bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical implementation of MRI-based organs-at-risk auto-segmentation with convolutional networks for prostate radiotherapy
Authors: Savenije Mark H. F. , Maspero Matteo , Sikkes Gonda G. , van der Voort van Zyp Jochem R. N. , T. J. Kotte Alexis N. , Bol Gijsbert H. , T. van den Berg Cornelis A. 
Published: May 2020

Abstract
Background
Structure delineation is a necessary, yet time-consuming manual procedure in radiotherapy. Recently, convolutional neural networks have been proposed to speed-up and automatise this procedure, obtaining promising results. With the advent of magnetic resonance imaging (MRI)-guided radiotherapy, MR-based segmentation is becoming increasingly relevant. However, the majority of the studies investigated automatic contouring based on computed tomography (CT).

Purpose
In this study, we investigate the feasibility of clinical use of deep learning-based automatic OARs delineation on MRI.

Materials and methods
We included 150 patients diagnosed with prostate cancer who underwent MR-only radiotherapy. A three-dimensional (3D) T1-weighted dual spoiled gradient-recalled echo sequence was acquired with 3T MRI for the generation of the synthetic-CT. The first 48 patients were included in a feasibility study training two 3D convolutional networks called DeepMedic and dense V-net (dV-net) to segment bladder, rectum and femurs. A research version of an atlas-based software was considered for comparison. Dice similarity coefficient, 95% Hausdorff distances (HD95), and mean distances were calculated against clinical delineations. For eight patients, an expert RTT scored the quality of the contouring for all the three methods. A choice among the three approaches was made, and the chosen approach was retrained on 97 patients and implemented for automatic use in the clinical workflow. For the successive 53 patients, Dice, HD95 and mean distances were calculated against the clinically used delineations.

Results
DeepMedic, dV-net and the atlas-based software generated contours in 60 s, 4 s and 10-15 min, respectively. Performances were higher for both the networks compared to the atlas-based software. The qualitative analysis demonstrated that delineation from DeepMedic required fewer adaptations, followed by dV-net and the atlas-based software. DeepMedic was clinically implemented. After retraining DeepMedic and testing on the successive patients, the performances slightly improved.

Conclusion
High conformality for OARs delineation was achieved with two in-house trained networks, obtaining a significant speed-up of the delineation procedure. Comparison of different approaches has been performed leading to the succesful adoption of one of the neural networks, DeepMedic, in the clinical workflow. DeepMedic maintained in a clinical setting the accuracy obtained in the feasibility study.
EVI5 is an oncogene that regulates the proliferation and metastasis of NSCLC cells
Authors: Cai Tingting , Zhou Jieqi , Zeng Yuanyuan , Du Wenwen , Zhang Yang , Liu Ting , Fu Yulong , Huang Jian-an , Qian Qian , Zhu Jianjie , Ling Chunhua , Liu Zeyi 
Published: May 2020

Abstract
Background
The Ecotropic viral integration site 5 (EVI5), an important protein in regulating cell cycle, cytokinesis and cellular membrane traffic, functions as a stabilizing factor maintaining anaphase-promoting complex/cyclosome (APC/C) inhibitor Emi1 in S/G2 phase. However, the mechanism by which EVI5 promotes malignant transformation of non-small cell lung cancer (NSCLC) remains unknown. In the present study, we addressed the role of EVI5 in NSCLC by regulating tumor growth, migration and invasion.

Methods
The expression levels of EVI5 and miR-486-5p in NSCLC tissues and cells were measured by real-time PCR. Meanwhile, EVI5 and its associated protein expression were analyzed by western blot and co-immunoprecipitation assay. Flow cytometry was performed to determine cell proliferation and apoptosis. CCK-8 and clonogenic assays were used to analyze cell viability. Wound healing, transwell migration and matrigel invasion assays were utilized to assess the motility of tumor cells. To investigate the role of EVI5 in vivo, lung carcinoma xenograft mouse model was applied..

Results
EVI5 was upregulated in NSCLC tissues and cell lines when compared with that in normal tissues and cell line. Knockdown of EVI5 in vitro inhibited tumor cell proliferation, migration and invasion in NSCLC cells. Further, inoculation of EVI5-deficient tumor cells into nude mice suppressed tumor proliferation and metastasis compared to control mice inoculated with unmanipulated tumor cells. These data indicated that EVI5 promote the proliferation of NSCLC cells which was consistent with our previous results. Additionally, we showed that EVI5 was directly regulated by miR-486-5p, and miR-486-5p-EVI5 axis affected the NSCLC migration and invasion through TGF-β/Smad signaling pathway by interacting with TGF-β receptor II and TGF-β receptor I.

Conclusions
Based on these results, we demonstrated a new post-transcriptional mechanism of EVI5 regulation via miR-486-5p and the protumoral function of EVI5 in NSCLC by interacting with Emi1 and/or TGF-β receptors, which provides a new insight into the targeted therapy of NSCLC.
MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data
Authors: Argelaguet Ricard , Arnol Damien , Bredikhin Danila , Deloro Yonatan , Velten Britta , Marioni John C. , Stegle Oliver 
Published: May 2020

AbstractTechnological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational strategies to analyze data from complex experimental designs that include multiple data modalities and multiple groups of samples. We present Multi-Omics Factor Analysis v2 (MOFA+), a statistical framework for the comprehensive and scalable integration of single-cell multi-modal data. MOFA+ reconstructs a low-dimensional representation of the data using computationally efficient variational inference and supports flexible sparsity constraints, allowing to jointly model variation across multiple sample groups and data modalities.
Usual care including home exercise with versus without spa therapy for chronic low back pain: protocol for the LOMBATHERM’ study, a multicentric randomised controlled trial
Authors: Forestier Romain , Suehs Carey , Françon Alain , Marty Marc , Genevay Stéphane , Sellam Jérémie , Chauveton Claire , Erol Forestier Fatma Begüm , Molinari Nicolas 
Published: May 2020

Abstract
Background
Low back pain is highly prevalent and a major source of disability worldwide. Spa therapy is frequently used to treat low back pain, but the associated level of evidence for efficacy is insufficient. To fill this knowledge gap, this protocol proposes an appropriately powered, prospective, evaluator-blinded, multi-centre, two-parallel-arm, randomised (1:1), controlled trial that will compare spa therapy in addition to usual care including home exercise (UCHE) versus UCHE alone for the treatment of chronic low back pain.

Methods
Eligible patients (anticipated sample size of 358) will have had low back pain for more than 3 months and scores for pain greater than 40 mm on a visual analogue scale (VAS). Following initial consent for UCHE and baseline evaluations, patients are randomised (1:1) to UCHE alone, or UCHE plus spa therapy (18 days of mud packs, underwater massages, showers and water exercises under medical supervision). Patients in the latter arm will be requested to sign an additional consent form as per Zelen randomisation. Follow-up visits will occur at approximately months 1, 6 and 12 and (along with baseline assessments) will cover changes over time in VAS pain scores, the impact of lower back pain on daily life (the Rolland and Morris Disability Questionnaire (RMDQ)), inappropriate fears and beliefs about lower back pain (the fear, avoidance, belief questionnaire (FABQ)), general quality of life (the Euroqol Group 5 dimension, 5 level questionnaire (EQ-5D-5 L)), Patient Acceptable Symptom State (PASS), consumption of analgesic drugs and nonsteroidal anti-inflammatory drugs (NSAIDs), and overall state of health. Health resource use and days of sick leave (and subsequently the associated costs) will also be recorded. The primary outcome is the presence/absence of a clinically relevant change (improvement of at least 30%) in the VAS score for pain at 6 months.

Discussion
Despite the fact that previous, rather dated recommendations encourage spa therapy for the treatment of low back pain, the current literary corpus is methodologically poor. This protocol has been designed to provide results spanning a thorough range of outcomes at the highest evidence level possible.

Trial registration
ClinicalTrials.gov: NCT03910023. Registered on 10 April 2019.
Australian Aedes aegypti mosquitoes are susceptible to infection with a highly divergent and sylvatic strain of dengue virus type 2 but are unlikely to transmit it
Authors: Pickering Paul , Hugo Leon E. , Devine Gregor J. , Aaskov John G. , Liu Wenjun 
Published: May 2020

Abstract
Background
Humans are the primary hosts of dengue viruses (DENV). However, sylvatic cycles of transmission can occur among non-human primates and human encroachment into forested regions can be a source of emergence of new strains such as the highly divergent and sylvatic strain of DENV2, QML22, recovered from a dengue fever patient returning to Australia from Borneo. The objective of the present study was to evaluate the vector competence of Australian Aedes aegypti mosquitoes for this virus.

Methods
Four- to five-day-old mosquitoes from two strains of Ae. aegypti from Queensland, Australia, were fed a meal of sheep blood containing 108 50% cell culture infectious dose per ml (CCID50/ml) of either QML22 or an epidemic strain of DENV serotype 2 (QML16) isolated from a dengue fever patient in Australia in 2015. Mosquitoes were maintained at 28 °C, 75% relative humidity and sampled 7, 10 and 14 days post-infection (dpi). Live virions in mosquito bodies (abdomen/thorax), legs and wings and saliva expectorates from individual mosquitoes were quantified using a cell culture enzyme-linked immunosorbent assay (CCELISA) to determine infection, dissemination and transmission rates.

Results
The infection and dissemination rates of the sylvatic DENV2 strain, QML22, were significantly lower than that for QML16. While the titres of virus in the bodies of mosquitoes infected with either of these viruses were similar, titres in legs and wings were significantly lower in mosquitoes infected with QML22 at most time points although they reached similar levels by 14 dpi. QML16 was detected in 16% (n = 25) and 28% (n = 25) of saliva expectorates at 10 and 14 dpi, respectively. In contrast, no virus was detected in the saliva expectorates of QML22 infected mosquitoes.

Conclusions
Australia urban/peri-urban Ae. aegypti species are susceptible to infection by the sylvatic and highly divergent DENV 2 QML22 but replication of QML22 is attenuated relative to the contemporary strain, QML16. A salivary gland infection or escape barrier may be acting to prevent infection of saliva and would prevent onward transmission of this highly divergent virus in Australia.
Reliability and validity of a novel Kinect-based software program for measuring a single leg squat
Authors: Ressman John , Rasmussen-Barr Eva , Grooten Wilhelmus Johannes Andreas 
Published: May 2020

Abstract
Background
The Single leg squat (SLS) is a movement screening test widely used in clinical settings. The SLS is highly subjective in its nature. Objective measures, such as 3D-motion analyses, are seldom used in daily clinical work. An interactive, Kinect-based 3D-movement analysis system, the Qinematic™, is proposed to be easily used in clinical settings to assess the SLS. The aim of this study was to establish the test-retest reliability and construct validity of Qinematic™ for assessing the SLS. A further aim was to identify angles of medial knee displacement, to summarise the discriminative ability of the SLS measured by Qinematic™.

Methods
We performed a test-retest reliability study (n = 37) of the SLS using Qinematic™ and a construct validity study, in which Qinematic™ data were compared with visual assessment of video-recorded SLS.

Results
Three variables (left knee down, right knee up and down) reached “substantial reliability” (ICC = 0.64–0.69). One variable, “left knee up”, showed a significant difference between the two test occasions (T1–6.34°, T2 0.66°, p = 0.013, ICC = 0.50), and “poor absolute reliability” was seen for all variables (SEM = 9.04–10.66, SDC = 25.06–29.55). A moderate agreement between the visual assessment and Qinematic™ data for various knee angles was shown (Kappa = 0.45–0.58). The best discriminative ability of the SLS was found at a knee angle of 6° (AUC = 0.82, sensitivity = 0.86, specificity = 0.78, PPV = 0.58, NPV = 0.94).

Conclusions
Qinematic™ shows a poor absolute reliability, and a substantial relative reliability, in measuring a SLS at the way down. This indicates that Qinematic™ should not be recommended for the use on an individual level, but it can possibly be used on a group level. The merged results of the construct validity study indicate that Qinematic™ at 6° of medial displacement can identify subjects with a knee over foot position. In summary, the use of the Qinematic™ net trajectory angle, which estimates the “line of best fit” cannot be recommended to assess a knee medial to foot position and should be reconsidered.
Automated recognition of spontaneous facial expression in individuals with autism spectrum disorder: parsing response variability
Authors: Bangerter Abigail , Chatterjee Meenakshi , Manfredonia Joseph , Manyakov Nikolay V. , Ness Seth , Boice Matthew A. , Skalkin Andrew , Goodwin Matthew S. , Dawson Geraldine , Hendren Robert , Leventhal Bennett , Shic Frederick , Pandina Gahan 
Published: May 2020

AbstractBackgroundReduction or differences in facial expression are a core diagnostic feature of autism spectrum disorder (ASD), yet evidence regarding the extent of this discrepancy is limited and inconsistent. Use of automated facial expression detection technology enables accurate and efficient tracking of facial expressions that has potential to identify individual response differences.MethodsChildren and adults with ASD (N= 124) and typically developing (TD,N= 41) were shown short clips of “funny videos.” Using automated facial analysis software, we investigated differences between ASD and TD groups and within the ASD group in evidence of facial action unit (AU) activation related to the expression of positive facial expression, in particular, a smile.ResultsIndividuals with ASD on average showed less evidence of facial AUs (AU12, AU6) relating to positive facial expression, compared to the TD group (p< .05,r= − 0.17). Using Gaussian mixture model for clustering, we identified two distinct distributions within the ASD group, which were then compared to the TD group. One subgroup (n= 35), termed “over-responsive,” expressed more intense positive facial expressions in response to the videos than the TD group (p< .001,r= 0.31). The second subgroup (n= 89), (“under-responsive”), displayed fewer, less intense positive facial expressions in response to videos than the TD group (p< .001;r= − 0.36). The over-responsive subgroup differed from the under-responsive subgroup in age and caregiver-reported impulsivity (p< .05,r= 0.21). Reduced expression in the under-responsive, but not the over-responsive group, was related to caregiver-reported social withdrawal (p< .01,r= − 0.3).LimitationsThis exploratory study does not account for multiple comparisons, and future work will have to ascertain the strength and reproducibility of all results. Reduced displays of positive facial expressions do not mean individuals with ASD do not experience positive emotions.ConclusionsIndividuals with ASD differed from the TD group in their facial expressions of positive emotion in response to “funny videos.” Identification of subgroups based on response may help in parsing heterogeneity in ASD and enable targeting of treatment based on subtypes.Trial registrationClinicalTrials.gov,NCT02299700. Registration date: November 24, 2014
The diatomic molecular spectroscopy database
Authors: Liu Xiangyue , Truppe Stefan , Meijer Gerard , Pérez-Ríos Jesús 
Published: May 2020

Abstract
Motivation
The spectroscopy of diatomic molecules is an important research area in chemical physics due to its relevance in astrochemistry, combustion chemistry, and ultracold physics. However, there is currently no database where the user can easily retrieve, in a useful format, the spectroscopic constants of a given molecule. A similar situation appears concerning the vibrational Franck–Condon factors for diatomic molecules, a crucial parameter to infer laser cooling prospects for molecules. To address this problem, and inspired by the idea that data should be open and freely accessible, we have developed a user-friendly website (https://rios.mp.fhi.mpg.de) where the user can retrieve spectroscopic constants and Franck–Condon factors in useful formats.

Implementation
In this database, the spectroscopic constants of the ground states and first excited states of the diatomic molecules are accessible from the website and can be retrieved in readable formats. The website is implemented within the LAMP web service stacks. In particular, using Linux as the operative system, Apache as the HTTP Server, MySQL as the database management system, and PHP as the programming language for the web. Furthermore, the user can register and upload new data. This project is licensed under the Free-Libre/Open Source Software (FLOSS) license Apache License 2.0 which allows free and open access to the codes as well as efficient collaboration in the maintenance of the software.

Conclusions and impact
The present data-driven website presents essential information in a user-friendly manner and may help the chemical physics community to identify molecules that should be explored through spectroscopic techniques.
Biotransformation of 5-hydroxymethylfurfural into 2,5-dihydroxymethylfuran by Ganoderma sessile and toxicological assessment of both compounds
Authors: Hou Ya-nan , Wang Ya-rong , Zheng Chun-hui , Feng Kun 
Published: May 2020

AbstractBiotransformation has the advantages of low cost and environmental protection and is a preferred method for production of compounds. At present, most 2,5-dihydroxymethylfuran (DHMF) is synthesized by chemical methods. In this study, 12.008 μg/mL DHMF was produced from 9.045 μg/mL 5-hydroxymethylfurfural (5-HMF) with a yield of 1.33 g/g using the crude enzymes from fungus Ganoderma sessile. To elucidate the toxic potential for both compounds, cytotoxicity tests and acute toxicity were evaluated respectively. 5-HMF induced weak cytotoxicity in HCT-8, A549 and SGC-7901 cells and DHMF exerted no cytotoxicity on HCT-8 while induced inhibition proliferation of A549 and SGC-7901 cells. The acute toxicity study showed no mortality happened in any group even at the single dose of 2000 mg/kg body weight. These results suggest it is feasible to convert 5-HMF to DHMF via crude enzymes from fungus G. sessile under mild condition, and that DHMF displays a potential effect of antitumor in vitro with little acute toxicity.
Thenar oxygen saturation (StO2) alterations during a spontaneous breathing trial predict extubation failure
Authors: Mesquida Jaume , Gruartmoner Guillem , Espinal Cristina , Masip Jordi , Sabatier Caroline , Villagrá Ana , Gómez Hernando , Pinsky Michael , Baigorri Francisco , Artigas Antonio 
Published: May 2020

Abstract
Background
Weaning from mechanical ventilation (MV) is a cardiovascular stress test. Monitoring the regional oxygenation status has shown promising results in predicting the tolerance to spontaneously breathe in the process of weaning from MV. Our aim was to determine whether changes in skeletal muscle oxygen saturation (StO2) measured by near-infrared spectroscopy (NIRS) on the thenar eminence during a vascular occlusion test (VOT) can be used to predict extubation failure from mechanical ventilation.

Methods
We prospectively studied 206 adult patients with acute respiratory failure receiving MV for at least 48 h from a 30-bed mixed ICU, who were deemed ready to wean by their physicians. Patients underwent a 30-min spontaneous breathing trial (SBT), and were extubated according to the local protocol. Continuous StO2 was measured non-invasively on the thenar eminence. A VOT was performed prior to and at 30 min of the SBT (SBT30). The rate of StO2 deoxygenation (DeO2), StO2 reoxygenation (ReO2) rate and StO2 hyperemic response to ischemia (HAUC) were calculated.

Results
Thirty-six of the 206 patients (17%) failed their SBT. The remainder 170 patients (83%) were extubated. Twenty-three of these patients (13.5%) needed reinstitution of MV within 24 h. Reintubated patients displayed a lower HAUC at baseline, and higher relative changes in their StO2 deoxygenation rate between baseline and SBT30 (DeO2 Ratio). A logistic regression-derived StO2 score, combining baseline StO2, HAUC and DeO2 ratio, showed an AUC of 0.84 (95% CI 0.74–0.91) for prediction of extubation failure.

Conclusions
Extubation failure was associated to baseline and dynamic StO2 alterations during the SBT. Monitoring StO2-derived parameters might be useful in predicting extubation outcome.
On Grüss inequalities within generalized K-fractional integrals
Authors: Rashid Saima , Jarad Fahd , Noor Muhammad Aslam , Noor Khalida Inayat , Baleanu Dumitru , Liu Jia-Bao 
Published: May 2020

AbstractIn this paper, we introduce the generalized $\mathcal{K}$K-fractional integral in the frame of a new parameter $\mathcal{K}>0$K>0. This paper offers some new important inequalities of Grüss type using the generalized $\mathcal{K}$K-fractional integral and associated integral inequalities. Our results with this new integral operator have the abilities to be implemented for the evaluation of many mathematical problems related to the real world applications.
Women in household decision-making and implications for dietary quality in Bhutan
Authors: Sariyev Orkhan , Loos Tim K. , Zeller Manfred , Gurung Tulsi 
Published: May 2020

AbstractDespite the wide range of literature supporting the linkages between women’s empowerment and food security, it is not examined in social contexts where females historically enjoy equality and even favoritism, for instance where there is female succession and/or polyandry. This study was done in the Kingdom of Bhutan where matrilineal succession and polyandry were prevalent during the twentieth century.Both quantitative and qualitative survey methods were employed with the objectives of (i) investigating women’s participation in crucial domestic decision-making processes and (ii) identifying the implications of female involvement in domestic decision-making on household-level dietary quality.While descriptive analyses and qualitative interviews revealed that women do not lack significant participation in domestic decision-making, the estimations indicate that the relationship between women’s participation in decision-making and dietary diversity is non-linear. Further analyses indicate a positive association between (perfect) gender equal decision-making regarding household livelihoods and household-level dietary quality.