gebhart/patrepeval huggingface dataset:
A Universal Influenza A Vaccine Based on Adenovirus Expressing Matrix-2 Ectodomain and Nucleoprotein Protects Mice From Lethal Challenge (2010)

A universal influenza vaccine, designed to induce broadly cross-reactive immunity against current and future influenza A virus strains, is in critical demand to reduce the need for annual vaccinations with vaccines chosen upon predicting the predominant circulating viral strains, and to ameliorate the threat of cyclically occurring pandemics that have, in the past, killed tens of millions. Here, we describe a vaccine regimen based on sequential immunization with two serologically distinct chimpanzee-derived replication-defective adenovirus (Ad) vectors expressing the matrix-2 protein ectodomain (M2e) from three divergent strains of influenza A virus fused to the influenza virus nucleoprotein (NP) for induction of antibodies to M2e and virus-specific CD8(+) T cells to NP. In preclinical mouse models, the Ad vaccines expressing M2e and NP elicit robust NP-specific CD8(+) T-cell responses and moderate antibody responses to all three M2e sequences. Most importantly, vaccinated mice are protected against morbidity and mortality following challenge with high doses of different influenza virus strains. Protection requires both antibodies to M2e and cellular immune responses to NP.
A New Dithienylbenzotriazole‐Based Poly(2,7‐carbazole) for Efficient Photovoltaics (2010)

Abstract A new dithienyl benzotriazole‐based conjugated polymer was synthesized by Suzuki coupling reaction. The polymer was found to be soluble in common organic solvents, such as chloroform, tetrahydrofuran and chlorobenzene, with excellent film‐forming properties. The structure of the polymer was confirmed by 1 H NMR, the molecular weights determined by GPC and the thermal properties investigated by TGA and DSC. The polymer films exhibited an absorption band in the wavelength range 300 to 610 nm. Preliminary photovoltaic cells based on the composite structure of indium tin oxide (ITO)/PEDOT:PSS/ PCDTBTz:PC 60 BM (1:2 w/w)/Al showed an open‐circuit voltage of 0.92 V, a power conversion efficiency of 2.2% and a short circuit current of 5.33 mA cm −2 . magnified image
The Art of Molecular Dynamics Simulation (2004)

The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.
Fluorescent Nucleotide Derivatives as Specific Probes for the Uncoupling Protein: Thermodynamics and Kinetics of Binding and the Control by pH (1995)

Fluorescent 2'-O-dansylated (DANS) purine nucleotides were synthesized. The fluorescence of the nucleotide derivatives is quenched in aqueous solutions but strongly enhanced on binding to the uncoupling protein (UCP) from brown adipose tissue mitochondria. The fluorescence enhancement was 30-, 10-, and 10-fold for DANSGTP, DANSATP, and DANSADP. One mole of DANS nucleotide binds to 1 mol of dimeric UCP. The binding affinity ranges from 10(5) to 10(8) M-1, similar to that of the unsubstituted nucleotides, while dansylation of AMP increases the affinity 50-fold. The pH dependence in the pKD/pH plots for the DANS nucleotides is basically similar to that for the unsubstituted nucleotides, i.e., for nucleoside diphosphates the slope delta pKD/delta pH < -1 at pH 5-6.5, = -1 at pH > 6.8, and only for triphosphates = -2 at pH > 7.2. Two different protonation sites with a pKH approximately 4 (Asp/Glu) and pKH approximately 7.2 (His), only for nucleoside triphosphates, are suggested to be involved in binding. The higher affinity of DANSGTP indicates additional participation in binding of the C-6 oxygen on the guanine. The binding as measured with the anion exchange method agrees with the fluorescence measurement for DANSGTP, whereas for the more loosely binding DANSATP it is 40% lower. This is interpreted in terms of tight/loose UCP-nucleotide complexes, 100% tight complex for DANSGTP (as well GTP or ATP) but 40% loose complex for DANSATP. By measuring the rapid kinetics using the fluorescence signal, the binding rate is found to be fast and fairly constant for the various nucleotides, whereas the dissociation is slow and strongly nucleotide dependent. The rates are pH dependent with delta pkon/delta pH = 1 for all the nucleotides and delta pkoff/delta pH = -1 for DANSNTP but more weakly with delta pkoff/delta pH < -0.5 for DANSADP and DAN-ATP. The pH dependence of the binding rate corresponds to a protonation at the carboxylate group (Glu/Asp). The high pH dependence of the dissociation rate only for DANSNTP is explained by deprotonation at the HisH+ which is involved only in nucleoside triphosphate binding. This is in line with the very strong pH dependence of nucleoside triphosphate affinity above pH 7 with a delta pKD/delta pH = -2 as an important regulatory mechanism for the H+ transport activity of UCP. The differences of the DANS nucleotides versus the DAN and unsubstituted nucleotides as well as the nucleoside tri- versus diphosphate are rationalized in a specific H+ dependent regulatory mechanism at the binding site.
Comparative neurovirulence of attenuated and non-attenuated strains of Venezuelan equine encephalitis virus in mice. (2001)

A candidate live-attenuated virus vaccine for protection against Venezuelan equine encephalitis (VEE) (designated V3526) was tested in mice to measure the magnitude, duration, and kinetics of virus replication in the blood and the central nervous system and its phenotypic stability after multiple passages in mice and cell culture. All results were compared to parallel experiments with parental virus and the existing VEE virus vaccine, TC-83. Maximum virus titers in the brains of V3526-inoculated mice were between 10- and 100-fold less than those observed in brains of mice inoculated intracranially (i.c.) with either the parental virus or TC-83. Neither V3526 nor TC-83 was lethal in BALB/c mice inoculated i.c.. However, mice inoculated with TC-83 developed acute symptoms lasting at least 14 days. In contrast, i.c. inoculation of TC-83 was uniformly lethal for C3H/HeN mice. V3526 was avirulent in both BALB/c and C3H/HeN mice after i.c. inoculation. The virulence characteristics of V3526 remained unchanged after five serial i.c. passages in mouse brains or after five cell culture passages. Finally, pathologic changes induced after i.c. inoculation of V3526 were consistently less severe and of shorter duration than those observed in TC-83-inoculated mice. Based on these results, V3526 is stable and appears to be significantly less neurovirulent in mice than TC-83.
BCG vaccination and the PPD test: what the clinician needs to know. (1995)

The resurgence in tuberculosis necessitates careful surveillance and sensitive detection of cases. The purified protein derivative (PPD) test is the foundation of tuberculosis control. Primary care clinicans are encountering increasing numbers of persons immigrating from countries in which BCG (bacille Calmette-Guérin) vaccination is common. Many health care providers believe that previous BCG vaccination usually results in a positive PPD test, and therefore consider BCG vaccination status when interpreting a positive result on the PPD test. All articles listed in MEDLINE that included BCG and PPD as key words, a total of 62, were reviewed. Articles published before computerization of the medical literature, a total of 35, were reviewed in Index Medicus. This literature review indicates that there is little relationship between BCG vaccination and PPD positivity, and that BCG vaccination status should not be considered in the interpretation of a positive PPD test.
Recognizing sublanguages in scientific journal articles through closure properties (2013)

It has long been realized that sublanguages are relevant to natural language processing and text mining. However, practical methods for recognizing or characterizing them have been lacking. This paper describes a publicly available set of tools for sublanguage recognition. Closure properties are used to assess the goodness of fit of two biomedical corpora to the sublanguage model. Scientific journal articles are compared to general English text, and it is shown that the journal articles fit the sublanguage model, while the general English text does not. A number of examples of implications of the sublanguage characteristics for natural language processing are pointed out. The software is made publicly available at [edited for anonymization].
THE LINKS BETWEEN THE ADOLESCENT DISSOCIATIVE EXPERIENCES SCALE (A-DES), FANTASY PRONENESS, AND ANXIETY SYMPTOMS (2003)

The purpose of this study was to further examine the psychometric properties of the Adolescent Dissociative Experiences Scale (A-DES). A sample of normal adolescents (N = 331) aged 12 to 18 years completed the A-DES and questionnaires measuring posttraumatic stress disorder (PTSD) symptoms, other anxiety disorder symptoms, and fantasy proneness. Factor analysis indicated that the A-DES, at least in nonreferred youths, is assessing a single dimension of dissociation. Furthermore, A-DES scores are not only significantly related to PTSD symptoms but also to other anxiety disorder symptoms (i.e., generalized anxiety disorder, obsessive-compulsive disorder, and panic disorder) and fantasy proneness. Theoretical and practical implications of these findings are briefly discussed.
Historical control monotherapy design in the treatment of epilepsy (2010)

There is justification for proposing that these data can serve as a historical control for future monotherapy studies, obviating the need for a placebo/pseudo-placebo arm in trials intended to demonstrate the efficacy of approved drugs as monotherapy in treatment-resistant patients.
Microscopic structure of athabasca oil sand (1982)

Abstract A refined structural model for in situ oil sands is proposed in terms of the mutual arrangement of sand grains, fines, water and bitumen. In the Athabasca deposit, the sand grains consist mainly of quartz and their packing is such that the porosity is about 35%. In rich oil sand, 10–15% of the pore space is occupied by connate water whereas the remainder is occupied by bitumen. For lower grade oil sands, a direct correlation exists between the water content and the amount of fines (particles smaller than 44 μm) and an inverse correlation exists between the bitumen content and the amount of fines. These relationships are successfully explained in terms of the irreducible water saturation in a porous medium and the double layer interaction between sand and bitumen surfaces.
Directed evolution of the TALE N-terminal domain for recognition of all 5′ bases (2013)

Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5'-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5' T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5' T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes.
Human dystrophin expression corrects the myopathic phenotype in transgenic mdx mice (1992)

Duchenne and the less severe Becker form of muscular dystrophy (DMD,BMD) result from genetic deficiency in the level and/or activity of the protein dystrophin. The recent availability of cDNA based minigenes encoding recombinant dystrophin polypeptides has raised the possibility of somatic gene transfer as a therapeutic approach to treat dystrophin deficiency. In this respect, the mdx mouse provides a useful model of DMD exhibiting features characteristic of both the early myopathic and later fibrotic phases of the human disease. Using a mutated human cDNA, compatible in size with virus-based somatic gene transfer vectors, the pathophysiological consequences of restoring dystrophin expression have been examined in transgenic mdx mice. Transgene expression was correlated with a marked reduction of the skeletal myofibre necrosis and regeneration which is a major feature of the dystrophin-deficient phenotype in young mdx mice. The cDNA construct which is based on a very mild BMD phenotype thus encodes a highly functional dystrophin molecule whose reduced size renders it an attractive candidate for development as a therapeutic gene transfer reagent.
ChemInform Abstract: PHOSPHORUS‐NITROGEN COMPOUNDS. 24. PHOSPHORAMIDE MUSTARD CARRIER DERIVATIVES (1984)

Abstract Dargestellt und auf Antitumor‐Aktivität untersucht werden die Verbindungen (I)‐(III).
A simulation tool for the analysis and verification of the steady state of circuit designs (1995)

Abstract Analogue and microwave design requires accurate and reliable simulation tools and methods to meet the design specifications. System properties are often measured in the steady state. Well‐suited algorithms for calculating the steady state can be classified into shooting methods, finite difference methods and the harmonic balance (HB) technique. Harmonic balance is a frequency domain method which approaches the problem of finding the steady state by a trigonometric polynomial. Depending on the size of the circuit and the number of Fourier coefficients of the polynomial, the resulting system of non‐linear equations can become very large. These non‐linear equations are solved by using Newton's method. The sparse linear system arising from Newton's method can be solved by direct, stationary or non‐stationary iterative solvers. Iterative methods are normally easy to parallelize or vectorize. In this paper a tool for the simulation of the steady state of electronic circuits is presented. the steady state is calculated using the harmonic balance technique. Non‐linear equations are solved by Newton's method and linear equations by preconditioned non‐stationary iterative solvers (CGS, Bi‐CGSTAB, BiCGSTAB(2), TFQMR). the run time is reduced dramatically, by up to an order of magnitude.
Yeast tRNA-splicing endonuclease cleaves precursor tRNA in a random pathway. (1993)

Introns interrupt many of the tRNA genes of Saccharomyces cerevisiae at a constant position in the anticodon loop. Pre-tRNA transcripts must be accurately cleaved at 3' and 5' splice sites by tRNA endonuclease to release these introns. In order to study splice site cleavage order, substrates were prepared in which the ribose 2'-OH at each of the splice sites was phosphorylated. This modification blocked cleavage by the endonuclease. We found that whichever splice site was blocked the endonuclease can cleave the other site, indicating that the two splice sites were cleaved independently. The endonuclease also cleaved both 3'- and 5'-nicked pre-tRNA(Phe). In addition, both kinds of "2/3 molecules" (exon+intron) were observed in kinetic studies, indicating that they were true biochemical intermediates. The rates of cleavage at the 3' and 5' splice sites of pre-tRNA were compared in several ways. The results showed that the endonuclease cleaves 3' and 5' sites at almost the same rate in the first cleavage, whereas in the second cleavage the 3' site was cleaved faster, indicating that the rates of the two routes for cleavage were unequal. These results demonstrated that the endonuclease cleaved pre-tRNA in a random order, creating two routes for removal of introns from pre-tRNA.
Stochastic Dynamics: Simulating the Effects of Turbulence on Flexible Structures (1997)

This paper addresses the problem of realistically simulating the motion of tree‐branches subjected to turbulence. Since the resulting motion is random in nature, we model it as a stochastic process. We synthesize this process directly by filtering a white noise in the Fourier domain. The filter is constructed by performing a modal analysis of the tree. We use a sophisticated numerical technique which is able to compute the first few significant modes of large trees. The main advantage of our technique over previous methods is that we are able to compute complicated motions without the necessity of integrating dynamical equations over time. Consequently, a user can view and manipulate tree‐motions in real‐time. Our technique can be further extended to other flexible structures such as two‐dimensional plates.
Vagus nerve stimulation therapy in depression and epilepsy: therapeutic parameter settings (2006)

Vagus nerve stimulation (VNS) therapy is an effective adjunctive treatment for chronic or recurrent treatment-resistant depression in adults, and for pharmacoresistant epilepsy in adults and adolescents. VNS therapy is administered through an implanted pulse generator that delivers programmed electrical pulses through an implanted lead to the left vagus nerve. Programmable pulse parameters include output current, frequency, pulse width, and ON/OFF times. Within a range of typical values, individual patients respond best to different combinations of parameter settings. The physician must identify the optimum settings for each patient while balancing the goals of maximizing efficacy, minimizing side effects, and preserving battery life. Output current is gradually increased from 0.25 mA to the maximum tolerable level (maximum, 3.5 mA); typical therapeutic settings range from 1.0 to 1.5 mA. Greater output current is associated with increased side effects, including voice alteration, cough, a feeling of throat tightening, and dyspnea. Frequency is typically programmed at 20 Hz in depression and 30 Hz in epilepsy. Pulse width is typically 250 or 500 micros. The recommended initial ON time is 30 s, followed by 5 min OFF; OFF time > ON time is recommended. As with pharmacotherapy, VNS therapy must be adjusted in a gradual, systematic fashion to individualize therapy for each patient.
A Probabilistic Reasoning Tool for Circulation Monitoring Based on Flow Measurements (1999)

Abstract An expert system is being developed to automatically detect and diagnose several important circulation system problems in geothermal drilling. The system is called the Circulation Monitoring System (CMS) and will be useful for detecting, characterizing, and quantifying lost circulation, fluid influx, gas/steam kicks, loss of mud pump efficiency, washouts, plugged nozzles, and sensor problems. Data from the outflow meter, pump-stroke counter, inflow meter, pit volume indicator, standpipe pressure sensor, and other sensors are processed by a Kalman filter and examined for deviations from expected patterns. The deviations are transformed into evidence for a Bayesian Network, which estimates the probability of each fault. The results are displayed by a Graphical User Interface, which also allows the user to see data related to a specific fault. A prototype has been field-tested and has successfully detected and diagnosed a variety of faults. The ability of the expert system to analyze circulation system problems is dependent on having high quality inflow and outflow measurements. Sandia National Laboratories has developed a Rolling Float Meter (RFM) to measure outflow and is testing commercially available ultrasonic inflow meters. The RFM has proven rig worthy and is ready for commercialization. Most recently it has been tested by Epoch Wellsite Services on a relief well in California where it has successfully detected kicks that were not observable by standard outflow measuring devices.
Atypical depression in growth hormone deficient adults, and the beneficial effects of growth hormone treatment on depression and quality of life (2004)

The results of our study confirm that a large proportion of GHDAs have unequivocal psychiatric morbidity, and suggest that a response to treatment can be seen after a short trial of GH therapy. We hypothesise that this rapid improvement of symptoms of atypical depression represents a direct central effect of GH therapy.
Stem cell therapy after myocardial infarction: ready for clinical application? (2006)

The discovery of stem cells capable of generating angiogenic or contractile cells and structures might offer new treatment options for patients suffering from heart disease. In particular, embryonic stem cells are considered to have great potential for regenerative medicine and tissue engineering. Studies suggest that delivery or mobilization of stem and progenitor cells might improve tissue perfusion and contractile performance of the damaged heart; however, the underlying mechanisms are poorly understood. Fusion or trans-differentiation into cardiomyocytes or vascular cells are considered rare events of cellular engraftment, and adult stem cells are now considered as 'regenerator cells', acting via paracrine effects of cytokines, or by activation of resident stent cells, thereby supporting the myocardial healing mechanisms after injury. Administration of autologous hematopoietic stem cells or mobilization of endogenous stem cells has been shown to be safe after myocardial infarction or cardiomyopathies, whereas skeletal myoblasts are considered to be hazardous due to the occurrence of life-threatening arrhythmias. This review focuses on the use of adult human stem cells for treating myocardial infarction and cardiomyopathy, and discusses recent preliminary efficacy data, which suggest that 'regenerator cells' might have the potential to improve myocardial perfusion and contractile performance in patients suffering from myocardial infarction, severe ischemic heart disease and chronic heart failure.
ChemInform Abstract: An Iodide‐Based Li7P2S8I Superionic Conductor. (2015)

Abstract The title compound is synthesized from a dispersion of Li 3 PS 4 (obtained from a stoichiometric mixture of Li 2 S and P 2 S 5 in MeCN for 24 h) and LiI in MeCN at ambient conditions for 12 h, followed by heat treatment at 200 °C in vacuum.