nils-herrmann/clean_scirepeval huggingface dataset:
Analysis of Long Non-Coding RNA Expression of Lymphatic Endothelial Cells in Response to Type 2 Diabetes

Recent evidence has indicated that long non-coding RNA (lncRNA) is involved in the pathogenesis of type 2 diabetes, but nothing is known about lncRNA expression changes of lymphatic endothelial cells in response to type 2 diabetes.  The GSE38396 dataset was downloaded from the Gene Expression Omnibus database and the probe sets of Human Gnome U133 Plus2.0 microarray were annotated for lncRNA. Differentially expressed lncRNAs between diabetic and non-diabetic lymphatic endothelial cells were calculated.  Compared with lymphatic endothelial cells in non-diabetic patients, 31 lncRNAs were down-regulated and 79 lncRNAs were up-regualted in lymphatic endothelial cells of type 2 diabetic patients. Several known lncRNAs were found, such as H19, GAS5, UCA1, CRNDE, GAS5, and LINC00312. Co-expression network of differentially expressed lncRNAs and mRNAs were constructed. Based on genomic regions of these lncRNAs, we found that binding sites of MAF and TCF3 were enriched and these lncRNAs may be related to insulin reporter signaling pathway and response to insulin stimulus.  In a word, we found a set of lncRNAs were differentially expressed in lymphatic endothelial cells in response to type 2 diabetes and these lncRNAs may be involved in the pathogenesis of diabetes-related complications.

Field of study: Biology, Chemistry
Comparative analysis of portal hepatic infiltrating leucocytes in acute drug‐induced liver injury, idiopathic autoimmune and viral hepatitis

Drug‐induced liver injury (DILI) is often caused by innate and adaptive host immune responses. Characterization of inflammatory infiltrates in the liver may improve understanding of the underlying pathogenesis of DILI. This study aimed to enumerate and characterize leucocytes infiltrating liver tissue from subjects with acute DILI (n = 32) versus non‐DILI causes of acute liver injury (n = 25). Immunostains for CD11b/CD4 (Kupffer and T helper cells), CD3/CD20 (T and B cells) and CD8/CD56 [T cytotoxic and natural killer (NK) cells] were evaluated in biopsies from subjects with acute DILI, either immunoallergic (IAD) or autoimmune (AID) and idiopathic autoimmune (AIH) and viral hepatitis (VH) and correlated with clinical and pathological features. All biopsies showed numerous CD8+ T cells and macrophages. DILI cases had significantly fewer B lymphocytes than AIH and VH and significantly fewer NK cells than VH. Prominent plasma cells were unusual in IAD (three of 10 cases), but were associated strongly with AIH (eight of nine) and also observed in most with AID (six of nine). They were also found in five of 10 cases with VH. Liver biopsies from subjects with DILI were characterized by low counts of mature B cells and NK cells in portal triads in contrast to VH. NK cells were found only in cases of VH, whereas AIH and VH both showed higher counts of B cells than DILI. Plasma cells were associated most strongly with AIH and less so with AID, but were uncommon in IAD.

Field of study: Biology, Medicine
The regular approach for identifying the atomic displacements in ABO3 crystals and its application to high-temperature phases of KNbO3.

The approach for identifying the atomic displacements from the ideal positions in perovskite structure is proposed, based: on characteristic features in the Fourier Transforms (FT) for different models of atomic displacements and on the results of EXAFS calculations lot alternative models of ideal structure distortions, generated using the value of averaged atomic displacement provided by diffraction methods. The approach is applied to study the local structure distortions in tetragonal and cubic phases of KNbO3. The effect of anharmonic motion of atoms on the obtained structure information is simulated through the cumulant expansion.

Field of study: Physics
Systematic Review and Meta-Analysis to Establish the Association of Common Genetic Variations in Vitamin D Binding Protein With Chronic Obstructive Pulmonary Disease

Vitamin-D binding protein (DBP) also known as GC protein, is a major determinant for vitamin- D metabolism and transport. GC1F, GC1S, and GC2 are the three allelic variants (denoted as rs4588 and rs7041) of GC, and known to be associated with chronic obstructive pulmonary disease (COPD). However, contradictory reports and population specific risk attributed by these alleles warranted detailed genetic epidemiology study to establish the association between GC variants and COPD. In this study we performed a meta-analysis and investigated the genetic architecture of GC locus to establish the association and uncover the plausible reason for allelic heterogeneity.  Published cross-sectional case control studies were screened and meta-analysis was performed between GC variants and COPD outcome. RevMan-v5.3 software was used to perform random and/or fixed models to calculate pooled odds ratio (Meta-OR). Linkage disequilibrium (LD) and haplotypes at GC locus were evaluated using 1000 Genomes genotype data. In silico functional implications of rs4588 and rs7041 was tested using publicly available tools.  GC1F allele and GC1F/1F genotype were found to confer COPD risk in overall meta-analysis. GC1S/1S was found to confer risk only among Europeans. In silico investigation of rs4588 and rs7041 identified strong eQTL effects and potential role in regulation of GC expression. Large differences in allele frequencies, linkage disequilibrium (LD) and haplotypes were identified at GC locus across different populations (Japanese, African, Europeans, and Indians), which may explain the variable association of different GC alleles in different populations.  GC1F and GC1F/1F impose significant genetic risk for COPD, among Asians. Considerable differences in allele frequencies and LD structure in GC locus may impose population specific risk.

Field of study: Biology
RESIDUA CHARACTERIZATION BY MODIFIED MOLECULAR CONNECTIVITY INDEX

Molecular structural characterization of the SCFE narrow-cuts of various residua was made by using molecular connectivity index (MCI) method in order to predict their physical properties and chemical reactivity. First-order MCI 1X was calculated for hundreds of SCFE narrow-cuts and correlated with their physical properties.The MCI 1X of SCFE narrow-cuts correlated very well with their physical properties for a given residue. The predicted physical properties of the SCFE narrow-cuts from various residua varied dramatically although they had the same MCI 1X.Apparently only the carbon atoms in the molecular skeletons are considered for calculating MCI. The existence of hydrogen atoms and their effects on the molecular structure and properties are neglected. Subsequently,the MCI was modified by integrating the atomic ratio of hydrogen to carbon (H/C) into the MCI to characterize the SCFE narrow-cuts of vacuum residua appropriately. A modified MCI K M was proposed by combining H/C and 1X. The quantitative structure property relation (QSPR) derived from the modified MCI K M and residue properties was developed to predict the physical properties and chemical reactivity appropriately. This MCI method was applied to the residue characterization successfully.

Field of study: Chemistry, Environmental science
Degradation of silicone in white LEDs during device operation: A finite element approach to product reliability prediction

Silicone, which is a very common material for Light Emitting Diode (LED) packaging components like lens, casting and housing, undergoes degradation during high temperature and current operation. Indeed, electrical and optical losses cause material shrinkage and hardening, inducing mechanical stress within the LED assembly, which can end up into crack formation in silicone. In order to evaluate the reliability of LED package regarding the silicone crack, a degradation material model is developed, which is based on the experimental investigation of the mechanical properties of silicone during degradation. A coupled thermo-optical model is used for the calculation of the temperature distribution in the device during steady-state operation. The crack reliability model, which is build combining the stress simulation results based on finite element approach and the visual inspection of the corresponding LED package during steady-state operation, is used to estimate the package lifetime depending on the operation conditions.

Field of study: Engineering
Macro and Micro-Scale Features of Thermoelectric PbTe 
(Br, Na) Systems: Micro-FTIR Spectroscopy, Micro-Seebeck Measurements, and SEM/EDX Observations

In this work, n-type and p-type PbTe doped with Br and Na, respectively, were thoroughly examined to determine the effect of the dopant on microstructure. Macro and micro homogeneity of the samples were studied by means of micro-Fourier-transform infrared (micro-FTIR) spectroscopy, micro-Seebeck measurements, and scanning electron microscopy with energy-dispersive x-ray analysis (SEM/EDX). SEM/EDX observations showed the samples were not single-phase materials—second phases were created by inclusions that disturbed the coherence of the matrix and, subsequently, drastically affected the Seebeck coefficient. In a micro-scale study, local variations of sodium content were detected in Na-doped samples; in Br-doped samples a second, PbBr2, phase was observed in the PbTe matrix. A direct effect of matrix dopant on Seebeck coefficient and plasmon frequency for the Br-doped and Na-doped samples was observed by use of the three complementary techniques.

Field of study: Materials science
Guido Miranda Gutiérrez: Pilar de la seguridad social Costarricense

Conoci a mi maestro y luego amigo en septiembre de 1961, cuando me presente al concurso para realizar el internado en el Hospital Calderon Guardia. Desde ese dia pude captar “la fuerza vital” que emanaba el Dr. Miranda, quien, como dice el filosofo Nietzche, era de esas personas que tenia un mandamiento “atrevete a ser lo que eres”, el, desde nino y joven y lleno de aspiraciones como audaz aventurero, no tenia temor a las dificultades, se realizaba superandolas y estas a su vez le ayudaron a desarrollar al maximo sus grandes capacidades personales. Con los anos, sus aspiraciones se llenaron de realizaciones en Medicina y en esa area que el tanto queria, como era la seguridad social del pais.

Field of study: Mathematics
Carbonaceous aerosol characteristics on the Third Pole: A primary study based on the Atmospheric Pollution and Cryospheric Change (APCC) network.

Carbonaceous aerosols (CAs) scatter and absorb incident solar radiation in the atmosphere, thereby influencing the regional climate and hydrological cycle, particularly in the Third Pole (TP). Here, we present the characteristics of CAs at 19 observation stations from the Atmospheric Pollution and Cryospheric Change network to obtain a deep understanding of pollutant status in the TP. The organic carbon (OC) and elemental carbon (EC) concentrations decreased noticeably inwards from outside to inland of the TP, consistent with their emission load and also affected by transport process and meteorological condition. Urban areas, such as Kathmandu, Karachi, and Mardan, exhibited extremely high OC and EC concentrations, with low and high values occurring in the monsoon and non-monsoon seasons, respectively. However, remote regions inland the TP (e.g., Nam Co and Ngari) demonstrated much lower OC and EC concentrations. Different seasonal variations were observed between the southern and northern parts of the TP, suggesting differences in the patterns of pollutant sources and in distance from the sources between the two regions. In addition to the influence of long-range transported pollutants from the Indo-Gangetic Plain (IGP), the TP was affected by local emissions (e.g., biomass burning). The OC/EC ratio also suggested that biomass burning was prevalent in the center TP, whereas the marginal sites (e.g., Jomsom, Dhunche, and Laohugou) were affected by fossil fuel combustion from the up-wind regions. The mass absorption cross-section of EC (MACEC) at 632 nm ranged from 6.56 to 14.7 m2 g-1, with an increasing trend from outside to inland of the TP. Urban areas had low MACEC values because such regions were mainly affected by local fresh emissions. In addition, large amount of brown carbon can decrease the MACEC values in cities of South Asia. Remote sites had high MACEC values because of the coating enhancement of aerosols. Influenced by emission, transport process, and weather condition, the CA concentrations and MACEC presented decreasing and increasing trends, respectively, from outside to inland of the TP.

Field of study: Environmental science
BRIEF COMMUNICATIONS: Lasing in YAG:Nd3+ and KGdW:Nd3+ crystals pumped with semiconductor lasers

Lasing in crystals with narrow absorption bands was achieved for the first time by excitation with radiation emitted from electron-beam-pumped CdSxSe1–x semiconductor lasers. The lasing thresholds of YAG:Nd3+ and KGdW:Nd3+ crystals pumped with λ = 586 nm radiation were ~ 2 and ~ 1 mJ, respectively. The efficiency of conversion of the pump radiation into the output radiation in the KGdW:Nd3+ laser was 0.27%.

Field of study: Engineering, Physics
Nine Things Genomics Can Tell Us About Candida auris

Candida auris is a recently emerged multidrug-resistant fungal pathogen causing severe illness in hospitalized patients. C. auris is most closely related to a few environmental or rarely observed but cosmopolitan Candida species. However, C. auris is unique in the concern it is generating among public health agencies for its rapid emergence, difficulty to treat, and the likelihood for further and more extensive outbreaks and spread. To date, five geographically distributed and genetically divergent lineages have been identified, none of which includes isolates that were collected prior to 1996. Indeed, C. auris’ ecological niche(s) and emergence remain enigmatic, although a number of hypotheses have been proposed. Recent genomic and transcriptomic work has also identified a variety of gene and chromosomal features that may have conferred C. auris with several important clinical phenotypes including its drug-resistance and growth at high temperatures. In this review we discuss nine major lines of enquiry into C. auris that big-data technologies and analytical approaches are beginning to answer.

Field of study: Biology
Caspase 3 is Activated through Caspase 8 instead of Caspase 9 during H2O2-induced Apoptosis in HeLa Cells

Oxidative stress is known to be involved in a variety of pathological processes including atherosclerosis, diabetes, and neurodegenerative diseases. Understanding how intracellular signaling pathways respond to oxidative stress will have a significant implication in the therapy of these diseases. In this study, we applied hydrogen peroxide (H2O2) to trigger apoptosis and investigated the dynamic activation of various caspases using a FRET technique. We measured the activation dynamics of caspase 3 and caspase 9 based on two reporter systems, SCAT 3 and SCAT 9. We found that caspase 3 activation was earlier than that of caspase 9 following H2O2 treatment. Caspase 3 was activated rapidly, reaching a maximum in 12±3 min, while the average duration of caspase 9 activation was 21±3 min. When cells were pretreated with Z-LEHD-fmk, a caspase 9 specific inhibitor, caspase 3 activation and apoptosis by H2O2 treatment were little affected, although the caspase 9 activation was completely inhibited. When cells were pretreated with Z-DEVD-fmk, a caspase 3 specific inhibitor, the activation of both caspase 3 and caspase 9, as well as apoptosis, were inhibited. When cells were pretreated with Z-IETD-fmk, a caspase 8 specific inhibitor, the activation of caspase 3 and caspase 9 were significantly delayed. Finally, we found that Bax did not translocate from the cytosol to the mitochondrial membrane during H2O2-induced apoptosis. Our results suggest that, during H H2O2-induced apoptosis, caspase 3 is activated directly through caspase 8 and is not through the mitochondria-dependent caspase 9 activation.

Field of study: Biology, Chemistry
Assessment of the anterior osteotomy role in the restoration of normal pelvic floor anatomy for bladder exstrophy patients using pre and postoperative pelvic floor MRI.

Our aim was to evaluate the effectiveness of anterior osteotomy in the restoration of normal pelvic floor anatomy in classic bladder exstrophy repair using pelvic floor MRI as an imaging tool for evaluation.



This study is a pilot prospective randomized controlled study that included 20 infants with classic bladder exstrophy older than three months with no history of previous surgical operations. All patients underwent complete primary repair and were randomized into two groups, with or without osteotomy. Both groups were assessed preoperatively & postoperatively after three months with pelvic floor MRI and compared to age & gender-matched control group infants with normal pelvic anatomy infants who underwent pelvic MRI for other medical conditions.



There was not any significant statistical difference between osteotomy and non-osteotomy groups in pre-operative demographic data and all pelvic floor MRI measurements, emphasizing that both groups were equal in all characters at the start point of the study before the operation. The mean change difference between pre-operative and post-operative pelvic floor MRI measurements were compared in both groups, and there was not any significant statistical difference in all pelvic floor MRI measurements. Both groups showed the same statistical significance when compared with the control group in all pelvic floor MRI measurements except the posterior bladder neck distance, which was in favor of the osteotomy group, closer to the normal pelvic floor anatomy.



Anterior osteotomy did not have a significant difference in the restoration of the normal pelvic floor anatomy when combined with complete primary repair of classic bladder exstrophy in newly diagnosed neonates older than three months, except for a single measurement, posterior bladder neck distance. Future studies needed to determine the effect of osteotomy on continence.

Field of study: Medicine
Studies in Bibliography: VI.-Agriculture from the Restoration to Anne

U NTIL R. Lennard found some of the results of the Royal Society' enquiry, the only guide there was to farming development in the post-Commonwealth period was a comparison of the few textbooks published then. These must be used with some care and their inadequacy is shown by the current textbooks, whose authors have used them.2 Even Godfrey Davies3 has been unable to indicate how far they might be used satisfactorily. All he can say is that since they commanded a ready sale there must have been something to be learned from them, but that where they were most original they, are probably most untrustworthy. I have demonstrated how such seventeenth-century works must be supplemented by other sources of evidence in an essay on pre-Commonwealth farming,4 and here I propose to show how far it is safe to use the didactic treatises of the late seventeenth century as a guide to the history of the development of our farming practice then. The actual number of books strictly confined to farming that was published in the half-century is small, about a dozen in all, but there were several dealing with horses, farriery which was the contemporary term for what is now known as veterinary science, botany, draining fens, fruit and forest trees, and so on. Most of these I propose to ignore, and to deal only with farming books pure and simple. Both Ernle5 and Godfrey Davies6 agree in selecting two works as the best of those which appeared during the period. These were John Worlidge's Systema Agricultura, i669, and J. Mortimer's Whole Art of Husbandry,) I707. The first is the most practical and the most systematic work on farming that had yet appeared, and the second the best and most complete work on practical farming yet published. These two books are examples of the merits and defects of textbooks when drawn upon for evidence of the contemporary state of farming. Both rely often enough on the authority of earlier works, but Worlidge has the grace to acknowledge his sources, while Mortimer rarely does, a common fault of the time and a proceeding that needs to be carefully watched to determine how far a practice described is contemporary or

Field of study: Economics, History
Loss-efficiency model of single and variable-speed compressors using neural networks

Compressor is the critical component to the performance of a vapor-compression refrigeration system. The loss-efficiency model including the volumetric efficiency and the isentropic efficiency is widely used for representing the compressor performance. A neural network loss-efficiency model is developed to simulate the performance of positive displacement compressors like the reciprocating, screw and scroll compressors. With one more input, frequency, it can be easily extended to the variable speed compressors. The three-layer polynomial perceptron network is developed because the polynomial transfer function is found very effective in training and free of over-learning. The selection of input parameters of neural networks is also found critical to the network prediction accuracy. The proposed neural networks give less than 0.4% standard deviations and ±1.3% maximum deviations against the manufacturer data.

Field of study: Engineering
Description of (n, p) and (n, 2n-activation cross sections for medium-mass nuclei within statistical multistep theory

A unique description of (n, p) and (n, 2n) activation cross sections as well as emission spectra is proposed within a pure multistep approach. Calculations are presented for 8 nuclei (A=47 ... 65) in the incident energy range from zero up to 20 MeV.

Field of study: Physics
Interpretation of English reflexives by adolescent speakers of Serbo-Croatian

This article addresses the question of L1 transfer in L2 acquisition of reflexive binding. It incorporates recent research on Binding Theory which focuses on the relationship between morphological complexity of anaphors and the occurrence of long-distance binding of reflexives (cf. Yang, 1983;  1987; Hellan, 1988; Battistella, 1989; Huang and Tang, 1989; Cole et al., 1990; Progovac, 1992). Reflexives typically fall into two categories: simple (X0) reflexives that may take long-distance antecedents and complex (XP) refle xives that may not. Acquisition of the English binding pattern by native speakers of Serbo-Croatian requires recognition of the morphological com plexity of English reflexives. Prior to reanalysis, learners are predicted to transfer the L1 X0 anaphor type and incorrectly assign long-distance antece dents to English XP reflexives. The interpretation of English reflexives by native speakers of Serbo- Croatian was investigated using two types of written sentence comprehension tasks. A picture identification task and a multiple-choice questionnaire were administered to intermediate (n = 20) and advanced (n = 20) L2 learners and a group of English native speaker controls (n = 20). Results consistent across task type support the transfer hypothesis and suggest learners have access to Universal Grammar in second language acquisition.

Field of study: Linguistics