Miracle-dz/UniFAR-FTUs huggingface dataset:
MRI-Based Radiomics Predicts Tumor Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer

Background: Conventional methods for predicting treatment response to neoadjuvant chemoradiotherapy (nCRT) in patients with locally advanced rectal cancer (LARC) are limited. Methods: This study retrospectively recruited 134 LARC patients who underwent standard nCRT followed by total mesorectal excision surgery in our institution. Based on pre-operative axial T2-weighted images, machine learning radiomics was performed. A receiver operating characteristic (ROC) curve was performed to test the efficiencies of the predictive model. Results: Among the 134 patients, 32 (23.9%) achieved pathological complete response (pCR), 69 (51.5%) achieved a good response, and 91 (67.9%) achieved down-staging. For prediction of pCR, good-response, and down-staging, the predictive model demonstrated high classification efficiencies, with an AUC value of 0.91 (95% CI: 0.83–0.98), 0.90 (95% CI: 0.83–0.97), and 0.93 (95% CI: 0.87–0.98), respectively. Conclusion: Our machine learning radiomics model showed promise for predicting response to nCRT in patients with LARC. Our predictive model based on the commonly used T2-weighted images on pelvic Magnetic Resonance Imaging (MRI) scans has the potential to be adapted in clinical practice. Novelty and Impact Statements: Methods for predicting the response of the locally advanced rectal cancer (LARC, T3-4, or N+) to neoadjuvant chemoradiotherapy (nCRT) is lacking. In the present study, we developed a new machine learning radiomics method based on T2-weighted images. As a non-invasive tool, this method facilitates prediction performance effectively. It achieves a satisfactory overall diagnostic accuracy for predicting of pCR, good response, and down-staging show an AUC of 0.908, 0.902, and 0.930 in LARC patients, respectively.
Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma

This study examined the structural diversity and bioactivity of peptaibol compounds produced by species from the phylogenetically separated Longibrachiatum Clade of the filamentous fungal genus Trichoderma, which contains several biotechnologically, agriculturally and clinically important species. HPLC-ESI-MS investigations of crude extracts from 17 species of the Longibrachiatum Clade (T. aethiopicum, T. andinense, T. capillare, T. citrinoviride, T. effusum, T. flagellatum, T. ghanense, T. konilangbra, T. longibrachiatum, T. novae-zelandiae, T. pinnatum, T. parareesei, T. pseudokoningii, T. reesei, T. saturnisporum, T. sinensis, and T. orientale) revealed several new and recurrent 20-residue peptaibols related to trichobrachins, paracelsins, suzukacillins, saturnisporins, trichoaureocins, trichocellins, longibrachins, hyporientalins, trichokonins, trilongins, metanicins, trichosporins, gliodeliquescins, alamethicins and hypophellins, as well as eight 19-residue sequences from a new subfamily of peptaibols named brevicelsins. Non-ribosomal peptide synthetase genes were mined from the available genome sequences of the Longibrachiatum Clade. Their annotation and product prediction were performed in silico and revealed full agreement in 11 out of 20 positions regarding the amino acids predicted based on the signature sequences and the detected amino acids incorporated. Molecular dynamics simulations were performed for structural characterization of four selected peptaibol sequences: paracelsins B, H and their 19-residue counterparts brevicelsins I and IV. Loss of position R6 in brevicelsins resulted in smaller helical structures with higher atomic fluctuation for every residue than the structures formed by paracelsins. We observed the formation of highly bent, almost hairpin-like, helical structures throughout the trajectory, along with linear conformation. Bioactivity tests were performed on the purified peptaibol extract of T. reesei on clinically and phytopathologically important filamentous fungi, mammalian cells, and Arabidopsis thaliana seedlings. Porcine kidney cells and boar spermatozoa proved to be sensitive to the purified peptaibol extract. Peptaibol concentrations ≥0.3 mg ml−1 deterred the growth of A. thaliana. However, negative effects to plants were not detected at concentrations below 0.1 mg ml−1, which could still inhibit plant pathogenic filamentous fungi, suggesting that those peptaibols reported here may have applications for plant protection.
Placebo Effects in Psychotherapy: A Framework

The issue of placebo response and the extent of its effect on psychotherapy is complex for two specific reasons: i) Current standards for drug trials, e.g., true placebo interventions, double-blinding, cannot be applied to most psychotherapy techniques, and ii) some of the “nonspecific effects” in drug therapy have very specific effects in psychotherapy, such as the frequency and intensity of patient–therapist interaction. In addition, different psychotherapy approaches share many such specific effects (the “dodo bird verdict”) and lack specificity with respect to therapy outcome. Here, we discuss the placebo effect in psychotherapy under four aspects: a) nonspecific factors shared with drug therapy (context factors); b) nonspecific factors shared among all psychotherapy traditions (common factors); c) specific placebo-controlled options with different psychotherapy modalities; and d) nonspecific control options for the specific placebo effect in psychotherapy. The resulting framework proposes that the exploration and enumeration of context factors, common factors, and specific factors contributes to the placebo effects in psychotherapy.
A New Analysis on Self-Control in Intertemporal Choice and Mediterranean Dietary Pattern

This paper completes Muñoz Torrecillas et al. (1) results and conclusions investigating the relationship between adherence to healthy dietary habits, specifically the Mediterranean Diet (hereinafter, MD), and impulsivity in intertemporal choices. Impulsivity can be defined as the strong preference for small immediate payoffs over larger delayed payoffs, and in the original study this behavior was captured by the parameter k (discount rate of the hyperbolic discount function), calculated using an automated scoring mechanism. Adherence to MD was measured by the KIDMED index and then grouped into three levels: high, medium, and low. While the authors observed that individuals in the high adherence group had the shallowest discounting and individuals in the low adherence group had the steepest discounting, the data were not statistically analyzed in depth. Therefore, the purpose of the present paper is to propose a preliminary quantitative model for this relationship and evaluate its significance. Tests revealed a significant interaction between adherence to MD and magnitude of delayed rewards when predicting discount rates. Specifically, the degree to which impulsivity decreases as adherence to MD increases is strongly influenced by delayed rewards of smaller magnitude. These findings are consistent with the authors' claims that healthy dietary habits may be closely linked with greater self-control when payoffs are small, and thus warrant further examination. The results do not indicate causality though, so future studies could also investigate the directions of this relationship as a means of developing behavioral interventions.
Cumulative Live Birth Rates of Good and Low Prognosis Patients According to POSEIDON Criteria: A Single Center Analysis of 18,455 Treatment Cycles

Objective: To investigate the characteristics and outcomes of low prognosis patients defined by POSEIDON criteria undergoing IVF treatment. Design: Retrospective cohort analysis. Setting: An IVF clinic in a public hospital. Patients: 18,455 fresh aspirated IVF cycles with subsequently frozen embryo transfer from Jan 2014 to Jan 2017 in a single IVF clinic were included in the analysis. The low prognosis patients were categorized into 4 groups based on POSEIDON criteria: group 1: age < 35, antral follicle count (AFC) ≥ 5, number of oocytes retrieved ≤ 9 in the previous cycle; group 2: age ≥ 35, AFC≥5, number of oocytes retrieved ≤ 9 in the previous cycle; group 3: age < 35, AFC < 5; group 4: age ≥ 35, AFC < 5. The non-low prognosis patients: group 5: AFC ≥ 5, previous number of oocytes retrieved > 9 oocytes; group 6: AFC ≥ 5, no previous ovarian stimulation. Intervention(s): None. Main Outcome Measure: The primary outcome was cumulative live birth rate (CLBR). Result(s): Taking group 1 as reference, the CLBR from young women in group 3 (35.5%, OR 0.9, 95% CI 0.7–1.2) was slightly lower than that in group 1 (44.6%, p = 0.615). The CLBR in group 2 (24.5%, OR 0.6, 95% CI 0.4–0.8, p = 0.004) and group 4 (12.7%, OR 0.4, 95% CI 0.3–0.6, p < 0.001) was significant lower than that in group 1. In non-poor prognosis patients, the CLBR from young women in group 5 (53.5% OR 1.3 95% CI 0.9, 1.7, p = 0.111) was a slight higher than the reference group 1 while the highest CLBR was originated from the first IVF patients with good ovarian reserve in group 6 (66.9%, OR 2.0, 95% CI 1.6, 2.4). Conclusion(s): The CLBRs and implantation rates in the young women (group 3) with diminished ovarian reserve was similar in those young women (group 1), and was significantly higher than in advanced age women with a fair ovarian reserve (group 2). Though patients in group 2 had better ovarian reserve, more oocytes and more embryos, the pregnancy outcome was inferior to that of group 3 patients with poorer ovarian reserve, fewer oocytes and fewer embryos.
A Hierarchical QoS Routing Protocol for the Wireless Sensor Networks

The large wireless sensor networks are often structured hierarchically by grouping nodes into different domains in order to deal with the scaling problem. This paper proposes a new protocol called hierarchical QoS routing protocol (HQRP) that achieves scalability by organizing the network as a hierarchy of domains using the full-mesh aggregation technique. In HQRP, each local node just only needs to maintain local routing and summary information of other domains, but does not requires any global states maintained. The HQRP uses a Reverse Best Metric Path Forwarding approach with hierarchical, topological and QoS forwarding conditions to construct the multicast tree while minimizing message overhead and satisfying delay-bandwidth and minimum energy consumption. The paper presents proof of correctness and complexity analysis of the HQRP. Simulation results show very good performance in terms of success ratio and message overhead.
The Moderating Effect of Mindfulness on the Mediated Relation Between Critical Thinking and Psychological Distress via Cognitive Distortions Among Adolescents

Critical thinking has been widely regarded as an indispensable cognitive skill in the 21st century. However, its associations with the affective aspects of psychological functioning are not well understood. This study explored the interrelations between trait mindfulness, critical thinking, cognitive distortions, and psychological distress using a moderated mediation model. The sample comprised 287 senior secondary school students (57% male and 43% female) aged 14–19 from a local secondary school in Hong Kong. The results revealed that high critical thinking was significantly associated with high levels of psychological distress when mindful awareness was low among adolescents. Trait mindfulness was found to moderate the indirect effects of critical thinking on psychological distress via cognitive distortions as the mediator. Specifically, in low trait mindfulness conditions, critical thinking was found to associate positively with cognitive distortions and psychological distress. Such associations were not observed in high trait mindfulness conditions. The findings reveal that though critical thinking has positive associations with cognitive functioning, its associations with affective well-being might be negative. The results also suggest that mindfulness might play an important role in preventing the possible psychological distress associated with critical thinking. Educational implications relating to the fostering of critical thinking and mindful awareness are discussed.
Offsetting Expression Profiles of Prognostic Markers in Prostate Tumor vs. Its Microenvironment

Diagnosis of the presence of tumors and subsequent prognosis based on tumor microenvironment becomes more clinically practical because tumor-adjacent tissues are easy to collect and they are more genetically homogeneous. The purpose of this study was to identify new prognostic markers in prostate stroma that are near the tumor. We have demonstrated the prognostic features of FGFR1, FRS2, S6K1, LDHB, MYPT1, and P-LDHA in prostate tumors using tissue microarrays (TMAs) which consist of 241 patient samples from Massachusetts General Hospital (MGH). In this study, we investigated these six markers in the tumor microenvironment using an Aperio Imagescope system in the same TMAs. The joint prognostic power of markers was further evaluated and classified using a new algorithm named Weighted Dichotomizing. The classifier was verified via rigorous 10-fold cross validation. Statistical analysis of the protein expression indicated that in tumor-adjacent stroma FGFR1 and MYPT1 were significantly correlated with patient outcomes and LDHB showed the outcome-association tendency. More interestingly, these correlations were completely opposite regarding tumor tissue as previously reported. The results suggest that prognostic testing should utilize either tumor-enriched tissue or stroma with distinct signature profiles rather than using mixture of both tissue types. The new classifier based on stroma tissue has potential value in the clinical management of prostate cancer patients.
Mind the Gap: The Implications of Not Acting in Line With Your Planned Actions After Installing Solar Photovoltaics

To realize the full potential of solar photovoltaics (PV), PV adopters need to adapt their energy demand to the production of self-generated solar energy as much as possible (i.e., use their PV sustainably). In a longitudinal questionnaire study (N = 74) in the Netherlands, we compared the intention to use PV in a sustainable way before the installation of PV with actual PV use. Wave 1 took place before respondents adopted PV, while Wave 2 took place after they installed PV. We examined whether potential differences between actual sustainable PV use and initial intentions may have implications for how people see themselves and for the motivation they ascribe to their decision to adopt PV. Our results show that the vast majority of people use their PV in a less sustainable way than they anticipated. Furthermore, after the installation of PV, respondents are less likely to see themselves as a sustainable PV user and less likely to believe that PV have positive environmental consequences than before the installation, while environmental self-identity did not differ pre and post-installation of PV. Moreover, the stronger the discrepancy between intended and actual sustainable use of the PV, the less likely people were to see themselves as a sustainable PV user and as a person who acts pro-environmentally in general. These findings suggest that it is important to support people to use their PV in a sustainable way to facilitate them to act upon their intentions.
Effects of Neuromuscular Fatigue on Eccentric Strength and Electromechanical Delay of the Knee Flexors: The Role of Training Status

Purpose: To examine the effects of fatiguing isometric contractions on maximal eccentric strength and electromechanical delay (EMD) of the knee flexors in healthy young adults of different training status. Methods: Seventy-five male participants (27.7 ± 5.0 years) were enrolled in this study and allocated to three experimental groups according to their training status: athletes (ATH, n = 25), physically active adults (ACT, n = 25), and sedentary participants (SED, n = 25). The fatigue protocol comprised intermittent isometric knee flexions (6-s contraction, 4-s rest) at 60% of the maximum voluntary contraction until failure. Pre- and post-fatigue, maximal eccentric knee flexor strength and EMDs of the biceps femoris, semimembranosus, and semitendinosus muscles were assessed during maximal eccentric knee flexor actions at 60, 180, and 300°/s angular velocity. An analysis of covariance was computed with baseline (unfatigued) data included as a covariate. Results: Significant and large-sized main effects of group (p ≤ 0.017, 0.87 ≤ d ≤ 3.69) and/or angular velocity (p < 0.001, d = 1.81) were observed. Post hoc tests indicated that regardless of angular velocity, maximal eccentric knee flexor strength was lower and EMD was longer in SED compared with ATH and ACT (p ≤ 0.025, 0.76 ≤ d ≤ 1.82) and in ACT compared with ATH (p = ≤0.025, 0.76 ≤ d ≤ 1.82). Additionally, EMD at post-test was significantly longer at 300°/s compared with 60 and 180°/s (p < 0.001, 2.95 ≤ d ≤ 4.64) and at 180°/s compared with 60°/s (p < 0.001, d = 2.56), irrespective of training status. Conclusion: The main outcomes revealed significantly higher maximal eccentric strength and shorter eccentric EMDs of knee flexors in individuals with higher training status (i.e., athletes) following fatiguing exercises. Therefore, higher training status is associated with better neuromuscular functioning (i.e., strength, EMD) of the hamstring muscles in fatigued condition. Future longitudinal studies are needed to substantiate the clinical relevance of these findings.
Comparing the Pathway to Success in European Countries Competing in the Swimming World Championships

Purpose: This study aimed to compare the performance progression model of the European countries that participated in the World Championships (WCs) from 2006 to 2017. Data from all championships were compared between the top five (1–5) and the next five (6–10) countries on the medal table. The study also identifies the ages of peak performance in senior swimmers, the annual ratio of progression and the effect of junior performance on senior success by these groups of countries. We hypothesized that: (1) countries with swimmers achieving better performances at the Junior WCs would also be higher in the medal ranking at the Senior WCs and (2) a higher annual performance progression in their swimmers increases the chances of countries being ranked in the top 5 at the Senior World Championships. Methods: Participant’s data from all Junior and Senior WCs between 2006 and 2017 were obtained from FINA. The final, filtered database included 629 swimmers after removing those participating only in the Junior WCs and selecting swimmers from the top 10 countries. One-way ANOVA, F test, and decision tree methods were used to examine differences between the top (1–5) and the next best (6–10) countries on the medal table for first participation age, annual progress, and best-time in junior and senior championships. Results: There was no difference (p = 0.492 and p = 0.97) between 1–5 and 6–10 ranked countries for best senior time and annual progression, respectively. Countries ranked in the top 5 at the Senior WCs had swimmers with faster times at the Junior WCs (p > 0.001). Decision tree analysis found that best-time at the Junior WC had the greatest explanatory capacity (94%). Conclusion: European countries with swimmers who perform best at the Junior WCs are also likely to be in the top 5 countries that win medals at the Senior WCs.
Spatial signatures of visual object recognition events learned from single-trial analysis of EEG

In this paper we use linear discrimination for learning EEG signatures of object recognition events in a rapid serial visual presentation (RSVP) task. We record EEG using a high spatial density array (63 electrodes) during the rapid presentation (50-200 msec per image) of natural images. Each trial consists of 100 images, with a 50% chance of a single target being in a trial. Subjects are instructed to press a left mouse button at the end of the trial if they detected a target image, otherwise they are instructed to press the right button. Subject EEG was analyzed on a single-trial basis with an optimal spatial linear discriminator learned at multiple time windows after the presentation of an image. Analysis of discrimination results indicated a periodic fluctuation (time-localized oscillation) in A/sub z/ performance. Analysis of the EEG using the discrimination components learned at the peaks of the A/sub z/ fluctuations indicate 1) the presence of a positive evoked response, followed in time by a negative evoked response in strongly overlapping areas and 2) a component which is not correlated with the discriminator learned during the time-localized fluctuation. Results suggest that multiple signatures, varying over time, may exist for discriminating between target and distractor trials.
Amaranth as a Dual-Use Crop for Leafy Greens and Seeds: Stable Responses to Leaf Harvest Across Genotypes and Environments

Dual-use production systems that utilize the green leaves as well as seeds from amaranth are highly promising for small-scale farmers around the world. The leaves are an important source of nutrients for farming families, while seeds can provide income. Farmers who use amaranth as a dual-use crop are concerned about the impacts of defoliation on seed yield. This experiment tested defoliation at various intensities and frequencies (0, 25, 50, 75, and 100% defoliation, 1, 2, and 3 times) under controlled conditions as well as under Danish and Mexican field conditions. Defoliation tolerance was tested in a total of seven varieties, spanning the three primary grain amaranth species: A. cruentus, A. hypocondriacus, and A. caudatus. In all of the varieties and environments tested, we found that neither seed yield nor quality was impacted by a single defoliation event at intensities up to 50% leaf removal. We observed similar responses with two and three consecutive defoliations in which we removed 25% of all leaves. Greater frequency and intensity of defoliation resulted in reduced seed yield in some environments, while seed quality (protein content and 1000 KW) did not appear to be affected. Dual-use production systems should be promoted with small-scale farmers around the world as promising systems for improving local nutrition while maintaining profits from seed production. This paper provides baseline guidelines for farmers regarding optimal defoliation intensities and frequencies.
Adaptive Object-Oriented Software: The Demeter Method with Propagation Patterns

From the Publisher: This ground-breaking book presents a complete methodology for adaptive programming in any object-oriented programming language. Lieberherr's adaptive method signals a new approach to object-oriented program design that goes beyond object encapsulation and hard-coded navigation paths to achieve more flexible interactions among objects. Programmers using this method work at a higher, schematic level of abstraction; graph notation represents the class structure and a "propagation pattern" language tells how to distribute meaningful methods - including navigation - across the structure. Using this method, programmers can easily adapt and modify programs as they evolve. This book can be used with any object-oriented programming environment, or with the Demeter Tools Version 5.5, a complete, professional software system for creating and maintaining adaptive programs.