gebhart/patrepeval huggingface dataset:
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors (2012)

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones. The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion. We frequently detected secondary motifs in addition to the canonical motifs of the TFs, indicating tethered binding and cobinding between multiple TFs. We observed significant position and orientation preferences between many cobinding TFs. Genes specifically expressed in a cell line are often associated with a greater occurrence of nearby TF binding in that cell line. We observed cell-line-specific secondary motifs that mediate the binding of the histone deacetylase HDAC2 and the enhancer-binding protein EP300. TF binding sites are located in GC-rich, nucleosome-depleted, and DNase I sensitive regions, flanked by well-positioned nucleosomes, and many of these features show cell type specificity. The GC-richness may be beneficial for regulating TF binding because, when unoccupied by a TF, these regions are occupied by nucleosomes in vivo. We present the results of our analysis in a TF-centric web repository Factorbook (http://factorbook.org) and will continually update this repository as more ENCODE data are generated.
Resveratrol Modulates Drug- and Carcinogen-Metabolizing Enzymes in a Healthy Volunteer Study (2010)

Resveratrol has been shown to exhibit cancer-preventive activities in preclinical studies. We conducted a clinical study to determine the effect of pharmacologic doses of resveratrol on drug- and carcinogen-metabolizing enzymes. Forty-two healthy volunteers underwent baseline assessment of cytochrome P450 (CYP) and phase II detoxification enzymes. CYP1A2, CYP2D6, CYP2C9, and CYP3A4 enzyme activities were measured by the metabolism of caffeine, dextromethorphan, losartan, and buspirone, respectively. Blood lymphocyte glutathione S-transferase (GST) activity and GST-pi level and serum total and direct bilirubin, a surrogate for UDP-glucuronosyl transferase (UGT) 1A1 activity, were measured to assess phase II enzymes. After the baseline evaluation, study participants took 1 g of resveratrol once daily for 4 weeks. Enzyme assessment was repeated upon intervention completion. Resveratrol intervention was found to inhibit the phenotypic indices of CYP3A4, CYP2D6, and CYP2C9 and to induce the phenotypic index of 1A2. Overall, GST and UGT1A1 activities were minimally affected by the intervention, although an induction of GST-pi level and UGT1A1 activity was observed in individuals with low baseline enzyme level/activity. We conclude that resveratrol can modulate enzyme systems involved in carcinogen activation and detoxification, which may be one mechanism by which resveratrol inhibits carcinogenesis. However, pharmacologic doses of resveratrol could potentially lead to increased adverse drug reactions or altered drug efficacy due to inhibition or induction of certain CYPs. Further clinical development of resveratrol for cancer prevention should consider evaluation of lower doses of resveratrol to minimize adverse metabolic drug interactions.
A reading aid for the partially sighted (1978)

There are several reading aids to help the partially sighted, the more sophisticated of which employ closed-circuit television. However, this latter type is very expensive and generally non-portable. A new reading aid has been devised by engineers at Philips Research Laboratories which retains most of the c.c.t.v. system advantages while at the same time being portable and costing less
Reduction of Intersubcarrier Interference and Frequency-Selective Fading in OFDM-ROF Systems (2010)

This paper theoretically investigates the signal degradation induced by intersubcarrier interference and frequency-selective fading in orthogonal frequency-division-multiplexing radio-over-fiber systems. Turbo codes and bit interleaver technologies are proposed to effectively mitigate unbalanced error distribution because of intersubcarrier interference and frequency-selective fading. Experimental results show that the receiver sensitivities are improved as far as 5 dB after 50-km SMF-28 transmission for 6.25-Gb/s wireless signals on optical generated 60-GHz carrier.
Synthesis and photophysical properties of novel biphenyl derivatives containing furan and thiophene groups (2010)

( Z)-2-(4-Bromophenyl)-3-(furan-2-yl)acrylonitrile and ( Z)-2-(4-bromophenyl)-3- (thiophen-2-yl)acrylonitrile were prepared by condensation of furan-2-carbaldehyde and thiophene-2-carbaldehyde with (4-bromophenyl)acetonitrile in the presence of catalytic amount of NaOCH 3 at room temperature. A series of novel biphenyl derivatives containing furan and thiophene groups was synthesised from (Z)-2-(4-bromophenyl)-3-(furan-2-yl)acrylonitrile and ( Z)-2-(4-bromophenyl)-3- (thiophen-2-yl)acrylonitrile via Suzuki coupling to arylboronic acids. The structures of these compounds were characterised by FTIR, 1 H NMR, 13 C NMR, and HRMS. The UV-Vis absorption and photoluminescence spectra of the novel compounds in CH 2 Cl 2 solution were investigated.
A Helical-Scan Color Videotape Recorder for the Broadcaster (1970)

A low-cost helical-scan color videotape recorder for the broadcaster has many of the features previously found only on quadruples recorders, and provides some features never before found on a videotape recorder. Until recently, most helicalscan videotape recorders introduced time-base errors too large to meet the EIA and FCC broadcast specifications and did not have a sufficient signal-to-noise ratio for the discriminating broadcaster, and until recently, electronic editing, color reproduction, missing video information and other similar problems remained unsolved. This helical-scan VTR can record the full NTSC color signal in its original form with a 4.2-MHz bandwidth and excellent signal-to-noise ratio.
An Investigation on Initialization Schemes for Multilayer Perceptron Training Using Multilingual Data and Their Effect on ASR Performance (2018)

In this paper we present our latest investigation on initialization schemes for Multilayer Perceptron (MLP) training using multilingual data. We show that the overall performance of an MLP network improves significantly by initializing it with a multilingual MLP. We propose a new strategy called "open target language" MLP to train more flexible models for language adaptation, which is particularly suited for small amounts of training data. Furthermore, by applying Bottle-Neck feature (BN) initialized with multilingual MLP the ASR performance increases on both, on those languages which were used for multilingual MLP training, and on a new language. Our experiments show word error rate improvements of up to 16.9% relative on a range of tasks for different target languages (Creole and Vietnamese) with manually and automatically transcribed training data.
Analysis and evaluation of a lossless turn-on snubber (2002)

A lossless turn-on snubber was studied analytically, by simulation and experimentally. Limits were found for the proper operation of the snubber and are expressed as permissible duty cycle as a function of input current. It was found that a modified version of the snubber, which includes a tapped main inductor, improves the performance by allowing a wider operational range. The experimental results confirm the theoretical analysis. A reduction of power losses of about 19 W was observed when the snubber was implemented in a 1 kW boost power converter.
Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database (2012)

The results of our study give us an intriguing picture of the molecular complexity of HD. Our analyses can be seen as a first step towards a comprehensive list of biological processes, molecular functions, and pathways involved in HD, and may provide a basis for the development of more holistic disease models and new therapeutics.
Origin of primordial germ cells in the prestreak chick embryo (1996)

The temporal and spatial pattern of segregation of the avian germline from the formation of the area pellucida to the beginning of primitive streak formation (stages VII-XIV, EG&K) was investigated using the culture of whole embryos and central and peripheral embryo fragments on vitelline membranes at stages VII-IX, immunohistological analysis of whole mount embryos and sections with monoclonal antibodies MC-480 against stage-specific embryonic antigen-1 (SSEA-1) and EMA-1, and with the culture of dispersed blastoderms at stages IX-XIV with and without on STO feeder layer. Whole embryos at intrauterine stages developed up to the formation of the primitive streak despite the absence of area pellucida expansion. Primordial germ cells (PGCs) appeared in the cultures of whole embryos and only in central fragments containing a partially formed area pellucida at stages VII-IX. When individual stage IX-XIV embryos were dispersed and cultured without a feeder layer, 25-45 PGCs/embryo were detected only with stage X-XIV, but not with stage IX blastoderms. However, the culture of dispersed cells from the area pellucida of stages IX-XIII on STO feeder layers yielded about 150 PGCs/embryo. The carbohydrate epitopes recognized by anti-SSEA-1 and EMA-1 first appeared at stage X on cells in association with polyingressing cells on the ventral surface of the epiblast and later on the dorsal surface of the hypoblast. The SSEA-1-positive hypoblast cells gave rise to chicken PGCs when cultured on a feeder layer of quail blastodermal cells. From these observations, we propose that the segregation and development of avian germline is a gradual, epigenetic process associated with the translocation of SSEA-1/EMA-1-positive cells from the ventral surface of the area pellucida at stage X to the dorsal side of the hypoblast at stages XI-XIV.
Multicenter Phase II Study to Evaluate a 28-Day Regimen of Oral Fluorouracil Plus Eniluracil in the Treatment of Patients With Previously Untreated Metastatic Colorectal Cancer (2000)

PURPOSE: To determine the efficacy of fluorouracil (5-FU) plus eniluracil when administered to patients with previously untreated metastatic colorectal cancer. PATIENTS AND METHODS: In this single-arm phase II study, patients with previously untreated metastatic colorectal cancer received oral eniluracil plus 5-FU (10:1 dose ratio), at 5-FU doses of 1.00 mg/m 2 or 1.15 mg/m 2 twice daily (every 12 hours) for 28 consecutive days repeated every 5 weeks (one cycle). Treatment continued until there was documented disease progression or unacceptable toxicity. RESULTS: Thirty and 25 patients were enrolled at a starting dose of 1.00 mg/m 2 and 1.15 mg/m 2 , respectively. Fourteen (25%) of 55 patients (95% confidence interval, 15% to 39%) had a partial response, and 20 patients (36%) had stable disease. The median durations of the partial responses and stable disease were 23.9 weeks (range, 12.3 to 52.1+ weeks) and 24.1 weeks (range, 17.1 to 55.6+ weeks), respectively. The median durations of progression-free and overall survival were 22.6 weeks (range, 21.0 to 29.0 weeks) and 59 weeks (range, 4 to 84+ weeks), respectively. The response rate in the 1.15 mg/m 2 –dose group was similar to the 1.00 mg/m 2 –dose group (28% v 23%, respectively). Severe (grade 3/4) nonhematologic treatment-related toxicity included diarrhea (nine patients), nausea/vomiting (one patient each), mucositis (two patients), and anorexia (one patient). Severe hematologic toxicities were rare. At the 1.15 mg/m 2 –dose level, two patients exhibited grade 3 granulocytopenia, and two patients had grade 3 anemia. CONCLUSION: The response rate with oral 5-FU plus eniluracil is comparable with that observed with infusional 5-FU or bolus 5-FU and leucovorin. The toxicity profile of this oral regimen is acceptable for use in an outpatient home-based setting.
Refractory migraine headache controlled with alprazolam: case report. (1985)

A woman with major depressive disorder and refractory, incapacitating migraine headaches responded to alprazolam in a double-blind, placebo-controlled study. Migraine, but not depression, recurred following tapering of the drug, suggesting efficacy of alprazolam for control of refractory migraine.
An efficient algorithm for signal flow determination in digital CMOS VLSI (1996)

Signal flow determination of CMOS/VLSI digital circuits is a key issue for switch-level CAD tools such as timing and testability analyzers, or functional abstractors, ATPGs etc .. and even some simulators. It is used to preprocess circuit MOS transistors in order to improve both the accuracy and the running time of these CAD tools. Existing algorithms can be classified into two main categories: the rule based approach and the algorithmic approach. However, both of them have several drawbacks. This paper presents an efficient algorithm based on a novel mixed algorithmic and rule based approach, that overcomes most of the drawbacks of the pure algorithmic and rule based approaches. It is based on a set of safe general topological rules rather than ad hoc or technology dependent ones. Due to the algorithmic aspect of our approach, some rules consider circuit global effects such as path informations. Our approach provide the advantages of the rule based one (ie : the flexibility and the adaptability toward the great variety of CMOS design styles) as well as the advantages of the algorithmic approach (ie: the fast processing time and the ability to consider circuits global effects). The result is that the software is very accurate since all the unidirectional and bi-directional transistors are correctly identified in all the pathological benchmarks reported in the literature. Besides, the software is fast (about 50 000 transistors/second) with a linear processing time.
Model calibration of a real petroleum reservoir using a parallel real-coded genetic algorithm (2007)

An application of a Real-coded Genetic Algorithm (GA) to the model calibration of a real petroleum reservoir is presented. In order to shorten the computation time, the possible solutions generated by the GA are evaluated in parallel on a group of computers. This required the GA to be adapted to a multi-processor structure, so that the scalability of the computation is maximised. The best solutions of each run enter the ensemble of calibrated models, which is finally analysed using a clustering algorithm. The aim is to identify the optimal regions contained in the ensemble and thus to reveal the distinct types of reservoir models consistent with the historic production data, as a way to assess the uncertainty in the Reservoir Characterisation due to the limited reliability of optimisation algorithms. The developed methodology is applied to the characterisation of a real petroleum reservoir. Results show a large improvement with respect to previous studies on that reservoir in terms of the quality and diversity of the obtained calibrated models. Our main conclusion is that, even with regularisation, many distinct calibrated models are possible, which highlights the importance of applying optimisation methods capable of identifying all such solutions.
A simulation model of foraging behaviour and the effect of predation risk (2000)

Summary 1. The effect of predation risk on the distribution of animals foraging in a patchy environment was explored using a simulation model based on the work of Bernstein, Kacelnik & Krebs (1988, 1991 ), extended to incorporate predation risk. 2. Modelled foragers consume prey within patches, having different prey densities, at a rate that depends only on prey density and interference from other foragers in the patch. Prey density remains constant (no depletion). A forager leaves a patch if its intake rate drops below its estimate of the average intake rate available in the environment. This estimate is continually updated by taking a weighted average of current intake and the previous estimate, giving a simple learning process. Decisions on whether to leave are made at regular intervals and a forager leaving a patch may arrive at random at any other patch. 3. Simulation results were sensitive to the computational scheme used to represent estimates of average intake rate in the environment and to the way in which foragers’ decisions were distributed over time, illustrating the need for careful formulation of such models. 4. Predation risk was modelled as a cost that reduced effective intake, and could be distributed uniformly or skewed to patches of high prey density. The effects of different levels and distributions of predation risk on distribution of foragers were examined using model parameters broadly appropriate to hedgehogs ( Erinaceous europaeus L.) foraging for earthworms ( Lumbricus spp.) and risking opportunistic predation by badgers ( Meles meles L.). The distribution of foragers with respect to prey density took an ‘ideal free’ form for zero or uniform risk, and was domed when cost of predation risk was relatively high and concentrated in the richer patches, as might be the case when predators and foragers share a common food resource.
Managing pests and their resistance to<i>Bacillus thuringiensis:</i>Can transgenic crops be better than sprays? (1994)

Insecticidal toxins from Bacillus thuringiensis (Bt) can now be deployed either in sprays or transgenic plants. Some entomologists and environmentalists have argued that the sprays are preferable to plants because they are less likely to cause resistance. However Bt sprays are not generally competitive with chemical insecticides and seem unlikely to displace them. In contrast, transgenic plants appear to be sufficiently effective to displace chemicals, making such plants attractive from the standpoint of environmental protection. Further, simulation models using data from the diamondback moth and a laboratory experiment using the Indianmeal moth suggest that wider at least some circumstances, transgenic plants bearing only one Bt gene may be more effective than sprays for delaying resistance to Bt Resistance in a laboratory‐selected strain of the Colorado potato beetle is especially interesting because a strain that can survive Bt sprays and develop to maturity cannot develop successfully on transgenic plants, not even on some showing very low expression. This suggests that more mechanisms are available for resistance to sprays than to transgenic plants, perhaps making resistance to sprays more ‘evolutionarily available’. When the use of two toxin genes is considered, simulation models suggest that transgenic plants may be much more durable than sprays of similar efficacy.
Über asymm. Methyl‐Tolyl‐Hydrazine und Ihre Reaktionen mit Zuckern (1957)

Abstract Die 3 isomeren asymm. Methyl‐tolyl‐hydrazine wurden dargestellt und deren Kondensationsfähigkeit mit Zuckern geprüft. Das α‐Methyl‐ p ‐tolylhydrazin erwies sich als brauchbares Reagens zur Abtrennung und Isolierung von Aldosen bestimmter Konfiguration aus Zuckergemischen.
Evolving trends in the treatment of anorectal diseases (1999)

During the first half of this century, the safe and effective treatment of benign anorectal disorders perhaps did more to establish our specialty as a viable and distinct entity than anything else. A thorough understanding of anorectal anatomy and physiology, improved methods of local anesthesia, and an appreciation of proper postoperative care made the care of patients with diseases of the rectum and anus the domain of true specialists. Hirschman stated, "It is the action of the profession itself which has created the special field of proctology--the anus and rectum being organs peculiar to themselves and being subject to many medical and surgical diseases in the same way as the eye, the ear, the nose, the genital and urinary organs; and call for just as much special medical and surgical care. The general surgeon knows nothing about, and cares less for, the medical treatment of these organs; and the general practitioner who is able to treat the medical conditions is not, as a rule, properly equipped to do so. Thus, the proctologist came into existence--a man who, by special study of this particular region of the body, is able to give special care of either a surgical or medical nature, and often both in the same case, as may be required."
Experimental and Numerical Modeling of Convective Proppant Transport (1994)

Abstract Slurry transport and settling experiments were conducted to improve current descriptions of proppant transport. Results of these experiments were used to formulate a new slurry transport model which was incorporated in a fully three-dimensional fracture simulator. The model was tested and verified against experimental observations of slurry transport in a 4 foot by 16 foot slot model. Results of the study indicate that proppant slurry transport can be accurately modeled when the effects of single particle settling, density driven flow, particle velocity profiles, and slurry rheology are accounted for.
Antibody Response to Diphtheria, Tetanus, and Poliomyelitis Vaccines in Relation to the Number of CD4+ T Lymphocytes in Adults Infected with Human Immunodeficiency Virus (1995)

A prospective study of antibody production by adults infected with human immunodeficiency virus (HIV) after vaccination with T lymphocyte-dependent diphtheria toxoid, tetanus toxoid, and inactivated trivalent poliovirus vaccine was conducted. Individuals were divided into three groups according to CD4+ T-lymphocyte count: group 1 had a count of < or = 100-300 x 10(6)/L; and group 3, > 300 x 10(6)/L. After vaccination, 61%, 70%, and 73% of the individuals in groups 1, 2, and 3, respectively, developed protective titers of antibody to diphtheria toxin; the mean postvaccination antibody titer of HIV-infected individuals was significantly lower than that of healthy controls not infected with HIV. Furthermore, the mean titers of antibodies to tetanus toxin and poliovirus were significantly lower in HIV-infected individuals with CD4+ lymphocyte counts of < 300 x 10(6)/L than in controls. Of the HIV-infected vaccinees, 83%-100% were protected against tetanus and 78%-100% against polio. We conclude that HIV-infected individuals with CD4+ lymphocyte counts of < 300 x 10(6)/L have an impaired (secondary) antibody response after receipt of T lymphocyte-dependent vaccines.
Routing strategies for fault recovery in wide area packet networks (2002)

We present the results of a study of routing algorithms for traffic restoration after a failure in a virtual circuit packet switched wide area network. Standard routing algorithms based on minimizing the steady state network delay may not be appropriate for rerouting the calls after a failure, in view of the transient congestion. We propose alternative routing schemes to reduce the congestion. The results of a simulation study of a 10 node network comparing the performance of the different routing algorithms (i.e., minimum delay, minimum hop, load distribution on paths, load distribution on links) are presented.
Inside-out meniscal repair using zone-specific instruments. (1996)

In the last decade, arthroscopic meniscus repair has become established as the treatment of choice for many meniscal lesions previously managed by meniscectomy. Biomechanical and clinical evidence supports meniscus repair for healable tears, especially in adolescents and young adults, while partial meniscectomy is appropriate for most of the remainder. Meniscus repair is a demanding technique that requires the skill of a dedicated arthroscopist. Special suturing tools and techniques often are required, but these are no substitute for appropriate selection and thorough preparation of specific tears that are likely to heal. Complete rehabilitation and a stable knee are required postoperatively to ensure a successful result.