Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions

High-confidence assemblies enabled comparative genomics analyses of the centromeric regions of Oryza genomes and provided insight into centromere evolution. Centromeres are dynamic chromosomal regions, and the genetic and epigenetic environment of the centromere is often regarded as oppressive to protein-coding genes. Here, we used comparative genomic and phylogenomic approaches to study the evolution of centromeres and centromere-linked genes in the genus Oryza. We report a 12.4-Mb high-quality BAC-based pericentromeric assembly for Oryza brachyantha, which diverged from cultivated rice (Oryza sativa) ∼15 million years ago. The synteny analyses reveal seven medium (>50 kb) pericentric inversions in O. sativa and 10 in O. brachyantha. Of these inversions, three resulted in centromere movement (Chr1, Chr7, and Chr9). Additionally, we identified a potential centromere-repositioning event, in which the ancestral centromere on chromosome 12 in O. brachyantha jumped ∼400 kb away, possibly mediated by a duplicated transposition event (>28 kb). More strikingly, we observed an excess of syntenic gene loss at and near the centromeric regions (P < 2.2 × 10−16). Most (33/47) of the missing genes moved to other genomic regions; therefore such excess could be explained by the selective loss of the copy in or near centromeric regions after gene duplication. The pattern of gene loss immediately adjacent to centromeric regions suggests centromere chromatin dynamics (e.g., spreading or microrepositioning) may drive such gene loss.
The paradigm shift for drug delivery systems for oral and maxillofacial implants

Abstract Along with the development of nanotechnological strategies for biomaterials associated with the prevention of infections, a myriad of clinically unproven techniques have been described to date. In this work, the aim was to perform a critical analysis of the literature available concerning antibacterial biomaterials for oral implantology and to provide a practical derivation for such a purpose. As anti-adhesive strategies may affect osseointegration, they should no longer be recommended for inclusion in this class of biomaterials, despite promising results in biomedical engineering for other, non-bone load bearing organs. Targeted, antibacterial drug delivery is most likely desirable in the case of intraosseous implants. Interfering factors such as the oral cavity environment, saliva, the bacterial microbiome, as well as, the characteristics of the alveolar mucosa and peri-implant space must be taken into account when calculating the local pharmacokinetics for antibacterial coatings. Effective release is crucial for tailoring antibacterial implant longevity providing minimal inhibitory concentration (MIC) for the desired amount of time, which for oral implants, should be at least the cumulative time for the osseointegration period and functional loading period within the tissues. These parameters may differ between the implant type and its anatomical site. Also, the functional drug concentration in the peri-implant space should be calculated as the amount of the drug released from the implant surface including the concentration of the drug inactivated by biological fluids of the peri-implant space or saliva flow throughout the effective release time.
Learning scenarios and encouraging algorithmic thinking

Although contemporary education places learners at the center of the teaching process, in most of our schools, students are mostly educated by traditional outdated teaching methods. Students should be active participants in the educational process that will, through research in collaboration with the teacher and other students, acquire new knowledge and develop various competencies, especially in the STEM field. The traditional role of the teacher, as the main source and knowledge transferor, is changing, so preparation for teaching should be adapted to such changes. Learning scenarios can contribute to the development of innovative ideas for the implementation of educational activities, including modern teaching methods using digital tools and digital contents. The Erasmus+ project “Games for Learning Algorithmic Thinking” begins with the education of primary school junior grade teachers, who will develop such learning scenarios and apply them with their students. The paper presents how the appropriate learning scenarios can stimulate the algorithmic thinking of young students in everyday situations.
Physical activity behaviours of persons living with HIV of low socioeconomic status: domain, intensity and sociodemographic correlates

ABSTRACT Physical activity (PA) is healthy for People Living with HIV and AIDS (PLWHA). This study examined the PA profile of 978 PLWHA based on PA domains and PA intensity. The study also sought to determine whether employment status and level of education can predict PA among PLWHA of low SES. PA and sociodemographic data of 978 PLWHA of mean age 35 (8.77) years were collected using the global physical activity questionnaire and a sociodemographic questionnaire. Results showed that, participants engaged more in work-related PA [160.11 (346.95) min/wk], followed by transport related PA [115.21(SD = 142.04) min/wk], and lastly in leisure related PA [40.84 (SD = 110.37) min/wk]. Participants also engaged more in moderate PA [265.86 (SD = 335.45) min/wk], than in vigorous PA [50.29 (SD = 205.30) min/wk]. Employment was a significant predictor of overall PA controlling for age, CD4 count and education level. The model explained 2.5% of the variance (R2 = 0.025) on overall PA and tested significant at a 0.01 alpha level (p < 0.01). PA interventions for this population should be domain- and intensity-specific. Researchers promoting healthy lifestyle behaviour change can benefit from determining the factors that facilitate domain-specific PA.
Split-Lists and Initial Thresholds for WAND-based Search

We examine search engine performance for rank-safe query execution using the WAND and state-of-the-art BMW algorithms. Supported by extensive experiments, we suggest two approaches to improve query performance: initial list thresholds should be used when k values are large, and our split-list WAND approach should be used instead of the normal WAND or BMW approaches. We also recommend that reranking-based distributed systems use smaller k values when selecting the results to return from each partition.
Motivating Job Characteristics and Happiness at Work: A Multilevel Perspective

Employees may react differently to the perceived availability of motivating job characteristics during work activities, depending on the degree to which such motivating job characteristics are also present at the job level and individual differences. This study expands Job Characteristics Theory (JCT) by using a multilevel approach to predict how variations in motivating job characteristics relate to employee happiness during daily work activities. Based on adaptation level theory and the affective-reactivity hypothesis, we predicted that the positive relationship between perceived motivating job characteristics and happiness during work activities is moderated by motivating job characteristics at the job level and individual differences in trait positive affect. A sample of 68 employees filled out a general survey and reported on their job characteristics and happiness during 741 work activities using a day reconstruction method across five working days. In line with adaptation level theory, multilevel results confirmed that the perceived availability of motivating job characteristics during work activities relates positively to happiness during that same work activity, but only when similar motivating job characteristics at the job level are low. In addition, trait positive affect further moderated this cross-level interaction. In line with the affective-reactivity hypothesis, the 3-way interaction effect showed that for employees who are high in positive affect, the perceived availability of motivating job characteristics related positively to happiness during specific work activities, regardless of whether similar motivating job characteristics at the job level were high or low. We discuss how these findings add important temporal dynamics to JCT.
Turning problems and freezing of gait in Parkinson’s disease: a systematic review and meta-analysis

Abstract Objective: To understand the differences of step and turn parameters between freezers and non-freezers during turning and determine the influence of turn angle and turn characteristics on freezing of gait. Data sources: PubMed and Web of Science were searched from the earliest data available to August 2017. Study selection: Case–control studies that examined the differences in turning while walking between freezers and non-freezers were included. Two reviewers selected studies independently. Data extraction: Methodological quality was evaluated by two independent reviewers using the STROBE checklist for case–control studies. Mean differences and 95% confidence intervals were calculated from pooled data for turn duration, peak turn velocity, number of steps and cadence. Center of mass deviation, segmental rotation, phase coordination and freezing of gait frequency were also extracted. When possible, different turning angles or spatial confounds were compared. Data synthesis: Sixteen studies met the inclusion criteria. Freezing of gait occurred in 38.2% of the freezers. Freezing appeared most frequently at the end of a turn and at the inner leg of the turn cycle. The meta-analysis revealed that turning in freezers was characterized by an increased turn duration, cadence and number of steps and a decreased peak turn velocity. Qualitative analysis showed that results concerning step width, step length and step time variability were inconsistent. Turning was characterized by an increased head–pelvis coupling and worse coordination in freezers compared to non-freezers. A decreased medial deviation of the center of mass was present prior to a freezing episode. Conclusions: Both step and rotational parameters differed in freezers compared to non-freezers while turning. These differences increased with increasing task complexity (i.e., larger turning angle or spatial confounds during turning). The results suggest that improving axial rotation could be a valuable rehabilitation target to ameliorate freezing. Implications for rehabilitation Patients with freezing of gait turn with a larger arc and a smaller angle compared to non-freezing patients Freezing–related turning deficits have both spatiotemporal and rotational motor control components Improving axial rotation could be a novel rehabilitation target to ameliorate freezing
An Accurate Bioimpedance Measurement System for Blood Pressure Monitoring

One potential method to estimate noninvasive cuffless blood pressure (BP) is through measurement of pulse wave velocity (PWV), which can be characterized by measuring the distance and the transit time of the pulse between two arterial sites. To obtain the pulse waveform, bioimpedance (BI) measurement is a promising approach because it continuously reflects the change in BP through the change in the arterial cross-sectional area. Several studies have investigated BI channels in a vertical direction with electrodes located along the wrist and the finger to calculate PWV and convert to BP; however, the measurement systems were relatively large in size. In order to reduce the total device size for use in a PWV-based BP smartwatch, this study proposes and examines a horizontal BI structure. The BI device is also designed to apply in a very small body area. Our proposed structure is based on two sets of four-electrode BI interface attached around the wrist. The effectiveness of our system and approach is evaluated on 15 human subjects; the PWV values are obtained with various distances between two BI channels to assess the efficacy. The results show that our BI system can monitor pulse rate efficiently in only a 0.5 × 1.75 cm2 area of the body. The correlation of pulse rate from the proposed design against the reference is 0.98 ± 0.07 (p < 0.001). Our structure yields higher detection ratios for PWV measurements of 99.0 ± 2.2%, 99.0 ± 2.1%, and 94.8 ± 3.7% at 1, 2, and 3 cm between two BI channels, respectively. The measured PWVs correlate well with the BP standard device at 0.81 ± 0.08 and 0.84 ± 0.07 with low root-mean-squared-errors at 7.47 ± 2.15 mmHg and 5.17 ± 1.81 mmHg for SBP and DBP, respectively. Our results inform future designs of smart watches capable of measuring blood pressure.
Effects of high-intensity interval training on vascular function in breast cancer survivors undergoing anthracycline chemotherapy: design of a pilot study

Introduction Cardiovascular disease (CVD) mortality is higher among breast cancer survivors (BCS) who receive chemotherapy compared with those not receiving chemotherapy. Anthracycline chemotherapy is of particular concern due to anthracycline-related impairment of vascular endothelial cells and dysregulation of the extracellular matrix. One strategy proven to offset these impairments is a form of exercise known as high-intensity interval training (HIIT). HIIT improves endothelial function in non-cancer populations by decreasing oxidative stress, the main contributor to anthracycline-induced vascular dysfunction. The purpose of this pilot study is to assess the feasibility of an 8-week HIIT, as well as the HIIT effects on endothelial function and extracellular matrix remodelling, in BCS undergoing anthracycline chemotherapy. Methods and analysis Thirty BCS are randomised to either HIIT, an 8-week HIIT intervention occurring three times per week (seven alternating bouts of 90% of peak power output followed by 10% peak power output), or delayed group (DEL). Feasibility of HIIT is assessed by (1) the percentage of completed exercise sessions and (2) the number of minutes of exercise completed over the course of the study. Vascular function is assessed using brachial artery flow-mediated dilation and carotid intima media thickness. Extracellular matrix remodelling is assessed by the level of matrix metalloproteinases in the plasma. A repeated-measures analysis of covariance model will be performed with group (HIIT and DEL group) and time (pre/post assessment) as independent factors. We hypothesise that HIIT will be feasible in BCS undergoing anthracycline chemotherapy, and that HIIT will improve endothelial function and extracellular matrix remodelling, compared with the DEL group. Success of this study will provide evidence of feasibility and efficacy to support a larger definitive trial which will impact cancer survivorship by decreasing anthracycline-induced vascular dysfunction, thereby benefiting cardiovascular markers that are related to CVD risk. Ethics and dissemination This trial was approved by the University of Southern California Institutional Review Board (HS-15–00227). Trial registration number NCT02454777; Pre-results.
Age and health-related quality of life, general self-efficacy, and functional level 12 months following dysvascular major lower limb amputation: a prospective longitudinal study

Abstract Aim: This study investigates the effect of time and age on health-related quality of life, general self-efficacy, and functional level 12 months following dysvascular major lower limb amputation (LLA). Methods: A prospective cohort study design with assessments at baseline and follow-up 3, 6, and 12 months post-amputation. Data were collected via in-person interviews using Short Form 36, the General Self-efficacy scale and Barthel Index 100. Out of a consecutive sample of 103 patients having dysvascular major LLA (tibia, knee, or femoral), 38 patients completed the study. Outcome at follow-up was compared with baseline and analyzed in age groups. Results: All SF36 subscale scores were below population norms at baseline. At 12 months, two out of eight scores—physical function and role-physical—had not improved. Different patterns of change over the 12 months were detected among the subscales, and psychosocial problems persisted and fluctuated throughout the 12 months in all age groups. Large differences were identified between age groups in physical function with the loss of physical function almost solely evident among the oldest (aged 75+ years) patients. Conclusions: Special attention should be given to the oldest patients need for rehabilitation so that they gain higher quality of life. Implications for rehabilitation Psychosocial problems persist and fluctuate throughout the first 12 months after major LLAs in all age groups and rehabilitation services should include psychosocial support throughout the first year to all patients independent of age. Waiting for an unnecessarily long period of time for a prosthesis can negatively impact both physical and psychosocial aspects of health-related QOL, and interventions to reduce waiting time are warranted. Differences between age groups in functional level after 12 months exist, with the loss of function almost solely evident among the oldest patients (aged 75+ years). A special focus should be given to the oldest patients’ need of everyday rehabilitation to regain basic physical functions.
Antithrombotic therapy for venous thromboembolism in patients with cancer: expert guidance

ABSTRACT Introduction: Most of the current clinical guidelines recommend the use of Low-Molecular-Weight Heparins (LMWHs) for cancer-associated thrombosis (CAT). The Hokusai VTE-cancer trial reported the first results of a direct comparison between a direct oral anticoagulant (DOAC), edoxaban, and LMWH in this setting. Areas covered: This review aims to critically appraise the currently available evidence on the efficacy and safety of anticoagulant agents for the long-term treatment of CAT and to provide an expert opinion and guidance in this field. Expert opinion: Based on the available evidence, DOACs represent a valid alternative to LMWH for the treatment of CAT for the majority of patients with active cancer. Currently, most solid evidence comes from the Hokusai VTE-cancer study, which showed that edoxaban is non-inferior to the LMWH dalteparin, with a trend toward fewer recurrent venous thromboembolic events, but with more major bleeding events. Similar findings were reported with rivaroxaban, although the study was not sufficiently powered to allow definitive conclusions. The majority of bleeding events occurred in the upper gastrointestinal tract and in patients with gastrointestinal cancer. Thus, LMWH remains the preferred option for patients with gastrointestinal cancer. Additional studies aimed to confirm these findings with other DOACs are now warranted.
Focused update of expert consensus statement: Use of invasive assessments of coronary physiology and structure: A position statement of the society of cardiac angiography and interventions

The rationale for adjunctive intracoronary diagnostic techniques is to supplement coronary angiography, the traditional method for determining the severity of coronary stenoses [1,2]. The purpose of this Focused Update is to incorporate the latest clinical evidence regarding these procedures into the 2014 SCAI Position Statement [2]. This document focuses on recommendations concerning the diagnostic potential of these modalities in specific lesion subsets and clinical circumstances.
Skeleton-based continuous extrinsic calibration of multiple RGB-D kinect cameras

Applications involving 3D scanning and reconstruction & 3D Tele-immersion provide an immersive experience by capturing a scene using multiple RGB-D cameras, such as Kinect. Prior knowledge of intrinsic calibration of each of the cameras, and extrinsic calibration between cameras, is essential to reconstruct the captured data. The intrinsic calibration for a given camera rarely ever changes, so only needs to be estimated once. However, the extrinsic calibration between cameras can change, even with a small nudge to the camera. Calibration accuracy depends on sensor noise, features used, sampling method, etc., resulting in the need for iterative calibration to achieve good calibration. In this paper, we introduce a skeleton based approach to calibrate multiple RGB-D Kinect cameras in a closed setup, automatically without any intervention, within a few seconds. The method uses only the person present in the scene to calibrate, removing the need for manually inserting, detecting and extracting other objects like plane, checker-board, sphere, etc. 3D joints of the extracted skeleton are used as correspondence points between cameras, after undergoing accuracy and orientation checks. Temporal, spatial, and motion constraints are applied during the point selection strategy. Our calibration error checking is inexpensive in terms of computational cost and time and hence is continuously run in the background. Automatic re-calibration of the cameras can be performed when the calibration error goes beyond a threshold due to any possible camera movement. Evaluations show that the method can provide fast, accurate and continuous calibration, as long as a human is moving around in the captured scene.
The acute effect of lower-limb warm-up on muscle performance

ABSTRACT It has been purported that the mechanism for muscular improvement after a gluteal warm-up protocol is likely to occur from neural activation. However, little is known about whether changes in muscular performance are due to changes in muscle activity. Therefore, the aim of this study was to determine whether a lower-limb warm-up that targets the gluteal muscle group would improve countermovement jump and short-distance sprinting through increased muscle activity. Ten semi-professional rugby union players (age 25.4 ± 2.9 yr; height 1.83 ± 6.7 m; body mass 96.8 ± 10.6 kg) with at least three years of resistance training experience volunteered for the study. In a cross-over design, participants performed countermovement jumps and 5 m sprints before and after a gluteal warm-up and a 10 min rest (control). Electromyography was used to measure muscle activity of the gluteus maximus and biceps femoris. Countermovement jump height significantly improved (7.9%, p < 0.05) after the lower-limb warm-up protocol compared with the control (3.2%). There was a significant (p < 0.05) improvement in sprint times over 2.5 m and 5 m regardless of the condition. There was no significant change in the muscle activity in any of the conditions. The results indicate that a lower-limb warm-up can acutely enhance countermovement jump performance compared to a control.
RETRACTED ARTICLE: miR-135 promotes proliferation and stemness of oesophageal squamous cell carcinoma by targeting RERG

Abstract We, the Editors and Publisher of the journal Artificial Cells, Nanomedicine, and Biotechnology, have retracted the following article: Yan Zhang, Shuang Ren, Fengfeng Yuan, Kaishang Zhang, Yingying Fan, Shaozhong Zheng, Zhen Gao, Jia Zhao, Teng Mu, Song Zhao, AnQuan Shang, Xiangnan Li and Ying Jie. (2018). miR-135 promotes proliferation and stemness of oesophageal squamous cell carcinoma by targeting RERG. Artificial Cells, Nanomedicine, and Biotechnology. 46:S2, S1210–S1219, DOI: 10.1080/21691401.2018. 1483379 Since publication, the authors noticed errors in their data calculation. As this error directly impacts the reported results and conclusions the authors alerted the issue to the Editor and Publisher and all have agreed to retract the article to ensure correction of the scholarly record. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.