Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of novel bat coronaviruses in south China that use the same receptor 1 as MERS coronavirus 2 3 Running title : Novel MERS-like-coronavirus binding to DPP 4 4 5

23 Middle East respiratory syndrome coronavirus (MERS-CoV) has represented a 24 human health threat since 2012. Although several MERS-related CoVs , which belong 25 to the same species as MERS-CoV, have been identified from bats, they do not use the 26 MERS-CoV receptor, dipeptidyl peptidase 4 (DPP4). Here, we screened 1059 bat 27 samples from at least 30 bat species collected in different regions in south China and 28 identified 89 strains of lineage C betacoronaviruses, including Tylonycteris pachypus 29 HKU4, Pipistrellus pipistrellus HKU5, and MERS-related CoVs. We sequenced the 30 full-length genomes of two positive samples collected from the great evening bat, Ia 31 io, from Guangdong Province. The two genomes were highly similar and exhibited 32 genomic structures identical to those of other lineage C betacoronaviruses. While they 33 exhibited genome-wide nucleotide identities of only 75.3 to 81.2% with other 34 MERS-related CoVs, their gene-coding regions were highly similar to their 35 counterparts, except in the case of the spike proteins. Further protein–protein 36 interaction assays demonstrated that the spike proteins of these MERS-related CoVs 37 bind to the receptor DPP4. Recombination analysis suggested that the newly 38 discovered MERS-related CoVs might have acquired their spike genes from a 39 DPP4-recognizing bat HKU4. Our study provides further evidence that bats represent 40 the evolutionary origins of MERS-CoV. 41 42 43 on M ay 3, 2018 by U nirsity of M inesota Liaries http/jvi.asm . rg/ D ow nladed fom Importance 44 Previous studies suggested that the Middle East respiratory syndrome coronavirus 45 (MERS-CoV) may have originated in bats. However, its evolutionary path from bats 46 to humans remains unclear. In this study, we discovered 89 novel lineage C 47 betacoronaviruses (BetaCoVs) in eight bat species. We provide the evidence of a 48 MERS-related CoV derived from the great evening bat that uses the same host 49 receptor as human MERS-CoV. This virus also provides evidence for a natural 50 recombination event between the bat MERS-related CoV and another bat coronavirus 51 HKU4. Our study expands the host ranges of MERS-related CoV and represents an 52 important step toward establishing bats as the natural reservoir of MERS-CoV. These 53 findings may lead to improved epidemiological surveillance of MERS-CoV and the 54 prevention and control of the spread of MERS-CoV to humans. 55
Conoscopic holography for image registration: a feasibility study

Preoperative image data can facilitate intrasurgical guidance by revealing interior features of opaque tissues, provided image data can be accurately registered to the physical patient. Registration is challenging in organs that are deformable and lack features suitable for use as alignment fiducials (e.g. liver, kidneys, etc.). However, provided intraoperative sensing of surface contours can be accomplished, a variety of rigid and deformable 3D surface registration techniques become applicable. In this paper, we evaluate the feasibility of conoscopic holography as a new method to sense organ surface shape. We also describe potential advantages of conoscopic holography, including the promise of replacing open surgery with a laparoscopic approach. Our feasibility study investigated use of a tracked off-the-shelf conoscopic holography unit to perform a surface scans on several types of biological and synthetic phantom tissues. After first exploring baseline accuracy and repeatability of distance measurements, we performed a number of surface scan experiments on the phantom and ex vivo tissues with a variety of surface properties and shapes. These indicate that conoscopic holography is capable of generating surface point clouds of at least comparable (and perhaps eventually improved) accuracy in comparison to published experimental laser triangulation-based surface scanning results.
An Entropy Maximizing Geohash for Distributed Spatiotemporal Database Indexing

We present a modification of the standard geohash algorithm based on maximum entropy encoding in which the data volume is approximately constant for a given hash prefix length. Distributed spatiotemporal databases, which typically require interleaving spatial and temporal elements into a single key, reap large benefits from a balanced geohash by creating a consistent ratio between spatial and temporal precision even across areas of varying data density. This property is also useful for indexing purely spatial datasets, where the load distribution of large range scans is an important aspect of query performance. We apply our algorithm to data generated proportional to population as given by census block population counts provided from the US Census Bureau.
Palatability of Beef from Cattle Fed Extruded Flaxseed before Hay or Mixed with Hay

This study was undertaken to evaluate the eating quality of longissimus thoracis steaks and hamburgers (80/20 gluteus medius to perirenal fat) with enhanced profiles of potentially healthy fatty acids. The profile of health favorable fatty acids (n-3, vaccenic and rumenic) was improved in beef by feeding co-extruded flaxseed (flaxseed, peas, and alfalfa) and alfalfa-grass hay as a total mixed ration (TMR), and further enhanced by feeding co-extruded flaxseed before alfalfa-grass hay (Non-TMR). Compared to TMR, feeding steers the Non-TMR resulted in tougher steaks (P < 0.05) with lower beef flavor (P < 0.01) and greater off-flavor (P < 0.01) intensity to an extent that might be detectable by consumers. High levels of trans-monounsaturated fatty acids, mainly of vaccenic acid, were associated with a fishy off-flavor, although actual changes in flavor may relate to correlated combined effects of conjugated fatty acids, atypical dienoic acids and ɑ-linolenic acid. Diet had no significant effect on sensory attributes of hamburgers, but when panelists described off-flavors, they noted more ‘other’ off-flavors (P < 0.05) with fishy and stale/cardboard notes being more prominant in Non-TMR hamburgers. Overall, beef samples with threshold levels of vaccenic acid over 6.12% of total fatty acids resulting from feeding flaxseed products, while of potentially greater health benefit, may pose challenges in terms of eating quality. Areas worthy of further investigation to ensure acceptable eating quality might be the influence of ageing on antioxidant capacity in beef with enhanced fatty acid profiles, and the potential use of protective packaging to limit deterioration.
Risk Factors for Functional Constipation in Young Children Attending Daycare Centers

Our objective was to determine the risk factors associated with the development of functional constipation (FC) in young children attending daycare centers. A cross-sectional survey using a questionnaire based on the Rome III criteria was conducted in children aged 25 to 84 months from 3 randomly selected daycare centers in January 2016. The items in a questionnaire were statistically compared in the constipated and non-constipated groups. A total of 212 children were included and FC was found in 8.5%. Multivariate logistic regression analyses revealed that maternal history of constipation (odds ratio [OR] = 4.1, 95% Confidence Interval [CI] 1.2-13.9), history of painful defecation before age 1 (OR = 10.4, 95% CI 1.1-101.3), history of painful defecation during toilet training (OR = 28.9, 95% CI 1.9-423.8), no or difficult defecation at a daycare center (OR = 5,804.6, 95% CI 134.4-250,718.4), no meat consumption (OR = 10.1, 95% CI 1.2-88.1), and 500 mL or less of water intake per day (OR = 9.9, 95% CI 0.9-99.5) were powerful predictors of FC in young children (P < 0.05). Additionally, the constipated group was significantly associated with 2 hours or less of outdoor play activities per day, entry into daycare centers before 24 months age, 6 hours or more of attendance at a daycare center per day, breastfeeding for less than 6 months, 3 meals or less per day, and 3 or fewer servings of fruits and vegetables per day (P < 0.05). The findings of this study can guide parents, daycare teachers, and clinicians in prevention, early recognition and early intervention for the risk factors associated with FC in young children.
Lymphoid enhancer binding factor-1 (LEF1) expression as a prognostic factor in adult acute promyelocytic leukemia

Lymphoid enhancer-binding factor 1 (LEF1) is a downstream effector of the Wnt/ β-catenin signaling pathway. High LEF1 expression has been reported as a prognostic marker in hematologic malignancies. We evaluated the prognostic significance of LEF1 expression in 78 adult acute promyelocytic leukemia (APL) patients. APL samples were dichotomized at the median value and divided into: LEF1low and LEF1high. LEF1high patients had lower WBC counts at baseline and were less likely to carry a FLT3 -ITD than LEF1low patients. Early death occurred only in the LEF1low group. Moreover, LEF1low expression was associated with a high Sanz score. Survival analysis of 61 APL patients < 60 years revealed that the LEF1high group had a significantly longer overall survival (OS). Cox analysis for OS confirmed only LEF1 expression as an independent prognostic factor. Of the 17 patients over the age of 60, those in the LEF1high group showed a higher median survival. In silico analysis identified 9 differentially expressed, up-modulated genes associated with a high expression of LEF1; the majority of these genes is involved in the regulation of apoptosis. Our study provides evidence that LEF1 expression is an independent prognostic factor in APL, and could be used in patients risk stratification.
Ecological Trade-offs between Migration and Reproduction Are Mediated by the Nutrition-Sensitive Insulin-Signaling Pathway

Crowding and changes in food availability are two critical environmental conditions that impact an animal's trajectory toward either migration or reproduction. Many insects facing this challenge have evolved wing polyphenisms. When conditions favor reproduction, wing polyphenic species produce adults that either have no wings or short, non-functional wings. Facultative wing growth reflects a physiological and evolutionary trade-off between migration and reproduction, triggered by environmental conditions. How environmental cues are transduced to produce these alternative forms, and their associated ecological shift from migration to reproduction, remains an important unsolved problem in evolutionary ecology. The brown planthopper, a wing polymorphic insect exhibiting strong trade-offs in investment between migration and reproduction, is one of the most serious rice pests in Asia. In this study, we investigated the function of four genes in the insulin-signaling pathway known to couple nutrition with growth, PI3 Kinase (PI3K), PDK1, Akt (Protein Kinase B), and the forkhead gene FOXO. Using a combination of RNA interference and pharmacological inhibitor treatment, we show that all four genes contribute to tissue level regulation of wing polymorphic development in this insect. As predicted, silencing of the NlPI3K, NlAkt and NlPDK1 through dsRNA and with the pharmacological inhibitor Perifosine resulted in short-winged brown planthoppers, whereas knockdown of NlFOXO resulted in long-winged planthoppers. Morphometric analyses confirm that phenotypes from our manipulations mimic what would be found in nature, i.e., major parameters such as bristle number, wing area and body weight are not significantly different from non-experimental animals. Taken together, these data implicate the insulin-signaling pathway in the transduction of environmental factors into condition-dependent patterns of wing growth in insects.
WITH: Human-Computer Collaboration for Data Annotation and Enrichment

The transformation that has been accomplished in Cultural Heritage (CH) during the last decades has resulted in the production of vast amounts of content from many different cultural institutions, such as museums, libraries and archives. A large part of this rich content has been aggregated in digital platforms that serve as cross-domain hubs, which however offer limited usability and accessibility of content due to insufficient data and metadata quality. In our effort to make CH more accessible and reusable, we introduce WITH, an aggregation platform that provides enhanced services and enables human-computer collaboration for data annotations and enrichment. WITH excels existing cultural content aggregation platforms by advancing digital cultural data through the combination of artificial intelligence automation and creative user engagement, thus facilitating its accessibility, visibility, and re-use. In particular, by using image and free text analysis methodologies for automatic metadata enrichment, in accordance to the human expertise for enrichment and validation through crowdsourcing approaches with gamification elements, WITH combines the intelligence of humans and computers to improve the quality of digital cultural content and its presentation, establishing new ways of collaboration between cultural organizations and their audiences.
Dynamic control of soft robots interacting with the environment

Despite the emergence of many soft-bodied robotic systems, model-based feedback control has remained an open challenge. This is largely due to the intrinsic difficulties in designing controllers for systems with infinite dimensions. In this paper we propose an alternative formulation of the soft robot dynamics which connects the robot's behavior with the one of a rigid bodied robot with elasticity in the joints. The matching between the two system is exact under the common hypothesis of Piecewise Constant Curvature. Based on this connection we introduce two control architectures, with the aim of achieving accurate curvature control and Cartesian regulation of the robot's impedance, respectively. The curvature controller accounts for the natural softness of the system, while the Cartesian controller adapts the impedance of the end effector for interactions with an unstructured environment. This work proposes the first closed loop dynamic controller for a continuous soft robot. The controllers are validated and evaluated on a physical soft robot capable of planar manipulation.
Pacifiers and breastfeeding: a systematic review.

OBJECTIVE To summarize current evidence on the association between infant pacifier use and breastfeeding. DATA SOURCES MEDLINE, CINAHL, the Cochrane Library, EMBASE, POPLINE, and bibliographies of identified articles. STUDY SELECTION A search for English-language records (from January 1950 through August 2006) containing the Medical Subject Heading terms pacifiers and breastfeeding was conducted, resulting in 1098 reports. Duplicate and irrelevant studies were excluded, yielding 29 studies that fit inclusion criteria for the review (4 randomized controlled trials, 20 cohort studies, and 5 cross-sectional studies). Two independent reviewers abstracted data and scored these studies for quality; disagreements were settled through consensus with a third investigator. MAIN EXPOSURE Pacifier use. MAIN OUTCOME MEASURES Breastfeeding duration or exclusivity. RESULTS Results from 4 randomized controlled trials revealed no difference in breastfeeding outcomes with different pacifier interventions (pacifier use during tube feeds, pacifier use at any time after delivery, an educational program for mothers emphasizing avoidance of pacifiers, and a UNICEF [United Nations Children's Fund]/World Health Organization Baby Friendly Hospital environment). Most observational studies reported an association between pacifier use and shortened duration of breastfeeding. CONCLUSIONS The highest level of evidence does not support an adverse relationship between pacifier use and breastfeeding duration or exclusivity. The association between shortened duration of breastfeeding and pacifier use in observational studies likely reflects a number of other complex factors, such as breastfeeding difficulties or intent to wean. Ongoing quantitative and qualitative research is needed to better understand the relationship between pacifier use and breastfeeding.
Timed Spider Diagrams: a temporal visual specication language

Spider Diagrams (SDs) are a well-established visual language used to specify sets, their relationships, and constraints on their cardinalities. We propose Timed SDs (TSDs) as an extension enabling the expression of temporal constraints. We adopt an interval-based model of calendar time, permitting diagram elements to be specied to exist only over some interval. We introduce basic TSDs, where time constraints refer to an entire diagram rather than to individual elements, as a canonical form for TSDs, and enable the decomposition of complex TSDs into lm-strip-like sequences of basic TSDs. Secondly, we introduce an innovative usage of SDs by specialising and adapting them to an OO-modelling context: in type-SDs a spider represents a type, whereas in instance-SDs a spider represents a specic object of a given type. A notion of conformance of an instance-SD to a type-SD ensues and we extend the concepts to instance-TSDs and type-TSDs. Finally, we extend the model to the application area of policy specication, introducing a notion of temporal policy, specifying the permissible states for instances of given types over a period without temporal gaps in it, and indicate when a sequence of time-annotated instances conforms to a policy.
Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays

General cognitive ability (g), which refers to what cognitive abilities have in common, is an important target for molecular genetic research because multivariate quantitative genetic analyses have shown that the same set of genes affects diverse cognitive abilities as well as learning disabilities. In this first autosomal genome‐wide association scan of g, we used a two‐stage quantitative trait locus (QTL) design with pooled DNA to screen more than 500 000 single nucleotide polymorphisms (SNPs) on microarrays, selecting from a sample of 7000 7‐year‐old children. In stage 1, we screened for allele frequency differences between groups pooled for low and high g. In stage 2, 47 SNPs nominated in stage 1 were tested by individually genotyping an independent sample of 3195 individuals, representative of the entire distribution of g scores in the full 7000 7‐year‐old children. Six SNPs yielded significant associations across the normal distribution of g, although only one SNP remained significant after a false discovery rate of 0.05 was imposed. However, none of these SNPs accounted for more than 0.4% of the variance of g, despite 95% power to detect associations of that size. It is likely that QTL effect sizes, even for highly heritable traits such as cognitive abilities and disabilities, are much smaller than previously assumed. Nonetheless, an aggregated ‘SNP set’ of the six SNPs correlated 0.11 (P < 0.00000003) with g. This shows that future SNP sets that will incorporate many more SNPs could be useful for predicting genetic risk and for investigating functional systems of effects from genes to brain to behavior.
The generation of regional pronunciations of English for speech synthesis

Welsh and Northern English), and two American ones (New York and South Carolina, to represent Eastern and Southern American); regional features were based primarily on the descriptions in [1], with native-speaker input where possible. The regional accents are abbreviated in this paper as: Br(Sc) = Edinburgh; Br(W) = Cardiff; Br(N) = Leeds; Am(E) = New York; and Am(S) = South Carolina. For the standard accents, Br(RP) = RP, and Am(Gen) = General American. Most speech synthesisers and recognisers for English currently use pronunciation lexicons in standard British or American accents, but as use of speech technology grows there will be more demand for the incorporation of regional accents. This paper describes the use of rules to transform existing lexicons of standard British and American pronunciations to a set of regional British and American accents. The paper briefly discusses some features describes of the regional accents in the project, and the framework used for generating pronunciations. Certain theoretical and practical problems are highlighted; for some of these, solutions are suggested, but it is shown that some difficulties cannot be resolved by automatic rules. However, although the method described cannot produce phonetic transcriptions with 100% accuracy, it is more accurate than using letter-to-sound rules, and faster than producing transcriptions by hand. The accents generated represent fairly educated regional speech, though some optional rules were included which produce broader accents. The division between 'obligatory' and 'optional' rules is somewhat artificial, as there may be speakers from the region who have a noticeably local accent but do not use all of the 'obligatory' rules as their speech is somewhat closer to the standard accent. However, it enables us to produce pronunciation lexicons which represent the main features of the regional accents, while allowing some freedom of variation.
Indexing visual features: Real-time loop closure detection using a tree structure

We propose a simple and effective method for visual loop closure detection in appearance-based robot SLAM. Unlike the Bag-of-Words (BoW hereafter) approach in most existing work of the problem, our method uses direct feature matching to detect loop closures and therefore avoid the perceptual aliasing problem caused by the vector quantization process of BoW. We show that a tree structure can be efficient in online loop closure detection. In our method, a KD-tree is built over all the key frame features and an indexing table is kept for retrieving relevant key frames. Due to the efficiency of the tree-based feature matching, loop closure detection can be achieved in real-time. To investigate the scalability of the method, we also apply the scale dependent feature selection in our method and show that the run time can be reduced significantly at the expense of sacrificing the performance to some extent. The proposed method is validated on an indoor SLAM dataset with 7,420 images.
Bayesian simulation optimization with input uncertainty

We consider simulation optimization in the presence of input uncertainty. In particular, we assume that the input distribution can be described by some continuous parameters, and that we have some prior knowledge defining the probability distribution for these parameters. We then seek the simulation design that has the best expected performance over the possible parameters of the input distributions. Assuming correlation of performance between solutions and also between input distributions, we propose modifications of two well-known simulation optimization algorithms, Efficient Global Optimization and Knowledge Gradient with Continuous Parameters, so that they work efficiently under input uncertainty.