Miracle-dz/UniFAR-FTUs huggingface dataset:
Decreased plasma soluble erythropoietin receptor in high-altitude excessive erythrocytosis and Chronic Mountain Sickness

Excessive erythrocytosis (EE) is the hallmark of chronic mountain sickness (CMS), a prevalent syndrome in high-altitude Andean populations. Although hypoxemia represents its underlying stimulus, why some individuals develop EE despite having altitude-normal blood erythropoietin (Epo) concentration is still unclear. A soluble form of the Epo receptor (sEpoR) has been identified in human blood and competes directly for Epo with its membrane counterpart (mEpoR). Thus, reduced levels of circulating sEpoR could lead to higher Epo availability and ultimately to EE. We characterized the relationship between Epo and sEpoR, with hematocrit and hemoglobin concentration in healthy highlanders and CMS patients at 4,340 m in Cerro de Pasco, Peru. Our results show that EE patients show decreased plasma sEpoR levels and can be subdivided into two subgroups of normal and high plasma Epo concentration for the altitude of residence, with hemoglobin concentration rising exponentially with an increasing Epo-to-sEpoR ratio (Epo/sEpoR). Also, we showed that the latter varies as an inverse exponential function of arterial pulse O2 saturation. Our findings suggests that EE is strongly associated with higher Epo/sEpoR values, leading to elevated plasma Epo availability to bind mEpoR, and thereby a stronger stimulus for augmented erythropoiesis. Differences in the altitude normal and high Epo CMS patients with a progressively higher Epo/sEpoR supports the hypothesis of the existence of two genetically different subgroups suffering from EE and possibly different degrees of adaptation to chronic high-altitude hypoxia.
Stimulation from Cochlear Implant Electrodes Assists with Recovery from Asymmetric Perceptual Tilt: Evidence from the Subjective Visual Vertical Test

Vestibular end organ impairment is highly prevalent in children who have sensorineural hearing loss (SNHL) rehabilitated with cochlear implants (CIs). As a result, spatial perception is likely to be impacted in this population. Of particular interest is the perception of visual vertical because it reflects a perceptual tilt in the roll axis and is sensitive to an imbalance in otolith function. The objectives of the present study were thus to identify abnormalities in perception of the vertical plane in children with SNHL and determine whether such abnormalities could be resolved with stimulation from the CI. Participants included 53 children (15.2 ± 4.0 years of age) with SNHL and vestibular loss, confirmed with vestibular evoked myogenic potential (VEMP) testing. Testing protocol was validated in a sample of nine young adults with normal hearing (28.8 ± 7.7 years). Perception of visual vertical was assessed using the static Subjective Visual Vertical (SVV) test performed with and without stimulation in the participants with cochleovestibular loss. Trains of electrical pulses were delivered by an electrode in the left and/or right ear. Asymmetric spatial orientation deficits were found in nearly half of the participants with CIs (24/53 [45%]). The abnormal perception in this cohort was exacerbated by visual tilts in the direction of their deficit. Electric pulse trains delivered using the CI shifted this abnormal perception towards center (i.e., normal; p = 0.007). Importantly, this benefit was realized regardless of which ear was stimulated. These results suggest a role for CI stimulation beyond the auditory system, in particular, for improving vestibular/balance function.
Pengaruh Radiasi Gamma Terhadap Sifat Mekanik UHMWPE Untuk Tibial Tray

Dalam ortopedi UHMWPE sering digunakan sebagai bantalan materi (tibial tray) pada sendi lutut buatan. Namun dalam penggunaannya, keausan bahan UHMWPE merupakan salah satu faktor utama yang memperpendek umur pakai sendi lutut buatan sehingga diperlukan metode untuk meningkatkan sifat mekanik UHMWPE. Tujuan penelitian ini adalah untuk mengetahui pengaruh radiasi sinar gamma terhadap sifat mekanik dan tingkat keausan dari UHMWPE sehingga dapat memenuhi kualifikasi bahan baku pembuatan tibial tray serta mengetahui dosis optimum yang diperlukan UHMWPE agar diperoleh bahan yang tahan terhadap keausan dan memiliki sifat mekanik yang lebih baik. Pembuatan tibial tray dilakukan dengan metode molding pressure dengan radiasi gamma. Pembuatan film UHMWPE dilakukan dengan hot press pada 170 °C selama 3 menit dan tekanan 200 kg/cm2. Kemudian film tersebut dipanaskan ke dalam furnace pada 128 oC selama 100 menit dan diradiasi dengan irradiator karet alam (IRKA) pada dosis 0 kGy, 50 kGy, 100 kGy, 125 kGy dan 150 kGy. Berdasarkan hasil karakterisasi sifat tibial tray dengan XRD, FT-IR, alat uji tarik, alat uji kekerasan, dan alat uji keausan, dapat disimpulkan bahwa efek radiasi terhadap polimer UHMWPE adalah terbentuknya ikatan silang dan degradasi bahan. Sehingga, semakin tinggi dosis radiasi dihasilkan sifat bahan yang semakin keras serta tahan terhadap aus. Selain itu, dapat diketahui bahwa dosis 100 kGy merupakan dosis optimal untuk meningkatkan sifat mekanik bahan.
Hit from both sides: tracking industrial and volcanic plumes in Mexico City with surface measurements and OMI SO 2 retrievals during the MILAGRO field campaign

Abstract. Large sulfur dioxide plumes were measured in the Mexico City Metropolitan Area (MCMA) during the MILAGRO field campaign. This paper seeks to identify the sources of these plumes and the meteorological processes that affect their dispersion in a complex mountain basin. Surface measurements of SO2 and winds are analysed in combination with radar wind profiler data to identify transport directions. Satellite retrievals of vertical SO2 columns from the Ozone Monitoring Instrument (OMI) reveal the dispersion from both the Tula industrial complex and the Popocatepetl volcano. Oversampling the OMI swath data to a fine grid (3 by 3 km) and averaging over the field campaign yielded a high resolution image of the average plume transport. Numerical simulations are used to identify possible transport scenarios. The analysis suggests that both Tula and Popocatepetl contribute to SO2 levels in the MCMA, sometimes on the same day due to strong vertical wind shear. During the field campaign, model estimates suggest that the volcano accounts for about one tenth of the SO2 in the MCMA, with a roughly equal split for the rest between urban sources and the Tula industrial complex. The evaluation of simulations with known sources and pollutants suggests that the combination of observations and meteorological models will be useful in identifying sources and transport processes of other plumes observed during MILAGRO.
A phase 2 study of tasisulam sodium (LY573636 sodium) as second‐line treatment for patients with unresectable or metastatic melanoma

Tasisulam sodium (hereafter, tasisulam) is a novel anticancer agent that induces apoptosis through the intrinsic pathway and has antiangiogenic activity in preclinical models. Tasisulam demonstrated activity across a broad range of tumors, including melanoma. The primary objective of this phase 2 study was to determine the objective response rate (ORR) in patients who had received 1 previous systemic chemotherapy for unresectable/metastatic melanoma; secondary objectives were to evaluate the clinical response rate (CRR), progression‐free survival (PFS), overall survival (OS), duration of response, safety, and pharmacokinetics.
Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia)

Bitter gourd (Momordica charantia) is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo) genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs) in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.
Effects of Uterine Manipulation on Surgical Outcomes in Laparoscopic Management of Endometrial Cancer: A Prospective Randomized Clinical Trial

Objective This study aimed to evaluate the influence of intrauterine manipulation on the surgical outcome in patients with early-stage endometrial cancer treated with 2 different laparoscopic approaches. Methods In a randomized parallel trial, 110 patients with clinical stage I endometrial cancer were randomly assigned for laparoscopic staging surgery with (group A, 55) or without (group B, 55) the use of a uterine manipulator (RUMI), between June 2009 and June 2011. Two sets of peritoneal washings were obtained, 1 before and 1 after the insertion of the uterine manipulator. Primary end points were the rates of positive cytology and lymphovascular space invasion. Results No difference was detected in patient characteristics between the groups. Mean operative time, estimated blood loss, and postoperative complications were similar between the groups. Group A had a similar incidence of lymphovascular space invasion compared with group B (12.7% vs 9.1%, respectively; P = 0.761). Four patients (7.3%) in group A had positive peritoneal cytology in the initial washing. One of these patients was classified as stage IIIA. One patient in group B was positive in the second washing. The agreement rate between the 2 sets of washings for both groups was 98.2%. During the median follow-up of 19 months, 6 patients had tumor recurrence without significant difference between the groups. Conclusions Despite concerns that the use of uterine manipulators may predispose the spread of early-stage disease, insertion of such uterine-manipulating systems did not increase rate of positive peritoneal cytology or lymphovascular space invasion in this study.
Citation for Published Item: Use Policy Evaluating Clone Detection Tools for Use during Preventative Maintenance

or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full DRO policy for further details. Abstract This paper describes the results of a process whereby the detection capability of 5 code replication detection tools for large software application are evaluated. Specifically this work focuses on the benefits of identification for preventative maintenance that is with the aim to remove some of the identified clones from the source code. A number of requirements are therefore identified upon which the tools are evaluated. The results of the analysis processes show that each tool has its own strengths and weaknesses and no single tool is able to identify all clones within the code. The paper proposes that it may be possible to use a combination of tools to perform the analysis process providing that adequate means of efficiently identifying false matches is found.
Solution structure of the methyl‐CpG‐binding domain of the methylation‐dependent transcriptional repressor MBD1

CpG methylation in vertebrates is important for gene silencing, alterations in chromatin structure and genomic stability, and differences in the DNA‐methylation status are correlated with imprinting phenomena, carcinogenesis and embryonic development. Methylation signals are interpreted by protein factors that contain shared methyl‐CpG‐binding domains (MBDs). We have determined the solution structure of the MBD of the human methylation‐dependent transcriptional repressor MBD1 by multi‐dimensional heteronuclear NMR spectroscopy. It folds into an α/β‐sandwich structure with characteristic loops. Basic residues conserved in the MBD family are largely confined to one face of this fold and a flexible loop, which together form a large positively charged surface. Site‐directed mutagenesis and chemical shift changes upon complexing with a methylated DNA facilitated identification of this surface as the DNA interaction site. In addition to three basic residues, conserved Tyr34 and Asp32 were shown to be important for the DNA binding.
All-optical mapping of barrel cortex circuits based on simultaneous voltage-sensitive dye imaging and channelrhodopsin-mediated photostimulation

Abstract. We describe an experimental approach that uses light to both control and detect neuronal activity in mouse barrel cortex slices: blue light patterned by a digital micromirror array system allowed us to photostimulate specific layers and columns, while a red-shifted voltage-sensitive dye was used to map out large-scale circuit activity. We demonstrate that such all-optical mapping can interrogate various circuits in somatosensory cortex by sequentially activating different layers and columns. Further, mapping in slices from whisker-deprived mice demonstrated that chronic sensory deprivation did not significantly alter feedforward inhibition driven by layer 5 pyramidal neurons. Further development of voltage-sensitive optical probes should allow this all-optical mapping approach to become an important and high-throughput tool for mapping circuit interactions in the brain.
Specific peroxidases differentiate Brachypodium distachyon accessions and are associated with drought tolerance traits.

BACKGROUND AND AIMS Brachypodium distachyon (Brachypodium) is a model system for studying cereal, bioenergy, forage and turf grasses. The genetic and evolutionary basis of the adaptation of this wild grass species to drought stress is largely unknown. Peroxidase (POD) may play a role in plant drought tolerance, but whether the allelic variations of genes encoding the specific POD isoenzymes are associated with plant response to drought stress is not well understood. The objectives of this study were to examine natural variation of POD isoenzyme patterns, to identify nucleotide diversity of POD genes and to relate the allelic variation of genes to drought tolerance traits of diverse Brachypodium accessions. METHODS Whole-plant drought tolerance and POD activity were examined in contrasting ecotypes. Non-denaturing PAGE and liquid chromatography-mass spectrometry were performed to detect distinct isozymes of POD in 34 accessions. Single nucleotide polymorphisms (SNPs) were identified by comparing DNA sequences of these accessions. Associations of POD genes encoding specific POD isoenzymes with drought tolerance traits were analysed using TASSEL software. KEY RESULTS Variations of POD isoenzymes were found among accessions with contrasting drought tolerance, while the most tolerant and susceptible accessions each had their own unique POD isoenzyme band. Eight POD genes were identified and a total of 90 SNPs were found among these genes across 34 accessions. After controlling population structure, significant associations of Bradi3g41340.1 and Bradi1g26870.1 with leaf water content or leaf wilting were identified. CONCLUSIONS Brachypodium ecotypes have distinct specific POD isozymes. This may contribute to natural variations of drought tolerance of this species. The role of specific POD genes in differentiating Brachypodium accessions with contrasting drought tolerance could be associated with the general fitness of Brachypodium during evolution.
Personalized services in online shopping: Enjoyment and privacy

Enjoyment and privacy are essential ingredients for successful personalization. However, the current understanding of the influence of personalization is limited. This study extends personalization literature into the area of enjoyment and privacy issues related to intention to purchase and into the context of online shopping. Responses from 148 online customers were used to examine the effects of personalization on enjoyment, privacy issues and intention to purchase. Results show that personalization affects positively enjoyment and intention, but has no effect on privacy. Additionally, privacy affects negatively both enjoyment and purchase intentions, while enjoyment has a positive influence on purchase intentions. This study suggests future research directions including the relation of trust with privacy, as well as different types of emotions, hedonic and utilitarian dimensions that relate with personalized services.
An Amphipathic α-Helix at the C Terminus of Hepatitis C Virus Nonstructural Protein 4B Mediates Membrane Association

ABSTRACT Nonstructural protein 4B (NS4B) plays an essential role in the formation of the hepatitis C virus (HCV) replication complex. It is an integral membrane protein that has been only poorly characterized to date. It is believed to comprise a cytosolic N-terminal part, a central part harboring four transmembrane passages, and a cytosolic C-terminal part. Here, we describe an amphipathic α-helix at the C terminus of NS4B (amino acid residues 229 to 253) that mediates membrane association and is involved in the formation of a functional HCV replication complex.
Ancient divisions, recent expansions: phylogeography and population genetics of the round goby Apollonia melanostoma

During the past two decades, the round goby Apollonia melanostoma (=Neogobius melanostomus) has expanded its range via shipping transport and canals, extending north and west from the Ponto‐Caspian region of Eurasia and to the North American Great Lakes. Exotic populations of the round goby have been very successful in the Baltic Sea and the Great Lakes regions, exerting significant ecological changes. Our study evaluates the population genetic and biogeographical structure of the round goby across its native and nonindigenous ranges, in light of geological history and its expansion pathways. We analyzed seven new nuclear microsatellite loci and mitochondrial DNA cytochrome b gene sequences from 432 individuals in 22 locations. Population structure was tested using FST‐analogs, phylogenetic trees, clustering diagrams, Bayesian assignment tests and nested clade analyses. Results show that native populations in the Black vs. the Caspian Sea basins diverge by 1.4% and c. 350 000 years, corresponding to closure of their prior connections and supporting the taxonomic separation of the Black Sea A. m. melanostoma from the Caspian Sea A. m. affinis. Their within‐basin populations diverge by ~0.4% and 100 000 years. Nonindigenous populations in the Baltic Sea and Danube and Dnieper Rivers trace to separate northern Black Sea origins, whereas the upper Volga River system houses mixed populations of A. m. melanostoma and A. m. affinis. Native populations average twice the genetic diversity of most exotic sites; however, sites in the Volga River system have high diversity due to mixing of the two taxa. Our results highlight how vicariance and anthropogenic disturbances have shaped a rapidly expanding species’ genetic heritage.
Ammonium Uptake by Rice Roots (I. Fluxes and Subcellular Distribution of 13NH4+)

The time course of 13NH4+ uptake and the distribution of 13NH4+ among plant parts and subcellular compartments was determined for 3-week-old rice (Oryza sativa L. cv M202) plants grown hydroponically in modified Johnson's nutrient solution containing 2,100, or 1000 [mu]M NH4+ (referred to hereafter as G2, G100, or G1000 plants, respectively). At steady state, the influx of 13NH4+ was determined to be 1.31, 5.78, and 10.11 [mu]mol g-1 fresh weight h-1, respectively, for G2, G100, and G1000 plants; efflux was 11, 20, and 29%, respectively, of influx. The NH4+ flux to the vacuole was calculated to be between 1 and 1.4 [mu]mol g-1 fresh weight h-1. By means of 13NH4+ efflux analysis, three kinetically distinct phases (superficial, cell wall, and cytoplasm) were identified, with t1/2 for 13NH4+ exchange of approximately 3 s and 1 and 8 min, respectively. Cytoplasmic [NH4+] was estimated to be 3.72, 20.55, and 38.08 mM for G2, G100, and G1000 plants, respectively. These concentrations were higher than vacuolar [NH4+], yet 72 to 92% of total root NH4+ was located in the vacuole. Distributions of newly absorbed 13NH4+ between plant parts and among the compartments were also examined. During a 30-min period G100 plants metabolized 19% of the influxed 13NH4+. The remainder (81%) was partitioned among the vacuole (20%), cytoplasm (41%), and efflux (20%). Of the metabolized 13N, roughly one-half was translocated to the shoots.
Continuity-of-Care Measures: An Analytic and Empirical Comparison

The authors compared four different continuity-of-care measures recently suggested in the literature. First, an analytic comparison is made and useful inequalities are derived. Then the continuity indexes are applied to an extensive data material from a Swedish ambulatory care center. The four indexes give fairly similar results, and the basic finding is the substantially higher index values for elderly patients. Finally, computed index values are compared with what could be expected under a scheme of random assignment of patients to doctors
Defining the roles of perforin, Fas/FasL, and tumour necrosis factor α in T cell induced mucosal damage in the mouse intestine

Background and aims: Mucosal flattening and epithelial cell apoptosis are typical features of T cell induced inflammatory diseases of the bowel, such as coeliac disease and graft versus host disease. Mice injected with a T cell activating anti-CD3 antibody develop a severe diarrhoeal illness. We describe the histological features of this enteropathy and define the effector mechanisms involved in T cell induced mucosal injury in this in vivo model. Methods: Wild-type and genetically modified mice were injected with the anti-CD3 antibody 3C11 (50 μg). Changes in the murine intestine were characterised by light microscopy analysis and terminal uridine nick-end labelling (TUNEL) assay. The role of perforin, Fas/Fas ligand (FasL), tumour necrosis factor α (TNF-α), and interferon γ (IFN-γ) in T cell induced mucosal damage was assessed using selected immunodeficient mouse strains. Results: T cell activation caused severe damage, including small intestinal mucosal flattening and apoptosis of crypt epithelial cells. Mucosal damage was unaltered in anti-CD3 treated mice lacking IFN-γ, Fas, or TNF-α receptors. In mice lacking TNF-α receptors and Fas (TNF-R1×R2 lpr/lpr strain), enterocyte apoptosis was diminished but there was no significant reduction in tissue damage. Apoptosis and mucosal injury were significantly reduced in perforin knockout mice. Abrogation of both FasL and perforin (perforin KO×gld mice) further significantly reduced tissue damage and apoptotic bodies. Conclusions: T cell induced mucosal injury is mediated by the combined effect of multiple pathways but predominantly by perforin. The redundancy of the mechanisms of tissue damage will have significant impact on therapeutic strategies aimed at specific and targeted inhibition of inflammatory processes.