Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification of Hantaan Virus with a SYBR Green Ⅰ-Based One-Step qRT-PCR Assay

Hantaan virus (HTNV) is a major zoonotic pathogen that causes hemorrhagic fever with renal syndrome (HFRS) in Asia, especially in China. Shaanxi province, which is located in northwest of China, is one of the areas in China most severely afflicted with HFRS epidemics annually. This study aims to establish a quantitative RT-PCR (qRT-PCR) assay to detect HTNV both in cell culture and clinical serum samples. We established a SYBR Green Ⅰ-based one-step qRT-PCR assay that targets the S segment of the HTNV genome for rapid detection and quantification. The HTNV cRNA standards were constructed by in vitro transcription, and the copy numbers of the HTNV cRNA were quantified. Standard curve was generated by determining the mean cycle threshold (Ct) values versus 10-fold serial dilutions of the HTNV cRNA over a range of 1×108 to 1×103 copies/μl. The standard curve had a reaction efficiency of 102.1%, a correlation coefficient (R2) of 0.998, and a slope of -3.273. The coefficient of variation (CV) of the intra- and inter-assays ranged from 0.68% to 3.00% and from 0.86% to 3.21%, respectively. The cycle intervals of the qRT-PCR assay between each dilution ranged from 2.9 to 3.8 cycles, and the lowest detection limit of the qRT-PCR assay was 10 copies/μl. The assay exhibited high specificity that was confirmed by melting curve analysis, and no cross reaction with the Seoul virus (SEOV) and other viruses (HBV, HCV and HIV) was observed. HTNV RNA was also detected in the 27 serum samples of clinical HFRS patients using the assay, and the HTNV RNA viral load ranged from 2.06×101 to 1.95×105 copies/μl. The SYBR Green Ⅰ-based one-step qRT-PCR assay is a sensitive, specific, reproducible, and simple method for detecting and quantifying HTNV in cell culture and clinical samples.
Exploiting Topic based Twitter Sentiment for Stock Prediction

This paper proposes a technique to leverage topic based sentiments from Twitter to help predict the stock market. We first utilize a con- tinuous Dirichlet Process Mixture model to learn the daily topic set. Then, for each topic we derive its sentiment according to its opin- ion words distribution to build a sentiment time series. We then regress the stock index and the Twitter sentiment time series to predict the market. Experiments on real-life S&P100 Index show that our approach is effective and performs better than existing state-of-the-art non-topic based methods.
The Relationship between Anemia and the Initiation of Dialysis in Patients with Type 2 Diabetic Nephropathy

Background Anemia is associated with various poor clinical outcomes in chronic kidney disease patients. The aim of this study was to investigate the relationship between anemia and the initiation degree and time of dialysis in type 2 diabetic nephropathy patients. Methods This observational retrospective study included 130 type 2 diabetic nephropathy patients in Korea. The existence of anemia, the degree and time of dialysis initiation were reviewed. Clinical characteristics and variables were also compared. Results The levels of hemoglobin and serum creatinine were significantly correlated with the dialysis initiation (P<0.05) during the 10-year follow-up period. Patients with anemia showed rapid decline of renal function, causing significantly more dialysis initiation (54.1% vs. 5.4%, P<0.05) compare to the patients without anemia. Average time to initiate dialysis in patients with anemia was 45.1 months (range, 8.0 to 115.8 months), which was significantly faster than that (68.3 months [range, 23.3 to 108.8 months]) in patients without anemia (P<0.01). The risk to dialysis initiation was significantly increased in patients with anemia compared to the patients without anemia (adjusted hazard ratio, 8.1; 95% confidence interval, 2.4 to 27.0; P<0.05). Conclusion Anemia is associated with rapid decline of renal dysfunction and faster initiation of dialysis in diabetic nephropathy patients. Therefore, clinicians should pay an earlier attention to anemia during the management of diabetes.
P-Curve: A Key to the File Drawer

Because scientists tend to report only studies (publication bias) or analyses (p-hacking) that "work," readers must ask, "Are these effects true, or do they merely reflect selective reporting? " We introduce p-curve as a way to answer this question. P-curve is the distribution of statistically significant p values for a set of studies (ps < .05). Because only true effects are expected to generate right-skewed p-curves-containing more low (.01s) than high (.04s) significant p values--only right-skewed p--curves are diagnostic of evidential value. By telling us whether we can rule out selective reporting as the sole explanation for a set of findings, p-curve offers a solution to the age-old inferential problems caused by file-drawers of failed studies and analyses.
Middle Cerebral Artery Flow Velocity Correlates With Common Carotid Artery Volume Flow Rate After CO2 Inhalation

Cerebral vasoreactivity can be studied with transcranial Doppler (TCD) by monitoring CO2‐induced middle cerebral artery (MCA) velocity changes. Expected MCA mean velocity (Vm) changes due to changes in end‐expiratory CO2(EE‐CO2) are established, but reactivity of common carotid artery (CCA) volume flow rate (VFR) has not been extensively reported. The authors assess the relationship between MCA Vm, CCA VFR, and EE‐CO2. Ten normal individuals without cerebrovascular disease and with CCA diameters of more than 3.0 mm were studied. CCA VFR was obtained by Color Velocity Imaging Quantification and ipsilateral MCA Vm by standard TCD methods. Each side was studied before, during, and after inhalation of 5% CO2. EE‐CO2, blood pressure, and pulse rate were monitored. Four women and 6 men with mean age of 36 years were included. Significant correlations between MCA Vm and EE‐CO2, CCA VFR and EE‐CO2, and MCA Vm and CCA VFR were found. MCA Vm and CCA VFR increased 5.2% and 4.3% per mm Hg increase in EE‐CO2, respectively. MCA Vm increased 0.3 cm/s per ml/min increase in CCA VFR. In normal individuals, there is a direct correlation between MCA Vm, CCA VFR, and EE‐CO2. Measurement of CCA VFR changes during CO2inhalation may be an alternative method to estimate cerebral vasoreactivity when the MCA velocity cannot be obtained because of inadequate acoustic temporal windows.
Auditory Cognitive Training for Pediatric Cochlear Implant Recipients

Objectives: Understanding speech in noise is the biggest challenge faced by individuals with cochlear implants (CIs). Improving speech-in-noise perception for pediatric CI recipients continues to remain a high priority for all stakeholders. This study was designed to investigate the efficacy of working memory training for improving speech-in-noise recognition for children with CIs. Design: Fourteen children with CIs (aged 6 to 15 years) received adaptive, home-based training on forward digit span task for 5 weeks, while 13 children with CIs participated in backward digit span training. Seventeen age-matched children with CIs in the control group received a placebo. Outcome measures included forward and backward digit span and speech recognition threshold for digit triplets in noise at pretraining, post-training, and 5-week follow-up. Performance measures from 26 age-matched children with normal hearing were also obtained only at the baseline session to generate normative standards for comparison. Results: Digit span scores were significantly higher at post-training and follow-up compared with pretraining for both forward- and backward-trained groups. Both trained groups showed similar training-induced shifts. The control group showed no such improvement. There was no effect of training on the speech recognition threshold. Children with CIs showed significantly lower digit span scores and a higher speech recognition threshold relative to children with normal hearing. Conclusions: Training improves working memory capacity as measured by digit spans for children with CIs. Training-induced improvements are stable for at least 5 weeks. Learning effects demonstrate near-transfer, from forward to backward digit span and vice versa, but failed to show far-transfer to speech-in-noise recognition. Current evidence is not supportive of cognitive training for improving speech-in-noise performance for children with CIs.
Poverty and the Impact of AIDS on Older Persons: Evidence from Cambodia and Thailand

The present study provides a comparative analysis of the impact of the AIDS epidemic in Cambodia and Thailand on the parents of adults who die of AIDS and how this impact interacts with poverty. It examines the relationship between economic status and routes through which losing an adult child can affect the parents, including caregiving during illness, payment of medical and living expenses, reduced economic activity, funeral expenses, loss of support from the deceased adult child, the fostering of orphaned grandchildren, and community reaction. Finally, an assessment is made of the impact on the overall economic situation of the parents. Generally, negative consequences appear more widespread in Cambodia, but economic status shows a stronger association with outcomes in Thailand. Thus the gap between poor Thais and Cambodians is often modest despite substantial differences in overall levels. The higher levels of hardship reported in Cambodia and the often minimal difference by economic status likely reflect the more severe levels of poverty in that country compared to Thailand. While differences in data collection methodologies may account for some of the contrasting findings, the results strongly suggest that setting matters and that the role of poverty in the AIDS epidemic is far from uniform.
Development of the projections from the dorsal lateral geniculate nucleus to the lateral suprasylvian visual area of cortex in the cat

In the study reported in the preceding paper, we used retrograde labeling methods to show that the enhanced projection from the thalamus to the posteromedial lateral suprasylvian (PMLS) visual area of cortex that is present in adult cats following neonatal visual cortex damage arises at least partly from surviving neurons in the dorsal lateral geniculate nucleus (LGN). In the C layers of the LGN, many more cells than normal are retrogradely labeled by horseradish peroxidase (HRP) injected into PMLS cortex ipsilateral to a visual cortex lesion. In addition, retrogradely labeled cells are found in the A layers, which normally have no projection to PMLS cortex in adult cats. The purpose of the present study was to investigate the mechanisms of this enhanced projection by examining the normal development of projections from the thalamus, especially the LGN, to PMLS cortex. Injections of HRP were made into PMLS cortex on the day of birth or at 1, 2, 4, or 8 weeks of age. Retrogradely labeled neurons were present in the lateral posterior nucleus, posterior nucleus of Rioch, pulvinar, and medial interlaminar nucleus, as well as in the LGN, at all ages studied. Within the LGN of the youngest kittens, a small number of retrogradely labeled cells was present in the interlaminar zones and among the cells in the A layers that border these zones. Such labeled cells were virtually absent by 8 weeks of age, and they are not found in normal adult cats. Sparse retrograde labeling of C‐layer neurons also was present in newborn kittens. The density of labeled C‐layer neurons increased 5‐ to 10‐fold between 1 day and 1 week of age and then increased further to adult values by 4 weeks of age. These results indicate that there is not an exuberant projection from the C layers of the LGN to the PMLS cortex in young kittens. This suggests, therefore, that the enhanced projection from the C layers to PMLS cortex after an early visual cortex lesion, described in the preceding paper, is due to new axonal growth. In contrast, at least part of the enhanced projection from the A layers after an early visual cortex lesion may result from the retention of an initially transient projection from the interlaminar zones and immediately adjacent cells in the A layers.
Microleakage of a condensable resin composite: an in vitro investigation.

OBJECTIVE The purpose of this investigation was to evaluate microleakage in Class II cavities restored with the condensable resin composite SureFil, placed with or without a liner and 1 of 2 different dentin bonding agents. METHOD AND MATERIALS Extracted noncarious human teeth were randomly divided into 4 groups of 15 each and restored according to manufacturer's instructions: group 1, SureFil and Prime & Bond NT; group 2, SureFil and PQ1; group 3, SureFil, PermaFlow, and PQ1; group 4, Heliomolar and Syntac Single-Component (control). Specimens were stored in 37 degrees C water for 24 hours. All specimens were thermocycled between 5 degrees C and 55 degrees C for 500 cycles. Each specimen was immersed in 0.2% basic fuchsin dye for 24 hours and then sectioned longitudinally and horizontally. Dye penetration at enamel and cementum margins were viewed at x30 magnification by 2 independent, calibrated evaluators. Specimens exhibiting dye penetration > or = 0.1 mm beyond the cavosurface margin were considered to have leakage. RESULTS Chi-square tests revealed no statistically significant differences in the presence of microleakage when all groups were analyzed together. However, 2 by 2 comparisons revealed that group 3 had significantly fewer specimens with microleakage than did group 1, 2, or 4. CONCLUSION To limit microleakage, a flowable composite should be used as a liner when a condensable composite material is used.
Magnetic resonance imaging for diagnosis of acute pulmonary embolism: not yet a suitable alternative to CT‐PA

See also Revel MP, Sanchez O, Couchon S, Planquette B, Hernigou A, Niarra R, Meyer G, Chatellier G. Diagnostic accuracy of magnetic resonance imaging for acute pulmonary embolism: results of the ‘IRM‐EP’ study. This issue, pp 743–50; and Sodhi KS, Saxena AK. Diagnostic accuracy of computed tomography pulmonary angiography and magnetic resonance imaging for an acute pulmonary embolism. This issue, pp 961.
Carbohydrate malabsorption in acutely malnourished children and infants: a systematic review

Context: Severe acute malnutrition (SAM) accounts for approximately 1 million child deaths per year. High mortality is linked with comorbidities, such as diarrhea and pneumonia. Objective: The aim of this systematic review was to determine the extent to which carbohydrate malabsorption occurs in children with SAM. Data Sources: The PubMed and Embase databases were searched. Reference lists of selected articles were checked. Data Extraction: All observational and controlled intervention studies involving children with SAM in which direct or indirect measures of carbohydrate absorption were analyzed were eligible for inclusion. A total of 20 articles were selected for this review. Data Synthesis: Most studies reported carbohydrate malabsorption, particularly lactose malabsorption, and suggested an increase in diarrhea and reduced weight gain in children on a lactose-containing diet. As most studies reviewed were observational, there was no conclusive scientific evidence of a causal relationship between lactose malabsorption and a worse clinical outcome among malnourished children. Conclusion: The combined data indicate that carbohydrate malabsorption is prevalent in children with SAM. Additional well-designed intervention studies are needed to determine whether outcomes of SAM complicated by carbohydrate malabsorption could be improved by altering the carbohydrate/lactose content of therapeutic feeds and to elucidate the precise mechanisms involved.
Phase I study of carboplatin, doxorubicin and weekly paclitaxel in patients with advanced ovarian carcinoma.

BACKGROUND Doxorubicin is an active compound in epithelial ovarian cancer (EOC), but adding it to carboplatin-paclitaxel causes toxicity. Toxicity can be reduced by weekly administration. We examined the tolerability of weekly paclitaxel in combination with carboplatin and doxorubicin. PATIENTS AND METHODS Chemotherapy naïve patients with EOC were treated with doxorubicin (50 mg/m(2) day 1), carboplatin (AUC 6 day 1) and paclitaxel (days 1, 8, 15, 21), 28-day cycle. Three patients were treated at each paclitaxel dose level, starting at 60, 75 and 90 mg/m(2)/week. If more than two patients in a cohort experienced dose-limiting toxicity (DLT) three more patients were treated at the dose level below. RESULTS Twelve patients with advanced EOC received a median of six cycles (range 2-6) of the three-drug combination. DLT occurred at dose level 3: prolonged grade 4 febrile neutropenia, 1 patient; grade 3 peripheral neuropathy, 1 patient. All six patients treated at dose level 2 experienced short-lived grade 4 neutropenia, which led to dose modifications resulting in an actual delivered dose of paclitaxel of 64 mg/m(2)/week. Eight out of 12 patients had measurable disease on CT scan: four obtained a partial remission; three had stable disease. CONCLUSIONS The combination of carboplatin, doxorubicin and paclitaxel in patients with EOC is active and its main toxicity is myelosuppression. Dose intensity of paclitaxel can be maintained in a three-drug combination through weekly administration (65 mg/m(2)).
From family damage to family challenge : stories of rebuilding lives after war and refugee trauma : Australia after the Balkans conflicts

The purpose of this study was to explore the effect of war-related psychological trauma on refugees from the former Yugoslavia who came to Australia in the last 20 years, and to examine how their process of recovery from trauma was assisted by the power of healing relationships, family strength and resilience. The aim was to explore the entire family unit in the context of whole-family interaction.
Bayesian Text Segmentation for Index Term Identification and Keyphrase Extraction

Automatically extracting terminology and index terms from scientific literature is useful for a variety of digital library, indexing and search applications. This task is non-trivial, compli- cated by domain-specific terminology and a steady introduction of new terminology. Correctly identifying nested terminology further adds to the challenge. We present a Dirichlet Process (DP) model of word segmentation where multiword segments are either retrieved from a cache or newly generated. We show how this DP-Segmentation model can be used to successfully extract nested terminology, outperforming previous methods for solving this problem.
Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.)

Genomic selection refers to the use of genotypic information for predicting breeding values of selection candidates. A prediction formula is calibrated with the genotypes and phenotypes of reference individuals constituting the calibration set. The size and the composition of this set are essential parameters affecting the prediction reliabilities. The objective of this study was to maximize reliabilities by optimizing the calibration set. Different criteria based on the diversity or on the prediction error variance (PEV) derived from the realized additive relationship matrix–best linear unbiased predictions model (RA–BLUP) were used to select the reference individuals. For the latter, we considered the mean of the PEV of the contrasts between each selection candidate and the mean of the population (PEVmean) and the mean of the expected reliabilities of the same contrasts (CDmean). These criteria were tested with phenotypic data collected on two diversity panels of maize (Zea mays L.) genotyped with a 50k SNPs array. In the two panels, samples chosen based on CDmean gave higher reliabilities than random samples for various calibration set sizes. CDmean also appeared superior to PEVmean, which can be explained by the fact that it takes into account the reduction of variance due to the relatedness between individuals. Selected samples were close to optimality for a wide range of trait heritabilities, which suggests that the strategy presented here can efficiently sample subsets in panels of inbred lines. A script to optimize reference samples based on CDmean is available on request.
Insights into the MCM functional mechanism: lessons learned from the archaeal MCM complex

The helicase function of the minichromosome maintenance protein (MCM) is essential for genomic DNA replication in archaea and eukaryotes. There has been rapid progress in studies of the structure and function of MCM proteins from different organisms, leading to better understanding of the MCM helicase mechanism. Because there are a number of excellent reviews on this topic, we will use this review to summarize some of the recent progress, with particular focus on the structural aspects of MCM and their implications for helicase function. Given the hexameric and double hexameric architecture observed by X-ray crystallography and electron microscopy of MCMs from archaeal and eukaryotic cells, we summarize and discuss possible unwinding modes by either a hexameric or a double hexameric helicase. Additionally, our recent crystal structure of a full length archaeal MCM has provided structural information on an intact, multi-domain MCM protein, which includes the salient features of four unusual β-hairpins from each monomer, and the side channels of a hexamer/double hexamer. These new structural data enable a closer examination of the structural basis of the unwinding mechanisms by MCM.
Capsular serotypes, virulence-associated genes and antimicrobial susceptibility of Streptococcus suis isolates from pigs in Korea

Streptococcus suis is an important pig pathogen with potential for human transmission. The serotype distributions and phenotypic characteristics vary over time and among regions; however, little is known about the characteristics of S. suis isolates in Korea. In this study, 240 S. suis isolates collected from pigs in Korea in 2009–2010 were serotyped by coagglutination tests, subsequently screened for three virulence-associated genes (mrp, epf and sly) and tested for antimicrobial susceptibility. As for 80 isolates, the serotypes of which were relevant to human infections, clonal complexes (CCs) were further identified by PCR. Serotype 3 was the most prevalent (15.8%), followed by serotype 2 (15.0%), with geographical variation for each serotype. Overall, 55.4% of the isolates carried mrp, whereas only 3.8% carried epf. CC25 was the most prevalent (41.3%) and was related to serotypes 2 and 9. The isolates showed higher susceptibility to ampicillin (93.4%) and ceftiofur (90.8%) than to the other antimicrobial agents tested. The highest resistance rate was observed to tetracycline (98.0%), followed by erythromycin (88.8%). In addition, the resistance to certain antimicrobials was significantly associated, in part, with virulence-associated genes or serotypes. Therefore, continuous characterization of S. suis is essential for the benefit of veterinary and human medicine.