nils-herrmann/clean_scirepeval huggingface dataset:
Apolipoprotein E Polymorphism in a Healthy Lebanese Population

The gene for apolipoprotein (apo) E, which modulates serum lipoprotein metabolism and concentration, is polymorphic with three major alleles, E2, E3, and E4, and a corresponding six apo E genotypes, E2/E2, E3/E2, E3/E3, E4/E2, E4/E3, and E4/E4. Due to its clinical importance in regulating lipid transport and redistribution, and coupled with the association of certain apo E alleles with metabolic disorders, we investigated apo E genotype in 155 healthy Lebanese individuals of both sexes, aged 5–77, by PCR/Cfo I restriction analysis.  Total genomic DNA was extracted from the peripheral blood of study subjects, and apo E genomic sequence was amplified by PCR using one set of primers defining a conserved region of apo E gene. Apo E genotype was determined by the digestion of the PCR products with Cfo I, followed by agarose gel electrophoresis.  Among the genotypes obtained the most prevalent were: E3/E3 (120/155; 77.42%), E2/E3 (20/155; 12.90%), E3/E4 (13/155; 8.39%), and E2/E4 (2/155; 1.29%). None of the homozygous E2/E2 or E4/E4 genotypes were detected. Furthermore, there was no difference in apo E genotype distribution with regard to age or sex, which is in accordance with the reports for other study populations.  The finding that apo E3/E3 is the most significant genotype in healthy Lebanese is similar to what was described for Caucasian populations. Further studies are required to establish the prevalence of homozygous E2/E2 and E4/E4.

Field of study: Medicine
An Improved Mix Transmission Algorithm for Privacy-Preserving

With the rapid development of the internet of things (IOT), personal privacy has been realized as the most important security issue in wireless sensor networks, especially in the Body Area Network (BAN) used in the medical field. Traditional encryption methods cannot defense against the attacks in which the communication signal vector is analyzed in time and space dimensions, while the data is transmitting in the wireless space. Based on the above requirements, an improved security data mix transmission algorithm for medical applications in the BAN is presented in this paper. Combined with the practical application scenarios, this algorithm can realize anonymous privacy protection of data transmission in the transmission process and present better transmission performance by dividing the whole network into many smaller ring networks and generating more tokens in the network. transmission simulations are conducted and the results show the method proposed offers less energy consumption and time delay

Field of study: Computer science
Pressure Induced Superconductivity in Ba0.5Sr0.5Fe2As2

High-pressure electrical resistance measurements have been performed on single crystal Ba0.5Sr0.5Fe2As2 platelets to pressures of 16 GPa and temperatures down to 10 K using designer diamond anvils under quasi-hydrostatic conditions with an insulating steatite pressure medium. The resistance measurements show evidence of pressure-induced superconductivity with an onset transition temperature at ~31 K and zero resistance at ~22 K for a pressure of 3.3 GPa. The transition temperature decreases gradually with increasing in pressure before completely disappearing for pressures above 12 GPa. The present results provide experimental evidence that a solid solution of two 122-type materials, e.g., Ba1-x.SrxFe2As2 (0 < x <1), can also exhibit superconductivity under high pressure

Field of study: Physics
High-Performance MWIR HgCdTe on Si Substrate Focal Plane Array Development

The development of low noise-equivalent differential temperature (NEDT), high-operability midwave infrared (MWIR) focal plane arrays (FPAs) fabricated from molecular beam epitaxial (MBE)-grown HgCdTe on Si-based substrates is reported. High-quality n-type MWIR HgCdTe layers with a cutoff wavelength of 4.90 μm at 77 K and a carrier concentration of 1–2 × 1015 cm−3 were grown on CdTe/Si substrates by MBE. Highly uniform composition and thickness over 3-inch areas were demonstrated, and low surface defect densities (voids ~5 × 102 cm−2, micro-defects ~5 × 103 cm−2) and etch pit density (~3.5 × 106 cm−2) were measured. This material was used to fabricate 320 × 256, 30 μm pitch FPAs with planar device architecture; arsenic implantation was used to achieve p-type doping. Radiometric and noise characterization was also performed. A low NEDT of 13.8 m K at 85 K for a 1 ms integration time with f/#2 optics was measured. The NEDT operability was 99% at 120 K with a mean dark current noise of 8.14 × 10−13 A/pixel. High-quality thermal images were obtained from the FPA up to a temperature of 150 K.

Field of study: Materials science
Meta-Analysis of Experimental Manipulations: Some Factors Affecting the Velten Mood Induction Procedure

Manipulation validity may be influenced by many factors, including specific aspects of experimental procedure. Meta-analysis is an ideal tool for assessing factors that influence manipulations because it is capable of equating, combining, and gauging the impact of different experimental procedures on a given manipulation. This use of meta-analysis is demonstrated by meta-analyzing experiments employing the Velten mood manipulation. This manipulation has been criticized for creating experimental demand. Procedures relevant to experimental demand include whether an honest or deceptive cover story is used and whether a self-report or non-self-report manipulation check measure is used. Effect sizes are smaller when a deceptive (vs. honest) cover story is used and when a non-self-report (vs. self-report) manipulation check measure is used. Discussion concerns how the Velten manipulation may be compromised and how meta-analysis may be employed to evaluate factors influencing manipulation validity.

Field of study: Psychology
Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.

Metabolic network reconstructions define metabolic information within a target organism and can therefore be used to address incomplete metabolic information. In the present study we used a computational approach to identify human metabolites whose metabolism is incomplete on the basis of their detection in humans but exclusion from the human metabolic network reconstruction RECON 1. Candidate solutions, composed of metabolic reactions capable of explaining the metabolism of these compounds, were then identified computationally from a global biochemical reaction database. Solutions were characterized with respect to how metabolites were incorporated into RECON 1 and their biological relevance. Through detailed case studies we show that biologically plausible non-intuitive hypotheses regarding the metabolism of these compounds can be proposed in a semi-automated manner, in an approach that is similar to de novo network reconstruction. We subsequently experimentally validated one of the proposed hypotheses and report that C9orf103, previously identified as a candidate tumour suppressor gene, encodes a functional human gluconokinase. The results of the present study demonstrate how semi-automatic gap filling can be used to refine and extend metabolic reconstructions, thereby increasing their biological scope. Furthermore, we illustrate how incomplete human metabolic knowledge can be coupled with gene annotation in order to prioritize and confirm gene functions.

Field of study: Biology, Computer science
CONTINUUM ASPECTS OF RF GRADIENT ACCELERATION OF PLASMA

A quasi-one-dimensional model of acceleration of a continuum plasma by r- f electric field gradient forces is examined. The conditions imposed on the electric field in order to effect sonic transitions are given. The case of isentropic flow is treated, and departure from the particle model is indicated for pressure> 100 mu and temperatures approx equal = 0.1 ev.

Field of study: Physics
SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination.

SGXPro consists of four components. (i) A parallel workflow engine that was designed to automatically manage communication between the different processes and build systematic searches of algorithm/program/parameter space to generate the best possible result for a given data set. This is performed by offering the user a palette of programs and techniques commonly used in X-ray structure determination in an environment that lets the user choose programs in a mix-and-match manner, without worrying about inter-program communication and file formats, during the structure-determination process. The current SGXPro program palette includes 3DSCALE, SHELXD, ISAS, SOLVE/RESOLVE, DM, SOLOMON, DMMULTI, BLAST, AMoRe, EPMR, XTALVIEW, ARP/wARP and MAID. (ii) A client/server architecture that allows the user to utilize the best computing facility available. (iii) Plug-in-and-play design, which allows easily integration of new programs into the system. (iv) User-friendly interface.

Field of study: Chemistry
Cancer immune checkpoint blockade therapy and its associated autoimmune cardiotoxicity

The immune checkpoint molecules are emerged in the evolution to protect the host from self-attacks by activated T cells. However, cancer cells, as a strategy to survive and expand, can hijack these molecules and mechanisms to suppress T cell-mediated immune responses. Therefore, an idea of blocking the checkpoint molecules to enhance the anti-tumor activities of the host immune system has been developed and applied to the cancer therapy after discovery of the inhibitory T cell co-receptor, cytotoxic T-lymphocyte associated protein 4 (CTLA-4), and further enhanced on the identification of PD-1 and its ligands. Since 2010, several checkpoint inhibitors have been approved by FDA and many more are in clinical trials. In the treatment of advanced cancers, these inhibitors significantly increased response rates and survival benefits. However, accompanied with the striking results, immune-related adverse events (irAEs) that broadly occurred in many organs were observed and reported, some of which were fatal. Herein, we first review the recent progressions in the research of the immune checkpoint molecules and the application of their blocking antibodies in cancer treatment, and then discuss the cardiac toxicity induced by the therapy and the strategy to monitor, manage this adverse event when it occurs.

Field of study: Biology, Chemistry, Medicine
Re: The early history of endoscopic correction of vesicoureteric reflux: the Dublin contribution.

Endoscopic correction of vesicoureteric reflux (VUR) is now the most common therapeutic intervention for the condition. Although much of the impetus for its use has emanated from Dublin, Ireland, there is some uncertainty about the origin of the innovation. Matouschek described the use of Teflon injected endoscopically under the ureteric ostium in 1981, in German and Spanish journals . In 1984, O’Donnell and Puri, while unaware of the previous publications, described a similar technique [3,4]. O’Donnell’s original concept of the endoscopic deposit of a bulking agent under the ureteric orifice was developed by Puri, who proposed Teflon (Polytef) as the agent. Experimental work on piglets was carried out but none of this was done endoscopically. The agent was introduced via a porcine cystotomy. The first endoscopic corrections of VUR in Dublin were not done on pigs but on human patients by O’Donnell, on 5 March 1984, and it was he who coined the acronym STING (Subureteric Teflon INGection). A series of successful clinical interventions followed and were reported in English [4]. We, the undersigned, were, with O’Donnell, the only three consultant paediatric surgeons on the staff of Our Lady’s Hospital for Sick Children, Dublin, at the time of the development of the procedure. Guiney was also Professor

Field of study: Medicine
Direct Evidence of Secondary Recoiled Nuclei From High Energy Protons

The production of secondary recoiled particles from interactions between high energy protons and microelectronics devices was investigated. By using NAND Flash memories, we were able to directly obtain analog information on recoil characteristics. While our results qualitatively confirm the role of nuclear reactions, in particular of those with tungsten, a quantitative model based on Monte Carlo and device-level simulations cannot describe the observed results in terms of recoils from proton-W reactions.

Field of study: Physics
Self-charging of the Eyjafjallajokull volcanic ash plume

Volcanic plumes generate lightning from the electrification of plume particles. Volcanic plume charging at over 1200 km from its source was observed from in situ balloon sampling of the April 2010 Eyjafjallajokull plume over Scotland. Whilst upper and lower edge charging of a horizontal plume is expected from fair weather atmospheric electricity, the plume over Scotland showed sustained positive charge well beneath the upper plume edge. At these distances from the source, the charging cannot be a remnant of the eruption itself because of charge relaxation in the finite conductivity of atmospheric air.

Field of study: Environmental science
COALESCENCE OF SPHERES BY SURFACE DIFFUSION

The shape evolution of small heated metal particles is dominated by surface diffusion. When two spheres touch, they will thus merge into one, as they continually decrease their surface area. Focusing on the asymptotic behavior when the radius r of the neck joining the two spheres is still small, it is found that the metal does not stay simply connected, but encloses an intricate succession of toroidal voids. The temporal evolution of r exhibits a new type of self-similar behavior resulting from a discrete sequence of secondary singularities. [S0031-9007(98)05587-2]

Field of study: Physics
Aptian dinosaur footprints from the Apulian platform (Bisceglie, Southern Italy) in the framework of periadriatic ichnosites

New dinosaur tracks have been found near Bisceglie (Bari, Apulia), on loose blocks ascribed to the Corato Member (late Bedoulian to early Gargasian) of the Calcare di Bari Fm. The material consists of isolated footprints as well as of short trackways of quadrupedal and bipedal dinosaurs. The new tracksite has yielded a quite differentiated dinosaur ichnocoenosis, including theropod, sauropod, thyreophoran and ornithopod footprints. The discovery of early Aptian dinosaur footprints in the limestone of the carbonate platform of southern Italy gives new insights on dinosaur distribution, and new palaeontological constraints for the palaeogeographic reconstruction of the Mediterranean Tethys during the Cretaceous. The analysis of this and others ichnosites of the periadriatic carbonate platforms, gives evidence of repeated emersions and of widespread land-vertebrates dwelling. The characteristics of the associations suggest that the trackmakers did not constitute a real coevolved association but the occasional co-occurrence of taxa after migration. The results emphasize the need of both structural and environmental continuity and walking ways between a southern continent and the periadriatic carbonate platforms during the Early Cretaceous.

Field of study: Environmental science, Geography
Dissection of a model for neuronal parabolic bursting

We have obtained new insight into the mechanisms for bursting in a class of theoretical models. We study Plant's model [24] for Aplysia R-15 to illustrate our view of these so-called “parabolic” bursters, which are characterized by low spike frequency at the beginning and end of a burst. By identifying and analyzing the fast and slow processes we show how they interact mutually to generate spike activity and the slow wave which underlies the burst pattern. Our treatment is essentially the first step of a singular perturbation approach presented from a geometrical viewpoint and carried out numerically with AUTO . We determine the solution sets (steady state and oscillatory) of the fast subsystem with the slow variables treated as parameters. These solutions form the slow manifold over which the slow dynamics then define a burst trajectory. During the silent phase of a burst, the solution trajectory lies approximately on the steady state branch of the slow manifold and during the active phase of spiking, the trajectory sweeps through the oscillation branch. The parabolic nature of bursting arises from the (degenerate) homoclinic transition between the oscillatory branch and the steady state branch. We show that, for some parameter values, the trajectory remains strictly on the steady state branch (to produce a resting steady state or a pure slow wave without spike activity) or strictly in the oscillatory branch (continuous spike activity without silent phases). Plant's model has two slow variables: a calcium conductance and the intracellular free calcium concentration, which activates a potassium conductance. We also show how bursting arises from an alternative mechanism in which calcium inactivates the calcium current and the potassium conductance is insensitive to calcium. These and other biophysical interpretations are discussed.

Field of study: Biology, Mathematics
Sphingosylphosphorylcholine stimulates human monocyte-derived dendritic cell chemotaxis

To investigate the effects of sphingosylphosphorylcholine (SPC) on human monocyte-derived dendritic cell (DC) chemotaxis.Human DC were generated from peripheral blood monocytes by culturing them with granulocyte macrophage-colony stimulating factor and interleukin-4. The effect of SPC on the DC chemotactic migration was measured by chemotaxis assay. Intracellular signaling event involved in the SPC-induced DC chemotaxis was investigated with several inhibitors for specific kinase. The expression of the SPC receptors was examined by reverse transcription polymerase chain reaction.We found that SPC induced chemotactic migration in immature DC (iDC) and mature DC (mDC). In terms of SPC-induced signaling events, mitogen activated protein kinase activation and Akt activation in iDC and mDC were stimulated. SPC-induced chemotaxis was mediated by extracellular signal-regulated protein kinase and phosphoino-sitide-3-kinase, but not by calcium in both iDC and mDC. Although mDC express ovarian cancer G protein-coupled receptor 1, but not G protein-coupled receptor 4, iDC do not express any of these receptors. To examine the involvement of sphin-gosine-1-phosphate (S1P) receptors, we checked the effect of an S1P receptor antagonist (VPC23019) on SPC-induced DC chemotaxis. VPC23019 did not affect SPC-induced DC chemotaxis.The results suggest that SPC may play a role in regulating DC trafficking during phagocytosis and the T cell-stimulating phase, and the unique SPC receptor, which is different from S1P receptors, is involved in SPC-induced chemotaxis.

Field of study: Biology, Chemistry, Medicine
Armature Reaction Analysis of a New Four-Phase Fault-Tolerant Doubly Salient Wound-Field Generator

To find the design basis of a new machine, the armature reaction should be first analyzed. With the given mathematical model of the excitation magnetic potential and the armature reaction magnetic potential of the wound-field doubly salient generator, the static armature reaction is presented in this paper. With the presented voltage equation, the simulated flux, current, and voltage waveforms are used to analyze the transient armature reaction in the normal state and fault-tolerant state. The analysis results show that the armature reaction can be concluded as “weakening in approaching and strengthening in leaving” by delaying the inflection point of the total phase flux. The finite-element anal-ysis and the prototype experiments of single-phase open-circuit, single-tube open-circuit and interturn short-circuit were carried out. The tested current waveforms with armature reaction verify the theoretical analysis and simulation results.

Field of study: Physics
Meningiomas: the role of preoperative angiography and embolization.

The field of interventional neuroradiology has experienced remarkable technological developments in microcatheters and embolic materials during the past two decades. The realm of meningioma therapy has benefited handsomely from the combination of these technical improvements and the knowledge of experienced practitioners in this field. Transarterial embolization has become a standard procedure in the preoperative management of meningiomas. The authors describe the indications, pretreatment evaluation, techniques, and outcomes when preoperative angiography and embolization are performed in the treatment of these tumors.

Field of study: Medicine
Use of pharmacogenomics in pediatric renal transplant recipients

Transplant recipients receive potent immunosuppressive drugs in order to prevent graft rejection. Therapeutic drug monitoring is the current approach to guide the dosing of calcineurin inhibitors, mammalian target of rapamycin inhibitors (mTORi) and mofetil mycophenolate. Target concentrations used in pediatric patients are extrapolated from adult studies. Gene polymorphisms in metabolizing enzymes and drug transporters such as cytochromes CYP3A4 and CYP3A5, UDP-glucuronosyl transferase, and P-glycoprotein are known to influence the pharmacokinetics and dose requirements of immunosuppressants. The implications of pharmacogenomics in this patient population is discussed. Genetic information can help with achieving target concentrations in the early post-transplant period, avoiding adverse drug reactions and drug-drug interactions. Evidence about genetic studies and transplant outcomes is revised.

Field of study: Biology
CD4+ T cells defined by their Vβ T cell receptor expression are associated with immunoregulatory profiles and lesion size in human leishmaniasis

Leishmaniasis is caused by infection with the protozoan parasite, Leishmania, that parasitizes human cells, and the cellular immune response is essential for controlling infection. In order to measure the host T cell response to Leishmania infection, we have measured the expansion, activation state and functional potential of specific T cells as identified by their T cell receptor Vβ region expression. In a group of cutaneous leishmaniasis (CL) patients, we evaluated these characteristics in nine different T cell subpopulations as identified by their Vβ region expression, before and after specific Leishmania antigen stimulation. Our results show: (1) an increase in CD4+ T cells expressing Vβ 5·2 and Vβ 24 in CL compared to controls; (2) a Leishmania antigen‐induced increase in CD4+ T cells expressing Vβ 5·2, 11, 12 and 17; (3) a profile of previous activation of CD4+ Vβ 5·2‐, 11‐ and 24‐positive T cells, with higher expression of CD45RO, HLA‐DR, interferon‐γ, tumour necrosis factor‐α and interleukin‐10 compared to other Vβ‐expressing subpopulations; (4) a positive correlation between higher frequencies of CD4+Vβ5·2+ T cells and larger lesions; and (5) biased homing of CD4+ T cells expressing Vβ 5·2 to the lesion site. Given that CL disease involves a level of pathology (ulcerated lesions) and is often followed by long‐lived protection and cure, the identification of specific subpopulations active in this form of disease could allow for the discovery of immunodominant Leishmania antigens important for triggering efficient host responses against the parasite, or identify cell populations most involved in pathology.

Field of study: Biology, Medicine