Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Visual Symptomatology Associated with Refractive, Accommodative, and Binocular Anomalies

Purpose. To characterize the symptomatology of refractive, accommodative, and nonstrabismic binocular dysfunctions and to assess the association between dysfunctions and symptoms. Methods. 175 randomised university students were examined. Subjects were given a subjective visual examination with accommodative and binocular tests, evaluating their symptomatology. Accommodative and binocular dysfunctions (AD, BD) were diagnosed according to the number of existing clinical signs: suspect AD or BD (one fundamental clinical sign), high suspect (one fundamental + 1 complementary clinical sign), and definite (one fundamental + 2 or more complementary clinical signs). A logistic regression was conducted in order to determine whether there was an association between dysfunctions and symptoms. Results. 78 subjects (44.6%) reported any kind of symptoms which were grouped into 18 categories, with “visual fatigue” being the most frequent (20% of the overall complaints). Logistic regression adjusted by the presence of an uncorrected refractive error showed no association between any grade of AD and symptoms. Subjects with BD had more likelihood of having symptoms than without dysfunction group (OR = 3.35), being greater when only definite BD were considered (OR = 8.79). Conclusions. An uncorrected refractive error is a confusion factor when considering AD symptomatology. For BD, the more the number of clinical signs used the greater the likelihood suffering symptoms.
THE EFFECT OF WEAK LENSING ON DISTANCE ESTIMATES FROM SUPERNOVAE

Using a sample of 608 Type Ia supernovae from the SDSS-II and BOSS surveys, combined with a sample of foreground galaxies from SDSS-II, we estimate the weak lensing convergence for each supernova line of sight. We find that the correlation between this measurement and the Hubble residuals is consistent with the prediction from lensing (at a significance of 1.7σ). Strong correlations are also found between the residuals and supernova nuisance parameters after a linear correction is applied. When these other correlations are taken into account, the lensing signal is detected at 1. 4σ. We show, for the first time, that distance estimates from supernovae can be improved when lensing is incorporated, by including a new parameter in the SALT2 methodology for determining distance moduli. The recovered value of the new parameter is consistent with the lensing prediction. Using cosmic microwave background data from WMAP7, H0 data from Hubble Space Telescope and Sloan Digital Sky Survey (SDSS) Baryon acoustic oscillations measurements, we find the best-fit value of the new lensing parameter and show that the central values and uncertainties on Ωm and w are unaffected. The lensing of supernovae, while only seen at marginal significance in this low-redshift sample, will be of vital importance for the next generation of surveys, such as DES and LSST, which will be systematics-dominated.
Hospital nurses' work motivation.

BACKGROUND The knowledge surrounding nurses' work motivation is currently insufficient, and previous studies have rarely taken into account the role of many influential background factors. AIM This study investigates the motivation of Estonian nurses in hospitals, and how individual and organisational background factors influence their motivation to work. METHODS The study is quantitative and cross-sectional. An electronically self-reported questionnaire was used for data collection. The sample comprised of 201 Registered Nurses working in various hospital settings in Estonia. Data were analysed using descriptive statistics, two-sample Wilcoxon rank-sum (Mann-Whitney) test, Kruskal-Wallis equality-of-populations rank test and Spearman's correlation. RESULTS Both extrinsic and intrinsic motivations were noted among hospital nurses. Nurses were moderately externally motivated (M = 3.63, SD = 0.89) and intrinsically strongly motivated (M = 4.98, SD = 1.03). A nurses' age and the duration of service were positively correlated with one particular area of extrinsic work motivation, namely introjected regulation (p < 0.001). Nurses who had professional training over 7 days per year had both a higher extrinsic motivation (p = 0.016) and intrinsic work motivation (p = 0.004). CONCLUSIONS The findings expand current knowledge of nurses' work motivation by describing the amount and orientation of work motivation among hospital nurses and highlighting background factors which should be taken into account in order to sustain and increase their intrinsic work motivation. The instrument used in the study can be an effective tool for nurse managers to determine a nurse's reasons to work and to choose a proper motivational strategy. Further research and testing of the instrument in different countries and in different contexts of nursing is however required.
Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan

Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108 to 3 × 109 genome copies per cm3 sediment, thus providing an estimation that the ssDNA viral populations represent 96.3–99.8% of the benthic total DNA viral assemblages. In the ssDNA viral metagenome, most of the identified viral sequences were associated with ssDNA viral families such as Circoviridae and Microviridae. The principle components analysis of the ssDNA viral sequence components from the sedimentary ssDNA viral metagenomic libraries found that the different depth viral communities at the study site all exhibited similar profiles compared with deep-sea sediment ones at other reference sites. Our results suggested that deep-sea benthic ssDNA viruses have been significantly underestimated by conventional direct virus counts and that their contributions to deep-sea benthic microbial mortality and geochemical cycles should be further addressed by such a new quantitative approach.
Health Care Transition Preparation and Experiences in a U.S. National Sample of Young Adults With Type 1 Diabetes

OBJECTIVE Young adults with type 1 diabetes transitioning from pediatric to adult care are at risk for adverse outcomes. We developed a survey to evaluate transition experiences in two groups of young adults with type 1 diabetes, before (PEDS) and after (ADULT) transition to adult care. RESEARCH DESIGN AND METHODS We fielded an electronic survey to young adults (18 to <30 years) at 60 T1D Exchange Clinic Registry centers. RESULTS Surveys were completed by 602 young adults, 303 in the PEDS group (60% female, age 20 ± 2 years) and 299 in the ADULT group (62% female, age 24 ± 3 years). In the PEDS group, mean anticipated transition age was 22 ± 2 years; 64% remained in pediatric care because of emotional attachment to the provider. The ADULT group transitioned at age 19 ± 2 years, mainly after pediatric provider recommendation. More than 80% of respondents reported receiving counseling on type 1 diabetes self-management and screening tests from pediatric providers, but less than half (43% PEDS and 33% ADULT) reported discussing reproductive health. In the PEDS group, half had discussed transfer with pediatric providers. Of the ADULT participants, 63% received an adult provider referral, and 66% felt mostly/completely prepared to transition. ADULT participants with fewer pretransition pediatric visits or who felt unprepared for transition had increased odds of gaps >6 months between pediatric and adult care. Receipt of transition preparation counseling was not associated with self-reported hemoglobin A1c <7.0% in either group. CONCLUSIONS These results support the need for intensive efforts to integrate transition preparation counseling and care coordination into pediatric type 1 diabetes care.
Cross-fitting and fast remainder rates for semiparametric estimation

There are many interesting and widely used estimators of a functional with ? nite semi-parametric variance bound that depend on nonparametric estimators of nuisance func-tions. We use cross-? tting to construct such estimators with fast remainder rates. We give cross-? t doubly robust estimators that use separate subsamples to estimate di? erent nuisance functions. We show that a cross-? t doubly robust spline regression estimator of the expected conditional covariance is semiparametric e? cient under minimal conditions. Corresponding estimators of other average linear functionals of a conditional expectation are shown to have the fastest known remainder rates under certain smoothness conditions. The cross-? t plug-in estimator shares some of these properties but has a remainder term that is larger than the cross-? t doubly robust estimator. As speci? c examples we consider the expected conditional covariance, mean with randomly missing data, and a weighted average derivative.
Safety, tolerability, and pharmacokinetics of l‐ornithine phenylacetate in patients with acute liver injury/failure and hyperammonemia

Cerebral edema remains a significant cause of morbidity and mortality in patients with acute liver failure (ALF) and has been linked to elevated blood ammonia levels. l‐ornithine phenylacetate (OPA) may decrease ammonia by promoting its renal excretion as phenylacetylglutamine (PAGN), decreasing the risk of cerebral edema. We evaluated the safety, tolerability, and pharmacokinetics of OPA in patients with ALF and acute liver injury (ALI), including those with renal failure. Forty‐seven patients with ALI/ALF and ammonia ≥60 μM were enrolled. Patients received OPA in a dose escalation scheme from 3.3 g every 24 hours to 10 g every 24 hours; 15 patients received 20 g every 24 hours throughout the infusion for up to 120 hours. Plasma phenylacetate (PA) concentrations were uniformly below target (<75 μg/mL) in those receiving 3.3 g every 24 hours (median [interquartile range] 5.0 [5.0] μg/mL), and increased to target levels in all but one who received 20 g every 24 hours (150 [100] μg/mL). Plasma [PAGN] increased, and conversion of PA to PAGN became saturated, with increasing OPA dose. Urinary PAGN clearance and creatinine clearance were linearly related (r = 0.831, P < 0.0001). Mean ammonia concentrations based on the area under the curve decreased to a greater extent in patients who received 20 g of OPA every 24 hours compared with those who received the maximal dose of 3.3 or 6.7 g every 24 hours (P = 0.046 and 0.022, respectively). Of the reported serious adverse events (AEs), which included 11 deaths, none was attributable to study medication. The only nonserious AEs possibly related to study drug were headache and nausea/vomiting. Conclusion: OPA was well‐tolerated in patients with ALI/ALF, and no safety signals were identified. Target [PA] was achieved at infusion rates of 20 g every 24 hours, leading to ammonia excretion in urine as PAGN in proportion to renal function. Randomized, controlled studies of high‐dose OPA are needed to determine its use as an ammonia‐scavenging agent in patients with ALF. (Hepatology 2018;67:1003–1013)
A Main Sequence for Quasars

The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called "main sequence" associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.
Recovering Latent Information in Treebanks

Many recent statistical parsers rely on a preprocessing step which uses hand-written, corpus-specific rules to augment the training data with extra information. For example, head-finding rules are used to augment node labels with lexical heads. In this paper, we provide machinery to reduce the amount of human effort needed to adapt existing models to new corpora: first, we propose a flexible notation for specifying these rules that would allow them to be shared by different models; second, we report on an experiment to see whether we can use Expectation-Maximization to automatically fine-tune a set of hand-written rules to a particular corpus.
iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC

Protein hydroxylation is a posttranslational modification (PTM), in which a CH group in Pro (P) or Lys (K) residue has been converted into a COH group, or a hydroxyl group (−OH) is converted into an organic compound. Closely associated with cellular signaling activities, this type of PTM is also involved in some major diseases, such as stomach cancer and lung cancer. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of P or K, which ones can be hydroxylated, and which ones cannot? With the explosive growth of protein sequences in the post-genomic age, the problem has become even more urgent. To address such a problem, we have developed a predictor called iHyd-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition (PseAAC) and introducing the “Random Forest” algorithm to operate the calculation. Rigorous jackknife tests indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for iHyd-PseCp has been established at http://www.jci-bioinfo.cn/iHyd-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.
Neuronal and glial alterations, increased anxiety, and cognitive impairment before hippocampal amyloid deposition in PDAPP mice, model of Alzheimer's disease

In the context of Alzheimer's disease (AD), hippocampal alterations have been well described in advanced stages of the pathology, when amyloid deposition, inflammation and glial activation occur, but less attention has been directed to studying early brain and behavioral changes. Using an animal model of AD, the transgenic PDAPP‐J20 mouse at 5 months of age, when no amyloid plaques are present and low cerebral levels of amyloid peptides are detectable, we found structural, morphological, and cellular alterations in the hippocampus. Young transgenic mice showed a reduced hippocampal volume with less number of pyramidal and granular neurons, which additionally exhibited cell atrophy. The neurogenic capability in this zone, measured as DCX+ cells, was strongly diminished and associated to alterations in cell maturity. A decrease in presynaptic synaptophysin optical density was detected in mossy fibers reaching CA3 subfield but not in Golgi stained‐ CA1 dendritic spine density. Employing confocal microscopy and accurate stereological tools we also found a reduction in the number of GFAP+ cells, along with decreased astrocyte complexity, suggesting a potential detriment of neural support. According with untimely neuroglial alterations, young PDAPP mice failed in the novel location recognition test, that depends on hippocampal function. Moreover, multivariate statistical analysis of the behavioral outcome in the open‐field test evidenced an elevated anxiety score in Tg mice compared with age‐matched control mice. In line with this, the transgenic group showed a higher number of c‐Fos+ nuclei in central and basolateral amygdala, a result that supports the early involvement of the emotionality factor in AD pathology. Applying an integrative approach, this work focuses on early structural, morphological and functional changes and provides new and compelling evidence of behavioral alterations that precede manifest AD. © 2013 Wiley Periodicals, Inc.
CircDOCK1 suppresses cell apoptosis via inhibition of miR-196a-5p by targeting BIRC3 in OSCC

Oral squamous cell carcinoma (OSCC) is the most frequent oral cancer in the world, accounting for more than 90% of all oral cancer diagnosis. Circular RNAs (circRNAs) are large types of non-coding RNAs, demonstrating a great capacity of regulating the expression of genes. However, most of the functions of circRNAs are still unknown. Recent research revealed that circRNAs could serve as a miRNA-sponge, consequently regulating the expression of target genes indirectly, including oncogenes. In this study, we built an apoptotic model with TNF-α, and then we confirmed a circRNA associated with the apoptosis of OSCC cells, circDOCK1 by comparing the expression profile of circRNAs in an apoptotic model with that in untreated OSCC cells. We ascertained the presence of circDOCK1 with qRT-PCR and circRNA sequencing. The knockdown of the expression of circDOCK1 led to the increase of apoptosis. Utilizing multiple bioinformatics methods, we predicted the interactions among circRNAs, miRNAs and genes, and built the circDOCK1/miR-196a-5p/BIRC3 axis. Both the silencing of circDOCK1 with small interfering RNA and the upregulation of the expression of miR-196a-5p with mimics led OSCC cells to increase apoptosis and decrease BIRC3 formation. We further confirmed this outcome by comparing the expression of circDOCK1, miR-196a-5p and BIRC3 in oral squamous carcinoma tissue with those in para-carcinoma tissue, and examining the expression profile of circRNAs in oral squamous carcinoma tissue and para-carcinoma tissue with microarray. Our results demonstrated that circDOCK1 regulated BIRC3 expression by functioning as a competing endogenous RNA (ceRNA) and participated in the process of OSCC apoptosis. Thus, we propose that circDOCK1 could represent a novel potential biomarker and therapeutic target of OSCC.
Multisourced metals enriched by magmatic-hydrothermal fluids in stratabound deposits of the Middle–Lower Yangtze River metallogenic belt, China

Stratabound deposits within late Carboniferous carbonate units in the Middle–Lower Yangtze River metallogenic belt are important copper producers in China. Hitherto, the genesis of these deposits has been debated, due to poor constraints regarding the timing and source of the mineralization. Proposed models include a late Carboniferous seafloor exhalative formation (SEDEX), or an Early Cretaceous magmatic-hydrothermal origin. These models imply different metal sources (basinal vs. magmatic fluid, respectively) and would require different exploration strategies. New pyrite Re-Os and trace-element results from the representative Xinqiao Cu-S-Fe-Au deposit favor a Cretaceous (ca. 138 Ma) magmatic-hydrothermal genesis over a SEDEX origin. The distinct initial 187Os/188Os compositions (Osi) of different pyrite types (colloform Osi = 1.35 and euhedral grains Osi = 0.79), coupled with the pyrite trace-element abundance, indicate that the Os, and by inference other metals (e.g., Cu, Ag, Au), was sourced from a Cretaceous magmatic-hydrothermal system (Osi = 0.74) and Late Permian metalliferous black shales (Osi = 7.56 ± 3.76). In addition, the genesis of Au-bearing stockwork pyrite veins hosted by the Carboniferous sandstone is best explained by the leaching of existing mineralization (e.g., porphyry Au-Mo) by Early Cretaceous magmatic-hydrothermal fluids. This is implied by the lack of common Os, high Re abundances (0.1–3.7 ppm), and highly variable Re-Os model ages (379 and 173 Ma), which are positively correlated with Re and total abundances of Co, Ni, Ag, Au, Tl, and Ba. This study highlights the importance of recycling of multisourced metals (sedimentary and existing mineralization) in the formation of intrusion-related stratabound deposits. Furthermore, it demonstrates the importance of integrating information regarding the source and timing of mineralization within a well-defined geological framework, which can yield information about the ore-forming processes and help to guide mineral exploration.
Intravoxel incoherent motion diffusion-weighted magnetic resonance imaging for predicting histological grade of hepatocellular carcinoma: Comparison with conventional diffusion-weighted imaging

AIM To compare intravoxel incoherent motion (IVIM)-derived parameters with conventional diffusion-weighted imaging (DWI) parameters in predicting the histological grade of hepatocellular carcinoma (HCC) and to evaluate the correlation between the parameters and the histological grades. METHODS A retrospective study was performed. Sixty-two patients with surgically confirmed HCCs underwent diffusion-weighted magnetic resonance imaging with twelve b values (10-1200 s/mm2). The apparent diffusion coefficient (ADC), pure diffusion coefficient (D), pseudo-diffusion coefficient (D*), and perfusion fraction (f) were calculated by two radiologists. The IVIM and conventional DWI parameters were compared among the different grades by using analysis of variance (ANOVA) and the Kruskal-Wallis test. Receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic efficiency of distinguishing between low-grade (grade 1, G1) and high-grade (grades 2 and 3, G2 and G3) HCC. The correlation between the parameters and the histological grades was assessed by using the Spearman correlation test. Bland-Altman analysis was used to evaluate the reproducibility of the two radiologists’ measurements. RESULTS The differences in the ADC and D values among the groups with G1, G2, and G3 histological grades of HCCs were statistically significant (P < 0.001). The D* and f values had no significant differences among the different histological grades of HCC (P > 0.05). The ROC analyses demonstrated that the D and ADC values had better diagnostic performance in differentiating the low-grade HCC from the high-grade HCC, with areas under the curve (AUCs) of 0.909 and 0.843, respectively, measured by radiologist 1 and of 0.911 and 0.852, respectively, measured by radiologist 2. The following significant correlations were obtained between the ADC, D, and D* values and the histological grades: r = -0.619 (P < 0.001), r = -0.628 (P < 0.001), and r = -0.299 (P = 0.018), respectively, as measured by radiologist 1; r = -0.622 (P < 0.001), r = -0.633 (P < 0.001), and r = -0.303 (P = 0.017), respectively, as measured by radiologist 2. The intra-class correlation coefficient (ICC) values between the two observers were 0.996 for ADC, 0.997 for D, 0.996 for D*, and 0.992 for f values, which indicated excellent inter-observer agreement in the measurements between the two observers. CONCLUSION The IVIM-derived D and ADC values show better diagnostic performance in differentiating high-grade HCC from low-grade HCC, and there is a moderate to good correlation between the ADC and D values and the histological grades.