Miracle-dz/UniFAR-FTUs huggingface dataset:
GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.

We describe a method (implemented in a program, GAZE) for assembling arbitrary evidence for individual gene components (features) into predictions of complete gene structures. Our system is generic in that both the features themselves, and the model of gene structure against which potential assemblies are validated and scored, are external to the system and supplied by the user. GAZE uses a dynamic programming algorithm to obtain the highest scoring gene structure according to the model and posterior probabilities that each input feature is part of a gene. A novel pruning strategy ensures that the algorithm has a run-time effectively linear in sequence length. To demonstrate the flexibility of our system in the incorporation of additional evidence into the gene prediction process, we show how it can be used to both represent nonstandard gene structures (in the form of trans-spliced genes in Caenorhabditis elegans), and make use of similarity information (in the form of Expressed Sequence Tag alignments), while requiring no change to the underlying software. GAZE is available at http://www.sanger. ac.uk/Software/analysis/GAZE.
Impact of Shading Net Color on PhytochemicalContents in Two Chili Pepper Hybrids CultivatedUnder Greenhouse Conditions

The objective of this study was to understand the combined effect of shading treatment and harvest time on pungency, ascorbic acid content, market-quality pepper yield, and photosynthetic activity in a yellow ‘Star Flame’ and ‘Fire Flame’ F1 hybrid pepper cultivar (Capsicum annuum). Plants were cultivated in a greenhouse under white, red, and green shading nets and compared to those grown under unshaded control conditions. The ascorbic acid and pungency parameters were analyzed by high-performance liquid chromatographic methods. Ascorbic acid, a compound of high nutritive value in pepper, was highest in fruits gathered during the first summer harvest in both hybrids. The ascorbic acid content was found to be further increased in fruits from plants grown under white net shading in both ‘Star Flame’ and ‘Fire Flame’. Total capsaicinoid contents in ‘Star Flame’ were influenced by the interaction of shading treatment and harvest time ( p = 0.004), with the lowest amounts (241.2-251.5 mg·kg fresh weight) resulting from white and red shading treatments at the early autumn harvest. In ‘Fire Flame’, both shading treatment ( p = 0.009) and harvest time ( p < 0.001) affected total capsaicinoid contents. We observed significantly higher total capsaicinoid contents in control fruits compared to that resulting from red and green shading treatments at the second harvest, and that resulting from red shading treatment at the third harvest. Analysis of photosynthetic activity revealed a significant and negative correlation between Fv/Fm values and total capsaicinoid contents in both hybrids ( p < 0.001). Based on the obtained results, the harvest of peppers during summer should be promoted to produce fruits with high pungency. OPEN ACCESS Received:
Relationship Between Bone Mineral Density and Disease Activity in Patients with Ankylosing Spondylitis

Objective: This retrospective study was planned to determine the relationship between bone mineral density (BMD) and clinical, radiological and laboratory parameters in patients with ankylosing spondylitis (AS). Materials and Methods: The study group consisted of 28 patients with a mean disease duration of 11.9±6.1 years. In addition to clinical and demographic variables, lumbar and femoral BMD were evaluated with dual energy X-ray absorbtiometry. Lumbar spine score (LSS) and sacroiliac score (SIS) were calculated by grading of standard radiographs. Erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) level were determined as laboratory parameters. Results: The rate of osteoporosis and osteopenia were 7.1% and 25% at the lumbar spine, and 14.2% and 17.8% at the femoral neck, respectively. LSS was significantly correlated with lumbar BMD (r=0.70, p<0.001), but not with femoral neck BMD (r=-0.11, p=0.55). SIS was negatively correlated with femoral neck BMD (r=-0.79, p<0.001), but not correlated with lumbar BMD (r=0.19, p=0.32). While lumbar BMD was positively correlated with disease duration (r=0.37, p=0.05), femoral neck BMD showed negative correlation with disease duration (r=-0.46, p=0.01). The evaluation of clinical paramaters and BMD showed that morning stiffness, spinal pain, ESR and CRP were not correlated with BMD. Only modified Schober's test was related to BMD on both lumbar spine and femoral neck. Conclusion: Ankylosing spondylitis patients are at risk for developing osteoporosis. In advanced disease, the lumbar BMD is misleadingly high because of paravertebral calcification and ossification. Therefore, it is more rational to evaluate the BMD at the femoral neck. (Turk J Rheumatol 2010; 25: 24-8)
On the Failure of Hindsight-Biased Principals to Delegate Optimally

With the help of a simple model, we show that the hindsight bias can lead to inefficient delegation decisions. This prediction is tested experimentally. In an online experiment that was conducted during the FIFA World Cup 2010, participants were asked to predict a number of outcomes of the ongoing World Cup and had to recall their assessments after the outcomes had been realized. Their answers were used to construct individual measures of the hindsight bias. The participants also had to make choices in a delegation game. Our data confirm that hindsight-biased subjects more frequently fail to delegate optimally than subjects whom we have classified as not hindsight biased. Data, as supplemental material, are available at http://dx.doi. org/10.1287/mnsc.2014. 2087 . This paper was accepted by Teck-Hua Ho, judgment and decision making.
Kizuna is a novel mitotic substrate for CDC25B phosphatase

CDC25 dual-specificity phosphatases play a central role in cell cycle control through the activation of Cyclin-Dependent Kinases (CDKs). Expression during mitosis of a stabilized CDC25B mutant (CDC25B-DDA), which cannot interact with the F-box protein βTrCP for proteasome-dependent degradation, causes mitotic defects and chromosome segregation errors in mammalian cells. We found, using the same CDC25B mutant, that stabilization and failure to degrade CDC25B during mitosis lead to the appearance of multipolar spindle cells resulting from a fragmentation of pericentriolar material (PCM) and abolish mitotic Plk1-dependent phosphorylation of Kizuna (Kiz), which is essential for the function of Kiz in maintaining spindle pole integrity. Thus, in mitosis Kiz is a new substrate of CDC25B whose dephosphorylation following CDC25B stabilization leads to the formation of multipolar spindles. Furthermore, endogenous Kiz and CDC25B interact only in mitosis, suggesting that Kiz phosphorylation depends on a balance between CDC25B and Plk1 activities. Our data identify a novel mitotic substrate of CDC25B phosphatase that plays a key role in mitosis control.
Towards physics-based helioseismic inversions of subsurface sunspot structure

Abstract Numerical computations of wave propagation through sunspot-like magnetic field structures are critical to developing and testing methods to deduce the subsurface structure of sunspots and active regions. We show that helioseismic analysis applied to the MHD sunspot simulations of Rempel and collaborators, as well as to translation-invariant models of umbral-like fields, yield wave travel-time measurements in qualitative agreement with those obtained in real sunspots. However, standard inversion methods applied to these data fail to reproduce the true wave-speed structure beneath the surface of the model. Inversion methods which incorporate direct effects of the magnetic field, including mode conversion, may be required.
How did the British media represent European political parties during the European parliament elections, 2014: A Europeanized media agenda?

The European Parliament election of 2014 generated much interest on account of the rise of a whole array of populist ‘anti-EU’ parties. This was widely reported in the British media but did that coverage give British news consumers an insight into the character of these parties, where they stood in relation to one another and where they stood in relation to Britain’s own UKIP? This article sets out to examine not only how much coverage there was in the British media about European political parties but also whether that coverage enabled citizens to get a sense of the political positioning of populist anti-EU parties. These questions touch on the extent to which British media reflect and comment on populist parties, European affairs and hence on the Europeanization of the news agenda.
Tuning the Catalytic Activity and Selectivity of Cu for CO2 Electroreduction in the Presence of Halides

In the present study we demonstrate that the activity and selectivity of copper during CO2 electrochemical reduction can be tuned by simply adding halides to the electrolyte. Comparing the production rate and Faradaic selectivity of the major products as a function the working potential in the presence of Cl–, Br–, and I–, we show that the activity and selectivity of Cu depends on the concentration and nature of the added halide. We find that the addition Cl– and Br– results in an increased CO selectivity. On the contrary, in the presence of I– the selectivity toward CO drops down and instead methane formation is enhanced up to 6 times compared with the halide-free electrolyte. Even though Br– and I– can induce morphology changes of the surface, the modification in the catalytic performance of Cu is mainly attributed to halides adsorption on the Cu surface. We hypothesizes that the adsorption of halides alters the catalytic performance of Cu by increasing the negative charge on the surface according to th.
Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks

Complex traits are determined by the combined effects of many loci and are affected by gene networks or biological pathways. Systems biology approaches have an important role in the identification of candidate genes related to complex diseases or traits at the system level. The present study systemically analyzed genes associated with bovine marbling score and identified their relationships. The candidate nodes were obtained using MedScan text-mining tools and linked by protein-protein interaction (PPI) from the Human Protein Reference Database (HPRD). To determine key node of marbling, the degree and betweenness centrality (BC) were used. The hub nodes and biological pathways of our network are consistent with the previous reports about marbling traits, and also suggest unknown candidate genes associated with intramuscular fat. Five nodes were identified as hub genes, which was consistent with the network analysis using quantitative reverse-transcription PCR (qRT-PCR). Key nodes of the PPI network have positive roles (PPARγ, C/EBPα, and RUNX1T1) and negative roles (RXRA, CAMK2A) in the development of intramuscular fat by several adipogenesis-related pathways. This study provides genetic information for identifying candidate genes for the marbling trait in bovine.
Multicolour imaging in a patient with optic disc pit maculopathy

Optic disc pit is a rare cavitary lesion of the optic nerve. Optic disc pit maculopathy, which is characterised by retinoschisis, serous macular detachment and atrophy of the retina, results from seepage of vitreous fluid into the retina through defects in the membrane overlying pit. This condition can present as a diagnostic dilemma if the pit is not discernible clinically or on colour fundus photography. Spectral domain optical coherence tomography is of great value in looking for optic disc pits in such cases. Multicolour imaging is novel imaging technology available with the Spectralis spectral domain optical coherence tomography system (Heidelberg Engineering, Heidelberg, Germany) and has recently been found useful in imaging several retinal conditions. Multicolour imaging uses three coloured lasers – blue (488 nm), green (515 nm) and infrared (820 nm) – which scan different layers of the retina. Blue reflectance imaging provides information about the inner retina and vitreoretinal interface. Green reflectance imaging reveals details of the middle retinal layers, such as retinal haemorrhages, blood vessels and exudates. Infrared reflectance imaging highlights features in the outer retina and choroid. A composite image of the three reflectance images constitutes the multicolour image. We herein report the utility of multicolour imaging in detecting optic disc pit maculopathy.
Public Policy And Management Challenges For Family Businesses

Public policies pose certain challenges for small businesses that are not seen as major problems for larger businesses. The purpose of this paper is to learn more about the extent to which respondents to a recent national survey of family business managers and owners perceive problems with policy and what might explain their perceptions. The data set includes business and owner-manager characteristics. Estimation results are obtained through an ordered probit model. Findings and their implications are discussed. This paper reports results from the Cooperative Regional Research Project, NE-167R, “Family Businesses: Interaction in Work and Family Spheres,” partially supported by the Cooperative States Research, Education and Extension Service (CSREES); U.S. Department of Agriculture; the experiment stations at the University of Hawaii at Manoa, University of Illinois, Purdue University (Indiana), Iowa State University, Michigan State University, University of Minnesota, Montana State University, University of Nebraska, Cornell University (New York), North Dakota State University, The Ohio State University, Pennsylvania State University, Texas A & M University, Utah State University, University of Vermont, and University of WisconsinMadison; and the Social Sciences and Humanities Research Council of Canada (for the University of Manitoba).
A Network Analysis of the Italian Overnight Money Market

The objective of this paper is to analyse the network topology of the Italian segment of the European overnight money market through methods of statistical mechanics applied to complex networks. We investigate differences in the activities of banks of different sizes and the evolution of their connectivity structure over the maintenance period. The main purpose of the analysis is to establish the potential implications of the current institutional arrangements on the stability of the banking system and to assess the efficiency of the interbank market in terms of absence of speculative and preferential trading relationships.
Forward Integration into Distribution: An Empirical Test of Transaction Cost Analysis

The issue of forward vertical integration has attracted a good deal of attention from researchers in several disciplines, including economics, marketing, and law. Many explanations have been offered for this phenomenon, including technological interrelationships involving economies of scale and scope (Chandler), uncertainty and risk considerations (Arrow, 1969), information externalities (Green), and strategic purposes. Blair and Kaserman (1983) offer an extensive survey of the extant literature in this area. Of particular note, however, is the recent rise in prominence of the transaction costs analysis (TCA) of vertical integration. This approach consists of a blend of institutional economics, organizational theory, and contract law, and has been developed primarily by Oliver Williamson (1979, 1985). He views vertical integration as a response to the inability of arms-length market relationships to govern exchange efficiently under particular circumstances. The level of specialized assets' required to support the exchange, the uncertainty2 surrounding the exchange, and the frequency3 of exchange are
Incidence and outcomes of incidental breast lesions detected on cross‐sectional imaging examinations

The aim of this study was to determine the frequency and outcomes of incidental breast lesions detected on nonbreast specific cross‐sectional imaging examinations. A retrospective review of the medical records was performed to identify all patients without a known history of breast cancer, who had an incidentally discovered breast lesion detected on a nonbreast imaging examination performed at our institution between September 2008 and August 2012 for this IRB‐approved, HIPAA compliant study. Outcomes of the incidental lesions were determined by follow‐up with dedicated breast imaging (mammography, breast ultrasound, and/or breast MRI) or results of biopsy, if performed. Imaging modality of detection, imaging features, patient age, patient location at the time of the nonbreast imaging examination, type of follow‐up, and final outcome were recorded. Rates of malignancy were also calculated, and comparison was made across the different cross‐sectional imaging modalities. Kruskal‐Wallis and Fisher's exact tests were used to identify factors associated with an increased rate of malignancy. Logistic regression was used to model the risk of malignancy as a function of continuous predictors (such as patient age or lesion size); odds ratios and 95% confidence intervals were obtained. A total of 292 patients with incidental breast lesions were identified, 242 of whom had incidental lesions were noted on computed tomography (CT) studies, 25 on magnetic resonance imaging (MRI), and 25 on positron emission tomography (PET). Although most of the incidental breast lesions were detected on CT examinations, PET studies had the highest rate of detection of incidental breast lesions per number of studies performed (rate of incidental breast lesion detection on PET studies was 0.29%, compared to 0.10% for CT and 0.01% for MRI). Of the 121 of 292 (41%) patients who received dedicated breast imaging work‐up at our institution, 40 of 121 (33%) underwent biopsy and 25 of 121 (21%) had malignancy. There was a significantly increased rate of malignancy in older patients (odds ratio: 1.05, 95% CI: 1.02‐1.093; P = .006). Additionally, patients with PET‐detected incidental breast lesions had a significantly higher rate of malignancy (55%), compared to patients with CT‐detected (35%) and MRI‐detected (8%) incidental breast lesions (P = .038). The rate of malignancy upon follow‐up of incidental breast lesions detected on nonbreast imaging examinations in this retrospective study was 21%, supporting the importance of emphasizing further work‐up of all incidentally detected breast lesions with dedicated breast imaging. Additionally, we found that PET examinations had the highest rate of detection of incidental breast lesions and the highest rate of malignancy, which suggests that PET examinations may be more specific for predicting the likelihood of malignancy of incidental breast lesions, compared to CT and MRI.
Colorectal Cancer Primary Tumor Location Implications on Biological Therapy in Metastatic Colorectal Cancer

A nti-epidermal growth factor receptors (anti-EGFRs) have been clinically proven to improve overall survival (OS) when combined with chemotherapy in the settings of extended RAS wild-type metastatic colorectal cancers. In addition, randomized phase III studies have confirmed the superiority of anti-EGFR therapy over bevacizumab in the front-line treatment of extended RAS wild-type metastatic colorectal cancer when it comes to response rate, and in select studies, OS. Recent updates from these clinical trials project convincing evidence that tumor sidedness is yet another predictive marker for response to anti-EGFR therapy. While left colonic RAS wild-type metastatic colorectal cancers derive major clinical benefit from anti-EGFR versus bevacizumab therapy, bevacizumab appears to have clear advantage in RAS wild-type metastatic right-sided tumors. In this review, we summarize recent reports from key clinical trials and their impact on day-to-day clinical practice.
Extracting Medication Information from French Clinical Texts

Much more Natural Language Processing (NLP) work has been performed on the English language than on any other. This general observation is also true of medical NLP, although clinical language processing needs are as strong in other languages as they are in English. In specific subdomains, such as drug prescription, the expression of information can be closely related across different languages, which should help transfer systems from English to other languages. We report here the implementation of a medication extraction system which extracts drugs and related information from French clinical texts, on the basis of an approach initially designed for English within the framework of the i2b2 2009 challenge. The system relies on specialized lexicons and a set of extraction rules. A first evaluation on 50 annotated texts obtains 86.7% F-measure, a level higher than the original English system and close to related work. This shows that the same rule-based approach can be applied to English and French languages, with a similar level of performance. We further discuss directions for improving both systems.
The influence of measurement uncertainties on the evaluation of the distribution volume ratio and binding potential in rat studies on a microPET® R4: a phantom study

In small animal positron emission tomography (PET) imaging, the injectable radiotracer dose is often limited by the tracer mass which, together with the tracer kinetics and scanner sensitivity, dictates the statistical quality of the time activity curves (TACs) used to extract biological parameters. We investigated the effect of measurement uncertainty on the determination of the distribution volume ratio (DVR) and binding potential (BP) as estimated using the tissue input Logan (DVRL, BPL) and the ratio (DVRr, BPr) methods for two tracers, with the Concorde microPET® R4 camera. Parameters' coefficients of variation (COV) were estimated from a combination of rat and phantom data. For 11C-dihydrotetrabenazine, the COV was 11% for the BPL and 13.4% for the BPr when using TACs obtained from individual regions of interest (ROIs) and segmented attenuation correction. The COVs were reduced to 7.5% (BPL) and 8.6% (BPr) when the striatal and cerebellar TACs were estimated as averages of 3 and 2 ROIs respectively. Results obtained for 11C-methylphenidate (MP) yielded approximately 30% higher COVs. With measured attenuation correction, the COVs were on average 100% higher. The presented method can be used to examine the contribution of a variety of imaging conditions to the uncertainty of biologically meaningful parameters.
Hydrochemical Characteristics and Multivariate Statistical Analysis of Natural Water System: A Case Study in Kangding County, Southwestern China

The utilization for water resource has been of great concern to human life. To assess the natural water system in Kangding County, the integrated methods of hydrochemical analysis, multivariate statistics and geochemical modelling were conducted on surface water, groundwater, and thermal water samples. Surface water and groundwater were dominated by Ca-HCO3 type, while thermal water belonged to Ca-HCO3 and Na-Cl-SO4 types. The analyzing results concluded the driving factors that affect hydrochemical components. Following the results of the combined assessments, hydrochemical process was controlled by the dissolution of carbonate and silicate minerals with slight influence from anthropogenic activity. The mixing model of groundwater and thermal water was calculated using silica-enthalpy method, yielding cold-water fraction of 0.56–0.79 and an estimated reservoir temperature of 130–199 °C, respectively. δD and δ18O isotopes suggested that surface water, groundwater and thermal springs were of meteoric origin. Thermal water should have deep circulation through the Xianshuihe fault zone, while groundwater flows through secondary fractures where it recharges with thermal water. Those analytical results were used to construct a hydrological conceptual model, providing a better understanding of the natural water system in Kangding County.