gebhart/patrepeval huggingface dataset:
Generic support for caching and disconnected operation (2002)

Current systems use caching to provide high performance and possibly support disconnected operation. However, current solutions are type specific. With the advent of modular distributed operating systems and mobile machines there is a need to provide generic support for implementing cacheable/disconnectable services. We present an architecture that can be used to implement cacheable/disconnectable services of any type. In addition we present the implementation of this architecture on the Spring operating system. We have used this architecture for implementing file caching and are currently working on other caching implementations and providing support for disconnected operation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sensitive, Seminested PCR Amplification of VP1 Sequences for Direct Identification of All Enterovirus Serotypes from Original Clinical Specimens (2006)

A reverse transcription-seminested PCR (RT-snPCR) assay was developed for the detection and identification of enterovirus (EV) RNA in clinical specimens. Three conserved protein motifs were identified by aligning the VP3 and VP1 sequences of prototype EV strains. Consensus degenerate primers were designed from a conserved VP3 motif and a distal VP1 motif for the first PCR. Consensus-degenerate hybrid oligonucleotide primers were designed from an internal VP1 motif and used with the same distal VP1 motif for the second, seminested PCR step. The primers were designed for broad target specificity and amplified all recognized and proposed EV serotypes and other antigenic variant strains tested. The VP1 RT-snPCR assay was slightly more sensitive than our in-house EV 5' nontranslated region RT-snPCR assay, detecting as few as 10 RNA copies per reaction. As an example application, the VP1 RT-snPCR assay was used to identify EVs in clinical specimens. A product of the expected size was successfully amplified and sequenced from cerebrospinal fluid; serum; stool suspensions; and nasopharyngeal, eye, and rectal swab specimens, allowing unambiguous identification of the infecting virus in all cases. The VP1 sequences derived from the RT-snPCR products allow rapid phylogenetic and molecular epidemiologic analysis of strains circulating during the EV season and comparison with EV sequences from past seasons or from different locations around the world.
Association between CARD8 rs2043211 Polymorphism and Inflammatory Bowel Disease: A Meta-Analysis (2015)

Our meta-analysis results indicated significant association between rs2043211 polymorphism and the susceptibility to CD under the dominant model and homozygote contrast in the European population.
Apoptosis in fetal nucleated erythrocytes circulating in maternal blood (2000)

The purpose of this study was to determine if apoptosis occurs in fetal cells that have crossed into the maternal circulation, which would potentially explain the difference between the number of intact fetal cells and the amount of fetal DNA detectable in maternal plasma. We flow-sorted fetal nucleated erythrocytes (FNRBCs) using antibody to the gamma chain of fetal haemoglobin and confirmed them to be fetal in origin by FISH analysis using chromosome-specific probes. Fetal cells were then analysed microscopically for the presence of terminal UdTP nuclear end labelling (TUNEL) staining. Apoptotic change was observed in 42.7% of fetal NRBCs (106/246) and 3.5% of maternal cells (29/818). Results of this study indicate that a significant number of fetal cells in maternal blood are undergoing apoptosis at the time of sampling. Apoptosis may be one mechanism by which fetal cells are cleared by the maternal circulation. Copyright © 2000 John Wiley & Sons, Ltd.
Determination of birefringence and absolute optic axis orientation using polarization-sensitive optical coherence tomography with PM fibers (2003)

A novel polarization-sensitive optical coherence tomography (PS-OCT) system was developed using polarization maintaining (PM) optical fibers and fiber coupler to measure birefringence properties of samples. Polarization distortion due to PM fibers and coupler can be calibrated with different polarization states during two consecutive A-scans. By processing the analytical interference fringe signals derived from two orthogonal polarization detection channels, the system can be used to measure phase retardation and optic axis orientation. Standard wave plates with different orientation and retardation were used as samples to test the system and calibrating method. We have also applied this system to image biological sample such as beef tendon.
Automated creation of clinical-practice guidelines from decision models (1998)

Development of effective clinical-practice guidelines (CPGs) requires input from experts in clinical medicine and in evidence synthesis; at the local level, such resources often are not available, or are prohibitively costly. Global CPGs may need to be adapted to local settings. In addition, traditional guidelines are normally static and thus may become out of date.
I developed a new approach that allows CPG developers to create, disseminate, and tailor CPGs, using normative decision models (DMs). I propose that guideline developers can use computer-based DMs that reflect known global and site-specific data to generate CPGs. Such CPGs are of high quality, can be tailored to specific clinical settings, and can be modified automatically over time as the underlying DM or evidence evolves.
To validate this hypothesis, I defined conceptual models for representing CPGs and DMs, and formalized a method for mapping between these two representations. To make this mapping possible, I designed a DM annotation editor that queries the decision analyst for missing knowledge. I describe implementation of the ALCHEMIST system that encompasses these two conceptual models, the mapping algorithm, and the resulting tailoring abilities.
I evaluated my thesis work in three ways. First, to show that the DM conceptual model and DM annotation editor provide information necessary for the efficient transformation of a DM into a CPG, I evaluated the design of both conceptual models, and demonstrated the accuracy of the mapping algorithm. Second, to show that ALCHEMIST produces CPGs that satisfy criteria for high-quality guidelines, I had guideline users rate the quality of produced CPGs using a guideline-rating key and the performance of ALCHEMIST's CPG browser. Finally, I evaluated ALCHEMIST's tailoring abilities.
Because it creates CPGs from normative DMs, ALCHEMIST can specify explicitly the alternatives, outcomes, and evidence in a clinical problem. ALCHEMIST automates the DM-to-CPG process and distributes the produced CPG over the web to allow guideline developers at local sites to apply, tailor, and maintain a globally produced CPG. I argue that my DM-to-CPG framework is a method for guideline developers to create and maintain automated CPGs, and that it thus promotes high-quality and cost-effective health care.
Expression of antibiotic resistance genes in the integrated cassettes of integrons (1995)

Plasmids containing cloned integron fragments which differ only with respect to either the sequence of the promoter(s) or the number and order of inserted cassettes were used to examine the expression of resistance genes encoded in integron-associated gene cassettes. All transcripts detected commenced at the common promoter P(ant), and alterations in the sequence of P(ant) affected the level of resistance expressed by cassette genes. When both P(ant) and the secondary promoter P2 were present, transcription from both promoters was detected. When more than one cassette was present, the position of the cassette in the array influenced the level of antibiotic resistance expressed by the cassette gene. In all cases, the resistance level was highest when the gene was in the first cassette, i.e., closest to P(ant), and was reduced to different extents by the presence of individual upstream cassettes. In Northern (RNA) blots, multiple discrete transcripts originating at P(ant) were detected, and only the longer transcripts contained the distal genes. Together, these data suggest that premature transcription termination occurs within the cassettes. The most abundant transcripts appeared to contain one or more complete cassettes, and is possible that the 59-base elements found at the end of the cassettes (3' to the coding region) not only function as recombination sites but may also function as transcription terminators.
AAV-mediated factor IX gene transfer to skeletal muscle in patients with severe hemophilia B (2003)

Hemophilia B is an X-linked coagulopathy caused by absence of functional coagulation factor IX (F.IX). Previously, we established an experimental basis for gene transfer as a method of treating the disease in mice and hemophilic dogs through intramuscular injection of a recombinant adeno-associated viral (rAAV) vector expressing F.IX. In this study we investigated the safety of this approach in patients with hemophilia B. In an open-label dose-escalation study, adult men with severe hemophilia B (F.IX < 1%) due to a missense mutation were injected at multiple intramuscular sites with an rAAV vector. At doses ranging from 2 x 10(11) vector genomes (vg)/kg to 1.8 x 10(12) vg/kg, there was no evidence of local or systemic toxicity up to 40 months after injection. Muscle biopsies of injection sites performed 2 to 10 months after vector administration confirmed gene transfer as evidenced by Southern blot and transgene expression as evidenced by immunohistochemical staining. Pre-existing high-titer antibodies to AAV did not prevent gene transfer or expression. Despite strong evidence for gene transfer and expression, circulating levels of F.IX were in all cases less than 2% and most were less than 1%. Although more extensive transduction of muscle fibers will be required to develop a therapy that reliably raises circulating levels to more than 1% in all subjects, these results of the first parenteral administration of rAAV demonstrate that administration of AAV vector by the intramuscular route is safe at the doses tested and effects gene transfer and expression in humans in a manner similar to that seen in animals.
A Critical Evaluation of the PAXgene Tissue Fixation System (2016)

While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.
Drug-Related Hepatotoxicity (2006)

Given its rarity, drug-related hepatotoxicity may not be seen during the initial clinical trials of a new medication. After approval, when many more patients are exposed, toxic effects that are very infrequent may emerge. This review explains the difficulties in identifying the cause of hepatotoxic effects in such situations and provides clinical guidance with regard to the detection, evaluation, and possible prevention of drug-related hepatotoxicity.
A Practical and Configurable Lip Sync Method for Games (2013)

We demonstrate a lip animation (lip sync) algorithm for real-time applications that can be used to generate synchronized facial movements with audio generated from natural speech or a text-to-speech engine. Our method requires an animator to construct animations using a canonical set of visemes for all pairwise combinations of a reduced phoneme set (phone bigrams). These animations are then stitched together to construct the final animation, adding velocity and lip-pose constraints. This method can be applied to any character that uses the same, small set of visemes. Our method can operate efficiently in multiple languages by reusing phone bigram animations that are shared among languages, and specific word sounds can be identified and changed on a per-character basis. Our method uses no machine learning, which offers two advantages over techniques that do: 1) data can be generated for non-human characters whose faces can not be easily retargeted from a human speaker's face, and 2) the specific facial poses or shapes used for animation can be specified during the setup and rigging stage, and before the lip animation stage, thus making it suitable for game pipelines or circumstances where the speech targets poses are predetermined, such as after acquisition from an online 3D marketplace.
Methylation of CpG in a small region of the hMLH1 promoter invariably correlates with the absence of gene expression. (1999)

Microsatellite instability (MSI) has been described in tumors from patients with hereditary nonpolyposis colorectal cancer, sporadic colorectal cancer, and other types of cancers. MSI is caused by the dysfunction of mismatch repairs genes. Loss of expression and mutation in one of the major mismatch repair genes, hMLH1, and the methylation of CpG sites in its promoter occur frequently in primary tumors and cell lines of colorectal cancer with MSI. To understand the mechanisms involved in the silencing of hMLH1 expression by methylation, we examined the methylation status of all CpG sites in the hMLH1 promoter in 24 colorectal cancer cell lines by the NaHSO3-sequencing method. We identified a small proximal region (-248 to -178, relative to the transcription start site) in the promoter in which the methylation status invariably correlates with the lack of hMLH1 expression. This correlation was further supported by the observation that cell lines that showed methylation-suppressed hMLH1 expression can be induced to reexpress hMLH1 by a methyl transferase inhibitor, 5-aza-2'-deoxycytidine, and the small region that we identified exhibited significant demethylation in all cell lines examined.
Parameterization and Sensitivity Analysis of the BIOME–BGC Terrestrial Ecosystem Model: Net Primary Production Controls (2000)

Ecosystem simulation models use descriptive input parameters to establish the physiology, biochemistry, structure, and allocation patterns of vegetation functional types, or biomes. For single-stand simulations it is possible to measure required data, but as spatial resolution increases, so too does data unavailability. Generalized biome parameterizations are then required. Undocumented parameter selection and unknown model sensitivity to parameter variation for larger-resolution simulations are currently the major limitations to global and regional modeling. The authors present documented input parameters for a process-based ecosystem simulation model, BIOME-BGC, for major natural temperate biomes. Parameter groups include the following: turnover and mortality; allocation; carbon to nitrogen ratios (C:N); the percent of plant material in labile, cellulose, and lignin pools; leaf morphology; leaf conductance rates and limitations; canopy water interception and light extinction; and the percent of leaf nitrogen in Rubisco (ribulose bisphosphate-1,5-carboxylase/oxygenase) (PLNR). Using climatic and site de-
L-929 Cells Harboring Ectopically Expressed RelA Resist Curcumin-induced Apoptosis (2000)

Curcumin (diferuloyl methane), the yellow pigment in turmeric (Curcuma longa), is a potent chemopreventive agent. Curcumin induces apoptosis of several, but not all, cancer cells. Many cancer cells protect themselves against apoptosis by activating nuclear factor-kappaB (NF-kappaB)/Rel, a transcription factor that helps in cell survival. Signal-induced activation of NF-kappaB is known to be inhibited by curcumin. To understand the role of NF-kappaB in curcumin-induced apoptosis, we stably transfected relA gene encoding the p65/RelA subunit of NF-kappaB, into l-929 cells (mouse fibrosarcoma) and the relA-transfected cells were resistant to varying doses of curcumin (10(-6)-10(-4) m), whereas the parental cells underwent apoptosis in a time- and dose-dependent manner. The relA-transfected cells showed constitutive NF-kappaB DNA binding activity that could not be inhibited by curcumin and did not show nuclear condensation and DNA fragmentation upon treatment with curcumin. When a super-repressor form of IkappaB-alpha (known to inhibit NF-kappaB) was transfected transiently into relA-transfected cells, the cells were no longer resistant to curcumin. Our results highlight a critical anti-apoptotic role for NF-kappaB in curcumin-induced apoptosis.
10 kHz linewidth 1.5 μm InGaAsP external cavity laser with 55 nm tuning range (1983)

An InGaAsP 1.5 μm laser, with one facet antireflection coated, has been incorporated into a diffraction grating external cavity. The lasing wavelength could be tuned over a 55 nm range about the centre wavelength of 1.5 μm by rotating the grating. Furthermore, it was found that the emission spectrum was extremely narrow; beat-frequency measurements at 1523 nm against an HeNe laser showed it to be of the order of 10 kHz.
The 3′‐untranslated region of brome mosaic virus RNA does not enhancetranslation of capped mRNAs in vitro (1995)

The translation enhancing ability of cis-acting 3'-terminal untranslated region (3'-UTR) of brome mosaic virus (BMV) was examined. Two chimeric mRNA constructs translated in rabbit reticulocyte lysates contained the BMV coat protein (CP) gene and NPTI gene, respectively. It was shown that the 3'-UTR of BMV RNA enhanced the translational efficiency of uncapped but not capped messages.
Phase control of wavepacket dynamics using shaped femtosecond pulses (1999)

Coherent vibrational and rotational dynamics of the Li2 molecule is controlled by varying the relative phases, φn, of the rovibrational wavepacket components, ∣n〉 e-i(ωnt+φn). The coherent superposition is created by excitation of a set of ten rovibronic E 1Σg+(νE=12–16, JE=17, 19) states from an intermediate state, A 1Σu+(νA=14, JA=18), using ultrashort optical pulses with well defined spectral amplitudes and phases encoded into the pulse by a liquid crystal spatial light modulator. The wavepacket is probed by time-dependent photoionization and the quantum interference signal is measured as a total ionization yield. The phases of the wavepacket components are optimized to produce partial localization of the wavepacket at a given time t, in specific regions of three-dimensional space defined by the radial and angular coordinates. As a result, the ionization yield, I(t), is maximized or minimized at a time t. The degree of control achieved in the experiment (Imax-Imin)/Imax=64(±12%). The experimental data are interpreted in terms of time-dependent radial and angular probability distributions, calculated for different initial conditions that are determined by the phase relationships in the excitation pulse.
“Put-that-there” (1980)

Recent technological advances in connected-speech recognition and position sensing in space have encouraged the notion that voice and gesture inputs at the graphics interface can converge to provide a concerted, natural user modality.
Greatly Enhanced Pressor Response to Antidiuretic Hormone in Patients with Impaired Cardiovascular Reflexes Due to Idiopathic Orthostatic Hypotension (1980)

Pressor responsiveness to infused arginine-vasopressin (AVP), noradrenaline (NA), and angiotensin II (Ang II) of two patients with idiopathic orthostatic hypotension (Shy-Drager's syndrome) was compared with that of normal subjects. During the AVP infusion studies, plasma AVP concentrations were measured by radioimmunoassay. Compared to normal subjects, the two patients showed a greatly increased slope of the curves relating doses or plasma concentrations of AVP to blood pressure (BP) increases. While in the normal subjects an increase of plasma AVP up to 450 fmoles/ml (normal range, 0.5–5.0 fmoles/ml) raised BP only by 5–7 mm Hg, in the two patients an increase of plasma AVP within or slightly above the normal range increased BP by up to 40 mm Hg. During AVP infusion, heart rate fell in the normal subjects but did not change in the two patients. A 10 mm Hg increase in BP would require doses or concentrations of AVP about 1,000 times higher in normals than in the patients. Equipressor doses of Ang II or NA were only 2 to 8 times lower in patients than in normals. Thus, in individuals whose cardiovascular reflex activity is greatly reduced or absent, plasma AVP concentrations within the physiological range are vasopressor. We conclude that in normal subjects the vasopressor effect of intravenously infused AVP is greatly buffered by activation of cardiovascular reflexes. Since this phenomenon is not apparent to the same extent during Ang II or NA infusion, it seems possible that rising AVP plasma concentrations specifically increase the feedback gain of cardiovascular reflex systems.
On code design for the Slepian-Wolf problem and lossless multiterminal networks (2006)

A Slepian-Wolf coding scheme for compressing two uniform memoryless binary sources using a single channel code that can achieve arbitrary rate allocation among encoders was outlined in the work of Pradhan and Ramchandran. Inspired by this work, we address the problem of practical code design for general multiterminal lossless networks where multiple memoryless correlated binary sources are separately compressed and sent; each decoder receives a set of compressed sources and attempts to jointly reconstruct them. First, we propose a near-lossless practical code design for the Slepian-Wolf system with multiple sources. For two uniform sources, if the code approaches the capacity of the channel that models the correlation between the sources, then the system will approach the theoretical limit. Thus, the great advantage of this design method is its possibility to approach the theoretical limits with a single channel code for any rate allocation among the encoders. Based on Slepian-Wolf code constructions, we continue with providing practical designs for the general lossless multiterminal network which consists of an arbitrary number of encoders and decoders. Using irregular repeat-accumulate and turbo codes in our designs, we obtain the best results reported so far and almost reach the theoretical bounds.
Analysis of Hysteresis Characteristics for Positioning Mechanism. Evaluation of Influences with No-Backlash Gearing. (1993)

It is very difficult to eliminate the mechanical hysteresis for positioning lnechanism. Weneed the allowable mechanical hysteresis magnitude, when we improve the mechanism performance.So that it has been proposed the evaluation methods of mechanical hysteresis influences on dynamic performance using the mechanical hysteresis test unit. In this report, these methodsare expanded to apply for positioning mechanism with reducer, which the mechanism includesthe mechanical hysteresis characteristics in these control system. Especially, the Amm parameter is newly defined to evaluate the influence on the system stability. And then it is testedand evaluated the closed looP Positioning mechanism system with the “No-backlash Gearing” reducer and the “Mechanical Hysteresis Test Unit”. It is proved that it can be quantified theseallowable mechanical hysteresis magnitude as like as the only Mechanical Hysteresis Test Unitcharacteristics.