gebhart/patrepeval huggingface dataset:
A recursive approach to low complexity codes (1981)

A method is described for constructing long error-correcting codes from one or more shorter error-correcting codes, referred to as subcodes, and a bipartite graph. A graph is shown which specifies carefully chosen subsets of the digits of the new codes that must be codewords in one of the shorter subcodes. Lower bounds to the rate and the minimum distance of the new code are derived in terms of the parameters of the graph and the subeodes. Both the encoders and decoders proposed are shown to take advantage of the code's explicit decomposition into subcodes to decompose and simplify the associated computational processes. Bounds on the performance of two specific decoding algorithms are established, and the asymptotic growth of the complexity of decoding for two types of codes and decoders is analyzed. The proposed decoders are able to make effective use of probabilistic information supplied by the channel receiver, e.g., reliability information, without greatly increasing the number of computations required. It is shown that choosing a transmission order for the digits that is appropriate for the graph and the subcodes can give the code excellent burst-error correction abilities. The construction principles
Efficient Methods for Direct Volume Rendering of Large Data Sets (2006)

Lacunar strokes (LS) are often preceded by repetitive transitory ischaemic attacks (TIAs) known as 'capsular warning syndrome'. The treatment of these symptoms remains controversial. Anticoagulants are often used in this situation, most of the time, however, with no or little benefit. Since it is not rare that these TIAs lead to a definite stroke, the therapeutic approach in the acute phase is very important. We report six patients presenting LS preceded by TIAs. All patients showed intermittent decrease of blood pressure (BP) coinciding with clinical worsening and leading to definite stroke in four of them. All were treated with full-dose intravenous heparin, which did not prevent further clinical deterioration. One patient received noradrenalin, which allowed stabilisation of the blood pressure values and complete resolution of the neurological symptoms. This observation suggests that in lacunar strokes preceded by TIAs monitoring and, if necessary, pharmacological increase of BP may prevent some patients from developing a definite stroke. Thus the 'capsular warning syndrome' could reflect a haemodynamic failure rather than repeated thrombo-embolism within the lumen of a single perforating arteriole.
57. Physical and dosimetric aspects of quality assurance in stereotactic radiotherapy (2001)

A quality assurance system in stereotactic radiosurgery and stereotactic fractionated radiotherapy, concerning the physical and dosimetric aspects, may be divided into three elements: (1) the preparation of reliable basic data for the computerized treatment planning system; (2) a control of the accelerator parameters prior to patient treatment; (3) preparation of the optimal treatment plan with the treatment planning system. Due to the small size of the beams formed by circular collimators (7.5–35 mm diameter, BrainLab System) the smallest available detectors should be used for measurements – a diamond diode (0.3 mm thickness) and a 0.015 cm3 ionization chamber (PTW Freiburg) are adequate to measure precisely TMR curves, beam profiles and output factors required for the treatment planning system BrainScan. The full control of accelerator parameters (Clinac 2300 C/D) necessary to safely carry out the treatment requires a comprehensive list of tests (an extended list of weekly checks including Winston-Lutz test). Testing procedure carried out with a set of specialized devices (Med-Tec, Radak, BrainLab) takes about two hours. Proper accelerator check and regulations allow for very precise patient positioning. Treatment planning (with the treatment planning system BrainScan) is based on a series of CT and MR scans with target volume and organs at risk marked on each slice by the radiotherapist. The planner has to select the positions of isocentres (up to 3), collimator diameters, number and range of the arcs. Additional parameters for optimization procedure are the total dose proportions delivered by each arc. The treatment plan evaluation is based on the analysis of DVHs for target volume and also for organs at risk (orbits, optical nerves, brain stem) in order to minimize the dose and volume irradiated. It was accepted that the dose uniformity factor, defined as a ratio Dmin/Dmax within the target volume, should be not less than 0.8, and should approach 0.9 as much as possible. The above-presented system of quality control, specifying tolerance limits of controlled parameters, assures safe and precise dose delivery in stereotactic radiotherapy.
Cotyledon Nuclear Proteins Bind to DNA Fragments Harboring Regulatory Elements of Phytohemagglutinin Genes (1989)

C. Daniel Riggs, Toni A. Voelker, Maarten J. Chrispeels, Cotyledon Nuclear Proteins Bind to DNA Fragments Harboring Regulatory Elements of Phytohemagglutinin Genes, The Plant Cell, Vol. 1, No. 6 (Jun., 1989), pp. 609-621
Reversal of motor impairments in parkinsonian rats by continuous intrastriatal delivery of l -dopa using rAAV-mediated gene transfer (2002)

Intrastriatal delivery of the tyrosine hydroxylase gene by viral vectors is being explored as a tool for local delivery of L-dopa in animals with lesions of the nigrostriatal pathway. The functional effects reported using this approach have been disappointing, probably because the striatal L-dopa levels attained have been too low. In the present study, we have defined a critical threshold level of L-dopa, 1.5 pmol/mg of tissue, that has to be reached to induce any significant functional effects. Using new generation high-titer recombinant adeno-associated virus vectors, we show that levels of striatal L-dopa production exceeding this threshold can be obtained provided that tyrosine hydroxylase is coexpressed with the cofactor synthetic enzyme, GTP-cyclohydrolase-1. After striatal transduction with this combination of vectors, substantial functional improvement in both drug-induced and spontaneous behavior was observed in rats with either complete or partial 6-hydroxydopamine lesions of the nigrostriatal pathway. However, complete reversal of motor deficits occurred only in animals in which part of the striatal dopamine innervation was left intact. Spared nigrostriatal fibers thus may convert L-dopa to dopamine and store and release dopamine in a more physiologically relevant manner in the denervated striatum to mediate better striatal output-dependent motor function. We conclude that intrastriatal L-dopa delivery may be a viable strategy for treatment and control of adverse side effects associated with oral L-dopa therapy such as on-off fluctuations and drug-induced dyskinesias in patients with Parkinson's disease.
Neisseria gonorrhoeae Treatment Failure and Susceptibility to Cefixime in Toronto, Canada (2013)

The rate of clinical failure following treatment of N. gonorrhoeae infections with cefixime was relatively high at a Toronto clinic and was associated with elevated MICs.
Intravenous iron therapy (2011)

Oral iron supplementation is usually the first choice for the treatment of iron deficiency anemia (IDA) because of its effectiveness and low cost. But unfortunately in many iron deficient conditions, oral iron is a less than the ideal treatment mainly because of adverse events related to the gastrointestinal tract as well as the long course required to treat anemia and replenish body iron stores. The first iron product for intravenous use was high-molecular-weight iron dextran. However, dextran-containing intravenous iron preparations are associated with an elevated risk of anaphylactic reactions, which made physicians reluctant to prescribe intravenous iron in the treatment of iron deficiency anemia for many years. In 1999 and 2001, two new intravenous iron preparations (ferric gluconate and iron sucrose) were introduced into the market as safer alternatives to iron dextran. Over the last five years, three new intravenous iron dextran-free preparations have been developed and have better safety profiles than the more traditional intravenous compounds, as none require test doses and all these products are promising in respect to a more rapid replacement of body iron stores (15-60 minutes/infusion) as they can be given at higher doses (from 500 mg to more than 1000 mg/infusion). The purpose of this review is to discuss some pertinent issues in relation to the history, pharmacology, administration, efficacy, safety profile and toxicity of intravenous iron for the treatment of iron deficiency anemia.
Bifocal Design Procedure for Dual-Reflectarray Antennas in Offset Configurations (2018)

This letter presents a new bifocal design procedure for dual-reflectarray antennas (DRAAs) in offset configurations. The technique starts by considering an axially symmetric geometry with the reflectarrays placed in parallel planes, which allows the rotation of a two-dimensional bifocal design around the symmetry axis. To reach a more compact configuration and to obtain smoother phase distributions, the reflectarrays are tilted and their phases are adjusted by means of a ray-tracing routine. The technique has been validated by numerical simulations through the comparison with a previous center-fed dual-reflectarray prototype. Finally, the simulations of an offset DRAA with tilted reflectarrays are presented, providing 0.56° beam spacing at 20 GHz for multispot satellite applications in Ka-band.
An Update on Clostridium difficile Toxinotyping (2015)

Toxinotyping is a PCR-restriction fragment length polymorphism (RFLP)-based method for differentiation of Clostridium difficile strains according to the changes in the pathogenicity locus (PaLoc), a region coding for toxins A and B. Toxinotypes are a heterogenous group of strains that are important in the development of molecular diagnostic tests and vaccines and are a good basis for C. difficile phylogenetic studies. Here we describe an overview of the 34 currently known toxinotypes (I to XXXIV) and some changes in nomenclature.
Catalytic Activation of the Phosphatase MKP-3 by ERK2 Mitogen-Activated Protein Kinase (1998)

MAP kinase phosphatase–3 (MKP-3) dephosphorylates phosphotyrosine and phosphothreonine and inactivates selectively ERK family mitogen-activated protein (MAP) kinases. MKP-3 was activated by direct binding to purified ERK2. Activation was independent of protein kinase activity and required binding of ERK2 to the noncatalytic amino-terminus of MKP-3. Neither the gain-of-function Sevenmaker ERK2 mutant D319N nor c-Jun amino-terminal kinase–stress-activated protein kinase (JNK/SAPK) or p38 MAP kinases bound MKP-3 or caused its catalytic activation. These kinases were also resistant to enzymatic inactivation by MKP-3. Another homologous but nonselective phosphatase, MKP-4, bound and was activated by ERK2, JNK/SAPK, and p38 MAP kinases. Catalytic activation of MAP kinase phosphatases through substrate binding may regulate MAP kinase activation by a large number of receptor systems.
Novel HER2 selective tyrosine kinase inhibitor, TAK‐165, inhibits bladder, kidney and androgen‐independent prostate cancer in vitro and in vivo (2006)

TAK-165 may be a hopeful new agent for bladder, kidney and androgen-independent prostate cancer.
Expression of human class II major histocompatibility complex antigens using retrovirus vectors. (1987)

Retrovirus vectors [direct orientation (DO) vectors] that permit the simultaneous expression of an inserted protein-coding sequence and a dominant-acting selectable marker have been constructed. In these vectors, an internal simian virus 40 or human metallothionein promoter sequence serves to drive the expression of the bacterial neomycin phosphotransferase or guanine-xanthine phosphoribosyltransferase genes, whereas the viral long terminal repeat sequences are utilized to promote expression of inserted sequences. In some of the vectors, the viral 5' splice site, normally used in the biogenesis of the subgenomic env-encoding mRNA, has been eliminated. These vectors yield high transient and stable titers of virus after transfection of viral packaging cell lines, show little or no depression of virus titer with a variety of inserts, and faithfully transmit recombinant proviral sequences to recipient cells. To characterize the expression potential of these vectors, a variety of inserts encoding the alpha and beta subunits of the human major histocompatibility complex class II antigen HLA-DR have been introduced into these vectors. NIH 3T3 cells infected by viruses containing HLA-DR alpha or beta cDNAs express these proteins as shown by immunoprecipitation of metabolically labeled extracts. In addition, through the sequential infection of cells with retrovirus constructions expressing two different selectable markers, both subunits of the class II antigen have been introduced into NIH 3T3 cells. Such infected cells express HLA-DR molecules at the cell surface.
Selective killing of glioma cells in culture and in vivo by retrovirus transfer of the herpes simplex virus thymidine kinase gene. (1991)

The thymidine kinase gene (tk) of herpes simplex type 1 virus (HSV-1) was inserted into a retroviral vector under the transcriptional control of the enhancer-promoter element of the Moloney murine leukemia virus long terminal repeat. Replication-defective viral particles were obtained by transfection of vector DNA into the packaging cell line psi2 and were used to infect C6 rat glioma-derived cell lines in culture. The sensitivity of these cells to the toxic effects of the nucleoside analog ganciclovir was found to be significantly increased by transfer of the HSV-1 tk gene. The difference in sensitivity between infected and uninfected cells defined ganciclovir concentrations that could be used to selectively kill essentially all infected cells while sparing uninfected ones. C6 glioma cells introduced subcutaneously into nude mice were highly tumorigenic. Growth of tumors produced from C6-derived cells bearing the HSV-1 tk gene, but not parental C6 cells, could be inhibited by intraperitoneal administration of ganciclovir. This work demonstrates the effectiveness of the thymidine kinase expressed by the HSV-1 ks gene in sensitizing brain tumor cells to the toxic effects of nucleoside analogs. Retrovirus vectors should thus prove useful in the selective delivery of this killer gene to dividing tumor cells in the nervous system, where most endogenous cells are not dividing.
Alcohol and the brain (1999)

An understanding of the pharmacology of alcohol use may lead to greater ability to treat psychiatric consequences of alcoholism, and may also prevent some of the secondary psychiatric comorbidity and later brain damage.
Emitter wrap-through solar cell (2002)

The authors present a new solar cell concept (emitter wrap-through or EWT) for a back-contact cell. The cell has laser-drilled vias to wrap the emitter on the front surface to contacts on the back surface and uses a potentially low-cost process sequence. Modeling calculations show that efficiencies of 18 and 21% are possible with large-area solar-grade multi- and monocrystalline silicon EWT cells, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Profiling genome-wide DNA methylation (2016)

DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dynamic, sequence-context-dependent and trans-generationally heritable, and these complex patterns of methylation highlight the significance of profiling DNA methylation to answer biological questions. In this review, we surveyed major methylation assays, along with comparisons and biological examples, to provide an overview of DNA methylation profiling techniques. The advances in microarray and sequencing technologies make genome-wide profiling possible at a single-nucleotide or even a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis, and selecting a feasible method requires knowledge of these methods. We first introduce the biological background of DNA methylation and its pattern in plants, animals and fungi. We present an overview of major experimental approaches to profiling genome-wide DNA methylation and hydroxymethylation and then extend to the single-cell methylome. To evaluate these methods, we outline their strengths and weaknesses and perform comparisons across the different platforms. Due to the increasing need to compute high-throughput epigenomic data, we interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially methylated regions (DMRs). This review summarizes the experimental and computational concepts for profiling genome-wide DNA methylation, followed by biological examples. Overall, this review provides researchers useful guidance for the selection of a profiling method suited to specific research questions.
Microarray analysis of Akt1 activation in transgenic mouse hearts reveals transcript expression profiles associated with compensatory hypertrophy and failure (2006)

To investigate molecular mechanisms involved in the development of cardiac hypertrophy and heart failure, we developed a tetracycline-regulated transgenic system to conditionally switch a constitutively active form of the Akt1 protein kinase on or off in the adult heart. Short-term activation (2 wk) of Akt1 resulted in completely reversible hypertrophy with maintained contractility. In contrast, chronic Akt1 activation (6 wk) induced extensive cardiac hypertrophy, severe contractile dysfunction, and massive interstitial fibrosis. The focus of this study was to create a transcript expression profile of the heart as it undergoes reversible Akt1-mediated hypertrophy and during the transition from compensated hypertrophy to heart failure. Heart tissue was analyzed before transgene induction, 2 wk after transgene induction, 2 wk of transgene induction followed by 2 days of repression, 6 wk after transgene induction, and 6 wk of transgene induction followed by 2 wk of repression. Acute overexpression of Akt1 (2 wk) leads to changes in the expression of 826 transcripts relative to noninduced hearts, whereas chronic induction (6 wk) led to changes in the expression of 1,611, of which 65% represented transcripts that were regulated during the pathological phase of heart growth. Another set of genes identified was uniquely regulated during heart regression but not growth, indicating that nonoverlapping transcription programs participate in the processes of cardiac hypertrophy and atrophy. These data define the gene regulatory programs downstream of Akt that control heart size and contribute to the transition from compensatory hypertrophy to heart failure.
Discovery, Synthesis, And Structure-Based Optimization of a Series of N-(tert-Butyl)-2-(N-arylamido)-2-(pyridin-3-yl) Acetamides (ML188) as Potent Noncovalent Small Molecule Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3CL Protease (2012)

A high-throughput screen of the NIH molecular libraries sample collection and subsequent optimization of a lead dipeptide-like series of severe acute respiratory syndrome (SARS) main protease (3CLpro) inhibitors led to the identification of probe compound ML188 (16-(R), (R)-N-(4-(tert-butyl)phenyl)-N-(2-(tert-butylamino)-2-oxo-1-(pyridin-3-yl)ethyl)furan-2-carboxamide, Pubchem CID: 46897844). Unlike the majority of reported coronavirus 3CLpro inhibitors that act via covalent modification of the enzyme, 16-(R) is a noncovalent SARS-CoV 3CLpro inhibitor with moderate MW and good enzyme and antiviral inhibitory activity. A multicomponent Ugi reaction was utilized to rapidly explore structure-activity relationships within S(1'), S(1), and S(2) enzyme binding pockets. The X-ray structure of SARS-CoV 3CLpro bound with 16-(R) was instrumental in guiding subsequent rounds of chemistry optimization. 16-(R) provides an excellent starting point for the further design and refinement of 3CLpro inhibitors that act by a noncovalent mechanism of action.
Reinfection of liver graft by hepatitis C virus after liver transplantation. (1992)

We have investigated hepatitis C virus (HCV) viremia before and after orthotopic liver transplantation (OLT). 38 patients were examined; 16 were anti-HCV positive and 22 anti-HCV negative pre-OLT in a RIBA-2 test (Ortho Diagnostic Systems Inc., Westwood, MA). HCV-RNA was detected using a modified nested polymerase chain reaction in 14/38 and 10/38 patients before and after OLT, respectively. 7 of these 14 subjects who were HCV-RNA positive before OLT were also positive for serum hepatitis B surface antigen. After OLT, six patients became HCV-RNA positive, likely as a result of transfusions, while four developed a probable recurrence of HCV infection. Infection of the liver graft by the same strain of HCV was indeed demonstrated by sequence analysis of a hypervariable domain (in the envelope region) in two cases. This establishes the possibility of HCV recurrence and shows the usefulness of polymerase chain reaction as the only assay currently capable of identifying HCV infection after OLT.
An Atmospheric-Pressure Glow Discharge Ionization Source (1990)

In this work, a novel atmospheric-pressure glow discharge source is explored. This discharge operates in the 1 kV range at typically 50–250 μA current in atmospheric-pressure helium. The characteristic I vs. V curve for a glow discharge is observed, and the discharge can operate in the positive or negative modes. The background ions observed in the positive mode from the atmospheric-pressure ionization (API) cell in the mass spectrometer are characteristic of water clusters from background water in the cell, and almost no helium background ions are detected. This atmospheric-pressure glow discharge source has been used to ionize various small biologicals, drugs, peptides, and explosives analogs that have been introduced into the API cell via a direct insertion probe. The resulting mass spectra exhibit generally the MH + with minimal or no fragmentation in the positive mode, indicating that ionization of the analyte occurs softly through proton transfer from water clusters. Detection limits in the low-pg range have been obtained in both the positive and negative modes.
S-N-S Josephson Junction Consisting of Y-Ba-Cu-O/Au/Nb Thin Films (1988)

An S-N-S Josephson junction consisting of Y-Ba-Cu-O/Au/Nb thin films has been fabricated by making use of the proximity effect. The ac-Josephson effect can be confirmed by the observation of the Shapiro steps in this S-N-S junction under microwave radiation. In addition, the effects of the magnetic field and temperature on the critical current have been demonstrated, which indicates that the junction behaves phenomenologically as a Josephson junction.