analysis, event correlation, interprocess communication, and full rate graphical displays. The Shuttle IAPU demonstrations are paving the way for incorporation into the Shuttle countdown procedures and the technologies developed will also be utilized by Rockwell's Reusable Launch Vehicle Design team. Accordingly, the overall architecture has been designed for growth using COTS tools and industry standards.&lt;/div&gt;
Critical Current Density Enhancement around a Matching Field in ErBa2Cu3O7-δ Films with BaZrO3 Nano-Rods (2005)

Field angular dependences of critical current density are measured for as-grown high crystalline quality ErBa 2 Cu 3 O 7-δ films with BaZrO 3 nano-rods. Large critical current density enhancement is observed. The magnetic field where the enhancement is observed coincides with the matching field calculated from the density of BaZrO 3 nano-rods. The largest enhancement is observed in B ∥ c -axis of ErBa 2 Cu 3 O 7-δ films. This anisotropic critical current density enhancement is thought to be caused by the direction of BaZrO 3 nano-rods which grow along the c -axis of the films. BaZrO 3 nano-rods in the films will promise the application of coated conductors in a magnetic field.
Association of plasma B lymphocyte stimulator levels and disease activity in systemic lupus erythematosus (2008)

The findings of association between a greater increase in the BLyS level from the previous visit and a greater increase in the SELENA-SLEDAI score at the subsequent visit, and between an elevated BLyS level at the previous visit and a greater SELENA-SLEDAI score at the subsequent visit, demonstrate a relationship between circulating BLyS levels and SLE disease activity. These results lend support to the notion that BLyS is a candidate for therapeutic targeting in SLE.
Carcinoembryonic antigen in malignant and nonmalignant gynecologic tumors.Circulating levels and tissue localization (1978)

Carcinoembryonic antigen (CEA) was determined in the serum and tissues of patients with gynecologic tumors utilizing radioimmunoassay and immunoperoxidase techniques. Among 328 patients with gynecologic cancer the serum CEA concentration was elevated over the normal background level of 5 ng/ml in 32 cases (9.8%), and the frequency of elevated CEA levels increased with advancing clinical stage. Among 84 patients with benign tumors CEA was elevated in 5 cases (6%). Elevated levels were most commonly seen in patients with ovarian cancer (20%). In squamous cell carcinoma of the uterine cervix elevated levels occurred in 10%, and in cervical adenocarcinoma CEA elevation took place in 19% of the cases. In endometrial cancer CEA became less frequently elevated (7%). After radical surgery the CEA concentration decreased and remained low in 20 of 24 cancer patients (83%). Fifteen of these remained clinically tumor free during the follow-up period of 4–24 months. Three of four patients whose CEA concentration did not significantly decrease after operation were found to have residual tumor. Radiotherapy resulted in an increased CEA concentration in 3 of 5 patients with advanced cancer. Immunoperoxidase staining of CEA was carried out in formalin-fixed paraffin-embedded sections of 64 tumors and 33 specimens from normal genital tract. Tissue CEA was demonstrable in early as well as in advanced stages of malignant tumors. All normal tissue specimens from the genital tract were CEA-negative, but the brushborder of normal colon was CEA-positive. CEA activity in tissue was found in 11 of 14 squamous cell carcinomas of the cervix (79%) and in 7 of 9 cervical adenocarcinomas (78%). By contrast, endometrial adenocarcinoma showed CEA staining in one of 11 tumors only, and in ovarian adenocarcinoma positive CEA staining was never seen. CEA reactions were sometimes found in benign mucinous cystadenomas of the ovary, but not in serous cysts. The serum CEA concentration was normal or sometimes slightly elevated in cases where the tumor was CEA-negative, whereas normal or even highly elevated serum CEA concentrations were seen in CEA-positive tumors. On the basis of these results the following conclusions can be made: 1) Serum CEA measurement is likely to be more effective in cervical and ovarian than in endometrial cancer for the detection of recurrent CEA-positive tumors. 2) It is possible by immunoperoxidase technique to identify certain CEA-positive cervical carcinomas before the serum CEA concentration becomes elevated. 3) Some benign ovarian tumors apparently produce high amounts of CEA without any clinical evidence of malignancy.
Applications of Aluminium Nitride Films Deposited by Reactive Sputtering to Silicon-On-Insulator Materials (1996)

Self-heating effects in silicon-on-insulator (SOI) devices limit the applicability of SOI materials in electronics in cases where high power dissipation is expected. Aluminium nitride as a potential candidate for buried insulator material in future SOI-structures is investigated. Reactive sputtering was used to manufacture the aluminium nitride films. The deposited films exhibit low stress and fairly low surface roughness. Further, resistivities above 10 14 Ωcm as well as low thermal resistances were obtained. Interfacial problems at the interface between silicon and aluminium nitride were handled by adding a thin (a few nm) film of thermally grown silicon dioxide to that interface. The deposited films could be bonded both directly and through an electrostatic technique to silicon wafers. The presented results show that it is possible to make SOI structures with aluminium nitride as buried insulator by means of wafer bonding and subsequent etch-back.
Efficacy of Paroxetine and Amitriptyline in Posttraumatic Stress Disorder: An Open-label Comparative Study (2011)

Objective: To evaluate the efficacy of amitriptyline and paroxetine in soldiers with combat-related post traumatic stress disorder (PTSD).Method: Fifty patients who were admitted to Gülhane Military Medical Academy Psychiatry Inpatient Clinic and who were diagnosed as chronic PTSD were enrolled. The primary outcome measures for the study was 17-item total severity score of the Clinician-Administered PTSD Scale (CAPS), Investigator-rated Clinical Global Impression (CGI-S) and CGI-Improvement Scales (CGI-I). Patients were randomized to 12 weeks of treatment with either paroxetine (25 patients) or amitriptyline (25 patients). Twenty-two patients from paroxetine group and 20 patients from amitriptyline group completed the study protocol.Results: Treatment response rates for paroxetine and amitriptyline was 31.8% and 55%, respectively. While there was a significant difference for CAPS-2 total score changes between the groups, no statistically significant difference was found for CGI severity, CGI progress, change in depression and anxiety scores.Conclusions: Both amitriptyline and paroxetine seem to be effective in the treatment of combat related PTSD cases. Despite no statistically significant difference between both groups, treatment response with amitriptyline seems to be higher. When we look at the changes in symptom patterns in terms of CAPS 2 scores, it was found that amitriptyline have decreased intrusive and increased arousal symptoms more than paroxetine.
Signaling through alternative Integrated Stress Response pathways compensates for GCN2 loss in a mouse model of soft tissue sarcoma (2015)

The tumor microenvironment is characterized by deficiencies in oxygen and nutrients, such as glucose and amino acids. Activation of the GCN2 arm of the Integrated Stress Response (ISR) in response to amino acid deprivation is one mechanism by which tumor cells cope with nutrient stress. GCN2 phosphorylates the alpha subunit of the eukaryotic translation initiation factor eIF2, leading to global downregulation of translation to conserve amino acids and initiation of a transcriptional program through ATF4 to promote recovery from nutrient deprivation. Loss of GCN2 results in decreased tumor cell survival in vitro under amino acid deprivation and attenuated tumor growth in xenograft tumor models. However, it is not known what effects GCN2 loss has on the growth of autochthonous tumors that arise in their native microenvironment. Here, we demonstrate in a genetically engineered mouse model of soft tissue sarcoma that loss of GCN2 has no effect on tumor growth or animal survival. The sarcomas displayed compensatory activation of PERK or phospho-eIF2α independent upregulation of ATF4 in order to maintain ISR signaling, indicating that this pathway is critical for tumorigenesis. These results have important implications for the development and testing of small molecule inhibitors of ISR kinases as cancer therapeutics.
Analyzing Packer's Deformation of Tubular for Unsetting Process in HTHP Wells under Variable (T, P) Fields (2012)

In this paper, the axial stress and deformation of high temperature high pressure super-deep deviated gas wells are studied. A new model presents multiple nonlinear equation systems, which comprehensively consider the axial load of the tubular string, internal and external fluid pressure, normal pressure between the tube and well wall, friction and the viscous friction of fluid flowing under variable temperature and pressure fields, instead of the traditional methods. The initial axial load, the pressure effect, the friction, temperature effect and sucker-rod pumping effect are derived using a dimensionless iterative interpolation algorithm. Basic data from the X Well (high temperature-high pressure gas well), 6115 meters deep, are used for case history calculations. The results and some useful conclusions could provide technical reliability in oil and gas well testing design.
A Novel Approach for the Production of Monoclonal Antibodies Using Infectious Vaccinia Virus Recombinants (1987)

We describe a novel approach of producing monoclonal antibodies (MABs) to one specific protein of a virus or other agent consisting of several proteins, without the use of purified antigen in either the immunization or screening phase of the procedure. This method has general application in the production of MABs when the antigen cannot be obtained in a pure form, but the gene is available. We illustrate this application by producing MAB specific to the nucleocapsid protein (N) of vesicular stomatitis virus serotype Indiana (VSV-IN) from BALB/c mice immunized with an infectious vaccinia virus recombinant vector (v38) that expresses the N gene of VSV-IN. This novel method of immunization obviates the need for initial purification of the protein antigen and injection of adjuvants with the isolated protein as is done in traditional MAB production.
Rapid induction of apoptosis in rat liver by cycloheximide. (1992)

A single administration of the inhibitor of protein synthesis cycloheximide results in the occurrence of apoptosis in rat liver. The presence of intracellular apoptotic bodies was detected as early as 2 hours after treatment. No evidence of cell necrosis could be observed by histologic and biochemical analysis. Apoptosis was followed by an increased expression of testosterone-repressed prostate message-2 RNA, a gene whose activity has been associated to apoptotic cell death in involuting rat prostate. The finding of in vivo induction of apoptosis in nonproliferating cells by an inhibitor of protein synthesis, together with the rapidity and synchrony in the occurrence of cell death make this model potentially useful for the analysis of the kinetics of the apoptotic cycle and in exploring some of the mechanisms of regulation of genes possibly involved in this type of cell death.