Miracle-dz/UniFAR-FTUs huggingface dataset:
The Wide Potential Trophic Niche of the Asiatic Fruit Fly Drosophila suzukii: The Key of Its Invasion Success in Temperate Europe?

The Asiatic fruit fly Drosophila suzukii has recently invaded Europe and North and South America, causing severe damage to fruit production systems. Although agronomic host plants of that fly are now well documented, little is known about the suitability of wild and ornamental hosts in its exotic area. In order to study the potential trophic niche of D. suzukii with relation to fruit characteristics, fleshy fruits from 67 plant species were sampled in natural and anthropic ecosystems (forests, hedgerows, grasslands, coastal areas, gardens and urban areas) of the north of France and submitted to experimental infestations. A set of fruit traits (structure, colour, shape, skin texture, diameter and weight, phenology) potentially interacting with oviposition choices and development success of D. suzukii was measured. Almost half of the tested plant species belonging to 17 plant families allowed the full development of D. suzukii. This suggests that the extreme polyphagy of the fly and the very large reservoir of hosts producing fruits all year round ensure temporal continuity in resource availability and contribute to the persistence and the exceptional invasion success of D. suzukii in natural habitats and neighbouring cultivated systems. Nevertheless, this very plastic trophic niche is not systematically beneficial to the fly. Some of the tested plants attractive to D. suzukii gravid females stimulate oviposition but do not allow full larval development. Planted near sensitive crops, these “trap plants” may attract and lure D. suzukii, therefore contributing to the control of the invasive fly.
The centriolar satellite protein CCDC66 interacts with CEP290 and functions in cilium formation and trafficking

ABSTRACT Centriolar satellites are membrane-less structures that localize and move around the centrosome and cilium complex in a microtubule-dependent manner. They play important roles in centrosome- and cilium-related processes, including protein trafficking to the centrosome and cilium complex, and ciliogenesis, and they are implicated in ciliopathies. Despite the important regulatory roles of centriolar satellites in the assembly and function of the centrosome and cilium complex, the molecular mechanisms of their functions remain poorly understood. To dissect the mechanism for their regulatory roles during ciliogenesis, we performed an analysis to determine the proteins that localize in close proximity to the satellite protein CEP72, among which was the retinal degeneration gene product CCDC66. We identified CCDC66 as a microtubule-associated protein that dynamically localizes to the centrosome, centriolar satellites and the primary cilium throughout the cell cycle. Like the BBSome component BBS4, CCDC66 distributes between satellites and the primary cilium during ciliogenesis. CCDC66 has extensive proximity interactions with centrosome and centriolar satellite proteins, and co-immunoprecipitation experiments revealed interactions between CCDC66, CEP290 and PCM1. Ciliogenesis, ciliary recruitment of BBS4 and centriolar satellite organization are impaired in cells depleted for CCDC66. Taken together, our findings identify CCDC66 as a targeting factor for centrosome and cilium proteins. Summary: The retinal degeneration gene product CCDC66 is a microtubule-associated protein that localizes to the centrosome and cilium complex, and functions in cilium formation and recruitment of BBS4 to the cilium.
Group Low-Rank Nonnegative Matrix Factorization With Semantic Regularizer for Hyperspectral Unmixing

In this paper, the low rank prior of abundances of hyperspectral data is explored and combined with semantic information to develop a new Group Low-rank constrained Nonnegative Matrix Factorization (GLrNMF) method for linear hyperspectral unmixing. First, hyperspectral image pixels are divided into several groups of superpixels, and then low-rank constraints are cast on them to explore the semantic geometry in both spatial and spectral domains. By incorporating semantic information into the NMF, we can recover more accurate endmembers and abundances in the linear unmixing model. Some experiments are taken on several synthetic and real hyperspectral data to investigate the performance of GLrNMF, and the results show that it can outperform some state-of-the-art unmixing results.
Bendamustine plus Rituximab Versus R-CHOP as First-Line Treatment for Patients with Follicular Lymphoma Grade 3A: Evidence from a Multicenter, Retrospective Study.

BACKGROUND Rituximab plus bendamustine (R-B) has been demonstrated to improve outcomes and reduce toxicity compared with rituximab, cyclophosphamide, doxorubicin, and prednisone (R-CHOP) in follicular lymphoma (FL). Nevertheless, in clinical practice, many centers still prefer R-CHOP to R-B in patients with FL grade 3A (FL3A). Therefore, we retrospectively assessed patients with FL3A treated with either R-CHOP or R-B in five European cancer centers and compared their outcomes. MATERIALS AND METHODS We retrospectively assessed 132 patients affected by FL grade 3A treated with either R-B or R-CHOP in the first line and evaluated outcome and toxicity according to the type of treatment. This study included 101 patients who were a subgroup of a previously published cohort. RESULTS R-B was less toxic and achieved a similar percentage of complete remissions compared with R-CHOP (97% vs. 96%, p = .3). During follow-up, 10 (16%) patients relapsed after R-B and 29 (41%) after R-CHOP (p = .001), leading to a median progression-free survival (PFS) of 15 versus 11.7 years, respectively (p = .03). Furthermore, R-B overcame the negative prognostic impact of BCL2 expression (15 vs. 4.8 years; p = .001). However, median overall survival was similar between both groups (not reached for both; p = .8). CONCLUSION R-B as a first-line treatment of FL3A is better tolerated than R-CHOP and seems to induce more profound responses, leading to a significantly lower relapse rate and prolonged PFS. Therefore, R-B is a valid treatment option for FL grade 3A. IMPLICATIONS FOR PRACTICE Rituximab plus bendamustine (R-B) has shown to be less toxic and more effective than rituximab, cyclophosphamide, doxorubicin, and prednisone (R-CHOP) in follicular lymphoma grade 3A. Although both regimens can induce a complete remission in >95% of patients, relapses occur more frequently after R-CHOP than R-B, leading to a significantly longer progression-free survival in the latter. R-B is also able to overcome the impact of negative prognosticators, such as BCL2 expression. However, because of the indolent course of this disease and efficient salvage treatments, overall survival was similar in both treatment groups. Therefore, R-B is a valid treatment option in this patient setting.
Robust Visual Tracking Using Exemplar-Based Detectors

Tracking by detection has become an attractive tracking technique, which treats tracking as an object detection problem and trains a detector to separate the target object from the background in each frame. While this strategy is effective to some extent, we argue that the task in tracking should be searching for a specific object instance instead of an object category. Based on this viewpoint, a novel framework based on object exemplar detectors is proposed for visual tracking. To build a specific and discriminative model to separate the object instance from the background, the proposed method trains an exemplar-based linear discriminant analysis (ELDA) classifier for the object exemplar, using the current tracked instance as the positive sample and massive negative samples obtained both offline and online. To improve the trackers’ adaptivity, we use an ensemble of the above ELDA detectors and update them during the tracking to cover the variation in object appearance. Extensive experimental results on a large benchmark data set show that the proposed method outperforms many state-of-the-art trackers, demonstrating the effectiveness and robustness of the ELDA tracker.
Identification of Key Factors Involved in the Biosorption of Patulin by Inactivated Lactic Acid Bacteria (LAB) Cells

The purpose of this study was to identify the key factors involved in patulin adsorption by heat-inactivated lactic acid bacteria (LAB) cells. For preventing bacterial contamination, a sterilization process was involved in the adsorption process. The effects of various physical, chemical, and enzymatic pre-treatments, simultaneous treatments, and post-treatments on the patulin adsorption performances of six LAB strains were evaluated. The pre-treated cells were characterized by scanning electron microscopy (SEM). Results showed that the removal of patulin by viable cells was mainly based on adsorption or degradation, depending on the specific strain. The adsorption abilities were widely increased by NaOH and esterification pre-treatments, and reduced by trypsin, lipase, iodate, and periodate pre-treatments. Additionally, the adsorption abilities were almost maintained at pH 2.2–4.0, and enhanced significantly at pH 4.0–6.0. The effects of sodium and magnesium ions on the adsorption abilities at pH 4 were slight and strain-specific. A lower proportion of patulin was released from the strain with higher adsorption ability. Analyses revealed that the physical structure of peptidoglycan was not a principal factor. Vicinal OH and carboxyl groups were not involved in patulin adsorption, while alkaline amino acids, thiol and ester compounds were important for patulin adsorption. Additionally, besides hydrophobic interaction, electrostatic interaction also participated in patulin adsorption, which was enhanced with the increase in pH (4.0–6.0).
Using Scripts to help in Biomedical Text Interpretation Working Note 30

Introduction This short note speculates on the use of world knowledge to help interpret a short paragraph of biomedical text about transcytosis (transport across a cell). The ultimate goal is to create a simple representation of the transcytosis process from the text (either automatically or semi-automatically). The challenges are formidable, as the process involves several steps that are often expressed opaquely (or even omitted) in the text, and the whole process is described over several non-contiguous sentences.
Global Ecosystem Response Types Derived from the Standardized Precipitation Evapotranspiration Index and FPAR3g Series

Observing trends in global ecosystem dynamics is an important first step, but attributing these trends to climate variability represents a further step in understanding Earth system changes. In the present study, we classified global Ecosystem Response Types (ERTs) based on common spatio-temporal patterns in time-series of Standardized Precipitation Evapotranspiration Index (SPEI) and FPAR3g anomalies (1982-2011) by using an extended Principal Component Analysis. The ERTs represent region specific spatio-temporal patterns of ecosystems responding to drought or ecosystems with decreasing severity in drought events as well as ecosystems where drought was not a dominant factor in a 30-year period. Highest explanatory values in the SPEI12-FPAR3g anomalies and strongest SPEI12-FPAR3g correlations were seen in the ERTs of Australia and South America whereas lowest explanatory value and lowest correlations were observed in Asia and North America. These ERTs complement traditional pixel based methods by enabling the combined assessment of the location, timing, duration, frequency and severity of climatic and vegetation anomalies with the joint assessment of wetting and drying climatic conditions. The ERTs produced here thus have potential in supporting global change studies by mapping reference conditions of long term ecosystem changes.
A Simple Parallel Algorithm with an O(1/t) Convergence Rate for General Convex Programs

This paper considers convex programs with a general (possibly non-differentiable) convex objective function and Lipschitz continuous convex inequality constraint functions. A simple algorithm is developed and achieves an $O(1/t)$ convergence rate. Similar to the classical dual subgradient algorithm and the ADMM algorithm, the new algorithm has a parallel implementation when the objective and constraint functions are separable. However, the new algorithm has a faster $O(1/t)$ convergence rate compared with the best known $O(1/\sqrt{t})$ convergence rate for the dual subgradient algorithm with primal averaging. Further, it can solve convex programs with nonlinear constraints, which cannot be handled by the ADMM algorithm. The new algorithm is applied to a multipath network utility maximization problem and yields a decentralized flow control algorithm with the fast $O(1/t)$ convergence rate.
Association between Diabetes and Risk of Aortic Dissection: A Case-Control Study in a Chinese Population

Background It is well-recognized that diabetes represents a powerful independent risk factor for cardiovascular diseases. However, very few studies have investigated the relationship between diabetes and risk of aortic dissection (AD). Aim The aim of this case-control study was to evaluate the association between diabetes and risk of AD in Chinese population. Methods A hospital-based case-control study, consisting of 2160 AD patients and 4320 controls, was conducted in a Chinese population. Demographic, clinical characteristics and risk factors were collected. Diabetes rate of patients with overall AD, Stanford type A AD and type B AD group was compared with that of corresponding matched control groups. Logistic regression analysis was used to estimate the odds ratios (OR) and 95% confidence intervals (95% CI) for relationship between diabetes and AD risk. Results The prevalence of diabetes was lower in AD cases than that of control subjects, whether it is the overall AD, type A AD or type B AD group (4.7% vs. 10.0%, 2.9% vs. 8.8%, 5.9% vs. 10.9%, all P<0.001). Furthermore, in multivariate model, diabetes was found to be associated with lower AD risk, which not only applies to the overall AD (OR = 0.2, 95%CI: 0.15–0.26), but also type A AD (OR = 0.12, 95% CI: 0.07–0.20) and type B AD (OR = 0.25, 95%CI: 0.18–0.33). Conclusions We observed the paradoxical inverse relationship between DM and risk of AD in the Chinese population. These results suggest diabetes may play a protective role in the development of AD. However, further studies are needed to enrich related evidence, especially with regard to underlying mechanisms for these trends.
Defining the appropriateness and inappropriateness of antibiotic prescribing in primary care

Objectives To assess the appropriateness of prescribing systemic antibiotics for different clinical conditions in primary care, and to quantify 'ideal' antibiotic prescribing proportions in conditions for which antibiotic treatment is sometimes but not always indicated. Methods Prescribing guidelines were consulted to define the appropriateness of antibiotic therapy for the conditions that resulted in antibiotic prescriptions between 2013 and 2015 in The Health Improvement Network (THIN) primary care database. The opinions of subject experts were then formally elicited to quantify ideal antibiotic prescribing proportions for 10 common conditions. Results Of the antibiotic prescriptions in THIN, 52.5% were for conditions that could be assessed using prescribing guidelines. Among these, the vast majority of prescriptions (91.4%) were for conditions where antibiotic appropriateness is conditional on patient-specific indicators. Experts estimated low ideal prescribing proportions in acute, non-comorbid presentations of many of these conditions, such as cough (10% of patients), rhinosinusitis (11%), bronchitis (13%) and sore throat (13%). Conversely, antibiotics were believed to be appropriate in 75% of non-pregnant women with non-recurrent urinary tract infection. In impetigo and acute exacerbation of chronic obstructive pulmonary disease, experts clustered into distinct groups that believed in either high or low prescribing. Conclusions In English primary care, most antibiotics are prescribed for conditions that only sometimes require antibiotic treatment, depending on patient-specific indicators. Experts estimated low ideal prescribing proportions in many of these conditions. Incomplete prescribing guidelines and disagreement about prescribing in some conditions highlight further research needs.
RESULTS Sensitivity of the In Vitro Human Corneal Wound Healing Model to Evaluate the Pattern and Rate of Reepithelialization

PURPOSE. The reepithelialization of the corneal surface is an important process for restoring the imaging properties of this tissue. The purpose of the present study was to characterize and validate a new human in vitro three-dimensional corneal wound healing model by studying the expression of basement membrane components and integrin subunits that play important roles during epithelial cell migration and to verify whether the presence of exogenous factors could accelerate the reepithelialization.
Universal hospital admission screening for carbapenemase-producing organisms in a low-prevalence setting.

BACKGROUND Carbapenemase-producing Enterobacteriaceae (CPE) are an emerging threat for healthcare providers worldwide. OBJECTIVES To determine CPE carriage rates and risk factors in an unselected hospital cohort at the time of admission. METHODS We approached 4567 patients within 72 h of admission to provide a rectal swab and answer a questionnaire on risk factors for carriage. Rectal swabs were cultured for carbapenem-resistant organisms on chromogenic and non-chromogenic agar, and tested for carbapenemase production by PCR (Check-Direct CPE). The study was approved by the NHS Research Ethics Committee. RESULTS Only 6 CPE were cultured from 5 (0.1%) of 4006 patients who provided a rectal swab; only 1 was cultured using non-chromogenic media. An additional 76 culture-negative rectal swabs were initially PCR positive, but none grew a carbapenem-resistant organism despite enrichment culture and only two were positive when retested several months later by Check-Direct and a second PCR assay (Cepheid GeneXpert® Carba-R). A modified Ct cut-off of <35 would have resolved these apparent false-positives. 40% of patients had a risk factor that should prompt screening and pre-emptive isolation as defined by UK CPE guidelines but only 8.1% and 20.2% of these patients had been screened and pre-emptively isolated by clinical teams, respectively. Overseas hospitalization was the only significant risk factor for CPE carriage (P < 0.001, OR 64.3, 95% CI 7.3-488.5). CONCLUSIONS This study highlights a very low carriage rate of CPE. Hospitalization abroad is the most important risk factor to guide admission screening in this low-prevalence setting.
Subcortical connections of the perirhinal, postrhinal, and entorhinal cortices of the rat. II. efferents

This is the second of two studies detailing the subcortical connections of the perirhinal (PER), the postrhinal (POR) and entorhinal (EC) cortices of the rat. In the present study, we analyzed the subcortical efferents of the rat PER areas 35 and 36, POR, and the lateral and medial entorhinal areas (LEA and MEA). Anterograde tracers were injected into these five regions, and the resulting density of fiber labeling was quantified in an extensive set of subcortical structures. Density and topography of fiber labeling were quantitatively assessed in 36 subcortical areas, including olfactory structures, claustrum, amygdala nuclei, septal nuclei, basal ganglia, thalamic nuclei, and hypothalamic structures. In addition to reporting the density of labeled fibers, we incorporated a new method for quantifying the size of anterograde projections that takes into account the volume of the target subcortical structure as well as the density of fiber labeling. The PER, POR, and EC displayed unique patterns of projections to subcortical areas. Interestingly, all regions examined provided strong input to the basal ganglia, although the projections arising in the PER and LEA were stronger and more widespread. PER areas 35 and 36 exhibited similar pattern of projections with some differences. PER area 36 projects more heavily to the lateral amygdala and much more heavily to thalamic nuclei including the lateral posterior nucleus, the posterior complex, and the nucleus reuniens. Area 35 projects more heavily to olfactory structures. The LEA provides the strongest and most widespread projections to subcortical structures including all those targeted by the PER as well as the medial and posterior septal nuclei. POR shows fewer subcortical projections overall, but contributes substantial input to the lateral posterior nucleus of the thalamus. The MEA projections are even weaker. Our results suggest that the PER and LEA have greater influence over olfactory, amygdala, and septal nuclei, whereas PER area 36 and the POR have greater influence over thalamic nuclei. © 2016 Wiley Periodicals, Inc.
Feature-Ensemble-Based Novelty Detection for Analyzing Plant Hyperspectral Datasets

Recently, there has been a significant increase in the use of proximal or remote hyperspectral imaging systems to study plant properties, types, and conditions. Numerous financial and environmental benefits of using such systems have been the driving force behind this growth. This paper is concerned with the analysis of hyperspectral data for detecting plant diseases and stress conditions and classifying crop types by means of advanced machine learning techniques. Main contribution of the work lies in the use of an innovative classification framework for the analysis, in which adaptive feature selection, novelty detection, and ensemble learning are integrated. Three hyperspectral datasets and a nonimaging hyperspectral dataset were used in the evaluation of the proposed framework. Experimental results show significant improvements achieved by the proposed method compared to the use of empirical spectral indices and existing classification methods.
A Streamlined, Automated Protocol for the Production of Milligram Quantities of Untagged Recombinant Rat Lactate Dehydrogenase A Using ÄKTAxpressTM

We developed an efficient, automated 2-step purification protocol for the production of milligram quantities of untagged recombinant rat lactate dehydrogenase A (rLDHA) from E. coli, using the ÄKTAxpress™ chromatography system. Cation exchange followed by size exclusion results in average final purity in excess of 93% and yields ~ 14 milligrams per 50 ml of original cell culture in EnPresso B media, in under 8 hrs, including all primary sample processing and column equilibration steps. The protein is highly active and coherent biophysically and a viable alternative to the more problematic human homolog for structural and ligand-binding studies; an apo structure of untagged rLDHA was solved to a resolution 2.29 Å (PDB ID 5ES3). Our automated methodology uses generic commercially available pre-packed columns and simple buffers, and represents a robust standard method for the production of milligram amounts of untagged rLDHA, facilitating a novel fragment screening approach for new inhibitors.