Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary dynamics and biogeography of Musaceae reveal a correlation between the diversification of the banana family and the geological and climatic history of Southeast Asia

Summary Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species‐rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo‐Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent. The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses. All three Musaceae genera – Ensete, Musa and Musella – originated in northern Indo‐Burma during the early Eocene. Musa species dispersed from ‘northwest to southeast’ into Southeast Asia with only few back‐dispersals towards northern Indo‐Burma. Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards.
Pleiotropic roles of Clostridium difficile sin locus

Clostridium difficile is the primary cause of nosocomial diarrhea and pseudomembranous colitis. It produces dormant spores, which serve as an infectious vehicle responsible for transmission of the disease and persistence of the organism in the environment. In Bacillus subtilis, the sin locus coding SinR (113 aa) and SinI (57 aa) is responsible for sporulation inhibition. In B. subtilis, SinR mainly acts as a repressor of its target genes to control sporulation, biofilm formation, and autolysis. SinI is an inhibitor of SinR, so their interaction determines whether SinR can inhibit its target gene expression. The C. difficile genome carries two sinR homologs in the operon that we named sinR and sinR’, coding for SinR (112 aa) and SinR’ (105 aa), respectively. In this study, we constructed and characterized sin locus mutants in two different C. difficile strains R20291 and JIR8094, to decipher the locus’s role in C. difficile physiology. Transcriptome analysis of the sinRR’ mutants revealed their pleiotropic roles in controlling several pathways including sporulation, toxin production, and motility in C. difficile. Through various genetic and biochemical experiments, we have shown that SinR can regulate transcription of key regulators in these pathways, which includes sigD, spo0A, and codY. We have found that SinR’ acts as an antagonist to SinR by blocking its repressor activity. Using a hamster model, we have also demonstrated that the sin locus is needed for successful C. difficile infection. This study reveals the sin locus as a central link that connects the gene regulatory networks of sporulation, toxin production, and motility; three key pathways that are important for C. difficile pathogenesis.
Using Super-Imposition by Translation And Rotation (SITAR) to relate pubertal growth to bone health in later life: the Medical Research Council (MRC) National Survey of Health and Development

Abstract Background: To explore associations between pubertal growth and later bone health in a cohort with infrequent measurements, using another cohort with more frequent measurements to support the modelling, data from the Medical Research Council (MRC) National Survey of Health and Development (2–26 years, 4901/30 004 subjects/measurements) and the Avon Longitudinal Study of Parents And Children (ALSPAC) (5–20 years) (10 896/74 120) were related to National Survey of Health and Development (NSHD) bone health outcomes at 60–64 years. Methods: NSHD data were analysed using Super-Imposition by Translation And Rotation (SITAR) growth curve analysis, either alone or jointly with ALSPAC data. Improved estimation of pubertal growth parameters of size, tempo and velocity was assessed by changes in model fit and correlations with contemporary measures of pubertal timing. Bone outcomes of radius [trabecular volumetric bone mineral density (vBMD) and diaphysis cross-sectional area (CSA)] were regressed on the SITAR parameters, adjusted for current body size. Results: The NSHD SITAR parameters were better estimated in conjunction with ALSPAC, i.e. more strongly correlated with pubertal timing. Trabecular vBMD was associated with early height tempo, whereas diaphysis CSA was related to weight size, early tempo and slow velocity, the bone outcomes being around 15% higher for the better vs worse growth pattern. Conclusions: By pooling NSHD and ALSPAC data, SITAR more accurately summarized pubertal growth and weight gain in NSHD, and in turn demonstrated notable associations between pubertal timing and later bone outcomes. These associations give insight into the importance of the pubertal period for future skeletal health and osteoporosis risk.
Predictors of weight‐loss response with glucagon‐like peptide‐1 receptor agonist treatment among adolescents with severe obesity

In two previous, separate clinical trials, we demonstrated significant reductions in body mass index (BMI) with exenatide in adolescents with severe obesity. In the present study, we pooled data from these near identical trials to evaluate factors that may predict BMI reduction at 3 months. Data from 32 patients (mean age 14.3 ± 2.2 years; 69% female; mean BMI 39.8 ± 5.8 kg m−2) were included. Exenatide treatment consisted of 5 mcg twice daily for 1 month, followed by an increase to 10 mcg twice daily for 2 additional months. Predictor variables included baseline BMI, BMI percent change at 1 month, incidence of nausea or vomiting and baseline appetite and satiety measures. Treatment effects of percent change in BMI from baseline were estimated within predictor subgroups using generalized estimating equations with exchangeable working correlation and robust variance estimation for confidence intervals and P‐values to account for paired observations. The pooled data treatment effect on absolute BMI at 3 months was −3.42% (95% confidence interval: −5.41%, −1.42%) compared to placebo. Within treated participants, appetite at baseline (treatment effect in high [−4.28%] vs. low [1.02%], P = 0.028) and sex (treatment effect in female [−4.78%] vs. male [0.76%], P = 0.007) were significant predictors of change in BMI at 3 months. Baseline BMI, BMI percent change at 1 month, age, incidence of nausea, vomiting, or other gastrointestinal symptoms and satiety scores did not predict 3‐month responses. Sex and measures of appetite may serve as useful predictors of glucagon‐like peptide‐1 receptor agonist treatment response among adolescents with severe obesity.
Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs

The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis. Results revealed the presence of five clusters within the populations differentiated principally by ploidy, taxonomy, origin and breeding program. The information obtained in this work could be readily used as a guide for parental introduction in new breeding programs that want to maximize variability by combination of contrasting variability sources such as those presented here.
A Generic Deep-Learning-Based Approach for Automated Surface Inspection

Automated surface inspection (ASI) is a challenging task in industry, as collecting training dataset is usually costly and related methods are highly dataset-dependent. In this paper, a generic approach that requires small training data for ASI is proposed. First, this approach builds classifier on the features of image patches, where the features are transferred from a pretrained deep learning network. Next, pixel-wise prediction is obtained by convolving the trained classifier over input image. An experiment on three public and one industrial data set is carried out. The experiment involves two tasks: 1) image classification and 2) defect segmentation. The results of proposed algorithm are compared against several best benchmarks in literature. In the classification tasks, the proposed method improves accuracy by 0.66%–25.50%. In the segmentation tasks, the proposed method reduces error escape rates by 6.00%–19.00% in three defect types and improves accuracies by 2.29%–9.86% in all seven defect types. In addition, the proposed method achieves 0.0% error escape rate in the segmentation task of industrial data.
Assimilating in situ soil moisture measurements into the DSSAT-CSM using a Kalman filter

With the ability to monitor soil moisture in time comes the opportunity to develop ways to incorporate these measurements into predictive models, without compromising or overriding the model physics. The importance of soil moisture to the growth of crops is well understood and because of this it is recognized as one of the more important parts of crop modeling programs. This research focused on improvements to the Decision Support System for Agrotechnology Transfer Cropping System Model (DSSAT-CSM) based on the accuracy of soil moisture estimates. To accomplish this, data assimilation techniques were implemented to process the uncertainty of the model related to state variables and the uncertainty found within in situ soil moisture measurements. Consideration of soil parameter uncertainty, which influences model estimates of soil moisture and model output, was taken into account using a Monte Carlo approach. A Kalman filter was used to combine the model estimates of soil moisture with in situ soil moisture measurements, while varying several important soil parameters in the model using a Monte Carlo approach. Covariances for the Kalman filter were calculated for the model and measurements based on the models standard deviation of soil moisture estimates and the standard deviation of the in situ soil moisture measurements. Data for this study was obtained from a research study conducted on irrigated wheat during the winters of 2003-04 and 2004-05 in Maricopa, Arizona in which thorough field and crop data were collected. The uncertainty of soil parameters was only moderately captured by the Monte Carlo approach for assimilation into the top layer of the soil profile. Improvement resulted for data assimilation of soil moisture through the reduction of the error between the measured and simulated
Retinoids regulate tight junctional resistance of cultured human cervical cells.

The objective of the study was to determine the effect of retinoids on paracellular resistance across the cervical epithelium and the mechanisms involved. The experimental model was cultures of human CaSki cells on filters, which retain phenotypic characteristics of the endocervical epithelium. End points for paracellular resistance were measurements of transepithelial electrical resistance and fluxes of pyranine (a trisulfonic acid that traverses the epithelium via the intercellular space). Paracellular resistance was significantly increased in cells grown in retinoid-free medium; the effect could be blocked and reversed with all- trans-retinoic acid (tRA) and with agonists of RAR and RXR receptors but only partially with retinol. The effect of tRA was dose dependent and saturable, with a 50% effective concentration of 0.8 nM. The increases in paracellular resistance induced by vitamin A deficiency required longer incubation in retinoid-free medium than decreases in resistance induced by retinoic acid. tRA had only a minimal effect on paracellular resistance in cells maintained in regular medium. Retinoid-free medium increased and tRA decreased the relative cation mobility across CaSki cultures. Also the effects of tRA were nonadditive to those of cytochalasin D (which decreases tight junctional resistance) and additive to those of ionomycin (which decreases the resistance of the lateral intercellular space), suggesting that tRA modulates tight junctional resistance. It is concluded that vitamin A determines the degree of paracellular resistance across cervical cells by a mechanism that involves modulation of tight junctional resistance.
Context Influences Interpretation of Eyewitness Confidence Statements

When an eyewitness makes an identification from a lineup, he or she is asked to provide a confidence statement to help jurors assess credibility. However, these are verbal statements and people must rely on metacognitive processes to correctly interpret them. Recently, Dodson and Dobolyi (2015) argued that a person’s interpretation of a witness’s verbal confidence is influenced by the diagnosticity of the features used to justify his or her identification. We tested this hypothesis in 2 experiments. Experiment 1 found that, relative to a confidence-only control, participants reduced their ratings of confidence when statements were justified using a facial feature that was shared by lineup members, but not when the feature was unique to the member chosen from the lineup. In Experiment 2, we found that participants integrated across the dimensions of witness confidence and accuracy, even when asked to make separate ratings. Altogether, the results suggest that people readily incorporate contextual information into their interpretations of witnesses’ verbal expressions of confidence and evaluations of accuracy.
Consistency of the EKF-SLAM Algorithm

This paper presents an analysis of the extended Kalman filter formulation of simultaneous localisation and mapping (EKF-SLAM). We show that the algorithm produces very optimistic estimates once the "true" uncertainty in vehicle heading exceeds a limit. This failure is subtle and cannot, in general, be detected without ground-truth, although a very inconsistent filter may exhibit observable symptoms, such as disproportionately large jumps in the vehicle pose update. Conventional solutions - adding stabilising noise, using an iterated EKF or unscented filter, etc., - do not improve the situation. However, if "small" heading uncertainty is maintained, EKF-SLAM exhibits consistent behaviour over an extended time-period. Although the uncertainty estimate slowly becomes optimistic, inconsistency can be mitigated indefinitely by applying tactics such as batch updates or stabilising noise. The manageable degradation of small heading variance SLAM indicates the efficacy of submap methods for large-scale maps
Time-dependent hypoxic ventilatory responses in rats: effects of ketanserin and 5-carboxamidotryptamine.

We hypothesized that the 5-hydroxytryptamine (5-HT) active drugs ketanserin and 5-carboxamidotryptamine (5-CT) would modulate time-dependent hypoxic phrenic and hypoglossal responses, including 1) short-term hypoxic response, 2) posthypoxia frequency decline (PHFD), and 3) long-term facilitation (LTF) of respiratory motor output. Phrenic and hypoglossal nerve activities were recorded in urethan-anesthetized, paralyzed, vagotomized, and artificially ventilated rats pretreated either with ketanserin (5-HT2A/C antagonist; 2 mg/kg iv), 5-CT (5-HT1A/B agonist; 10 μg/kg iv), or saline (sham). Rats were exposed to three 5-min episodes of hypoxia [fractional inspired O2([Formula: see text]) = 0.11], separated by 5 min of hyperoxia ([Formula: see text] = 0.5). During hypoxia, ketanserin augmented phrenic but not hypoglossal burst amplitude; 5-CT had no effect. Both drugs accentuated PHFD. Ketanserin blocked phrenic LTF; hypoglossal LTF was not apparent, even in sham-treated rats. 5-CT reversed LTF, resulting in a long-lasting depression of phrenic burst frequency and amplitude without effect on hypoglossal burst amplitude. The data suggest that 1) 5-HT2A/C receptor activation modulates the short-term hypoxic phrenic response and PHFD and is necessary for LTF; and 2) 5-CT may affect time-dependent hypoxic ventilatory responses by reducing serotonin release via 5-HT1A/Bautoreceptor activation.
The Planar Directed K-Vertex-Disjoint Paths Problem Is Fixed-Parameter Tractable

Given a graph G and k pairs of vertices (s<sub>1</sub>, t<sub>1</sub>), . , (s<sub>k</sub>, t<sub>k</sub>), the k-Vertex-Disjoint Paths problem asks for pair wise vertex-disjoint paths P<sub>1</sub>, . , Pk such that Pi goes from si to ti. Schrijver [SICOMP'94] proved that the k-Vertex-Disjoint Paths problem on planar directed graphs can be solved in time <sup>nO(k)</sup>. We give an algorithm with running time 2<sup>2O(k2)</sup> * n<sup>O(1)</sup> for the problem, that is, we show the fixed-parameter tractability of the problem.
Mock Juror Sampling Issues in Jury Simulation Research: A Meta-Analysis

The advantages and disadvantages of jury simulation research have often been debated in the literature. Critics chiefly argue that jury simulations lack verisimilitude, particularly through their use of student mock jurors, and that this limits the generalizabilty of the findings. In the present article, the question of sample differences (student v. nonstudent) in jury research was meta-analyzed for 6 dependent variables: 3 criminal (guilty verdicts, culpability, and sentencing) and 3 civil (liability verdicts, continuous liability, and damages). In total, 53 studies (N = 17,716) were included in the analysis (40 criminal and 13 civil). The results revealed that guilty verdicts, culpability ratings, and damage awards did not vary with sample. Furthermore, the variables that revealed significant or marginally significant differences, sentencing and liability judgments, had small or contradictory effect sizes (e.g., effects on dichotomous and continuous liability judgments were in opposite directions). In addition, with the exception of trial presentation medium, moderator effects were small and inconsistent. These results may help to alleviate concerns regarding the use of student samples in jury simulation research.
Dietary BCAA Intake Is Associated with Demographic, Socioeconomic and Lifestyle Factors in Residents of São Paulo, Brazil

Background: Identifying which risk groups have a higher intake of branched chain amino acids (BCAA) is important for the planning of public policies. This study was undertaken to investigate BCAA consumption, the foods contributing to that consumption and their association with demographic, socioeconomic and lifestyle factors. Methods: Data from the Health Survey of São Paulo, a cross-sectional population-based survey (n = 1662; age range 12–97 years), were used. Dietary intake was measured using 24-h dietary recalls. Baseline characteristics were collected. Associations between BCAA intake and demographic, socioeconomic and lifestyle factors were determined using linear regression. Results: Total BCAA intake was 217.14 mg/kg·day (Leu: 97.16 mg/kg·day; Ile: 56.44 mg/kg·day; Val: 63.54 mg/kg·day). BCAA intake was negatively associated with female sex in adolescents and adult groups, with no white race in adolescents, and with former smoker status in adults. Conversely, BCAA was positively associated with household per capita income in adolescents and adults. No associations were observed in the older adults group. Main food contributors to BCAA were unprocessed red meat, unprocessed poultry, bread and toast, beans and rice. Conclusions: Adolescents and adults were the most vulnerable to having their BCCA intake influenced by demographic, socioeconomic and lifestyle factors.
Time, Resident Involvement, and Supply Drive Cost Variability in Septoplasty with Turbinate Reduction

Objective To determine factors that influence cost variability in septoplasty with inferior turbinate reduction. Study Design Case series with chart review. Setting Tertiary care hospital and affiliated ambulatory surgical center. Subjects and Methods Surgical costs were reviewed for adult patients undergoing septoplasty with inferior turbinate reduction between December 2014 and September 2017. Cases where additional procedures were performed were excluded. Operative supply costs, operative time, room time, and resident involvement were determined. Contribution of these factors to total costs and variability were analyzed. Results The study included 116 patients (mean age, 38 years) and 4 faculty surgeons. Total cost was primarily driven by operative time (74%), with a smaller portion of total cost arising from supplies (26%). Time cost (P < .0001) and supply cost (P = .006) varied significantly among surgeons. A resident was involved in 46.6% of cases. When subanalyzed by resident year, no-resident and senior resident (postgraduate years 4 and 5) cases had nearly identical mean times, while junior resident (postgraduate years 1-3) cases had mean times and operative time costs that were 39% greater (P < .001). Conclusion For septoplasty with inferior turbinate reduction, the greatest driver of cost variation was operative time. Resident involvement correlated with increased time and cost. Supply costs had a much smaller impact. When subanalyzed by resident year, junior resident–involved cases were significantly longer than no-resident cases.
Measurement of body joint angles for physical therapy based on mean shift tracking using two low cost Kinect images

Range of motion (ROM) is commonly used to assess a patient's joint function in physical therapy. Because motion capture systems are generally very expensive, physical therapists mostly use simple rulers to measure patients' joint angles in clinical diagnosis, which will suffer from low accuracy, low reliability, and subjective. In this study we used color and depth image feature from two sets of low-cost Microsoft Kinect to reconstruct 3D joint positions, and then calculate moveable joint angles to assess the ROM. A Gaussian background model is first used to segment the human body from the depth images. The 3D coordinates of the joints are reconstructed from both color and depth images. To track the location of joints throughout the sequence more precisely, we adopt the mean shift algorithm to find out the center of voxels upon the joints. The two sets of Kinect are placed three meters away from each other and facing to the subject. The joint moveable angles and the motion data are calculated from the position of joints frame by frame. To verify the results of our system, we take the results from a motion capture system called VICON as golden standard. Our 150 test results showed that the deviation of joint moveable angles between those obtained by VICON and our system is about 4 to 8 degree in six different upper limb exercises, which are acceptable in clinical environment.