gebhart/patrepeval huggingface dataset:
A corpus-based approach to help-desk response generation (2006)

We are developing a corpus-based approach for the prediction of help-desk responses from features in customers' emails, where responses are represented at two levels of granularity: document and sentence. We present an automatic evaluation of the responses generated by our system, as well as a manual one involving human judges. The automatic evaluation involves textual comparisons between generated responses and responses composed by the help-desk operators. The results show that both levels of granularity produce good responses, addressing inquiries of different kinds. The human-based evaluation measures response in- formativeness, and confirms our conclusion that both levels of granularity produce useful responses.
Microtechnology: Meet neurobiology (2006)

The field of neuroscience has always been attractive to engineers. Neurons and their connections, like tiny circuit elements, process and transmit information in a dramatic way that is intimately curious to researchers in the computer science and engineering fields. Of particular interest has been the recent push in applying microtechnology to the field of neuroscience. This review is meant to provide an overview of some of the subtle nuances of the nervous system and outline recent advances in lab on a chip applications in neurobiology. It also aims to highlight some of the challenges the field faces in the hopes of encouraging new engineering researchers to collaborate with neurobiologists to help advance our basic understanding of the nervous system and create novel applications based on neuroengineering principles.
A Sharp Photocurrent Enhancement in Photoelectrochemical Cells with a Photocathode Sensitized by Dye Films of Rhodamine-C18 and Methylviolet-C18 Prepared by Langmuir-Blodgett Techniques (1995)

It was found that the photocurrent quantum efficiency of photoelectrochemical cells with p-CuSCN photo-cathode sensitized with double dye layers such as Rhodamine- C 18 and Methylviolet- C 18 is greatly enhanced (∼15%), when the double dye system is prepared using Langmuir-Blodgett (LB) technique. An ordered arrangement of dye molecules in LB films provides a suitable condition to transfer photogenerated holes and electrons between two dye layers, so that photogenerated holes upon excitation can transfer effectively into the valence band of p-CuSCN.
Detecting Associations Between Knee Rotational Laxity and Kinematics in a Healthy Population (2013)

Passive knee laxity, which is determined by the soft tissues and articular structures of the knee, allows for the translation and rotation of the knee 1. While laxity increases following soft tissue injury, there is a lack of clinical evidence demonstrating a relationship between increased passive laxity and subsequent clinical problems such as osteoarthritis. However, there is increasing evidence that abnormal active rotational kinematics during walking are a potential risk factor for osteoarthritis (OA) initiation and progression 2. Establishing a relationship between passive knee laxity and active knee kinematics is therefore clinically important, but at present there is a paucity of information on the interaction between passive and active knee rotational movement.
High‐Resolution Multi‐Contrast MRI of the Carotid Artery Wall for Evaluation of Atherosclerotic Plaques (2003)

Abstract Carotid atherosclerosis is an important medical condition associated with a high potential risk of stroke. In addition to the degree of artery stenosis, the size and tissue composition of the atherosclerotic plaque are thought to be important factors for disease management and prognosis. This unit presents a protocol for high‐resolution multi‐contrast MRI of the carotid artery wall. The protocol employs a combination of bright‐blood magnetic resonance angiography and black‐blood imaging with different contrast weightings (T1, T2, and proton‐density contrasts) in order to provide comprehensive characterization of the atherosclerotic lesion. The images obtained with the protocol presented here can be used to identify basic tissue components of the atherosclerotic plaque (fibrous matrix, lipid core, calcificates, and hemorrhage) and to conduct morphological measurements of plaque size and distribution.
Inducible expression of human hepatitis B virus (HBV) in stably transfected hepatoblastoma cells: a novel system for screening potential inhibitors of HBV replication (1997)

We report the development and isolation of a cell line, termed HepAD38, that replicates human hepatitis B virus (HBV) under conditions that can be regulated with tetracycline. In the presence of the antibiotic, this cell line is free of virus due to the repression of pregenomic (pg) RNA synthesis. Upon removal of tetracycline from the culture medium, the cells express viral pg RNA, accumulate subviral particles in the cytoplasm that contain DNA intermediates characteristic of viral replication, and secrete virus-like particles into the supernatant. Since the HepAD38 cell line can produce high levels of HBV DNA, it should be useful for analyses of the viral replication cycle that depend upon viral DNA synthesis in a synchronized fashion. In addition, this cell line has been formatted into a high-throughput, cell-based assay that permits the large-scale screening of diverse compound libraries for new classes of inhibitors of HBV replication.
Retraction for Zehorai and Seger, “Beta-Like Importins Mediate the Nuclear Translocation of Mitogen-Activated Protein Kinases” (2018)

Volume 34, no. 2, p. 259–270, 2014, [https://doi.org/10.1128/MCB.00799-13][1]. We retract this article. After a recent correction of some figures (E. Zehorai and R. Seger, Mol Cell Biol 37:e00215-17, 2017, [https://doi.org/10.1128/MCB.00215-17][2]), we were made aware of additional problems,
An ultrasensitive electrochemiluminescence biosensor for multiple detection of microRNAs based on a novel dual circuit catalyzed hairpin assembly (2018)

A novel double-hairpin DNA inducing a dual circuit catalyzed hairpin assembly (DC-CHA) strategy was proposed to fabricate electrochemiluminescence (ECL) biosensors for multiple target (microRNA-21 and microRNA-155) ultrasensitive detection.
[Comparison of the radial and femoral arterial approaches for coronary angioplasty in acute myocardial infarction]. (2004)

In patients with acute myocardial infarction treated with coronary angioplasty, the transradial access is efficacious with fewer major access site complications than transfemoral access. Transradial approach produces a shorter length of stay, as compared to the transfemoral approach although with longer times of radiation and higher dose area-product.
Implementing Quality Service-Learning Programs in Community Colleges (2013)

This cross-case comparative study at Western Community College and the University of the Coast explored through a constructive lens the characteristics that lead to sustainable, high quality service-learning programs and how they are implemented at institutions of higher education. The researchers determined that both Western Community College and the University of the Coast (a) have diverse collaborative partnerships that promote excellent communication between all of the entities, (b) offer a wide variety of service-learning courses to connect curricular and cocurricular experiences, (c) have a stable funding base, (d) provide the necessary resources, (e) have continuity in staffing, and (f) incorporate feedback and assessment into their respective service-learning programs. The findings from this study, based on one-on-one interviews, focus groups, observations, and document analysis, serve as a model on how to create quality and sustainable service-learning programs that combine academic scholarship, off-campus learning discoveries, reflection, civic engagement, and meaningful community service. The research may be applicable for educators at community colleges at various stages in developing service-learning programs, or who are transforming faltering programs, trying to make them sustainable.
A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides (2019)

We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, <sup>15</sup>N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
Preliminary Evidence for Techniques Used to Optimally Align (Tune) Fixed Ankle-Foot Orthoses in Children (2011)

In Brief An angle of 10° to 12° incline between the anterior border of the tibia (shank) and the vertical (SAV) at mid-midstance has been recommended as a starting point from which the “moment arm” at the knee can be optimized (tuned) in children wearing fixed ankle-foot orthoses. The aim of this study was to document the SAV and “moment arm” at the knee throughout stance in normally developing children. Data were collected from 11 healthy children aged 5 to 16 years, and SAV and “moment arm” at the knee plotted throughout stance, both barefoot and shod. The mean (standard deviation) SAV at mid-midstance was 11.4° (3.4°) barefoot and 10.5° (3.6°) shod. The mean (standard deviation) “moment arm” at the knee (normalized to leg length) at mid-midstance was 2.5% (1.7%) barefoot and 1.3% (2.4%) shod. The study provides preliminary evidence for current tuning techniques. An angle of 10–12° incline between the anterior border of the tibia (shank) and the vertical (SAV) at mid-midstance has been recommended as a starting point from which the moment arm at the knee can be optimized (tuned) in children wearing fixed ankle-foot orthoses (AFOs). The aim of this study was to document the SAV and moment arm at the knee throughout stance in normally developing children. This preliminary study identifies patterns of the SAV and moment arm at the knee, throughout stance in this population. Measures of moment arm at the knee were similar to previously published work from smaller cohorts, indicating that its use as an outcome measure for tuning may be appropriate, especially if measures are taken over more than one gait cycle.
Synthetic-Aperture Radar Based on Nonsinusoidal Functions: VI-Pulse-Position and Pulse-Shape Coding (1980)

Previous papers of this series have used coded radio signals with desirable features, without explaining how these signals were obtained. This paper supplies the explanation. The concept of coding is generalized from the baseband signals, modulated onto sinusoidal carriers, to the radio signals actually transmitted. The conventional radar signals have coded baseband signals, which are referred to as the fine structure of the radar signals, while the carrier, referred to as the hyperfine structure, has always sinusoidal time variation. The more general radio signals discussed here have both a coded fine structure and hyperfine structure. Two classic problems of radar are readily solved by this generalized coding. 1) A class of signals is derived that approaches the ideal thumbtack ambiguity function in the range-Doppler domain as closely as one wants to. 2) The same class of signals makes it possible to increase the average-to- peak power ratio significantly over that achievable with frequency- modulated sinusoidal carriers. An estimate of the number of terms of a Fourier-series expansion of the signals, as well as the number of components of each term, is given; this estimate shows that a Fourier representation is too complicated for practical purposes, but also that the signals are ideal for frequency-sharing and spread-spectrum transmission.
A Fourier descriptor model of hysteresis loops for sinusoidal and distorted waveforms (1997)

This work is concerned with the use of the Fourier descriptor technique for reproducing the hysteresis loop for both sinusoidal and distorted flux-density waveforms that produce minor hysteresis loops. The hysteresis curve is characterized only at discrete points. Approximating the curve by a polygon with a limited number of sides, the Fourier series coefficients of the normalized cumulative angular function are computed. The shape of the hysteresis loop for a pure sinusoidal waveform can be reconstructed easily when these coefficients are determined. The procedure can be extended for the distorted waveform by taking account of the dips in the exiting waveform that cause minor loops in the hysteresis curve. The deviation between the original curve and the generated one depends upon the number of Fourier coefficients. As the number of the Fourier coefficients used in the synthesis is increased, the generated curve becomes closer to the original one. However, the use of a large number of the Fourier coefficients requires a greater execution time.
Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks (2008)

These findings establish a functional link between two previously unrelated genes. Microarray analysis indicates that sticky and dFmr1 are both required for regulation of many developmental genes in a variety of cell types. The diversity of transcripts regulated by these two genes suggests a clear cause of the pleiotropy that sticky and dFmr1 mutants display and provides many novel, testable hypotheses about the functions of these genes. As both of these genes are implicated in the development and function of the mammalian brain, these results have relevance to human health as well as to understanding more general biological processes.
Penile Plication Using the 16-Dot Technique (2007)

Peyronie’s disease, characterized by the formation of a fibrous plaque within the tunica albuginea of the corpora cavernosa, has long caused sexual dysfunction. Plication surgery has allowed a simple technique to correct the penile curvature caused by Peyronie’ s disease. The 16-dot plication technique corrects the penile curvature with a high level of patient satisfaction and yet can be performed under local anesthesia. Slight adjustments can be made during the procedure, which allows greater precision toward penile strengthening. The 16-dot penile plication procedure has an 85% long-term success rate for achieving a straight erection by patient reporting. Minimal complications are reported, with penile shortening (0.5–1.5 cm) reported at 41%. With a mean operative time of 45 min and the ability to perform the procedure under local anesthesia, the 16-dot plication procedure is an important tool for the urologist for treatment of Peyronie’s disease.
Average Modeling and Hybrid Control of a Three-Phase Series Hybrid Power Filter (2006)

This paper presents a detailed study of a series hybrid power filter (SHPF). The system consists of a small-rated series active power filter and a series tuned passive filter. This combination is suitable for compensating voltage type harmonics-producing load. The hybrid control approach adopted is based on detecting both source current and load voltage harmonics. This technique enhances the compensation characteristics of the proposed system. A low-frequency mathematical model of the series hybrid filter is established. The elaboration of the control law is based on a small-signal averaged model of the converter, computed in the (d,q) synchronous frame. Then, suitable multiple-loops PI controllers are designed on the basis of the system's transfer functions and the use of the linear feedback control. Simulation results are shown in an attempt to verify the mathematical model of the filter and the effectiveness of the hybrid control approach for voltage harmonics compensation
Calcium Channel Blockers Suppress Cytokine-induced Activation of Human Neutrophils (2007)

These findings suggest that (i) some calcium channel blockers can suppress cytokine-induced neutrophil activation, leading to possible prevention of the progression of atherosclerosis; and (ii) that activation of the ERK and phosphatidylinositol 3-kinase (PI3K)/Akt pathways, induced by TNF-alpha but not by GM-CSF, is selectively affected by some blockers.
Structure and Expression of the Human L- myc Gene Reveal a Complex Pattern of Alternative mRNA Processing (1988)

We analyzed in detail the structure of the L-myc gene isolated from human placental DNA and characterized its expression in several small-cell lung cancer cell lines. The gene is composed of three exons and two introns spanning 6.6 kilobases in human DNA. Several distinct mRNA species are produced in all small-cell lung cancer cell lines that express L-myc. These transcripts are generated from a single gene by alternative splicing of introns 1 and 2 and by use of alternative polyadenylation signals. In some mRNAs there is a long open reading frame with a predicted translated protein of 364 residues. Amino acid sequence comparison with c-myc and N-myc demonstrated multiple discrete regions with extensive homology. In contrast, other mRNA transcripts, generated by alternative processing, could encode a truncated protein with a novel carboxy-terminal end.
Analysis of the major Auger transitions in CO andCO2with the use of the self-consistent-fieldXαmultiple-scattering method (1984)

The two-hole final-state binding energies for the major Auger transitions in CO and ${\mathrm{CO}}_{2}$ are calculated with the use of the self-consistent-field $X\ensuremath{\alpha}$ multiple-scattering (SCF-$X\ensuremath{\alpha}$-MS) method. A simple modification of Slater's transition-state approach is used, and the results give essentially the same degree of agreement with experiment as more first-principles Hartree-Fock methods. The relative transition intensities for the $\mathrm{C}(\mathrm{KVV})$ and the $\mathrm{O}(\mathrm{KVV})$ spectra are calculated and compared both with experimental measurements and Hartree-Fock calculations. The utility of the method lies in the ease to which it can be applied to more-complex systems such as large molecules and clusters of atoms simulating molecules absorbed on surfaces.
Chlamydia trachomatis Oligopeptide Transporter Performs Dual Functions of Oligopeptide Transport and Peptidoglycan Recycling (2020)

Peptidoglycan, the sugar-amino acid polymer that composes the bacterial cell wall, requires a significant expenditure of energy to synthesize and is highly immunogenic. To minimize the loss of an energetically expensive metabolite and avoid host detection, bacteria often recycle their peptidoglycan, transporting its components back into the cytoplasm, where they can be used for subsequent rounds of new synthesis. The peptidoglycan-recycling substrate binding protein (SBP) MppA, which is responsible for recycling peptidoglycan fragments in <i>Escherichia coli</i>, has not been annotated for most intracellular pathogens. One such pathogen, <i>Chlamydia trachomatis</i>, has a limited capacity to synthesize amino acids <i>de novo</i> and therefore must obtain oligopeptides from its host cell for growth. Bioinformatics analysis suggests that the putative <i>C. trachomatis</i> oligopeptide transporter OppABCDF (OppABCDF <i><sub>Ct</sub></i> ) encodes multiple SBPs (OppA1 <i><sub>Ct</sub></i> , OppA2 <i><sub>Ct</sub></i> , and OppA3 <i><sub>Ct</sub></i> ). Intracellular pathogens often encode multiple SBPs, while only one, OppA, is encoded in the <i>E. coli</i><i>opp</i> operon. We hypothesized that the putative OppABCDF transporter of <i>C. trachomatis</i> functions in both oligopeptide transport and peptidoglycan recycling. We coexpressed the putative SBP genes (<i>oppA1<sub>Ct</sub></i> , <i>oppA2<sub>Ct</sub></i> , <i>oppA3<sub>Ct</sub></i> ) along with <i>oppBCDF<sub>Ct</sub></i> in an <i>E. coli</i> mutant lacking the Opp transporter and determined that all three chlamydial OppA subunits supported oligopeptide transport. We also demonstrated the <i>in vivo</i> functionality of the chlamydial Opp transporter in <i>C. trachomatis</i> Importantly, we found that one chlamydial SBP, OppA3 <i><sub>Ct</sub></i> , possessed dual substrate recognition properties and is capable of transporting peptidoglycan fragments (tri-diaminopimelic acid) in <i>E. coli</i> and in <i>C. trachomatis</i> These findings suggest that <i>Chlamydia</i> evolved an oligopeptide transporter to facilitate the acquisition of oligopeptides for growth while simultaneously reducing the accumulation of immunostimulatory peptidoglycan fragments in the host cell cytosol. The latter property reflects bacterial pathoadaptation that dampens the host innate immune response to <i>Chlamydia</i> infection.
Release of mitochondrial Ca2 via the permeability transition activates endoplasmic reticulum Ca2 uptake (2001)

SPECIFIC AIMSRegulatory interactions between the endoplasmic reticulum (ER) and the mitochondria in the control of intracellular free Ca2+ [Ca2+]i may be important in the control of many cell functions, especially those involved in initiating cell death. We used targeted Ca2+ sensors (cameleons) to investigate the movement of Ca2+ between the ER and mitochondria of intact cells and focused on the role of the mitochondrial permeability transition (MPT) in this interaction. We hypothesized that release of Ca2+ from mitochondria in response to a known MPT agonist (atractyloside) would cause release of ER Ca2+, perpetuating cellular Ca2+ overload and cell death.PRINCIPAL FINDINGS1. Targeting and Ca2+ sensitivity of cameleonsThe cDNA for yellow cameleon 2.1 (YC2.1) and ER targeted cameleon-3ER (Cam3ER) were provided by Roger Tsien (Howard Hughes Medical Institute, University of California, San Diego). We constructed a mitochondrial targeted YC2.1 (YC2.1mito) by amplifying YC2.1 from pCDNA3 by PCR and subclonin...