gebhart/patrepeval huggingface dataset:
Forward current propagation beyond the virtual cathode formed by a high injection current (2001)

A virtual cathode is formed in a cavity, if the injection current from the diode exceeds the critical current. The propagation properties of the forward current beyond the virtual cathode are investigated. It is shown that the forward current increases significantly as the diode gap distance LCA increases, although the injection current from the diode decreases drastically. Experimental data agree well with theoretical results obtained analytically.
Early Detection of<i>Aspergillus</i>Infection after Allogeneic Stem Cell Transplantation by Polymerase Chain Reaction Screening (2000)

Invasive aspergillosis (IA) has become a major cause of mortality in patients after allogeneic stem cell transplantation. To assess the potential of prospective polymerase chain reaction (PCR) screening for early diagnosis of IA, 84 recipients of an allogeneic stem cell transplant were analyzed with the investigators blinded to clinical and microbiologic data. Of 1193 blood samples analyzed, 169 (14.2%) were positive by PCR. In patients with newly diagnosed IA (n=7), PCR positivity preceded the first clinical signs by a median of 2 days (range, 1-23 days) and preceded clinical diagnosis of IA by a median of 9 days (range, 2-34 days). Pretransplantation IA (relative risk [RR], 2.37), acute graft-versus-host disease (RR, 2.75), and corticosteroid treatment (RR, 6.5) were associated with PCR positivity. The PCR assay revealed a sensitivity of 100% (95% confidence interval [CI], 48%-100%) and a specificity of 65% (95% CI, 53%-75%). None of the PCR-negative patients developed IA during the study period. Thus, prospective PCR screening allows for identification of patients at high risk for subsequent onset of IA.
IP6K2 is a client for HSP90 and a target for cancer therapeutics development (2008)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
A nonvolatile programmable solid-electrolyte nanometer switch (2005)

A reconfigurable LSI employing a nonvolatile nanometer-scale switch, NanoBridge, is proposed, and its basic operations are demonstrated. The switch, composed of solid electrolyte copper sulfide, has a <30-nm contact diameter and <100-/spl Omega/ on-resistance. Because of its small size, it can be used to create extremely dense field-programmable logic arrays. A 4 /spl times/ 4 crossbar switch and a 2-input look-up-table circuit are fabricated with 0.18-/spl mu/m CMOS technology, and operational tests with them have confirmed the switch's potential for use in programmable logic arrays. A 1-kb nonvolatile memory is also presented, and its potential for use as a low-voltage memory device is demonstrated.
Accelerated and reproducible oxidation of strain-compensated short-period superlattice structures for incorporation in InP based devices (2001)

An accelerated oxidation process has been demonstrated in InAs/AlAs-based strain-compensated ultrashort-period superlattices grown on an InP substrate. It has been observed that the uniformity as well as the rate of the oxidation process in the strain-compensated short-period superlattice depends on the composition of the surrounding semiconductor layers. A suitable layer structure has been designed to obtain accelerated and reproducible oxidation rate in InP based optoelectronic devices.
Genome Sequence of African Swine Fever Virus BA71, the Virulent Parental Strain of the Nonpathogenic and Tissue-Culture Adapted BA71V (2015)

The strain BA71V has played a key role in African swine fever virus (ASFV) research. It was the first genome sequenced, and remains the only genome completely determined. A large part of the studies on the function of ASFV genes, viral transcription, replication, DNA repair and morphogenesis, has been performed using this model. This avirulent strain was obtained by adaptation to grow in Vero cells of the highly virulent BA71 strain. We report here the analysis of the genome sequence of BA71 in comparison with that of BA71V. They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes. We discuss the possible contribution of these changes to virulence. Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network.
Structure of the baboon endogenous virus genome: nucleotide sequences of the long terminal repeat (1981)

The entire nucleotide sequence of the long terminal repeat (LTR) of baboon endogenous virus (BaEV) M7 was determined, which consisted of 554 base pairs (bp). At both ends of the LTR, 13 bp sequences, AAATGAAAAGTAA and TGATTCTAACATC, were detected to be inverted repeats. The structure with these inverted repeats resembles those of other retroviruses and transposable elements. a Hogness box, TATAAAA, and a putative poly(A)-addition signal, AGTAAA, were present within the right-hand half of the LTR, where the initiation and termination of the viral RNA synthesis seems to occur in the integrated BaEV genome. The primer-binding site of at least 14 bp long was found just outside of the LTR where the strong stop DNA started, and the primer for reverse transcription in BaEV seemed to be tRNAPro. Several structural features are commonly detected in the LTRs of BaEV and other retroviruses. Our studies suggest that BaEV has evolved from a common ancestor with other mammalian type C viruses. Close relationships between BaEV and a feline endogenous virus, RD114, are demonstrated.
Expression in <i>Mycoplasma pneumoniae</i> of the recombinant gene encoding the cytadherence‐associated protein HMW1 and identification of HMW4 as a product (1996)

Mycoplasma pneumoniae is a major cause of tracheobronchitis and pneumonia in older children and young adults. The lack of adequate tools for genetic analysis has hindered the elucidation of function and regulation of mycoplasma virulence determinants. We describe here the use of a transposon vector to deliver the cloned gene for the cytadherence-associated protein HMW1 in M. pneumoniae. A 4.95 kbp BamHI fragment encoding all but the C-terminal end of HMW1 was cloned into a modified Tn4001 and transformed into wild-type M. pneumoniae and into a non-cytadhering mutant lacking HMW1-HMW5. Southern blot hybridizations confirmed insertion of the transposon and the presence of both the resident and recombinant hmw1 alleles. Analysis by Western immunoblotting revealed a truncated HMW1 (HMW1') in the transformants, the level of HMW1' being dependent upon the orientation of the hmw1 gene in the transposon and the site of insertion. Similar expression patterns were noted in wild-type and mutant backgrounds. However, expression of wild-type levels of HMW1' in the mutant did not restore adherence. Finally, HMW4 and HMW1 were shown to be products of the same gene, HMW4 being a heat-modified derivative of HMW1.
Beating Atrial Septal Defect Closure Monitored by Epicardial Real-Time Three-Dimensional Echocardiography Without Cardiopulmonary Bypass (2003)

Introduction of RT3DE, a semiautomatic suture device, and a suture cutting system made beating ASD closure without cardiopulmonary bypass possible.
The Type VI Secretion System Spike Protein VgrG5 Mediates Membrane Fusion during Intercellular Spread by Pseudomallei Group Burkholderia Species (2014)

Pseudomallei group Burkholderia species are facultative intracellular parasites that spread efficiently from cell to cell by a mechanism involving the fusion of adjacent cell membranes. Intercellular fusion requires the function of the cluster 5 type VI secretion system (T6SS-5) and its associated valine-glycine repeat protein, VgrG5. Here we show that VgrG5 alleles are conserved and functionally interchangeable between Burkholderia pseudomallei and its relatives B. mallei, B. oklahomensis, and B. thailandensis. We also demonstrate that the integrity of the VgrG5 C-terminal domain is required for fusogenic activity, and we identify sequence motifs, including two hydrophobic segments, that are important for fusion. Mutagenesis and secretion experiments using B. pseudomallei strains engineered to express T6SS-5 in vitro show that the VgrG5 C-terminal domain is dispensable for T6SS-mediated secretion of Hcp5, demonstrating that the ability of VgrG5 to mediate membrane fusion can be uncoupled from its essential role in type VI secretion. We propose a model in which a unique fusogenic activity at the C terminus of VgrG5 facilitates intercellular spread by B. pseudomallei and related species following injection across the plasma membranes of infected cells.
PLASMINOGEN ACTIVATOR INHIBITOR-1 PROMOTES INFLAMMATORY PROCESS INDUCED BY CIGARETTE SMOKE EXTRACTION OR LIPOPOLYSACCHARIDES IN ALVEOLAR EPITHELIAL CELLS (2009)

Plasminogen activator inhibitor-1 (PAI-1) plays a role in regulating levels of some cytokines and cell migration in addition to its classic role in inhibiting fibrinolysis. PAI-1 levels in induced-sputum of chronic obstructive pulmonary disease (COPD) patients were elevated significantly and correlated negatively with pulmonary function. To study the role of PAI-1 in inflammatory process in COPD, the authors transfected alveolar epithelial cells (AECs) with siRNA-targeted PAI-1 and stimulated the cells by cigarette smoke extraction (CSE) or lipopolysaccharides (LPS). The expression of inflammatory factors, interleukin-8 (IL-8) and leukotriene B4 (LTB4), and the monocyte migration were detected. The exposure to CSE or LPS induced the expression of PAI-1, IL-8, and LTB4 in AECs and monocyte migration to AECs. However, they were attenuated after transfection with siRNA-targeted PAI-1. In conclusion, PAI-1 stimulates inflammation induced by CSE or LPS in AECs through up-regulation of inflammatory factors and promoting inflammatory cell migration. PAI-1 may play a proinflammatory role in the pathogenesis of COPD.
Fairing recursive subdivision surfaces with curve interpolation constraints (2002)

Given a polygonal mesh with a set of tagged control polygons, a subdivision surface that interpolates the B-spline curves of these control polygons can be obtained by constructing a set of polygonal complexes, each of which converges to one of the given curves. The construction process will geometrically and topologically disturb the initial and/or the subdivided polygonal meshes in the vicinity of the polygonal complexes. This may result in poorly shaped surfaces across the interpolated curves. Based on signal fairing, this paper describes a method to fair such a surface and paves the way to achieve further constraints such as interpolating curves with predefined tangent plane or cross curvature.
Acute Metabolic Alkalosis Enhances Response of C3H Mouse Mammary Tumors to the Weak Base Mitoxantrone (2001)

Uptake of weak acid and weak base chemotherapeutic drugs by tumors is greatly influenced by the tumor extracellular/interstitial pH (pH(e)), the intracellular pH (pH(i)) maintained by the tumor cells, and by the ionization properties of the drug itself. The acid-outside plasmalemmal pH gradient in tumors acts to exclude weak base drugs like the anthracyclines, anthraquinones, and vinca alkaloids from the cells, leading to a substantial degree of "physiological drug resistance" in tumors. We have induced acute metabolic alkalosis in C3H tumor-bearing C3H/hen mice, by gavage and by intraperitoneal (i.p.) administration of NaHCO(3). (31)P magnetic resonance spectroscopic measurements of 3-aminopropylphosphonate show increases of up to 0.6 pH units in tumor pH(e), and 0.2 to 0.3 pH units in hind leg tissue pH(e), within 2 hours of i.p. administration of NaHCO(3). Theoretical calculations of mitoxantrone uptake into tumor and normal (hind leg) tissue at the measured pH(e) and pH(i) values indicate that a gain in therapeutic index of up to 3.3-fold is possible with NaHCO(3) pretreatment. Treatment of C3H tumor-bearing mice with 12 mg/kg mitoxantrone resulted in a tumor growth delay of 9 days, whereas combined NaHCO(3)--mitoxantrone therapy resulted in an enhancement of the TGD to 16 days.
Shutdown decay of mRNA (2006)

Although plasmid-borne and chromosomal toxin-antitoxin (TA) operons have been known for some time, the recent identification of mRNA as the target of at least two different classes of toxins has led to a dramatic renewal of interest in these systems as mediators of stress responses. Members of the MazF/PemK family, the so-called mRNA interferases, are ribonucleases that inhibit translation by destroying cellular mRNAs under stress conditions, while the founder member of the RelE family promotes cleavage of mRNAs through the ribosome. Detailed structures of these enzymes, often in complex with their inhibitors, have provided vital clues to their mechanisms of action. The primary role and regulation of these systems has been the subject of some controversy. One model suggests they play a beneficial role by wiping the slate clean and preventing wasteful energy consumption by the translational apparatus during adaptation to stress conditions, while another favours the idea that their main function is programmed cell death. The two models might not be mutually exclusive if a side-effect of prolonged exposure to toxic RNase activity without de novo synthesis of the inhibitor were a state of dormancy for which we do not yet understand the key to recovery. In this review, I discuss the recent developments in the rapidly expanding field of what I refer to as bacterial shutdown decay.
Algorithms for quad-double precision floating point arithmetic (2002)

A quad-double number is an unevaluated sum of four IEEE double precision numbers, capable of representing at least 212 bits of significand. We present the algorithms for various arithmetic operations (including the four basic operations and various algebraic and transcendental operations) on quad-double numbers. The performance of the algorithms, implemented in C++, is also presented.
Vapour pressure and enthalpy of sublimation of 1,3,5,7-tetranitro-1,3,5,7-tetra-azacyclo-octane (HMX) (1976)

The vapour pressure of 1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetra-azacyclo-octane (HMX) has been measured in the temperature range 188 to 213°C by the Knudsen effusion method, and the enthalpy of sublimation over this range calculated to be 38.7 kcal mol–1. Similar measurements on anthracene have been made which confirm literature values.A marked dependence of the vapour pressure, but not of its temperature variation, on the size of the effusion orifice has been observed.
Key pathways and genes controlling the development and progression of clear cell renal cell carcinoma (ccRCC) based on gene set enrichment analysis (2013)

The gene pathways that we identified could provide insight concerning the development of ccRCC. Further studies are needed to determine the biological function for the positive genes.
Mode-locking of thulium-doped and erbium-doped fiber lasers (1997)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.
Platelet‐Leukocyte Aggregates During Hemodialysis: Effect of Membrane Type (1999)

Hemodialysis is associated with the formation of platelet-leukocyte aggregates. Whether this phenomenon is hemodialysis (HD) membrane dependent is unclear. To evaluate this process, we examined respectively platelet activation (anti-CD41, anti-CD62, and antifibrinogen monoclonal antibodies [MoAb] binding), leukocyte activation (CD11b expression), and the appearance of platelet specific antigens on leukocytes as an index of platelet-leukocyte aggregation during HD using 3 different membrane materials, Cuprophan, Hemophan, and polysulfone. Flow cytometric techniques and specific MoAb were used. All parameters were assayed 5 min after initiation of HD to avoid the confounding variable of leukopenia and resultant cell subpopulation analysis. Platelet activation (anti-CD62 and antifibrinogen binding) occurred only with Cuprophan. All 3 membranes induced equivalent increases in CD11b expression on neutrophils and similarly increased the binding of anti-CD41 to neutrophils, reflecting an increment in the formation of platelet neutrophil aggregates. However, only Cuprophan induced an increase in anti-CD62 binding to neutrophils, suggesting that the aggregated platelets linked to neutrophils were activated. Increased anti-CD41 binding by monocytes was similarly observed with all 3 membranes. However, only polysulfone induced an increase in CD11b expression and fibrinogen binding to monocytes. We conclude that while the formation of platelet leukocyte aggregates appears to be a universal phenomenon in HD occurring with a variety of membrane types, subtypes of this phenomenon consisting of activated platelets and fibrinogen binding may be membrane dependent. This phenomenon may serve as a new biocompatibility parameter and may shed light on some of the biologic consequences of hemodialysis.
Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic (2011)

The abundance and structure of archaeal and bacterial communities from the active layer and the associated permafrost of a moderately acidic (pH < 5.0) High Arctic wetland (Axel Heiberg Island, Nunavut, Canada) were investigated using culture- and molecular-based methods. Aerobic viable cell counts from the active layer were ∼100-fold greater than those from the permafrost (2.5 × 10(5) CFU·(g soil dry mass)(-1)); however, a greater diversity of isolates were cultured from permafrost, as determined by 16S rRNA gene sequencing. Isolates from both layers demonstrated growth characteristics of a psychrotolerant, halotolerant, and acidotolerant community. Archaea constituted 0.1% of the total 16S rRNA gene copy number and, in the 16S rRNA gene clone library, predominantly (71% and 95%) consisted of Crenarchaeota related to Group I. 1b. In contrast, bacterial communities were diverse (Shannon's diversity index, H = ∼4), with Acidobacteria constituting the largest division of active layer clones (30%) and Actinobacteria most abundant in permafrost (28%). Direct comparisons of 16S rRNA gene sequence data highlighted significant differences between the bacterial communities of each layer, with the greatest differences occurring within Actinobacteria. Comparisons of 16S rRNA gene sequences with those from other Arctic permafrost and cold-temperature wetlands revealed commonly occurring taxa within the phyla Chloroflexi, Acidobacteria, and Actinobacteria (families Intrasporangiaceae and Rubrobacteraceae).
Selection and characterization of new microorganisms for the manufacture of 9‐OH‐AD from sterols (1992)

Using a special selection procedure, several mutants of Mycobacterium vaccae were isolated which were capable of converting sterols to 9 alpha-hydroxyandrost-4-ene-3,17-dion (9-OH-AD). Two mutants, Mycobacterium vaccae ZIMET 11052 and 11053, respectively, were further investigated. Strains of the species Mycobacterium fortuitum are mainly used for commercially obtaining 9-OH-AD from sterols. In contrast to the species Mycobacterium fortuitum the species Mycobacterium vaccae has not been reported to contain pathogenic strains. This seems an advantage for industrial application. Mutants with the ability of converting sterols to 9 alpha-hydroxysteroids have a defect in the steroid-1-dehydrogenase activity which is, however, only a partial one. The remaining activity may cause an undesirable degradation of the steroid nucleus. The steroid-1-dehydrogenase activity was tested using an assay developed by ATRAT (1986). We confirmed two apparently distinct steroid-1-dehydrogenases in Mycobacterium fortuitum NRRL B-8119 as reported by WOVCHA et al. (1979). One of them has an activity on androst-4-ene-3,17-dion (AD). The activity is increased by induction with sitosterol. The other one is active on 9-OH-AD. But Mycobacterium vaccae does not possess steroid-1-dehydrogenase activity on 9-OH-AD, and the AD specific steroid-1-dehydrogenase is not effected by sitosterol. The consequence is a high level of protection against steroid nucleus degradation yielding an effective accumulation of 9-OH-AD in fermentations with Mycobacterium vaccae mutants.
Towards strain gauges based on a self-assembled nanoparticle monolayer—SAXS study (2010)

An in situ small-angle x-ray scattering study of the nanoparticle displacement in a self-assembled monolayer as a function of a supporting membrane strain is presented. The average nanoparticle spacing is 6.7 nm in the unstrained state and increases in the applied force direction, following linearly the membrane strain which reaches the maximum value of 11%. The experimental results suggest a continuous mutual shift of the nanoparticles and their gradual separation with the growing stress rather than nanoparticle islands formation. No measurable shift of the nanoparticles was observed in the direction perpendicular to the applied stress.
Transcatheter closure of secundum atrial septal defects. (2013)

Atrial septal defect (ASD) is one of the most common congenital heart defects, accounting for 7%-10% of all congenital heart disease (CHD) in children and 30%-33% of defects diagnosed in adults with CHD. This review highlights the evolution of transcatheter ASD closure, indications, follow-up, outcomes, and complications with a focus on the erosion issue with certain devices.
Simplification and Analysis of Transitive Trust Networks (2006)

When transacting and interacting through open computer networks, traditional methods used in the physical world for establishing trust can no longer be used. Creating virtual network substitutes with which people, organisations and software agents can derive trust in other parties requires computerised analysis of the underlying trust networks. This article describes an approach to trust network analysis using subjective logic (TNA-SL), that consists of the three following elements. Firstly it uses a concise notation with which trust transitivity and parallel combination of trust paths can be expressed. Secondly it defines a method for simplifying complex trust networks so that they can be expressed in this concise form. Finally it allows trust measures to be expressed as beliefs, so that derived trust can be automatically and securely computed with subjective logic. We compare our approach with trust derivation algorithms that are based on normalisation such as PageRank and EigenTrust. We also provide a numerical example to illustrates how TNA-SL can be applied.
Pharmacokinetics, Safety, and Antiviral Effects of Hypericin, a Derivative of St. John's Wort Plant, in Patients with Chronic Hepatitis C Virus Infection (2001)

Hypericin is a natural derivative of the common St. Johns wort plant, Hypericum perforatum. It has in vitro activity against several viruses, including bovine diarrhea virus, a pestivirus with structural similarities to hepatitis C virus (HCV). We conducted a phase I dose escalation study to determine the safety and antiviral activity of hypericin in patients with chronic HCV infection. The first 12 patients received an 8-week course of 0.05 mg of hypericin per kg of body weight orally once a day; 7 patients received an 8-week course of 0.10 mg/kg orally once a day. At the end of the 8-week period of treatment, no subject had a change of plasma HCV RNA level of more than 1.0 log(10). Five of 12 subjects receiving the 0.05-mg/kg/day dosing schedule and 6 of 7 subjects receiving the 0.10-mg/kg/day dosing schedule developed phototoxic reactions. No other serious adverse events associated with hypericin use occurred. The pharmacokinetic data revealed a long elimination half-life (mean values of 36.1 and 33.8 h, respectively, for the doses of 0.05 and 0.1 mg/kg) and mean area under the curve determinations of 1.5 and 3.1 microg/ml x hr, respectively. In sum, hypericin given orally in doses of 0.05 and 0.10 mg/kg/d caused considerable phototoxicity and had no detectable anti-HCV activity in patients with chronic HCV infection.