Miracle-dz/UniFAR-FTUs huggingface dataset:
Site of metabolism prediction for oxidation reactions mediated by oxidoreductases based on chemical bond

Motivation: The metabolites of exogenous and endogenous compounds play a pivotal role in the domain of metabolism research. However, they are still unclear for most chemicals in our environment. The in silico methods for predicting the site of metabolism (SOM) are considered to be efficient and low‐cost in SOM discovery. However, many in silico methods are focused on metabolism processes catalyzed by several specified Cytochromes P450s, and only apply to substrates with special skeleton. A SOM prediction model always deserves more attention, which demands no special requirements to structures of substrates and applies to more metabolic enzymes. Results: By incorporating the use of hybrid feature selection techniques (CHI, IG, GR, Relief) and multiple classification procedures (KStar, BN, IBK, J48, RF, SVM, AdaBoostM1, Bagging), SOM prediction models for six oxidation reactions mediated by oxidoreductases were established by the integration of enzyme data and chemical bond information. The advantage of the method is the introduction of unlabeled SOM. We defined the SOM which not reported in the literature as unlabeled SOM, where negative SOM was filtered. Consequently, for each type of reaction, a series of SOM prediction models were built based on information about metabolism of 1237 heterogeneous chemicals. Then optimal models were attained through comparisons among these models. Finally, independent test set was used to validate optimal models. It demonstrated that all models gave accuracies above 0.90. For receiver operating characteristic analysis, the area under curve values of all these models over 0.906. The results suggested that these models showed good predicting power. Availability and implementation: All the models will be available when contact with wangyun@bucm.edu. cn Contacts: wangyun@bucm.edu. cn or yjqiao@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.
Barriers and facilitators to implementing family support and education in Early Psychosis Intervention programmes: A systematic review

Family support is a core component of the Early Psychosis Intervention (EPI) model, yet it continues to have relatively low rates of implementation in practice. This paper reports results of a literature review on facilitators and barriers to delivering family interventions in EPI programmes. A search was conducted of 4 electronic databases, Medline, EMBASE, PsycINFO and Joanna Briggs, from 2000 to 2015 using terms related to early onset psychosis, family work and implementation. Four thousand four hundred and two unique studies were identified, 7 of which met inclusion criteria. Barriers and facilitators were coded and aggregated to higher‐level themes using a consensus approach. Five of 7 studies examined structured multifamily psychoeducation. Uptake by families was affected by: family/client interest and readiness to participate; ability to access supports; and support needs/preferences. Implementation by programmes was affected by staff access to training and resources to provide family support. A key finding across the identified studies was that families have different needs and preferences regarding the timing, length, intensity and content of the intervention. One size does not fit all and many families do not require the intensive psychoeducational programmes typically provided. The reviewed literature suggests that flexible, tiered approaches to care may better meet family needs and increase rates of uptake of family support. However, more research is needed on the effectiveness of different models of family support in early psychosis and how they can be successfully implemented.
Uncovering the wisdom hidden between the lines: the Collaborative Reflexive Deliberative Approach

Abstract Background Meta-analysis and meta-synthesis have been developed to synthesize results across published studies; however, they are still largely grounded in what is already published, missing the tacit ‘between the lines’ knowledge generated during many research projects that are not intrinsic to the main objectives of studies. Objective To develop a novel approach to expand and deepen meta-syntheses using researchers’ experience, tacit knowledge and relevant unpublished materials. Methods We established new collaborations among primary health care researchers from different contexts based on common interests in reforming primary care service delivery and a diversity of perspectives. Over 2 years, the team met face-to-face and via tele- and video-conferences to employ the Collaborative Reflexive Deliberative Approach (CRDA) to discuss and reflect on published and unpublished results from participants’ studies to identify new patterns and insights. Results CRDA focuses on uncovering critical insights, interpretations hidden within multiple research contexts. For the process to work, careful attention must be paid to ensure sufficient diversity among participants while also having people who are able to collaborate effectively. Ensuring there are enough studies for contextual variation also matters. It is necessary to balance rigorous facilitation techniques with the creation of safe space for diverse contributions. Conclusions The CRDA requires large commitments of investigator time, the expense of convening facilitated retreats, considerable coordination, and strong leadership. The process creates an environment where interactions among diverse participants can illuminate hidden information within the contexts of studies, effectively enhancing theory development and generating new research questions and strategies.
Tomato ethylene sensitivity determines interaction with plant growth-promoting bacteria

Background and Aims Plant growth-promoting bacteria (PGPB) are soil micro-organisms able to interact with plants and stimulate their growth, positively affecting plant physiology and development. Although ethylene plays a key role in plant growth, little is known about the involvement of ethylene sensitivity in bacterial inoculation effects on plant physiology. Thus, the present study was pursued to establish whether ethylene perception is critical for plant-bacteria interaction and growth induction by two different PGPB strains, and to assess the physiological effects of these strains in juvenile and mature tomato ( Solanum lycopersicum ) plants. Methods An experiment was performed with the ethylene-insensitive tomato never ripe and its isogenic wild-type line in which these two strains were inoculated with either Bacillus megaterium or Enterobacter sp. C7. Plants were grown until juvenile and mature stages, when biomass, stomatal conductance, photosynthesis as well as nutritional, hormonal and metabolic statuses were analysed. Key Results Bacillus megaterium promoted growth only in mature wild type plants. However, Enterobacter C7 PGPB activity affected both wild-type and never ripe plants. Furthermore, PGPB inoculation affected physiological parameters and root metabolite levels in juvenile plants; meanwhile plant nutrition was highly dependent on ethylene sensitivity and was altered at the mature stage. Bacillus megaterium inoculation improved carbon assimilation in wild-type plants. However, insensitivity to ethylene compromised B. megaterium PGPB activity, affecting photosynthetic efficiency, plant nutrition and the root sugar content. Nevertheless, Enterobacter C7 inoculation modified the root amino acid content in addition to stomatal conductance and plant nutrition. Conclusions Insensitivity to ethylene severely impaired B. megaterium interaction with tomato plants, resulting in physiological modifications and loss of PGPB activity. In contrast, Enterobacter C7 inoculation stimulated growth independently of ethylene perception and improved nitrogen assimilation in ethylene-insensitive plants. Thus, ethylene sensitivity is a determinant for B. megaterium , but is not involved in Enterobacter C7 PGPB activity.
Sex Steroid Hormones and Tumors in Domestic Animals

Sex steroid hormones play a role in the development and control of animal tumours, partic‐ ularly in those arising in their target organs. Due to their incidence and prevalence, mamma‐ ry tumours of female dogs and cats are among the most frequently studied with focus on the role of ovarian oestrogen and progesterone. In these tumours, sex steroid hormones have been shown to act during the three steps of the carcinogenesis cascade: initiation, pro‐ motion and progression. Experimental data have shown the mutagenic effect of oestrogens [1] while epidemiologic and clinical studies highlighted the role of ovarian hormones as pro‐ moters on mammary tumours in both the dog and the cat [2-9]. Finally, oestrogens and pro‐ gesterone further act during tumour progression. Their role in the last two steps of carcinogenesis makes it possible to control the evolution of the disease.
Vaginal cuff brachytherapy in endometrial cancer – a technically easy treatment?

Endometrial cancer (EC) is one of the most common gynecological cancers among women in the developed countries. Vaginal cuff is the main location of relapses after a curative surgical procedure and postoperative radiation therapy have proven to diminish it. Nevertheless, these results have not translated into better survival results. The preeminent place of vaginal cuff brachytherapy (VCB) in the postoperative treatment of high- to intermediate-risk EC was given by the PORTEC-2 trial, which demonstrated a similar reduction in relapses with VCB than with external beam radiotherapy (EBRT), but VCB induced less late toxicity. As a result of this trial, the use of VCB has increased in clinical practice at the expense of EBRT. A majority of the clinical reviews of VCB usually address the risk categories and patient selection but pay little attention to technical aspects of the VCB procedure. Our review aimed to address both aspects. First of all, we described the risk groups, which guide patient selection for VCB in clinical practice. Then, we depicted several technical aspects that might influence dose deposition and toxicity. Bladder distension and rectal distension as well as applicator position or patient position are some of those variables that we reviewed.
NKG2D and Its Ligands: “One for All, All for One”

The activating receptor NKG2D is peculiar in its capability to bind to numerous and highly diversified MHC class I-like self-molecules. These ligands are poorly expressed on normal cells but can be induced on damaged, transformed or infected cells, with the final NKG2D ligand expression resulting from multiple levels of regulation. Although redundant molecular mechanisms can converge in the regulation of all NKG2D ligands, different stimuli can induce specific cellular responses, leading to the expression of one or few ligands. A large body of evidence demonstrates that NK cell activation can be triggered by different NKG2D ligands, often expressed on the same cell, suggesting a functional redundancy of these molecules. However, since a number of evasion mechanisms can reduce membrane expression of these molecules both on virus-infected and tumor cells, the co-expression of different ligands and/or the presence of allelic forms of the same ligand guarantee NKG2D activation in various stressful conditions and cell contexts. Noteworthy, NKG2D ligands can differ in their ability to down-modulate NKG2D membrane expression in human NK cells supporting the idea that NKG2D transduces different signals upon binding various ligands. Moreover, whether proteolytically shed and exosome-associated soluble NKG2D ligands share with their membrane-bound counterparts the same ability to induce NKG2D-mediated signaling is still a matter of debate. Here, we will review recent studies on the NKG2D/NKG2D ligand biology to summarize and discuss the redundancy and/or diversity in ligand expression, regulation, and receptor specificity.
The role of value in the attentional boost effect

Focusing attention on one item typically interferes with the ability to process other information. Yet, target detection can both facilitate memory for items paired with the target (the attentional boost effect) and increase the perceived value of those items (cued approach). Because long-term memory is better for valuable items than for neutral items, we asked whether the attentional boost effect is due to changes in the perceived value of items that are paired with targets. In three experiments, participants memorised a series of briefly presented images that depicted valuable (e.g., food) or neutral (e.g., children’s toys) items. Whenever an item appeared, a square flashed in its centre. Participants pressed a button if the square was a target colour but not if it was a distractor colour. Consistent with previous research, target-paired items were remembered better than distractor-paired items and were rated as more valuable. Importantly, if memory for target-paired items is enhanced because they increased in perceived value, then valuable items should have been better remembered than neutral items. However, we found no evidence that value enhanced memory for the items in this task. Thus, it is unlikely that the attentional boost effect is due to changes in perceived value.
Salient Region-Based Least-Squares Log-Density Gradient Clustering for Image-To-Video Person Re-Identification

Because of its distinction and reliability, the person-salient region has been applied to pedestrian re-identification (re-id) across disjoint camera views. Despite the great progress achieved, a few works have studied the more challenging image-to-video person re-id problem, in which the gallery consists of videos and the same pedestrian appears in a continuous video sequence. The intrinsic high redundancy of such video sequences makes it more difficult to obtain high performance for pedestrian re-id. To solve this problem, in this paper, we propose a new salient region clustering approach for image-to-video person re-id. Specifically, we use the mean shift to extract the person regions and obtain the salient region by computing the saliency for each region. Then, all salient regions are clustered by least-squares log-density gradient clustering, after which the salient regions that are extracted from the same person are marked as the same group. Finally, the rank of the person re-id can be obtained by computing the distance between the probe-salient region and the gallery clustered salient regions. We evaluate the proposed approach on two public pedestrian sequence data sets (PRID 2011 and MARS), and the experimental results validate the effectiveness of the proposed approach for the image-to-video person re-id.
Role of 5‐HT1A receptor in insular cortex mediating stress – induced visceral sensory dysfunction

5‐HT1A receptors (HTR1As) in the insular cortex are thought to be related with the generation of stress‐induced functional gastrointestinal disorders (FGIDs), but its mechanism is not clear. Visceral hypersensitivity is one important pathophysiological mechanism of FGIDs. This study aimed to explore the role of HTR1As in mediating stress‐induced visceral hypersensitivity and its mechanism in the insular cortex.
Friction Characteristics of CFRP Plates in Contact with Copper Plates under High Contact Pressure

Carbon fiber-reinforced-polymer (CFRP) plates have significant properties for applications in structural engineering, automotive, aviation, space, and shipbuilding. CFRP plates have the advantage over conventional materials owing to their resistance to corrosion, low weight, and high tensile strength. The coefficient of friction between CFRP plate and copper plate is an important parameter required for designing anchors for CFRP plates. The friction behavior of CFRP plates in contact with copper plates of different hardness (as-received and annealed) under high contact pressure (50–175 MPa) was investigated. The shear stress versus contact pressure relationship was linear for the as-received copper plates with a constant coefficient of friction of 0.31. However, for the annealed copper plates, the coefficient of friction decreased with contact pressure from 0.39 to 0.30. For all tests, the sliding distance before rupture of CFRP plate decreased with the increase of contact pressure. Ploughing, wear, debris accumulation, and stick-slip behavior were observed and illustrated in this article.
Wideband Optimization Process for EM Characterization of Low-Losses Dielectric and Dispersive Materials in a Quasi-TEM Cell

This paper presents an original wideband method (from 1 MHz to 1 GHz) for the characterization of dielectric and dispersive materials. The method is based on a full-wave calculation technique using the finite-difference time-domain (FDTD) method combined with a fast optimization process. The S-parameters are the metrics which have to be minimized. Only two S-parameters measurements of a quasi-TEM structure with and without the sample under test (SUT) are required. In parallel, the experiment is faithfully reproduced by simulation through the FDTD method still without and with the SUT model. This enables to determine the electromagnetic properties of the SUT by adjusting its properties in simulation in order to match the measured S-parameters of the cell thanks to the optimization process. The main advantage of the proposed method lies in the fact that no machining process of the sample is required provided that: 1) the size of the sample enables to insert it within the quasi-TEM cell; 2) the position of the SUT in the propagating device is known accurately; and 3) the insertion of the SUT sufficiently modifies the S-parameters of the quasi-TEM structure. The experimental results obtained on different dielectrics or ferrite samples are provided showing excellent agreements with results given in the literature or by the manufacturers.
An international survey of patients living with spasticity

Abstract Purpose: To better understand patient perspectives on the life impact of spasticity. Methods: Global Internet survey (April 2014–May 2015) of 281 people living with spasticity. Results: Respondents indicated that spasticity has a broad impact on their daily-life: 72% reported impact on quality of life, 44% reported loss of independence and 44% reported depression. Most respondents (64%) were cared for by family members, of whom half had stopped working or reduced their hours. Overall, 45% reported dissatisfaction with the information provided at diagnosis; main reasons were “not enough information” (67%) and “technical terminology” (36%). Respondents had high treatment expectations; 63% expected to be free of muscle spasm, 41% to take care of themselves and 36% to return to a normal routine. However, 33% of respondents had not discussed these expectations with their physician. The most common treatments were physiotherapy (75%), botulinum neurotoxin (BoNT, 73%) and oral spasmolytics (57%). Of those treated with BoNT, 47% waited >1 year from spasticity onset to treatment. Conclusions: This survey emphasises the broad impact of spasticity and highlights unmet needs in the patient journey. Improvements with regards to communication and the therapeutic relationship would be especially welcomed by patients, and would help manage treatment expectations. Implications of Rehabilitation Spasticity has broad impact on the lives of patients and their families that extends beyond the direct physical disability. Patients with spasticity need to be well informed about their condition and treatments available and should be given the opportunity to discuss their expectations. Physicians need to be aware of the patient’s individual needs and expectations in order to better help them achieve their therapeutic goals.
Use of Simulation Based on an Electronic Health Records Environment to Evaluate the Structure and Accuracy of Notes Generated by Medical Scribes: Proof-of-Concept Study

Background The increasing adoption of electronic health records (EHRs) has been associated with a number of unintended negative consequences with provider efficiency and job satisfaction. To address this, there has been a dramatic increase in the use of medical scribes to perform many of the required EHR functions. Despite this rapid growth, little has been published on the training or assessment tools to appraise the safety and efficacy of scribe-related EHR activities. Given the number of reports documenting that other professional groups suffer from a number of performance errors in EHR interface and data gathering, scribes likely face similar challenges. This highlights the need for new assessment tools for medical scribes. Objective The objective of this study was to develop a virtual video-based simulation to demonstrate and quantify the variability and accuracy of scribes’ transcribed notes in the EHR. Methods From a pool of 8 scribes in one department, a total of 5 female scribes, intent on pursuing careers in health care, with at least 6 months of experience were recruited for our simulation study. We created three simulated patient-provider scenarios. Each scenario contained a corresponding medical record in our simulation instance of our EHR. For each scenario, we video-recorded a standardized patient-provider encounter. Five scribes with at least 6 months of experience both with our EHR and in the specialty of the simulated cases were recruited. Each scribe watched the simulated encounter and transcribed notes into a simulated EHR environment. Transcribed notes were evaluated for interscribe variability and compared with a gold standard for accuracy. Results All scribes completed all simulated cases. There was significant interscribe variability in note structure and content. Overall, only 26% of all data elements were unique to the scribe writing them. The term data element was used to define the individual pieces of data that scribes perceived from the simulation. Note length was determined by counting the number of words varied by 31%, 37%, and 57% between longest and shortest note between the three cases, and word economy ranged between 23% and 71%. Overall, there was a wide inter- and intrascribe variation in accuracy for each section of the notes with ranges from 50% to 76%, resulting in an overall positive predictive value for each note between 38% and 81%. Conclusions We created a high-fidelity, video-based EHR simulation, capable of assessing multiple performance indicators in medical scribes. In this cohort, we demonstrate significant variability both in terms of structure and accuracy in clinical documentation. This form of simulation can provide a valuable tool for future development of scribe curriculum and assessment of competency.
Dyneins Across Eukaryotes: A Comparative Genomic Analysis

Dyneins are large minus‐end‐directed microtubule motors. Each dynein contains at least one dynein heavy chain (DHC) and a variable number of intermediate chains (IC), light intermediate chains (LIC) and light chains (LC). Here, we used genome sequence data from 24 diverse eukaryotes to assess the distribution of DHCs, ICs, LICs and LCs across Eukaryota. Phylogenetic inference identified nine DHC families (two cytoplasmic and seven axonemal) and six IC families (one cytoplasmic). We confirm that dyneins have been lost from higher plants and show that this is most likely because of a single loss of cytoplasmic dynein 1 from the ancestor of Rhodophyta and Viridiplantae, followed by lineage‐specific losses of other families. Independent losses in Entamoeba mean that at least three extant eukaryotic lineages are entirely devoid of dyneins. Cytoplasmic dynein 2 is associated with intraflagellar transport (IFT), but in two chromalveolate organisms, we find an IFT footprint without the retrograde motor. The distribution of one family of outer‐arm dyneins accounts for 2‐headed or 3‐headed outer‐arm ultrastructures observed in different organisms. One diatom species builds motile axonemes without any inner‐arm dyneins (IAD), and the unexpected conservation of IAD I1 in non‐flagellate algae and LC8 (DYNLL1/2) in all lineages reveals a surprising fluidity to dynein function.