gebhart/patrepeval huggingface dataset:
Mutational analysis of the transcriptional activator VirG of Agrobacterium tumefaciens (1994)

To find VirG proteins with altered properties, the virG gene was mutagenized. Random chemical mutagenesis of single-stranded DNA containing the Agrobacterium tumefaciens virG gene led with high frequency to the inactivation of the gene. Sequence analysis showed that 29% of the mutants contained a virG gene with one single-base-pair substitution somewhere in the open reading frame. Thirty-nine different mutations that rendered the VirG protein inactive were mapped. Besides these inactive mutants, two mutants in which the vir genes were active even in the absence of acetosyringone were found on indicator plates. A VirG protein with an N54D substitution turned out to be able to induce a virB-lacZ reporter gene to a high level even in the absence of the inducer acetosyringone. A VirG protein with an I77V substitution exhibited almost no induction in the absence of acetosyringone but showed a maximum induction level already at low concentrations of acetosyringone.
Prevention of Nozzle Wear in Abrasive Water Suspension Jets (AWSJ) Using Porous Lubricated Nozzles (2002)

This paper introduces a novel method for preventing nozzle wear in abrasive water jets. It consists of using a porous nozzle, surrounded by a reservoir containing high-viscosity lubricant, which is exposed to the same driving pressure as the flow in the nozzle. The pressure difference across the porous medium, generated due to the high-speed flow in the nozzle, continuously forces lubricant through it. The resulting thin oil film forming on the walls of the nozzle protects the walls from the impact and shear caused by the abrasive particles. The porous nozzles were manufactured using Electric Discharge Machining and examined with Scanning Electron Microscopy. Two test facilities were used for evaluating the porous lubricated nozzles. The first was a two-dimensional facility, supporting a 145 μm wide nozzle with windows on both sides, which enabled visualization of the oil film and measurements of the liquid and abrasive-particle velocities using Particle Image Velocimetry. The measured slip velocities were also compared to computed values from a simple numerical model involving one-way coupling. The second facility used a 200 μm axisymmetric nozzle to determine the extent of nozzle wear under different conditions. We found that the presence of an oil film substantially reduced the extent of nozzle wear, from 111 percent of the diameter, when the nozzle was not lubricated, to 4 percent, when the oil viscosity was 1800 mm2/s and its flow rate was 2.4 percent of the water flow (over the same period). The wear increased as the lubricant flow rate and viscosity decreased. The presence of the oil film also improved the coherence of the jet.
The late‐flowering phenotype of FRIGIDA and mutations in LUMINIDEPENDENS is suppressed in the Landsberg erecta strain of Arabidopsis (1994)

Summary The late‐flowering phenotype of mutations in the LUMINIDEPENDENS (LD) gene and the late flowering caused by the naturally occurring dominant gene FRIGIDA (FRI) are suppressed in the Landsberg erecta (L er ) strain of Arabidopsis thaliana . This suppression is dependent on a locus on chromosome 5 designated FLC . Of the ecotypes tested, only the L er strain contains the suppressor allele of FLC; ld mutations and FRI cause late flowering in the other genetic backgrounds. The allele at FLC also has a moderate effect on flowering time in the absence of FRI or ld mutations. The flowering time effects of FLC are gene dosage dependent.
SableVM: a research framework for the efficient execution of java bytecode (2001)

SableVM is an open-source virtual machine for Java, intended as a r esearch framework for efficient execution of Java bytecode. The framework is essentially composed of an extensible bytecode interpreter using state-of-the-art and innovative techniques. Written in the C programming language, and assuming minimal system dependencies, the interpreter emphasizes high-level techniques to support efficient execution. In particular, we introduce new data layouts for classes, virtual tables and object instances that reduce the cost of interface method calls to that of normal virtual calls, allow ecient garbage collection and light synchronization, and make effective use of memory space.
Prescribing and using self-injectable antiretrovirals: How concordant are physician and patient perspectives? (2009)

Physician and patient beliefs about SIAT influence prescribing behavior and compliance yet may not be concordant, with patients having more positive attitudes towards SIAT than anticipated by physicians.
Switch from αvβ5 to αvβ6 integrin expression protects squamous cell carcinomas from anoikis (2004)

Stratified squamous epithelia express the alphavbeta5 integrin, but in squamous cell carcinomas (SCCs) there is down-regulation of alphavbeta5 and up-regulation of alphavbeta6. To investigate the significance of this finding, we transduced an alphav-negative human SCC line with retroviral vectors encoding alphav integrins. alphavbeta5-expressing cells underwent suspension-induced apoptosis (anoikis), whereas alphav-negative cells and cells expressing alphavbeta6 did not. Resistance to anoikis correlated with PKB/Akt activation in suspension, but not with changes in PTEN or p110alpha PI3 kinase levels. Anoikis was induced in parental and alphavbeta6-expressing cells by inhibiting PI3 kinase. Conversely, activation of Akt or inhibition of caspases in alphavbeta5-expressing cells suppressed anoikis. Caspase inhibition resulted in increased phosphoAkt, placing caspase activation upstream of decreased Akt activation. Anoikis required the cytoplasmic domain of beta5 and was independent of the death receptor pathway. These results suggest that down-regulation of alphavbeta5 through up-regulation of alphavbeta6 may protect SCCs from anoikis by activating an Akt survival signal.
Induced Pluripotent Stem Cells in Regenerative Medicine: An Argument for Continued Research on Human Embryonic Stem Cells (2009)

Human embryonic stem cells (ESCs) can be induced to differentiate into a wide range of tissues that soon could be used for therapeutic applications in regenerative medicine. Despite their developmental potential, sources used to generate human ESC lines raise serious ethical concerns, which recently prompted efforts to reprogram somatic cells back to a pluripotent state. These efforts resulted in the generation of induced pluripotent stem (iPS) cells that are functionally similar to ESCs. However, the genetic manipulations required to generate iPS cells may complicate their growth and developmental characteristics, which poses serious problems in predicting how they will behave when used for tissue-regenerative purposes. In this article we summarize the recently developed methodologies used to generate iPS cells, including those that minimize their genetic manipulation, and discuss several important complicating features of iPS cells that may compromise their future use for therapies in regenerative medicine.
Synthesis, Structure, and Reactivity of the Phosphinimide Complexes (t-Bu3PN)nMX4-n (M = Ti, Zr) (2000)

The phosphinimide complexes (t-Bu3PN)TiCl3 (1) and (t-Bu3PN)2TiCl2 (4) are readily prepared in high yields from the stoichiometric reaction of t-Bu3PNSiMe3 and TiCl4, while (t-Bu3PN)3TiCl (11) is readily obtained from the reaction of t-Bu3PNLi and TiCl4. The analogous 1:1 or 2:1 reactions of ZrCl4 and t-Bu3PNLi afford mixtures of products, although in the 3:1 stoichiometric ratio (t-Bu3PN)3ZrCl (12) is isolable. These complexes are readily alkylated with a variety of reagents to give (t-Bu3PN)TiMe3 (2), (t-Bu3PN)Ti(CH2Ph)3 (3), (t-Bu3PN)2TiMe2 (5), (t-Bu3PN)2Ti(η3-C3H5)2 (6), (t-Bu3PN)2Ti(CH2Ph)2 (7), (t-Bu3PN)2TiPh2 (8), (t-Bu3PN)2Ti(η5-Cp)Cl (9), (t-Bu3PN)2Ti(η5-Cp)Me (10), (t-Bu3PN)3TiMe (13), (t-Bu3PN)3TiPh (14), (t-Bu3PN)3ZrMe (15), (t-Bu3PN)3Zr(CH2Ph) (16), and (t-Bu3PN)3Zr(η5-Cp) (17). Subsequent reactions of some of these alkyl derivatives with [PhNMe2H][B(C6F5)4], [Ph3C][B(C6F5)4], or B(C6F5)3 are investigated. A number of zwitterionic and cationic species complexes have been characterized. These include [(t-Bu3PN)Ti(CH2Ph)2(PhCH2)B(C6F5)3] (18), [(t-Bu3PN)2TiMe(PMe3)][B(C6F5)4] (19), (t-Bu3PN)2TiMe (μ-MeB(C6F5)3) (20), (t-Bu3PN)2Ti(μ-MeB(C6F5)3)2 (21), and (t-Bu3PN)2Ti(C6F5)2 (22). The implications of this chemistry are considered. Structural data for 1, 4, 5, 12, 16, 21, and 22 are described.
Lamb Waves and Resonant Modes in Rectangular-Bar Silicon Resonators (2010)

This paper presents two newly developed models of capacitive silicon bulk acoustic resonators (SiBARs) characterized by a rectangular-bar geometry. The first model is derived from an approximate analytical solution of the linear elastodynamic equations for a parallelepiped made of an orthotropic material. This solution, which is recognized to represent a Lamb wave propagating across the width of the resonator, yields the frequencies and shapes of the resonance modes that typically govern the operation of SiBARs. The second model is numerical and is based on a finite-element multiphysics simulation of both acoustic wave propagation in the resonator and electromechanical transduction in the capacitive gaps of the device. It is especially useful in the computation of the SiBAR performance parameters, which cannot be obtained from the analytical model, e.g., the relationship between the transduction area and the insertion loss. Comparisons with the measurements taken on a set of silicon resonators fabricated using electron-beam lithography show that both models can predict the resonance frequencies of SiBARs with a relative error, which, in most cases, is significantly smaller than 1%.
(Invited) Aspect Ratio Trapping: A Unique Technology for Integrating Ge and III-Vs with Silicon CMOS (2010)

This paper describes the recent development of the Aspect Ratio Trapping (ART) heterointegration technique. This technique uses high aspect ratio sub-micron trenches to trap threading dislocations, greatly reducing the dislocation density of lattice mismatched materials grown on silicon. ART is shown to be very effective for a wide variety of materials including Ge, GaAs and InP. It has been combined with epitaxial lateral overgrowth to create long, 18 micron wide strips of low dislocation density material. ART has been used to integrate many types of Ge and III-V devices on silicon including GaAs MOSFETs, GaAs lasers, GaAs tunnel diodes and a silicon infrared imager chip with monolithically integrated Ge photodiodes.
The uneven distribution of family responsabilities between women and men, and its link with low fertility: some evidence for European Union countries from Eurobarometer data. (2004)

L¿Eurobaròmetre és una enquesta realitzada per la Unió Europea dues vegades a l¿any, que té com a finalitat conèixer l¿opinió dels ciutadans europeus. Aquesta enquesta, que cobreix tant els estats membres de la UE com els països candidats a l¿adhesió, té una mostra molt àmplia a escala europea. Cada enquesta inclou una sèrie de qüestionaris temàtics que cobreixen diversos temes d¿interès pels polítics de la UE. Per exemple, l¿Eurobaròmetre Estàndard 56.2 (2001) inclou un conjunt de preguntes sobre fecunditat ideal i efectiva a la UE-15. Aquestes preguntes es varen repetir al 2002 pels països candidats: com a conseqüència, es disposa de resultats per 25 països. Alguns Eurobaròmetres recents inclouen, a més a més, preguntes sobre la distribució de les responsabilitats familiars entre homes i dones. Aquesta investigació analitza aquests resultats per demostrar si existeix alguna relació entre baixa fecunditat i repartiment de tasques en un context en el que les dones estan incrementant la seva participació en el mercat de treball, però continuen encarregant-se de la majoria de les tasques reproductives.
Detection and segmentation of generic shapes based on affine modeling of energy in eigenspace (2001)

This paper presents a novel approach for detection and segmentation of man made generic shapes in cluttered images. The set of shapes to be detected are members of affine transformed versions of basic geometric shapes such as rectangles, circles etc. The shape set is represented by its vectorial edge map transformed over a wide range of affine parameters. We use vectorial boundary instead of regular boundary to improve the robustness to noise, background clutter and partial occlusion. Our approach consists of a detection stage and a verification stage. In the detection stage, we first derive the energy from the principal eigenvectors of the set. Next, an a posteriori probability map of energy distribution is computed from the projection of the edge map representation in a vectorial eigen-space. Local peaks of the posterior probability map are located and indicate candidate detections. We use energy/probability based detection since we find that the underlying distribution is not Gaussian and resembles a hypertoroid. In the verification stage, each candidate is verified using a fast search algorithm based on a novel representation in angle space and the corresponding pose information of the detected shape is obtained. The angular representation used in the verification stage yields better results than a Euclidean distance representation. Experiments are performed in various interfering distortions, and robust detection and segmentation are achieved.
Development of a Multifunctional Cosmetic Prosthetic Hand (2007)

An innovative artificial hand is presented, which can help to restore both motor and sensory capabilities of upper extremity amputees. All requisite components of the revolutionary prosthesis fit into the small volume of the metacarpus. A new high-power actuating technology has been developed for maximizing the benefit in using the prosthetic hand by increasing the number of grasping patterns. An optional sensory feedback system has been designed for the prosthesis, which is based on mechanical vibration. First clinical trials with the prosthetic hand revealed a high acceptance, as the force necessary to hold an object securely was reduced significantly.
High speed spectral domain polarization sensitive optical coherence tomography of the human retina (2005)

We developed a high-speed polarization sensitive optical coherence tomography (PS-OCT) system for retinal imaging based on spectral domain OCT. The system uses two spectrometers, one for each polarization channel, that operate in parallel at 20000 A-lines/s each. It provides reflectivity, retardation, and cumulative optic axis orientation simultaneously. We present our instrument and discuss the requirements for the alignment of the two spectrometers specific for our setup. We show 2D spectral domain PS-OCT images and - to the best of our knowledge - the first 3D spectral domain PS-OCT data sets in form of fly-through movies and volume rendered data sets recorded in human retina in vivo.
A dual-drive Ti:LiNbO/sub 3/ Mach-Zehnder modulator used as an optoelectronic logic gate for 10-Gb/s simultaneous multiplexing and modulation (1992)

A dual-drive Ti:LiNbO/sub 3/ Mach-Zehnder modulator is used as an optoelectronic exclusive-OR gate. The logic capability is employed for simultaneously multiplexing and encoding two electrical 5-Gb/s signals on an optical beam. Demultiplexing schemes for differentially encoded signals involving optical or electrical time demultiplexing are presented. The dual-drive modulator offers a simple and relatively inexpensive way of encoding a 10-Gb/s pseudorandom bit string using one 5-Gb/s pattern generator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antipsychotic Augmentation of Serotonin Reuptake Inhibitors in Treatment-Resistant Obsessive-Compulsive Disorder: An Update Meta-Analysis of Double-Blind, Randomized, Placebo-Controlled Trials (2015)

Background: Many patients with obsessive-compulsive disorder do not respond adequately to serotonin reuptake inhibitors. Augmentation with antipsychotic drugs can be beneficial in this regard. However, since new relevant randomized controlled trials evaluating new antipsychotics were conducted, a recalculation of the effect sizes appears necessary. Methods: We meta-analyzed all double-blind, randomized, placebo-controlled trials comparing augmentation of serotonin reuptake inhibitors with antipsychotics to placebo supplementation in treatment-resistant obsessive-compulsive disorder. The primary outcome was mean change in the Yale-Brown Obsessive-Compulsive Scale total score. Secondary outcomes were obsessions, compulsions, response rates, and attrition rates. The data collection process was conducted independently by 2 authors. Hedges's g and risks ratios were calculated as effect sizes. In preplanned meta-regressions, subgroup analyses, and sensitivity analyses, we examined the robustness of the results and explored reasons for potential heterogeneity. Results: Altogether, 14 double-blind, randomized, placebo-controlled trials (n = 491) investigating quetiapine (N = 4, n = 142), risperidone (N = 4, n = 132), aripiprazole (N = 2, n = 79), olanzapine (N = 2, n = 70), paliperidone (N = 1, n = 34), and haloperidol (N = 1, n = 34) were incorporated. Augmentation with antipsychotics was significantly more efficacious than placebo in Yale-Brown Obsessive-Compulsive Scale total reduction (N = 14, n = 478; Hedges's g = -0.64, 95% CI: -0.87 to -0.41; P = <.01). Aripiprazole (Hedges's g = -1.35), haloperidol (Hedges's g = -0.82), and risperidone (Hedges's g = -0.59) significantly outperformed placebo. Antipsychotics were superior to placebo in treating obsessions, compulsions, and achieving response. There was no betweengroup difference concerning all-cause discontinuation. The nonsignificant meta-regressions suggest no influence of the antipsychotic dose or baseline symptom severity on the meta-analytic results. Conclusions: According to our findings, antipsychotic augmentation of serotonin reuptake inhibitors can be regarded as an evidence-based measure in treatment-resistant obsessive-compulsive disorder.
Characterization of Generalized Transducing Phage φw39 Heteroimmune to Phage P1 in Escherichia coli W39 (1984)

Generalized transducing phage similar to phage P1 in Escherichia coli was isolated from E. coli W39, an antigenic test strain of the O121 group. This phage, designated phi w39, was reciprocally heteroimmune to phages P1 and P7, but nonreciprocally heteroimmune to phage D6. Transduction experiments using various R plasmids with different molecular weights suggested that phage phi w39 could transduce at least 65 megadaltons DNA. As in the case of P1 prophage, phi w39 prophage existed as a plasmid belonging to incompatibility group Y and carried a dnaB-like function. The molecular weight of phi w39 plasmid was nearly the same as that of plasmid, i.e., 58.6 megadaltons. Despite the pronounced structural and functional similarity of phages phi w39 and P1, restriction cleavage patterns of their genomes differed considerably.
Novel therapies in lupus - focus on nephritis. (2008)

Lupus nephritis (LN) is one of the major complications of Systemic Lupus Erythematosus (SLE) and its treatment remains a challenge. Although the classical and widely used immunosuppressive agents have accounted for a significant improvement in the survival and decreased the progression to end-stage renal failure they lack selectivity for the underlying immune dysregulation. In addition the toxicity related to their use and the relapses after treatment are of major concern not least because of the adverse effect on the prognosis of the patients with SLE who have kidney involvement. The development of more specific pharmacological agents for patients with SLE is still a major research goal. Ideally these agents should provide a better long-term prognosis for SLE patients and be less toxic. In this review we summarise the mechanism of action and the results obtained with a variety of drugs that have recently been utilized in the treatment of patients with lupus especially those with nephritis. We discuss the clinical usefulness of B- -cell depletion principally anti-CD20 antibodies blockage of co-stimulatory pathways (anti-CD40 ligand antibody CTLA4Ig) the induction of immune tolerance (LJP 394 peptide specific vaccination) and therapy targeting cytokines (anti-IL10 antibody BLyS blockage) and the complement system (anti-C5 antibody). Immunoablative doses of Cyclophosphamide (CyC) with or without Haematopoietic Stem Cell Transplantation (HSCT) and the possibilities of gene therapy are also reviewed. The use of intravenous immunoglobulin (IVIg) and plasmapheresis are not discussed because these treatments have been used in clinical practice for several years.
A controlled trial of naltrexone in obese humans. (1985)

Based on reports that opiate antagonists can curtail short-term eating in several species including humans, the efficacy of naltrexone in promoting weight loss by obese subjects was examined. Naltrexone, a long-acting oral opiate antagonist, was studied in a randomized parallel double-blind placebo controlled ten week trial in 27 females and 14 males who were 30-100 percent overweight. Subjects on naltrexone lost an average of 1.8 kg and placebo subjects lost 1.5 kg, with no significant difference between groups. Three subjects who took naltrexone had elevations of liver transaminases, two times higher than normal. In the present study naltrexone at a daily dosage of 200 mg did not appear to have efficacy in producing weight loss after eight weeks of treatment. Studies of the effects of naltrexone at higher dosage or for longer periods should monitor hepatic function.
Natural Language Understanding (2021)

From the Publisher:
In addition, this title offers coverage of two entirely new subject areas. First, the text features a new chapter on statistically-based methods using large corpora. Second, it includes an appendix on speech recognition and spoken language understanding. Also, the information on semantics that was covered in the first edition has been largely expanded in this edition to include an emphasis on compositional interpretation.
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data (2011)

A program implemented in Java, Zinfandel, is available at http://www.cs.columbia.edu/~itsik/zinfandel/
Amino Acid Sequence of Bovine Glucagon (1971)

Bovine glucagon has been found to have the same amino acid sequence as porcine glucagon. This result is unusual from the standpoint of absolute conservation of primary structure.
Constitutively Active Adenosine Monophosphate–Activated Protein Kinase Regulates Voltage-Gated Sodium Channels in Ventricular Myocytes (2003)

We propose that sodium channels may be substrates for AMPK, possibly contributing to the observed arrhythmogenic activity in patients with some PRKAG2 mutations.