Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete genome sequence of soil actinobacteria Streptomyces cavourensis TJ430

A new actinobacteria Streptomyces cavourensis TJ430 was isolated from the mountain soil collected from the southwest of China. In previous study, TJ430 showed striking bactericidal activities and strong ability of antibiotic production. Here, we report complete genome of this bacterium, consisting of 7.6 Mb linear chromosome and 0.2 Mb plasmids. It was predicted 6450 genes in chromosome and 225 genes in plasmids, as well as 12 gene islands in chromosome. Abundant genes have predicted functions in antibiotic metabolism and stress resistance. A whole‐genome comparison of S. cavourensis TJ430, S. coelicolor A3(2), and S. lividans 66 indicates that TJ430 has a relatively high degree of strain specificity. The 16S rRNA phylogenetic tree shows the high identities (99.79%) of TJ430 with S. cavourensis DSM40300. TJ430 is a new and rare Streptomyces species, and analysis of its genome helps us to better understand primary metabolism mechanism of this isolate, as well as the evolutionary biology.
Assessing the Quality of Home Detection from Mobile Phone Data for Official Statistics

Abstract Mobile phone data are an interesting new data source for official statistics. However, multiple problems and uncertainties need to be solved before these data can inform, support or even become an integral part of statistical production processes. In this article, we focus on arguably the most important problem hindering the application of mobile phone data in official statistics: detecting home locations. We argue that current efforts to detect home locations suffer from a blind deployment of criteria to define a place of residence and from limited validation possibilities. We support our argument by analysing the performance of five home detection algorithms (HDAs) that have been applied to a large, French, Call Detailed Record (CDR) data set (~18 million users, five months). Our results show that criteria choice in HDAs influences the detection of home locations for up to about 40% of users, that HDAs perform poorly when compared with a validation data set (resulting in 358-gap), and that their performance is sensitive to the time period and the duration of observation. Based on our findings and experiences, we offer several recommendations for official statistics. If adopted, our recommendations would help ensure more reliable use of mobile phone data vis-à-vis official statistics.
Syntaxin 17 regulates the localization and function of PGAM5 in mitochondrial division and mitophagy

PGAM5, a mitochondrial protein phosphatase that is genetically and biochemically linked to PINK1, facilitates mitochondrial division by dephosphorylating the mitochondrial fission factor Drp1. At the onset of mitophagy, PGAM5 is cleaved by PARL, a rhomboid protease that degrades PINK1 in healthy cells, and the cleaved form facilitates the engulfment of damaged mitochondria by autophagosomes by dephosphorylating the mitophagy receptor FUNDC1. Here, we show that the function and localization of PGAM5 are regulated by syntaxin 17 (Stx17), a mitochondria‐associated membrane/mitochondria protein implicated in mitochondrial dynamics in fed cells and autophagy in starved cells. In healthy cells, loss of Stx17 causes PGAM5 aggregation within mitochondria and thereby failure of the dephosphorylation of Drp1, leading to mitochondrial elongation. In Parkin‐mediated mitophagy, Stx17 is prerequisite for PGAM5 to interact with FUNDC1. Our results reveal that the Stx17‐PGAM5 axis plays pivotal roles in mitochondrial division and PINK1/Parkin‐mediated mitophagy.
Sparsified SGD with Memory

Huge scale machine learning problems are nowadays tackled by distributed optimization algorithms, i.e. algorithms that leverage the compute power of many devices for training. The communication overhead is a key bottleneck that hinders perfect scalability. Various recent works proposed to use quantization or sparsification techniques to reduce the amount of data that needs to be communicated, for instance by only sending the most significant entries of the stochastic gradient (top-k sparsification). Whilst such schemes showed very promising performance in practice, they have eluded theoretical analysis so far. In this work we analyze Stochastic Gradient Descent (SGD) with k-sparsification or compression (for instance top-k or random-k) and show that this scheme converges at the same rate as vanilla SGD when equipped with error compensation (keeping track of accumulated errors in memory). That is, communication can be reduced by a factor of the dimension of the problem (sometimes even more) whilst still converging at the same rate. We present numerical experiments to illustrate the theoretical findings and the good scalability for distributed applications.
Influence of high-temperature exposure on the mating, oviposition and thermotaxis of Bactrocera cucurbitae (Coquillet) (Diptera:Tephritidae)

Background Bactrocera cucurbitae (Coquillett) is an important pest of cucurbit crops and certain vegetables in Asia, the Middle East, Africa and Hawaii. Most studies on B. cucurbitae have focussed on the effects of prolonged high temperature and very few have examined the effects of short-term exposures to high-temperature on behaviour. Results In this study, short-term of high-temperature treatments of 33°C, 37°C, 41°C and 45°C were maintained for 1-3hr, and long-term, variable high-temperature treatments were established that consisted of experienced one, two and three times high temperatures stages to 31°C, 33°C, 34°C, 35°C, 36°C, 37°C, 41°C and 45°C for 7hr. We compared the effects of the different high temperatures regimes changes treatments on the mating, oviposition and thermotactic taxis of the flies. The results showed that exposure to a 45°C/1hr treatment, delayed both initiation of mating and oviposition for 8 hr relative to the control but mating and was observed 41 times and oviposition 47 times. By comparison, in the control, mating commenced immediately and was observed 38.3 times and oviposition was observed 41.3 times. Under the other treatments, all the indices for the flies declined with the increase in temperature and duration of exposure. Conclusion Results showed that 1hr of exposure to 45°C significantly stimulated mating, oviposition and thermotactic behaviour of the flies. These results could improve our understanding of the mechanisms responsible for the population dynamics of B. cucurbitae during the high-temperature season.
Psychometric properties of the short-form UCLA Loneliness Scale (ULS-8) among Chinese adolescents

Abstract Loneliness is prevalent and severe among adolescents, indicating the need for a reliable, valid, and concise instrument for detecting adolescent loneliness. This study aims to examine the psychometric properties of the Chinese version of the short-form UCLA Loneliness Scale (ULS-8) among Chinese adolescents. Computer-assisted self-interviewing was used to complete the questionnaire among 3480 junior or senior high school students aged 10 to 19 years. Construct validity was assessed using exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). To test the concurrent validity and convergent validity of the scale, a single loneliness item and variables such as depression, suicidal ideation, and quality of interpersonal relationships were used. For reliability, Cronbach alpha and test–retest correlation were computed. Construct validity and internal consistency showed that the ULS-6, which excluded 2 reverse-scored items from the ULS-8, had stronger psychometric properties than the ULS-8. The convergent validity and concurrent validity were also supported by the study results. The overall Cronbach &agr; of the ULS-6 was 0.878 and the test–retest reliability coefficient was 0.663. The ULS-6 showed satisfactory reliability and validity in this study, suggesting that this instrument can be used in the measurement of loneliness among Chinese adolescents.
Development and Preliminary Validation of a Depression Assessment Tool for Maintenance Hemodialysis Patients

Patients undergoing maintenance hemodialysis (MHD) are subject to a higher‐than‐usual prevalence of depressive disorders. However, the lack of consensus regarding the best assessment method remains an important problem. Thus, there is a clear need for more effective screening tools and an easily administered, disease‐specific self‐report measure of depression in MHD patients. After we developed and administered an initial depression inventory for MHD patients (I‐DI‐MHD), we created the DI‐MHD and administered the DI‐MHD and the Beck Depression Inventory (BDI) to 354 patients from four hospitals. Reliability, construct validity and receiver operator characteristic curves were assessed. The 17‐item DI‐MHD instrument displayed good internal consistency (Cronbach's alpha =0.893), provided excellent convergent validity, and correlated with the BDI scale (kappa =0.785, P <0.001). A factor analysis pattern matrix analysis showed that a four‐factor model provided the best account of the data. Finally, the DI‐MHD cutoff yielded a sensitivity of 0.97 and a specificity of 0.86, which were slightly better than the corresponding values for the BDI. The DI‐MHD scale shows reasonable validity and reliability for assessing depression in MHD patients.
Small-airway obstruction, dynamic hyperinflation, and gas trapping despite normal airway sensitivity to methacholine in adults with chronic cough.

The clinical relevance of cough during methacholine challenge in individuals with normal airway sensitivity is unknown. We compared responses of individuals with chronic cough who cough during high-dose methacholine bronchoprovocation and have normal versus increased airway sensitivity to healthy controls. Fifteen healthy participants (CONTROL) aged 26 ± 7 yr (mean ± SD) and 32 participants aged 42 ± 14 yr with chronic cough and suspected asthma completed high-dose methacholine challenge testing. Three participants who did not cough and had normal airway sensitivity were excluded. Spirometry and lung volumes were compared at the maximum response (MAX) among 1) ASTHMA [ n = 15, provocative concentration of methacholine causing a 20% fall in forced expiratory volume in 1 s (FEV1) from baseline (PC20) 4.71 ± 1.37 mg/ml], 2) methacholine-induced cough with normal airway sensitivity (COUGH, n = 14, PC20 41.2 ± 18.7 mg/ml for 3 participants with a measurable PC20), and 3) CONTROL ( n = 15; PC20 93.4 ± 95.4 mg/ml for 4 participants with a measurable PC20). Esophageal pressure-derived pulmonary mechanics were compared at MAX for the ASTHMA and COUGH groups. From baseline to MAX, FEV1 and forced expiratory flow between 25% and 75% of forced vital capacity decreased more in ASTHMA (-36.2 ± 3.8 %pr; -47.1 ± 6.9 %pr, respectively) than COUGH (-12.2 ± 3.0 %pr ( P < 0.001); -24.7 ± 6.5 %pr ( P < 0.001), respectively) and CONTROL (-13.7 ± 2.0 %pr ( P < 0.001); -32.8 ± 5.4 %pr ( P < 0.017), respectively). In both ASTHMA and COUGH, inspiratory capacity decreased by 500-800 ml, and functional residual capacity and residual volume increased by ~800 ml. Individuals with COUGH develop dynamic hyperinflation and gas trapping comparable to individuals with ASTHMA despite less bronchoconstriction and smaller reductions in mid-to-late expiratory flows, which leads us to believe that COUGH is a distinct phenotype. NEW & NOTEWORTHY Healthy individuals and individuals with chronic cough who demonstrate normal airway sensitivity but cough during methacholine bronchoprovocation bronchoconstrict less than individuals with mild asthma. However, those who cough and have normal airway sensitivity develop dynamic hyperinflation and gas trapping comparable to individuals with mild asthma. Thus, methacholine-induced cough with normal airway sensitivity may be clinically relevant, related to reversible small airway obstruction and preservation of the bronchodilating and/or bronchoprotective effects of deep inspirations.
Caregiver burden after stroke: changes over time?

Abstract Introduction and aim: Many caregivers of stroke patients experience a high burden. This study aims to describe the course of burden in individual caregivers in the first year after stroke. Methods: This study is part of the Stroke Cohort Outcomes of REhabilitation study, a multicentre, longitudinal cohort study including consecutive stroke patients admitted to two rehabilitation facilities. Caregivers were asked to complete the Caregiver Strain Index and questions on their sociodemographic characteristics 6 and 12 months post admission. Patients’ sociodemographic and clinical characteristics were extracted from medical records. Results: A total of 129 caregivers were included, 72 completed the Caregiver Strain Index twice. Of them, 19 (26.4%) were men, median age 59 (range 27–78) years. A consistently high or low burden was reported by 15 (20.8%) and 49 (68.1%), respectively, whereas 8 (11.1%) reported a high burden at either 6 (n = 3) or 12 months (n = 5). Discussion: In the majority of caregivers of stroke patients the perceived caregiver burden is consistent over time. However, as in 11.1% caregiver burden changes from 6 to 12 months, caregiver burden should be measured repeatedly until 12 months after stroke. Caregivers living together with a patient who suffered a haemorrhagic stroke seem to be more at risk for a high burden. Implications for rehabilitation Many caregivers of stroke patients experience a high burden. The Caregiver Strain Index score at 6 months is a good predictor for the score at 12 months. In some caregivers the high burden is not yet present at 6 months, therefore monitoring caregiver burden throughout the first year after stroke seems warranted. Caregivers living together with a patient who suffered a haemorrhagic stroke seem to be more at risk for a high burden.
Fighting Redundancy and Model Decay with Embeddings

Every day, hundreds of millions of new Tweets containing over 40 languages of ever-shifting vernacular flow through Twitter. Models that attempt to extract insight from this firehose of information must face the torrential covariate shift that is endemic to the Twitter platform. While regularly-retrained algorithms can maintain performance in the face of this shift, fixed model features that fail to represent new trends and tokens can quickly become stale, resulting in performance degradation. To mitigate this problem we employ learned features, or embedding models, that can efficiently represent the most relevant aspects of a data distribution. Sharing these embedding models across teams can also reduce redundancy and multiplicatively increase cross-team modeling productivity. In this paper, we detail the commoditized tools, algorithms and pipelines that we have developed and are developing at Twitter to regularly generate high quality, up-to-date embeddings and share them broadly across the company.
Multisource domain adaptation and its application to early detection of fatigue

We consider the characterization of muscle fatigue through a noninvasive sensing mechanism such as Surface ElectroMyoGraphy (SEMG). While changes in the properties of SEMG signals with respect to muscle fatigue have been reported in the literature, the large variation in these signals across different individuals makes the task of modeling and classification of SEMG signals challenging. Indeed, the variation in SEMG parameters from subject to subject creates differences in the data distribution. In this article, we propose two transfer learning frameworks based on the multisource domain adaptation methodology for detecting different stages of fatigue using SEMG signals, that addresses the distribution differences. In the proposed frameworks, the SEMG data of a subject represent a domain; data from multiple subjects in the training set form the multiple source domains and the test subject data form the target domain. SEMG signals are predominantly different in conditional probability distribution across subjects. The key feature of the first framework is a novel weighting scheme that addresses the conditional probability distribution differences across multiple domains (subjects) and the key feature of the second framework is a two-stage domain adaptation methodology which combines weighted data from multiple sources based on marginal probability differences (first stage) as well as conditional probability differences (second stage), with the target domain data. The weights for minimizing the marginal probability differences are estimated independently, while the weights for minimizing conditional probability differences are computed simultaneously by exploiting the potential interaction among multiple sources. We also provide a theoretical analysis on the generalization performance of the proposed multisource domain adaptation formulation using the weighted Rademacher complexity measure. We have validated the proposed frameworks on Surface ElectroMyoGram signals collected from 8 people during a fatigue-causing repetitive gripping activity. Comprehensive experiments on the SEMG dataset demonstrate that the proposed method improves the classification accuracy by 20% to 30% over the cases without any domain adaptation method and by 13% to 30% over existing state-of-the-art domain adaptation methods.
mTORC1/2 inhibition re-sensitizes platinum-resistant ovarian cancer by disrupting selective translation of DNA damage and survival mRNAs

Platinum resistance is a major cause of treatment failure and mortality in epithelial ovarian cancer. mTORC1/2 inhibitors, which impair mRNA translation, can re-sensitize resistant ovarian cancer cells to platinum chemotherapy but the mechanism remains poorly described. Using platinum-resistant OVCAR-3 cells treated with the selective mTORC1/2 inhibitor INK128/MLN128, we conducted genome-wide transcription and translation studies and analyzed the effect on cell proliferation, AKT-mTOR signaling and cell survival, to determine whether carboplatin resistance involves selective mRNA translational reprogramming, and whether it is sensitive to mTORC1/2 inhibition. Gene ontology and Ingenuity Pathway Analysis (IPA) were used to categorize gene expression changes into experimentally authenticated biochemical and molecular networks. We show that carboplatin resistance involves increased mTORC1/2 signaling, resulting in selective translation of mRNAs involved in DNA damage and repair responses (DDR), cell cycle and anti-apoptosis (survival) pathways. Re-sensitization of ovarian cancer cell killing by carboplatin required only modest mTORC1/2 inhibition, with downregulation of protein synthesis by only 20-30%. Genome-wide transcriptomic and translatomic analyses in OVCAR-3 cells revealed that the modest downregulation of global protein synthesis by dual mTORC1/2 inhibition is associated with greater selective inhibition of DDR, cell cycle and survival mRNA translation, which was confirmed in platinum-resistant SKOV-3 cells. These data suggest a clinical path to re-sensitize platinum resistant ovarian cancer to platinum chemotherapy through partial inhibition of mTORC1/2, resulting in selective translation inhibition of DDR and anti-apoptosis protective mRNAs.
The Open Vision Computer: An Integrated Sensing and Compute System for Mobile Robots

In this paper we describe the Open Vision Computer (OVC) which was designed to support high speed, vision guided autonomous drone flight. In particular our aim was to develop a system that would be suitable for relatively small-scale flying platforms where size, weight, power consumption and computational performance were all important considerations. This manuscript describes the primary features of our OVC system and explains how they are used to support fully autonomous indoor and outdoor exploration and navigation operations on our Falcon 250 quadrotor platform.
GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components

Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these applications via their Graphical User Interfaces (GUI) is a key factor for their final success and real utility for researchers. Despite the existence of different packages and applications focused on advanced data visualization, there is a lack of specific libraries providing pertinent GUI components able to help scientific bioinformatics software developers. To that end, this paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development. Within GC4S, developers of new applications can focus on the specific GUI requirements of their projects, relying on GC4S for generalities and abstractions. GC4S is free software distributed under the terms of GNU Lesser General Public License and both source code and documentation are publicly available at http://www.sing-group.org/gc4s
Sub-Diffraction Visible Imaging Using Macroscopic Fourier Ptychography and Regularization by Denoising

Imaging past the diffraction limit is of significance to an optical system. Fourier ptychography (FP) is a novel coherent imaging technique that can achieve this goal and it is widely used in microscopic imaging. Most phase retrieval algorithms for FP reconstruction are based on Gaussian measurements which cannot extend straightforwardly to long range, sub-diffraction imaging setup because of laser speckle noise corruption. In this work, a new FP reconstruction framework is proposed for macroscopic visible imaging. When compared with existing research, the reweighted amplitude flow algorithm is adopted for better signal modeling, and the Regularization by Denoising (RED) scheme is introduced to reduce the effects of speckle. Experiments demonstrate that the proposed method can obtain state-of-the-art recovered results on both visual and quantitative metrics without increasing computation cost, and it is flexible for real imaging applications.