gebhart/patrepeval huggingface dataset:
Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli (2004)

The cAMP response protein (CRP) is a transcription factor known to regulate many genes in Escherichia coli. Computational studies of transcription factor binding to DNA are usually based on a simple matrix model of sequence-dependent binding energy. For CRP, this model predicts many binding sites that are not known to be functional. If they are indeed spurious, the underlying binding model is called into question. We use a species comparison method to assess the functionality of a population of such predicted CRP sites in E. coli. We compare them with orthologous sites in Salmonella typhimurium identified independently by CLUSTALW alignment, and find a dependence of mutation probability on position in the site. This dependence increases with predicted site binding energy. The positions where mutation is most strongly suppressed are those where mutation would have the biggest effect on predicted binding energy. This finding suggests that many of the novel sites are functional, that the matrix model correctly estimates their binding strength, and that calculated CRP binding strength is the quantity that is conserved between species. The analysis also identifies many new E. coli binding sites and genes likely to be functional for CRP.
PET and SPECT Exploration of Central Monoaminergic Transporters for the Development of New Drugs and Treatments in Brain Disorders (2005)

Membrane and vesicular monoaminergic transporters, responsible for the homeostasis of neurotransmitter pools at nerve endings, are very involved in the physiology and diseases of central nervous system. Recent progresses of cerebral molecular imaging using SPECT and PET methods allow the extend of in vivo exploration of these transporters. For this aim, an increasing number of radiopharmaceuticals labelled with [123I], [99mTc], [11C] or [18F] have been developed such as cocaine derivatives for the DAT, compounds from the diphenyl sulfide family for the SERT, and dihydrotetrabenazine derivatives for the VMAT2. These functional imaging methods can be very useful in several neurological and psychiatric disorders which involve the monoaminergic neurotransmission systems such as Parkinson's disease, ADHD, depression and autism. For example, the DAT is a specific index of the density of dopaminergic endings which progressively degenerate in Parkinson's disease. In vivo exploration of this transporter can therefore be a relevant way (i) to realize an early detection of the loss of dopaminergic neurons, (ii) to assess the progression of the disease, (iii) to validate and improve the efficacy of new therapeutic strategies such as neuroprotection and neuroreparation. In all, the extend of in vivo exploration of monoamine transporters will allow great progress for (1) knowledge of physiopathological mechanisms of brain disorders, (2) early diagnosis of cerebral dysfunctions, allowing early use of new therapies, (3) selection of homogenous classes of subjects for therapeutic assays, (4) objectiveness of drug-molecular target interaction, (5) follow-up of disease evolution and treatment.
The E3L and K3L vaccinia virus gene products stimulate translation through inhibition of the double-stranded RNA-dependent protein kinase by different mechanisms (1993)

Vaccinia virus has evolved multiple mechanisms to counteract the interferon-induced antiviral host cell response. Recently, two vaccinia virus gene products were shown to interfere with the activity of the double-stranded RNA-dependent protein kinase (PKR): the K3L gene product and the E3L gene product. We have evaluated the efficiency by which these gene products inhibit PKR and whether they act in a synergistic manner. The effects of the two vaccinia virus gene products were compared in an in vivo system in which translation of a reporter gene (dihydrofolate reductase or eukaryotic translation initiation factor 2 alpha [eIF-2 alpha]) was inhibited because of the localized activation of PKR. In this system, the E3L gene product, and to a lesser extent the K3L gene product, potentiated translation of the reporter gene and inhibited eIF-2 alpha phosphorylation. Analysis in vitro demonstrated that the E3L gene product inhibited PKR approximately 50- to 100-fold more efficiently than the K3L gene product. However, further studies demonstrated that the mechanism of action of these two inhibitors was different. Whereas the E3L inhibitor interfered with the binding of the kinase to double-stranded RNA, the K3L inhibitor did not. We propose that the K3L inhibitor acts through its homology to eIF-2 alpha to interfere with the interaction of eIF-2 alpha with PKR. The two inhibitors did not display a synergistic effect on translation or eIF-2 alpha phosphorylation. In addition, neither K3L nor E3L expression detectably altered cellular protein synthesis.
Wideband beamforming with broad nulls of nested array (2013)

A side lobe level constraints orthogonal method for wideband beamforming with broad nulls of harmonic nested array is proposed. Space-frequency structure based on nested array is applied. Nonuniform octave subband signals are implemented by harmonic nested array and general parameter filter banks with multirate method. The reference desired broad nulls pattern is designed with side lobe level constraints orthogonal method at the highest frequency bin. It is convenient to control side lobe level by this method. If we keep the side lobe levels within certain angle range low enough, it can be seen as a broad null within the frequency spans. Each subarray is operating with the lowest rate in parallel. Weightings and patterns are realized by IDFT and DFT. These contribute to decreasing the computational load significantly and improving the speed and performances as well. Simulations show that the proposed method is competent for broad nulls wideband beamforming.
The Effectiveness of Repetitive Paravertebral Injections with Local Anesthetics and Steroids for the Prevention of Postherpetic Neuralgia in Patients with Acute Herpes Zoster (2009)

Repetitive paravertebral anesthetic block in combination with steroids plus standard treatment with acyclovir and analgesics significantly reduced the incidence of PHN than the standard treatment alone.
Simplified Statistics for Small Numbers of Observations (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSimplified Statistics for Small Numbers of ObservationsR. B. Dean and W. J. DixonCite this: Anal. Chem. 1951, 23, 4, 636–638Publication Date (Print):April 15, 1951Publication History Published online1 May 2002Published inissue 15 April 1951https://pubs.acs.org/doi/10.1021/ac60052a025https://doi.org/10.1021/ac60052a025research-articleACS PublicationsRequest reuse permissionsArticle Views3267Altmetric-Citations712LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Dengue Virus Identification by the Plaque Reduction Neutralization Test (1967)

Summary A method for identification and serologic classification of dengue viruses using a plaque reduction neutralization test and monkey immune serum is described. Results of typing 40 strains confirm the usefulness of this method for classification of low passage strains. Adaptation of the isolates to suckling mice or tissue culture was not required and strains within each of the four dengue serotypes were readily identified. Cross neutralization tests using monkey antiserum confirmed the results of the one-way neutralization test using antiserum to reference dengue strains and also indicated antigenic variation within serotypes 1, 2 and 4.
Nano Si Cluster-SiO[sub x]-C Composite Material as High-Capacity Anode Material for Rechargeable Lithium Batteries (2006)

Nanosilicon cluster- composites including nanosize Si particles were prepared by using the disproportionation of silicon mono-oxide and the polymerization of furfuryl alcohol. The applicability of nanosilicon composites as anode material for rechargeable lithium batteries was investigated on the basis of X-ray diffraction measurement, observation by transmission electron microscopy (TEM) and electrochemical studies. TEM analysis showed that Si clusters in the range of 2–10 nm were distributed homogeneously within silicon oxide phases. The nanosilicon composite anode had a large capacity of ca. and a long cycle life of cycles. The improvement of cyclability is due to the nanosize Si particles and their uniform dispersion within the silicon oxide phase retained by the carbon matrix, which could effectively suppress the pulverizing of Si particles by the volume change during lithium insertion and extraction.
Mitogen-Activated Protein Kinase: Conservation of a Three-Kinase Module From Yeast to Human (1999)

Mitogen-activated protein kinases (MAPK) are serine-threonine protein kinases that are activated by diverse stimuli ranging from cytokines, growth factors, neurotransmitters, hormones, cellular stress, and cell adherence. Mitogen-activated protein kinases are expressed in all eukaryotic cells. The basic assembly of MAPK pathways is a three-component module conserved from yeast to humans. The MAPK module includes three kinases that establish a sequential activation pathway comprising a MAPK kinase kinase (MKKK), MAPK kinase (MKK), and MAPK. Currently, there have been 14 MKKK, 7 MKK, and 12 MAPK identified in mammalian cells. The mammalian MAPK can be subdivided into five families: MAPKerk1/2, MAPKp38, MAPKjnk, MAPKerk3/4, and MAPKerk5. Each MAPK family has distinct biological functions. In Saccharomyces cerevisiae, there are five MAPK pathways involved in mating, cell wall remodelling, nutrient deprivation, and responses to stress stimuli such as osmolarity changes. Component members of the yeast pathways have conserved counterparts in mammalian cells. The number of different MKKK in MAPK modules allows for the diversity of inputs capable of activating MAPK pathways. In this review, we define all known MAPK module kinases from yeast to humans, what is known about their regulation, defined MAPK substrates, and the function of MAPK in cell physiology.
Platelet Activation and Function after Trauma (2001)

Severe injury usually results in increased platelet activation and function. However, the combination of increased platelet activation with decreased function was associated with increased mortality.
A synthetic consensus anti–spike protein DNA vaccine induces protective immunity against Middle East respiratory syndrome coronavirus in nonhuman primates (2015)

First identified in 2012, Middle East respiratory syndrome (MERS) is caused by an emerging human coronavirus, which is distinct from the severe acute respiratory syndrome coronavirus (SARS-CoV), and represents a novel member of the lineage C betacoronoviruses. Since its identification, MERS coronavirus (MERS-CoV) has been linked to more than 1372 infections manifesting with severe morbidity and, often, mortality (about 495 deaths) in the Arabian Peninsula, Europe, and, most recently, the United States. Human-to-human transmission has been documented, with nosocomial transmission appearing to be an important route of infection. The recent increase in cases of MERS in the Middle East coupled with the lack of approved antiviral therapies or vaccines to treat or prevent this infection are causes for concern. We report on the development of a synthetic DNA vaccine against MERS-CoV. An optimized DNA vaccine encoding the MERS spike protein induced potent cellular immunity and antigen-specific neutralizing antibodies in mice, macaques, and camels. Vaccinated rhesus macaques seroconverted rapidly and exhibited high levels of virus-neutralizing activity. Upon MERS viral challenge, all of the monkeys in the control-vaccinated group developed characteristic disease, including pneumonia. Vaccinated macaques were protected and failed to demonstrate any clinical or radiographic signs of pneumonia. These studies demonstrate that a consensus MERS spike protein synthetic DNA vaccine can induce protective responses against viral challenge, indicating that this strategy may have value as a possible vaccine modality against this emerging pathogen.
Applications of diamond films and related materials; Proceedings of the 1st International Conference, Auburn, AL, Aug. 17-22, 1991 (1991)

The present conference discusses the nucleation and growth of diamond from hydrocarbons, the cutting tool performance of CVD thick-film diamond, the characterization of CVD diamond grinding powder, industrial applications of crystalline diamond-coated tools, standardized SEM tribometry of diamond-coated substrates, residual stress in CVD diamond films, the optical properties of CVD diamond films, polycrystalline diamond films for optical applications, and diamond growth on ferrous metals. Also discussed are ion beam-irradiation smoothing of diamond films, electronic circuits on diamond substrates, diamond-laminated surfaces for evaporative spray cooling, electron devices based on the unique properties of diamond, diamond cold cathodes, thin-film diamond microstructure applications, Schottky diodes from flame-grown diamond, diamond films for thermionic applications, methods of diamond nucleation and selective deposition, high-rate/large-area diamond film production, halogen-assisted diamond growth, the economics of diamond technology, and the optical and mechanical properties of diamondlike films.
Dengue: an escalating problem (2002)

The short-term impact of atrial fibrillation (AF) on cardiac surgery hospitalizations has been previously reported in cohorts of various sizes, but results have been variable. Using the 2005–2014 National Inpatient Sample, we identified all adult hospitalizations for cardiac surgery using the International Classification of Diseases, Ninth Revision, Clinical Modification as any procedure code and AF as any diagnosis code. We estimated the impact of AF on inpatient mortality, length of stay (LOS), and cost of hospitalization using survey-weighted, multivariable logistic, accelerated failure-time log-normal, and log-transformed linear regressions, respectively. Additionally, we exact-matched AF to non-AF hospitalizations on various confounders for the same outcomes. A total of 1,269,414 hospitalizations were noted for cardiac surgery during the study period. Coexistent AF was found in 44.9% of these hospitalizations. Overall mean age was 65.6 years, 40.9% were female, mean LOS was 11.6 days, and inpatient mortality was 4.5%. Stroke rate was lower in AF hospitalizations (1.8% vs 2.1%, p&lt;0.001). Mortality was lower in the AF (3.9%) versus the non-AF (5%) group (exact-matched OR or emOR=0.48, 95% CI 0.29 to 0.80, p&lt;0.001; 987 matched pairs, n=2423), with similar results after procedural stratification: isolated valve replacement/repair (emOR=0.38, p&lt;0.001), isolated coronary artery bypass graft (CABG) (emOR=0.33, p&lt;0.001), and CABG with valve replacement/repair (emOR=0.55, p&lt;0.001). A 12% increase was seen in LOS in the AF subgroup (exact-matched time ratio=1.12, 95% CI 1.10 to 1.14, p&lt;0.001) among hospitalizations which underwent valve replacement/repair with or without CABG. Hospitalizations for cardiac surgery which had coexistent AF were found to have lower inpatient mortality risk and stroke prevalence but higher LOS and hospitalization costs compared with hospitalizations without AF.
Functional and morphological effects of resistance exercise on disuse-induced skeletal muscle atrophy (2011)

Abstract quality of life. Since there is no currently effective and safe treatment available for skeletal muscle atrophy, the search for new alternatives is necessary. Resistance exercise (RE) seems to be an important tool in the treatment of disuse-induced skeletal muscle atrophy by promoting positive functional (strength and power) and structural (hypertrophy and phenotypic changes) adaptive responses. Human and animal studies using different types of resistance exercise (flywheel, vascular occlusion, dynamic, isometric, and eccentric) have obtained results of great importance. However, since RE is a complex phenomenon, lack of strict control of its variables (volume, frequency, intensity, muscle action, rest intervals) limits the interpretation of the impact of the manipulation on skeletal muscle remodeling and function under disuse. The aim of this review is to critically describe the functional and morphological role of resistance exercise in disuse-induced skeletal muscle atrophy with emphasis on the principles of training.
Intralesional Candida Antigen for Common Warts in People with HIV (2013)

This is the first reported case series using Candida antigen for warts in individuals with HIV. The use of Candida antigen represents a simple and novel approach to the management of treatment-refractory warts in those with HIV. This case series provides a foundation for future larger, randomized trials.
The influence of formation on tensile strength of papers made from mechanical pulps (2000)

The importance of paper formation is widely appreciated amongst papermakers in relation to sheet appearance, but much remains unclear about its role in paper strength, particularly for paper made from mechanical pulps. This paper addressed the question of how formation affects the tensile strength of such pulps. Two softwoods mechanical pulps from species of differing fibre length and coarseness were fractionated by fibre length and formed into handsheets at standard handsheet consistency and at a headbox consistency. As found by previous workers, handsheets from the shorter fibre fractions gave higher strength. These handsheets also had better formation, as expected from shorter fibres. To isolate the influence of formation from other factors which differ between species and fractions and may cause strength differences, we compared one fraction of one species at differing forming consistencies. This showed that the direct contribution of formation to tensile strength was significant, with poor formation giving lower strength for all fractions. In addition, we compared tensile strengths of whole pulps formed at standard handsheet consistency and headbox consistency at reduced grammages over the range 60-30 gsm.
Amino acid sequence of p15 from avian myeloblastosis virus complex (1981)

The complete amino acid sequence of the p15 gag protein from avian myeloblastosis virus (AMV) complex has been determined by sequential Edman degradation of the intact molecule and of peptide fragments generated by limited tryptic cleavage, cleavage with staphylococcal protease, and cyanogen bromide cleavage. AMV p15 is a single-chain protein containing 124 amino acids. The charged amino acids tend to be clustered in the primary structure. p15 contains a single cysteine at position 113 which may be essential for the p15 associated proteolytic activity. However, p15 shows no appreciable sequence homology with papain or other classical thiol proteases.
P2X7 Receptors Regulate NKT Cells in Autoimmune Hepatitis (2006)

Adenine nucleotides induce danger signals in T cells via purinergic receptors, raising the question whether they exert similar effects on innate immunity. Here we show that micromolar concentrations of nicotinamide adenine dinucleotide (NAD) induce a rapid increase of annexin V staining in NKT cells in vitro, a response that requires expression of P2X(7)Rs. Consistent with this result, treatment of mice with NAD causes a temporary decrease of NKT cells in the liver and protects from Con A- and alpha-galactosylceramide-induced hepatitis, both of which require functional NKT cells. Resistance to liver injury is associated with decreased cytokine production by NKT cells in NAD-treated mice. In contrast, when NAD is injected into Con A- or alpha-galactosylceramide-primed mice, liver injury is exacerbated and cytokine production by NKT cells is increased. This effect is caused by P2X(7)R-mediated stimulation of activated NKT cells. In agreement, mice lacking P2X(7)Rs on lymphocytes suffer reduced liver injury, and animals lacking ADP-ribosyltransferase, the enzyme that uses NAD to attach ADP-ribosyl groups to cell surfaces, are also resistant to Con A-induced hepatitis. These results prompt the conclusion that engagement of P2X(7)Rs on NKT cells inhibits naive, while stimulating activated cells, resulting in suppression or stimulation of autoimmune hepatitis.
On the Mechanism of Hemozoin Production in Malaria Parasites: Activated Erythrocyte Membranes Promote β-Hematin Synthesis (2001)

The ferriprotoporphyrin IX (FP) molecules released by intraerythrocytic malaria parasites during hemoglobin digestion are converted to beta-hematin and are stored in the parasites' food vacuoles. It has been demonstrated in cell-free medium that the incorporation of FP into beta-hematin under physiological conditions requires a catalyst from parasite lysates or pre-formed beta-hematin. In the present studies, lysates of Plasmodium falciparum-infected erythrocytes were suspended in 1 M NaOH and were washed with phosphate buffer, pH 7.6. When the cell extracts were incubated with hematin in 0.5 M sodium acetate buffer, pH 5, for 20 hr at 37 degrees C, a large quantity of beta-hematin was formed. To determine whether parasite components were necessary for the beta-hematin formation, normal erythrocyte ghosts were similarly treated with 1 M NaOH and then incubated with hematin. In repeated experiments it was found that, on the average, 70% of the hematin was converted to beta-hematin. Membranes treated with HCl or CH(3)COOH also promoted the formation of beta-hematin, while untreated membranes were ineffective. The possibility that metabolic activities in the food vacuoles of malaria parasites may activate membrane fragments, from hemoglobin vesicles, to promote beta-hematin formation is discussed in this paper.