Miracle-dz/UniFAR-FTUs huggingface dataset:
Target SSR-Seq: A Novel SSR Genotyping Technology Associate With Perfect SSRs in Genetic Analysis of Cucumber Varieties

Simple sequence repeats (SSR) – also known as microsatellites – have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques. Despite a plethora of studies reporting that perfect SSRs with stable motifs and flanking sequences are more efficient for genetic research, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. In this study, we developed a technology called Target SSR-seq that combined the multiplexed amplification of perfect SSRs with high throughput sequencing. This method can genotype plenty of SSR loci in hundreds of samples with highly accurate results, due to the substantial coverage afforded by high throughput sequencing. We also detected 844 perfect SSRs based on 182 resequencing datasets in cucumber, of which 91 SSRs were selected for Target SSR-seq. Finally, 122 SSRs, including 31 SSRs for varieties identification, were used to genotype 382 key cucumber varieties readily available in Chinese markets using our Target SSR-seq method. Libraries of PCR products were constructed and then sequenced on the Illumina HiSeq X Ten platform. Bioinformatics analysis revealed that 111 filtered SSRs were accurately genotyped with an average coverage of 1289× at an extremely low cost; furthermore, 398 alleles were observed in 382 cucumber cultivars. Genetic analysis identified four populations: northern China type, southern China type, European type, and Xishuangbanna type. Moreover, we acquired a set of 16 core SSRs for the identification of 382 cucumber varieties, of which 42 were isolated as backbone cucumber varieties. This study demonstrated that Target SSR-seq is a novel and efficient method for genetic research.
Sublinear-Time Non-Adaptive Group Testing With O(k log n) Tests via Bit-Mixing Coding

The group testing problem consists of determining a small set of defective items from a larger set of items based on tests on groups of items, and is relevant in applications such as medical testing, communication protocols, pattern matching, and many more. While rigorous group testing algorithms have long been known with runtime at least linear in the number of items, a recent line of works has sought to reduce the runtime to <inline-formula> <tex-math notation="LaTeX">${\mathrm{ poly}}({k} \log {n})$ </tex-math></inline-formula>, where n is the number of items and k is the number of defectives. In this paper, we present such an algorithm for non-adaptive group testing termed <italic>bit mixing coding</italic> (BMC), which builds on techniques that encode item indices in the test matrix, while incorporating novel ideas based on erasure-correction coding. We show that BMC achieves asymptotically vanishing error probability with <inline-formula> <tex-math notation="LaTeX">${O}({k} \log {n})$ </tex-math></inline-formula> tests and <inline-formula> <tex-math notation="LaTeX">${O}({k}^{2} \cdot \log {k} \cdot \log {n})$ </tex-math></inline-formula> runtime, in the limit as <inline-formula> <tex-math notation="LaTeX">${n} \to \infty $ </tex-math></inline-formula> (with k having an arbitrary dependence on n). This closes an open problem of simultaneously achieving <inline-formula> <tex-math notation="LaTeX">${\mathrm{ poly}}({k} \log {n})$ </tex-math></inline-formula> decoding time using <inline-formula> <tex-math notation="LaTeX">${O}({k} \log {n})$ </tex-math></inline-formula> tests without any assumptions on k. In addition, we show that the same scaling laws can be attained in a commonly-considered noisy setting, in which each test outcome is flipped with constant probability.
Emotion Regulation and Attitudes Toward Conflict in Colombia: Effects of Reappraisal Training on Negative Emotions and Support for Conciliatory and Aggressive Statements

Control of negative emotions (e.g., anger and fear) by political cues perpetuate intractable conflict by mobilizing public support for aggressive actions. Halperin et al. (2013) found that reappraisal – an adaptive form of emotion regulation – decreased negative emotions triggered by anger-inducing information related to the Israeli–Palestinian conflict, and increased support for conciliatory statements. We tested these effects in the context of the conflict between the Colombian government and the Fuerzas Armadas Revolucionarias de Colombia-Ejército del Pueblo (FARC-EP). Reappraisal training reduced negative emotions produced by a presentation that illustrated FARC’s violent actions, and increased support for conciliatory statements (with overall moderate effect magnitudes). We also found that negative emotions mediated the effects of reappraisal on the support for aggressive and conciliatory statements. These findings indicate a high degree of generality of the phenomena, especially considering the differences between the Israeli–Palestinian conflict and the Colombian conflict. Our findings also show promise for replicating these effects on other types of intergroup conflicts and guiding effective public policy.
The Positivity Scale: Concurrent and Factorial Validity Across Late Childhood and Early Adolescence

Despite the well-established protective functions of positivity (i.e., a dispositional self-evaluative tendency to view oneself, life, and future under a positive outlook) from middle adolescence to old age, its reliable assessment and contribution to a proper psychological functioning have received little attention during previous developmental phases. In this article, we aimed to evaluate the psychometric properties and construct validity of the eight-item Positivity Scale (P Scale; Caprara et al., 2012) during late childhood and early adolescence in a sample of British students (N = 742; 48% boys) from both primary (Mage = 10.75, SD = 0.52) and secondary schools (Mage = 13.38 years, SD = 0.94). First, results from confirmatory factor analysis (CFA) attested to the plausibility of the hypothesized 1-factor structure of the P Scale in a revised CFA model including the correlation between the residuals of two items similar in their wording. Next, we found evidence for strong (scalar) measurement invariance of the P Scale across late childhood and early adolescence as well as for its concurrent validity as indicated by expected relations of positivity to indicators of adjustment (i.e., prosocial behavior) and maladjustment (i.e., externalizing and internalizing problems). Overall, these findings support the concurrent and factorial validity of the P Scale as a short self-report instrument to measure children’s tendency to view their experience from a positive stance. We discuss the implications of our results for improving the wording of the items composing P Scale as well as for understanding the dispositional mechanisms conducive to psychological health and wellbeing across late childhood and early adolescence.
Robot-Assisted Therapy in Upper Extremity Hemiparesis: Overview of an Evidence-Based Approach

Robot-mediated therapy is an innovative form of rehabilitation that enables highly repetitive, intensive, adaptive, and quantifiable physical training. It has been increasingly used to restore loss of motor function, mainly in stroke survivors suffering from an upper limb paresis. Multiple studies collated in a growing number of review articles showed the positive effects on motor impairment, less clearly on functional limitations. After describing the current status of robotic therapy after upper limb paresis due to stroke, this overview addresses basic principles related to robotic therapy applied to upper limb paresis. We demonstrate how this innovation is an evidence-based approach in that it meets both the improved clinical and more fundamental knowledge-base about regaining effective motor function after stroke and the need of more objective, flexible and controlled therapeutic paradigms.
Functional Connectivity Changes Across the Spectrum of Subjective Cognitive Decline, Amnestic Mild Cognitive Impairment and Alzheimer’s Disease

The abnormality occurs at molecular, cellular as well as network levels in patients with Alzheimer’s disease (AD) prior to diagnosis. Most previous connectivity studies were conducted at 1 out of 3 (local, meso and global) scales in subjects covering only part of the entire AD spectrum (subjective cognitive decline, SCD; amnestic mild cognitive impairment, aMCI; and then fully manifest AD). Data interpretation within the framework of disease progression is therefore difficult. The current study included 3 age- and sex-matched cohorts: SCD (n = 32), aMCI (n = 37) and fully-established AD (n = 30). A group of healthy elderly subjects (n = 40) were included as a normal control (NC). Network connectivity was examined at the local (degree centrality), meso [subgraph centrality (SC)], and global (eigenvector and page-rank centralities) levels. As compared to NC, SCD subjects had isolated decrease of SC in primary (somatomotor and visual) networks. aMCI subjects had decreased centralities at all three scales in associative (frontoparietal control, dorsal attention, limbic and default) networks. AD subjects had increased centrality at the global scale in all seven networks. There was a positive association between Montreal Cognitive Assessment (MoCA) scores and DC in the frontoparietal control network in SCD, a negative relationship between Mini-Mental State Examination (MMSE) scores and EC in the somatomotor network in AD. These findings suggest that the primary network is impaired as early as in SCD. Impairment in the associative network also starts at the local level at this stage and may contribute to the cognitive decline. As associative network impairment extends from local to meso and global scales in aMCI, compensatory mechanisms in the primary network are activated.
Bonus Skills: Examining the Effect of an Unconditional Cash Transfer on Child Human Capital Formation

This paper evaluates the impact of the Australian Baby Bonus – a $3000 one-off cash transfer – on various aspects of child human capital development. Using high-quality longitudinal cohort data and difference-in-difference models, we compare the outcomes of cohort members whose younger sibling was born marginally on either side of July 1, 2004, when the Baby Bonus was introduced. Our results suggest that the Baby Bonus was not effective in boosting learning, socio-emotional or physical health outcomes of the average pre-school child. This finding is strengthened by the observation that the Baby Bonus did not impact parental well-being, parental behavior and labor supply, the potential mechanisms via which the cash transfer could have affected human capital formation. The muted effect for the Baby Bonus in comparison to significant effects for similar cash handouts in other countries may be explained by its non-targeted and one-off structure. We conclude that the large financial cost of $3000 per child is not justified as an intervention for the entire population to boost children's skills.
UvA-DARE ( Digital Academic Repository ) Macrophage regulatory mechanisms in atherosclerosis

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Clinical Significance of Serum Glutamine Level in Patients with Colorectal Cancer

Limited studies have assessed the associations of pretreatment serum glutamine level with clinicopathological characteristics and prognosis of colorectal cancer (CRC) patients. This study focuses on clarifying the clinical significance of baseline serum glutamine level in CRC patients. We retrospectively examine 123 patients with newly diagnosed CRC between 2009 and 2011. The associations of pretreatment serum glutamine level with clinicopathological characteristics, proinflammatory cytokines, overall survival (OS), and progression-free survival (PFS) were analyzed. We executed univariate and multivariate analyses to assess the associations between serum glutamine level and clinicopathological variables able to predict survival. Low glutamine levels were associated with older age, advanced stage, decreased albumin levels, elevated carcinoembryonic antigen levels, higher C-reactive protein levels, higher modified Glasgow prognostic scores, and higher proinflammatory cytokine levels. Furthermore, patients with low glutamine levels had poorer OS and PFS than those with high glutamine levels (p < 0.001 for both). In multivariate analysis, pretreatment glutamine level independently predicted OS (p = 0.016) and PFS (p = 0.037) in CRC patients. Pretreatment serum glutamine level constitutes an independent prognostic marker to predict survival and progression in CRC patients.
A Novel Method for Measuring the Timing of Heart Sound Components through Digital Phonocardiography

The auscultation of heart sounds has been for decades a fundamental diagnostic tool in clinical practice. Higher effectiveness can be achieved by recording the corresponding biomedical signal, namely the phonocardiographic signal, and processing it by means of traditional signal processing techniques. An unavoidable processing step is the heart sound segmentation, which is still a challenging task from a technical viewpoint—a limitation of state-of-the-art approaches is the unavailability of trustworthy techniques for the detection of heart sound components. The aim of this work is to design a reliable algorithm for the identification and the classification of heart sounds’ main components. The proposed methodology was tested on a sample population of 24 healthy subjects over 10-min-long simultaneous electrocardiographic and phonocardiographic recordings and it was found capable of correctly detecting and classifying an average of 99.2% of the heart sounds along with their components. Moreover, the delay of each component with respect to the corresponding R-wave peak and the delay among the components of the same heart sound were computed: the resulting experimental values are coherent with what is expected from the literature and what was obtained by other studies.
Misperception of Visual Verticality Measured with a Virtual Reality Device in Patients with Fibromyalgia Syndrome: A Cross-Sectional Study

The objective of this study was to analyze the perception of visual verticality (VV) in subjects with Fibromyalgia Syndrome (FMS) and to correlate this with the symptoms of the disease and balance capacity. A cross-sectional study including 54 patients (51 female) was conducted. The evaluation of visual verticality was carried out with a virtual reality device by calculating the Mean Absolute Error (MAE) of degrees deviation in two tests: the Subjective Visual Vertical (SVV) test for the contribution of the vestibular system to the perception of verticality and the Rod and Frame test (RFT) for the contribution of the visual system. In total, 16 subjects (29.6%) presented good VV perception, 6 subjects (11.1%) presented an exclusive alteration of the SVV test, 19 subjects (35.2%) presented an exclusive alteration of the RFT and 13 subjects (24.1%) showed alteration in the two tests. The MAE in the SVV test showed medium correlations with several variables such as the Fibromyalgia Impact Questionnaire (FIQ) (Rho = 0.399, p = 0.003), the Pain Catastrophizing Scale (PCS) (Rho = 0.417, p = 0.002), the Dizziness Handicap Inventory (DHI) (Rho = 0.376, p = 0.005), and the Activities-Specific Balance Confidence Scale (ABC-16) (Rho = −0.367, p = 0.006). The MAE in the RFT showed medium correlations with the Instability Support Reduced (Rho = 0.327, p = 0.016) and Instability Gait Eyes Open (Rho = 0.312, p = 0.022) subscales of the JAEN (Joined Assessment of Equilibrium and Neuro-motor) Scale. Conclusions: Around 70% of the subjects with FMS showed some alteration in the perception of VV; 60% of these patients presented visual system dependence. The SVV test correlates with the impact and health status of FMS, and the RFT correlates with the alteration in the dynamic balance.
Studying Human Behaviour with Virtual Reality: The Unity Experiment Framework

Virtual Reality systems offer a powerful tool for human behaviour research. The ability to create three-dimensional visual scenes and measure responses to the visual stimuli enables the behavioural researcher to test hypotheses in a manner and scale that were previously unfeasible. For example, a researcher wanting to understand interceptive timing behaviour might wish to violate Newtonian mechanics, so objects move in novel 3D trajectories. The same researcher may wish to collect such data with hundreds of participants outside the laboratory (e.g. in a museum), and the use of a VR headset makes this a realistic proposition. The difficulty facing the researcher is that sophisticated 3D graphics engines (such as Unity) have been created for game designers rather than behavioural scientists. In order to overcome this barrier, we have created a set of tools and programming syntaxes that allow logical encoding of the common experimental features required by the behavioural scientist. The Unity Experimental Framework (UXF) allows the researcher to readily implement several forms of data collection, and provides researchers with the ability to easily modify independent variables. UXF does not offer any stimulus presentation features, so the full power of the Unity game engine can be exploited. We use a case study to show how UXF can support behavioural research and remote deployment of experiments (where data are streamed over the internet and accessed later by researchers). In summary, UXF presents an opportunity to simplify and speed up development of virtual reality experiments created in commercial VR software.
The Relationship between Remote Working and Work-life Balance with Mediating and Moderating Effects of Social Support: An Empirical Study of Information Technology Employees

This study examined the relationship between remote working and work-life balance with mediating and moderating effects of social support on work-life balance. The study surveyed the information technology employees in and around Hyderabad. The data were gathered using a structured questionnaire for the three constructs remote working, social support, and work-life balance. Only the items for the three constructs with factor loadings of > . 5 were considered for this study. The reliability and internal consistency of the questionnaire were assessed by Cronbach’s alpha and Split -half (odd-even) correlation. The estimated composite reliability and average variance extracted /convergent validity for the constructs are reliable. The data from 301 valid responses were analyzed using structural equation modeling with IBM AMOS 28 version. The assessment with Shapiro Wilk’s test statistic indicates that data were normally distributed. The model fit indices demonstrated excellent model fit. There was a statistically insignificant direct effect between remote working and work-life balance; however, social support fully mediates and moderates the work-life balance of the information technology employees. The study assessed the moderating role of social support on the relationship between remote working and work-life balance. The results reveal positive and significant moderating effects of social support on the relationship between remote working and work-life balance. The slope analysis indicates that at a high level of social support, the impact of remote working on work-life balance is positively stronger than low social support, indicating more work-life balance during remote working with high social support.
Center of pressure progression patterns during level walking in adolescents with idiopathic scoliosis

The purpose of this study was to determine whether functional walking performance measured with Timed Up-and-Go (TUG) and center of pressure (CoP) progression pattern is different across adolescents with various curve severity of idiopathic scoliosis (IS). The CoP coordinates during a stance phase for self-paced level walking between adolescent with three different severities of IS (mild IS, moderate IS, and severe IS) and age-matched normal subjects were measured with foot pressure measurement. The average data of three trials were compared among groups with repeated measure analysis of variance. Results showed that the TUG was different between normal and AIS subjects, indicating use of TUG as a marker of functional walking performance in AIS is plausible but studies with larger sample size is needed before using TUG to identify AIS with different scoliosis severity. The results also showed that the CoP displacement, velocity and acceleration during a stance phase was different across groups, and with the most prominent deviations found in the moderate IS group. The medial-lateral shifting of the CoP trajectory at mid-foot regions in all IS groups deviated the most. A tendency of asymmetry in CoP progression pattern between feet in IS groups was also found. The deviation of the spine alignment in frontal plane could change the CoP progression patterns during level walking, suggesting the risk of the locomotors subjecting to abnormal loading during daily walking. Education and conservative interventions might be needed for preservation of medical outcome and prevention of back pain and/or musculoskeletal consequences later in the lives of AIS with and without surgical correction.
Commissioning of 6 and 10 MV Beams for Total Body Irradiation (TBI)

The objective of the TBI treatment is the ablation of the bone marrow and the destruction of the circulating leukemia cells, once they are widely distributed throughout the body. Using beam parameters acquired under conventional SSD in TBI treatments may add non-negligible uncertainties in the monitor units calculation or in the beam profiles. The study, aims to commission the 6 and 10 MV photon beams, of the Varian accelerator CX model. A slab phantom and dosimetric assembly were used under TBI conditions. The accuracy of the TPS was evaluated against the experimental data. A set of data were acquired, highlighting the TPR table and methodology for calculating MU has been implemented. The TPS has presented a statistical uncertainty of ± 2.7 % compared to the experimental data for monitor unit calculation. The use of an acrylic spoiler has been shown to be clinically advantageous where, for a 6 MV beam, the entrance PDD was 75 % without a spoiler and 99.5 % with a spoiler. For a 10 MV beam, it was verified that without a spoiler, the entrance PDD was about 55 %, but with a spoiler, it was about 93 %. For medium Heterogeneous the TPS underestimated dose values by up to - 3.5 % with a mean deviation of – 2.9 %, for 6 MV and for 10 MV, the TPS overestimated the dose values by up to 1.1 %, with an average deviation of 1.0 % using the acrylic thorax phantom. The data obtained can be used clinically.