nils-herrmann/clean_scirepeval huggingface dataset:
Sequence analysis of the full-length genome of Japanese encephalitis virus vaccine SA_(14)-14-2 strain

To sequence the full length genome of Japanese encephalitis virus attenuated live vaccine SA 14 14 2 strain, provide direct information about the genomic structure and the possible relationship to the attenuated mechanism, and set up the basis for investigating the genetic quality control markers of the vaccine.  Six pairs of overlaping primers were designed according to the published sequences of SA 14 14 2 and SA 14 strains. Using RT PCR, cDNA fragments of SA 14 14 2 strain were got and cloned into pGEM T vector, then transformed into competent TG1 hosts. Positive clones were screened, identified and sequenced.  Sequence analysis showed that genome of JEV vaccine SA 14 14 2 strain consisted of 10976 nucleotides and contained a single open reading frame of 10299 which encoded a polyprotein of 3432 amino acids. Compared with the published sequence of SA 14 14 2 and SA 14 strain, the homology of the nucleotide sequence and deduced amino acid sequence were all more than 99%, the mutation sites were located in different regions. Seven mutation sites responsible for the attenuation deduced were all consisted in. Among them, there were 4 mutated sites between 1296 and 1506 in the E region, this region may be used as genetic markers for the quality control of the vaccine.  Sequence of SA 14 14 2 vaccine genome is similar to the published data. Some mutations are among them probably due to passage of virus in difference cultures. The sequence analysis would be helpful to understanding attenuated mechanism of the vaccine and developing genetic quality control standard for vaccine production.

Field of study: Biology
Identification of Verapamil Binding Sites Within Human Kv1.5 Channel Using Mutagenesis and Docking Simulation.

The phenylalkylamine class of L-type Ca2+ channel antagonist verapamil prolongs the effective refractory period (ERP) of human atrium, which appears to contribute to the efficacy of verapamil in preventing reentrant-based atrial arrhythmias including atrial fibrillation. This study was designed to investigate the molecular and electrophysiological mechanism underlying the action of verapamil on human Kv1.5 (hKv1.5) channel that determines action potential duration and ERP in human atrium.



Site-directed mutagenesis created 10 single-point mutations within pore region of hKv1.5 channel. Wholecell patch-clamp method investigated the effect of verapamil on wild-type and mutant hKv1.5 channels heterologously expressed in Chinese hamster ovary cells. Docking simulation was conducted using open-state homology model of hKv1.5 channel pore.



Verapamil preferentially blocked hKv1.5 channel in its open state with IC50 of 2.4±0.6 μM (n = 6). The blocking effect of verapamil was significantly attenuated in T479A, T480A, I502A, V505A, I508A, L510A, V512A and V516A mutants, compared with wild-type hKv1.5 channel. Computer docking simulation predicted that verapamil is positioned within central cavity of channel pore and has contact with Thr479, Thr480, Val505, Ile508, Ala509, Val512, Pro513 and Val516.



Verapamil acts as an open-channel blocker of hKv1.5 channel, presumably due to direct binding to specific amino acids within pore region of hKv1.5 channel, such as Thr479, Thr480, Val505, Ile508, Val512 and Val516. This blocking effect of verapamil on hKv1.5 channel appears to contribute at least partly to prolongation of atrial ERP and resultant antiarrhythmic action on atrial fibrillation in humans.

Field of study: Biology, Chemistry
Ulna Autograft for Wrist Arthrodesis: A Novel Approach in Failed Wrist Arthoplasty

Rheumatoid arthritis is a polyarthropathy affecting approximately 1% of the population worldwide. Wrist involvement is observed around 75% of patients, resulting in substantial disability and morbidity. A multidisciplinary approach to management of such patients is undertaken to prevent disease progression, many go on to develop debilitating disease requiring surgical intervention. Total wrist arthroplasty and arthrodesis are the main options available for those with end-stage disease, with arthroplasty preferred due to its ability to preserve a good degree of wrist function. Where complications occur with total wrist arthroplasty, salvage surgery with arthrodesis can be considered, however this requires satisfactory bone stock to enable stable fusion of the joint following arthroplasty. We report our experience of Ulna strut allografts in wrist arthrodesis in the management of failed total wrist arthroplasty.

Field of study: Medicine
Characterization of gamma-aminobutyrate type A receptors with atypical coupling between agonist and convulsant binding sites in discrete brain regions.

Gamma-ainobutyric acid type A (GABA(A)) receptor ionophore ligand t-[35S]butylbicyclophosphorothionate ([35S]TBPS) was used in an autoradiographic assay on brain cryostat sections to visualize and characterize atypical GABA-insensitive [35S]TBPS binding previously described in certain recombinant GABA(A) receptors and the cerebellar granule cell layer. Picrotoxinin-sensitive but 1-mM GABA-insensitive [35S]TBPS binding was present in the rat cerebellar granule cell layer, many thalamic nuclei, subiculum and the internal rim of the cerebral cortex, amounting in these regions up to 6% of the basal binding determined in the absence of exogenous GABA. Similar binding properties were detected also in human and chicken brain sections. Like the GABA-sensitive [35S]TBPS binding, GABA-insensitive binding was profoundly decreased by pentobarbital, pregnanolone, loreclezole and Mg2+. The binding was reversible and apparently dependent on Cl- ions. Localization of the GABA-insensitive [35S]TBPS binding was not identical to that of high-affinity [3H]muscimol binding and diazepam-insensitive [3H]Ro 15-4513 binding, two previously established receptor subtype-dependent binding heterogeneities in the rat brain. The present study reveals a component of the GABA-ionophore enriched in the thalamus and cerebellar granule cells, possibly representing poorly desensitized or desensitizing receptors.

Field of study: Biology
Absence of intrinsic electric conductivity in single dsDNA molecules.

The intrinsic dc conductivity of long, individual lambda phage dsDNA molecules has been investigated by ultrasensitive low current-voltage-spectroscopy (IV) under ambient conditions and controlled low humidity inert gas atmosphere on microfabricated metal-insulator-metal gap structures. We found a strong dependence of the measured conductivity on the apparent humidity, which we attribute to capillary condensation of water to the immobilized DNA molecules, giving rise to additional ionic currents. Additional IV-spectroscopy experiments under controlled argon atmosphere always revealed a significant drop in electrical conductivity to 4 x 10(-15)AV(-1)microm(-1), indicating almost no considerable contribution of electrical long range charge transport.

Field of study: Biology, Engineering
Will the Real Federal Deficit Stand Up

In some circles, the federal budget deficit has become the hottest political issue since Vietnam. Democrats and Republicans echo each others' proclamations of disaster and largely restrict their differences to proposed remedies and the casting of blame. Scoring political points has replaced almost all efforts at sober economic analysis. Deficits do matter, but to know how and how much, you have to measure them right. And deficits can be good as well as bad. By official measure, the federal budget has been in deficit in all but eight of the fifty-five years from 1931 through 1985. In fact, in the twenty-five years since 1960 only one, 1969, had no deficit. The last sixteen years have presented an unbroken picture of deficits. World War II saw what were then huge deficits, totaling $170 billion for the years 1942 through 1945. The total gross federal debt over that period rose by $203 billion. From 1946 through 1984, budget deficits, net of surpluses, totaled $988 billion; including off-budget outlays, they totaled $1,112 billion. Over that period, the gross federal public debt increased by $1,317 billion. This is a history that, at least in general terms, is well etched into the public consciousness. It has been the stuff of many sober pronouncements and warnings and has frequently agitated political debate. A number of additional items of information, however, compli-

Field of study: Economics
In-situ EXAFS study of copper in the electrokinetic remediation process.

The speciation of copper in the early stage of the electrokinetic remediation (EKR) process has been studied by extended X-ray absorption fine structure (EXAFS) spectroscopy in the present work. By in-situ EXAFS, we found that copper in a contaminated soil possessed a Cu-O bond distance of 1.98 A with a coordination number (CN) of 5.8. In the second shell, the bond distance of Cu-(O)-Cu was 2.87 A with a CN of 6.4. However, possibly due to the fact that incompact copper atoms in the outer shells were distorted by EKR, the Cu-(O)-Cu (2nd shell) bond distance and the CN of copper in the contaminated soil decreased by 0.08 A and 5.4, respectively in the early stage of the EKR process. Interestingly, after prolonging the contact time to about 80 minutes, the 1st-shell copper atoms were also perturbed by EKR. This work is an example of usefulness of the in-situ EXAFS spectroscopy for detailed studies of the speciation of copper in the contaminated soil during EKR process.

Field of study: Physics
Engineering Consultancy Practice (ECP) Business Model in Malaysia: A Structural Equation Modeling (SEM) Approach

The implementation of liberalization in Malaysia has offered opportunities to the Malaysian to expand business. The salient point of liberalization of Engineering Consultancy Practices (ECP) is the opening of the flood gate for non-professionals (including foreigners) to register and operates consultancy practices. This would create an excessive competitive environment to the Malaysian ECP. The aim of this study is to identify the successful business model to be adopted by Engineering Consultancy Practice (ECP) for building its capacity and competitiveness. This study is important in the sense that it serves as one of the pioneer studies, focusing on the engineering consultancy practices, from the perspective of business model. Principal Component Analysis (PCA) is employed to analyze data from a quantitative survey. Three components are extracted through PCA approach: (1) Profit Structure factor, (2) Management Capability factor and (3) Stakeholder Relationship factor. Consequently, Structural Equation Modeling (SEM) is utilized to perform analysis on the data extracted from PCA. Two (2) Business Model Indices are formed to examine the business performance in terms of business model criteria and business performance. Through the data validation, it is found that ECP Business Performance Index is best to evaluate the business performance. Understanding the core values related to the Engineering Consultancy Practices could help the local stakeholders to have better preparation and planning to face a greater challenge lies as a result of the liberalization.

Field of study: Business
Meteoric water circulation in a rolling-hinge detachment system (northern Snake Range core complex, Nevada)

Combined petrofabric, microstructural, stable isotopic, and 40 Ar/ 39 Ar geochronologic data provide a new perspective on the Cenozoic evolution of the northern Snake Range metamorphic core complex in east-central Nevada. This core complex is bounded by the northern Snake Range detachment, interpreted as a rolling-hinge detachment, and by an underlying shear zone that is dominated by muscovite-bearing quartzite mylonite and interlayered micaschist. In addition to petrofabric, microstructural analysis, and 40 Ar/ 39 Ar geochronology, we use hydrogen isotope ratios (δD) in synkinematic white mica to characterize fluid-rock interaction across the rolling-hinge detachment. Results indicate that the western flank of the range preserves mostly Eocene deformation (49–45 Ma), characterized by coaxial quartz fabrics and the dominant presence of metamorphic fluids, although the imprint of meteoric fluids increases structurally downward and culminates in a shear zone with a white mica 40 Ar/ 39 Ar plateau age of ca. 27 Ma. In contrast, the eastern flank of the range displays pervasive noncoaxial (top-to-the-east) fabrics defined by white mica that formed in the presence of meteoric fluids and yield Oligocene–Miocene 40 Ar/ 39 Ar ages (27–21 Ma). Evolution of the Oligocene–Miocene rolling-hinge detachment controlled where and when faulting was active or became inactive owing to rotation, and therefore where fluids were able to circulate from the surface to the brittle-ductile transition. On the western flank (rotated detachment), faulting became inactive early, while continued active faulting on the eastern flank of the detachment allowed surface fluids to reach the mylonitic quartzite. The combined effects of synkinematic recrystallization and fluid interaction reset argon and hydrogen isotope ratios in white mica until the early Miocene (ca. 21 Ma), when the brittle-ductile transition was exhumed beneath the detachment.

Field of study: Geology
Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression.

The 2-oxoglutarate dehydrogenase (OGDH) complex is an important control point in vertebrate mitochondrial oxidative metabolism, including in the citrate cycle and catabolism of alternative fuels including glutamine. It is subject to allosteric regulation by NADH and the ATP/ADP ratio, and by Ca(2+) through binding to the E1 subunit. The latter involves a unique Ca(2+)-binding site which includes D(114)ADLD (site 1). Here, we describe three splice variants of E1 in which either the exon expressing this site is replaced with another exon (loss of site 1, LS1) or an additional exon is expressed leading to the insertion of 15 amino acids just downstream of site 1 (Insert), or both changes occur together (LS1/Insert). We show that all three variants are essentially Ca(2+)-insensitive. Comparison of massive parallel sequence (RNA-Seq) databases demonstrates predominant expression of the Ca(2+)-sensitive archetype form in heart and skeletal muscle, but substantial expression of the Ca(2+)-insensitive variants in brain, pancreatic islets and other tissues. Detailed proteomic and activity studies comparing OGDH complexes from rat heart and brain confirmed the substantial difference in expression between these tissues. The evolution of OGDH variants was explored using bioinformatics, and this indicated that Ca(2+)-sensitivity arose with the emergence of chordates. In all species examined, this was associated with the co-emergence of Ca(2+)-insensitive variants suggesting a retained requirement for the latter in some settings. Tissue-specific expression of OGDH splice variants may thus provide a mechanism that tunes the control of the enzyme to the specialized metabolic and signalling needs of individual cell types.

Field of study: Biology, Computer science
Approximate controllability of the nonlinear third-order dispersion equation

In this paper, we consider the approximate controllability of nonlinear third-order dispersion equation of the form ∂ w ∂ t ( x , t ) + ∂ 3 w ∂ x 3 ( x , t ) = ( Gu ) ( x , t ) + f ( t , w ( x , t ) ) on the interval 0 ⩽ x ⩽ 2π, t ⩾ 0 with initial and periodic boundary conditions w ( x , 0 ) = 0 , ∂ k w ∂ x k ( 0 , t ) = ∂ k w ∂ x k ( 2 π , t ) , k = 0 , 1 , 2 . We study the approximate controllability for nonlinear dispersion system under the assumption that the corresponding linear control system is approximately controllable. The solutions are given by a variation of constants formula which allows us to study the approximate controllability for nonlinear dispersion systems. Based on the semigroup theory and fixed point approach, sufficient conditions are formulated and proved.

Field of study: Mathematics
Supporting the Use of Health Technology Assessments by Decision-Makers.

A perceived gap exists in how well Canadian health technology assessment (HTA) producers are supporting the use of their HTAs by decision-makers. The authors propose that the newly released HTA Database Canadian search interface incorporate structured decision-relevant summaries of HTAs that would be developed by participating Canadian HTA organizations. The registry would serve as a "one-stop shop" by including HTA reports along with their structured summaries in a format that better meets decision-makers' needs. The Health Technology Analysis Exchange - a Canadian network of publicly funded HTA producers - is well-positioned to undertake this work and would welcome input about both the idea and its execution.

Field of study: Medicine, Political science
THE MAP ROOM: One Hundred Inches in One Hundred Hours

rom 22–27 November 2001, two complex Intermountain storm systems produced 108 inches of snow at Alta ski area in the Wasatch Mountains of northern Utah (Fig. 1; Steenburgh 2003). Since 100 in. fell in 100 h, local news media coined the phrases “100 inches in 100 hours” and “Hundred-Inch Storm Cycle” to describe the event (a storm cycle is a period where multiple winter storms occur in rapid succession). The storm cycle was the largest at Alta since 1991, provided a boost for preparations for the 2002 Winter Olympics, and produced substantial lowland precipitation. Salt Lake City International Airport (SLC) observed 1.27 in. of rain on 22 November, a record for a calendar day in that month, while during colder periods, up to 33 in. of snow fell in the Salt Lake City metropolitan area. The event provided an excellent example of the complex evolution of Intermountain winter storms, with storm stages delineated by the passage of large-scale weather features and their accompanying changes in stability and precipitation processes. Contrasts between mountain and lowland precipitation varied from stage to stage and storm to storm, illustrating the limitations of applying climatological precipitation–altitude relationships for short-range quantitative precipitation forecasting. The first storm system moved through Utah from 0600 UTC 22 to 0700 UTC 24 November, producing 50 in. of snow at Alta. Time–height sections for SLC, created from hourly National Centers for Environmental Prediction (NCEP) Rapid Update Cycle (RUC2) analyses, showed an intrusion of low-θe air aloft several hours ahead of a surface-based cold front . Widespread valley rain and mountain snow ONE HUNDRED INCHES IN ONE HUNDRED HOURS The Complex Evolution of an Intermountain Winter Storm Cycle

Field of study: Environmental science
Resonance excitation of intense acoustic beams in crystals of different syngonies

The resonance excitation of an intense elastic wave in a crystal, arising under conditions of the nonspecular reflection of an incident pump wave is described for a crystal geometry close to a cut that allows the existence of a bulk eigenwave satisfying the free boundary condition. It is shown that choosing a crystal surface parallel to the plane of symmetry optimizes reflection resonance due to the coincidence of the excited wave’s intensity maximum and the reflected (parasite) wave’s intensity minimum in the same geometry of reflection. Parameters of resonance are given for a number of crystals with monoclinic, orthorhombic, and hexagonal syngonies.

Field of study: Physics
Lipotoxic Palmitate Impairs the Rate of β-Oxidation and Citric Acid Cycle Flux in Rat Neonatal Cardiomyocytes

Diabetic hearts exhibit intracellular lipid accumulation. This suggests that the degree of fatty acid oxidation (FAO) in these hearts is insufficient to handle the elevated lipid uptake. We previously showed that palmitate impaired the rate of FAO in primary rat neonatal cardiomyocytes. Here we were interested in characterizing the site of FAO impairment induced by palmitate since it may shed light on the metabolic dysfunction that leads to lipid accumulation in diabetic hearts.  We measured fatty acid oxidation, acetyl-CoA oxidation, and carnitine palmitoyl transferase (Cpt1b) activity. We measured both forward and reverse aconitase activity, as well as NAD+ dependent isocitrate dehydrogenase activity. We also measured reactive oxygen species using the 2', 7'-Dichlorofluorescin Diacetate (DCFDA) assay. Finally we used thin layer chromatography to assess diacylglycerol (DAG) levels.  We found that palmitate significantly impaired mitochondrial β-oxidation as well as citric acid cycle flux, but not Cpt1b activity. Palmitate negatively affected net aconitase activity and isocitrate dehydrogenase activity. The impaired enzyme activities were not due to oxidative stress but may be due to DAG mediated PKC activation.  This work demonstrates that palmitate, a highly abundant fatty acid in human diets, causes impaired β-oxidation and citric acid cycle flux in primary neonatal cardiomyocytes. This metabolic defect occurs prior to cell death suggesting that it is a cause, rather than a consequence of palmitate mediated lipotoxicity. This impaired mitochondrial metabolism can have important implications for metabolic diseases such as diabetes and obesity.

Field of study: Biology, Chemistry
Effects of Tripterygium wilfordii saponins and interleukin-10 on dendritic cells from human peripheral blood.

To study the effects of Tripterygium wilfordii (TII) and IL-10 on human leukocyte antigen-DR (HLA-DR) and CD80 expressions and IL-12 p40 subunit production and transcription of dendritic cells (DC) in human peripheral blood from healthy volunteers in vitro.



DC were generated by culturing plastic-adherent peripheral blood mononuclear cells with GM-colony stimulating factor (GM-CSF), IL-4, and TNFalpha. The expressions of HLA-DR and CD80 were examined by flow cytometry after the cells were stained with immunofluorescence antibodies. Enzyme-linked immunosorbent assay and reverse transcriptase polymerase chain reaction analysis were used to detect IL-12 p40 protein level and mRNA transcription, respectively.



TII 5 - 20 mg/L and IL-10 50 - 200 microg/L greatly down-regulated the membrane expressions of HLA-DR and CD80 on DC in a concentration-dependent manner. IL-12 p40 production and mRNA transcription were also inhibited in DC both by TII and by IL-10.



TII and IL-10 exert immunosuppressive role via inhibiting membrane expressions of HLA-DR and CD80 and synthesis of IL-12 p40 subunit in DC.

Field of study: Biology, Chemistry, Medicine
Monitoring temporal and spatial variations in galactic cosmic rays (GCRs) in the inner heliosphere from data on cosmogenic radionuclides in freshly-fallen meteorites

Meteorite data on monitoring the variations in GCR gradients at 2–4 AU from the Sun over the period 1957–2010 demonstrate the effect of the inversion of solar magnetic fields (SMFs) during the solar maximum periods of 11-year solar cycles on the depth of GCR modulation in the heliosphere.

Field of study: Physics