Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation of Somatic Genomic Alterations Between Tissue Genomics and ctDNA Employing Next-Generation Sequencing: Analysis of Lung and Gastrointestinal Cancers

Next-generation Sequencing (NGS) of cancer tissues is increasingly being carried out to identify somatic genomic alterations that may guide physicians to make therapeutic decisions. However, a single tissue biopsy may not reflect complete genomic architecture due to the heterogeneous nature of tumors. Circulating tumor DNA (ctDNA) analysis is a robust noninvasive method to detect and monitor genomic alterations in blood in real time. We analyzed 28 matched tissue NGS and ctDNA from gastrointestinal and lung cancers for concordance of somatic genomic alterations, driver, and actionable alterations. Six patients (21%) had at least one concordant mutation between tissue and ctDNA sequencing. At the gene level, among all the mutations (n = 104) detected by tissue and blood sequencing, 7.7% (n = 8) of mutations were concordant. Tissue and ctDNA sequencing identified driver mutations in 60% and 64% of the tested samples, respectively. We found high discordance between tissue and ctDNA testing, especially with respect to the driver and actionable alterations. Both tissue and ctDNA NGS detected actionable alterations in 25% of patients. When somatic alterations identified by each test were combined, the total number of patients with actionable mutations increased to 32%. Our data show significant discordance between tissue NGS and ctDNA analysis. These results suggest tissue NGS and ctDNA NGS are complementary approaches rather than exclusive of each other. When performed in isolation, tissue and ctDNA NGS can each potentially miss driver and targetable alterations, suggesting that both approaches should be incorporated to enhance mutation detection rates. Larger prospective studies are needed to better clarify this emerging precision oncology landscape. Mol Cancer Ther; 17(5); 1123–32. ©2018 AACR.
Design of an 87% Fractional Bandwidth Doherty Power Amplifier Supported by a Simplified Bandwidth Estimation Method

This paper presents a novel technique for the design of broadband Doherty power amplifiers (DPAs), supported by a simplified approach for the initial bandwidth estimation that requires linear simulations only. The equivalent impedance of the Doherty inverter is determined by the value of the output capacitance of the power device, and the Doherty combiner is designed following this initial choice and using a microstrip network. A GaN-based single-input DPA designed adopting this method exhibits, on a state-of-the-art bandwidth of 87% (1.5–3.8 GHz), a measured output power of around 20 W with 6 dB back-off efficiency between 33% and 55%, with a gain higher than 10 dB. System-level measurements prove the linearizability of the designed Doherty amplifier when a modulated signal is applied.
Cylindrical M-sequence Markers and its Application to AR Fitting System for Kimono Obi

This paper proposes an m-sequence cylindrical marker, which is an optical barcode marker that can be applied on cylindrical objects, such as parts of a human body and everyday things such as furniture, bottles, and cups. We use two cycles of an m-sequence barcode to maintain continuity at the joint of the cylindrical marker. By using the m-sequence characteristics, the marker is able to acquire the rotation angle by recognizing only a certain part of the barcode. To confirm feasibility, we have made a cylindrical marker that fits on the waist of a human, and have implemented an AR fitting application for kimono obi.
Introgression of the Kinetoplast DNA: An Unusual Evolutionary Journey in Trypanosoma cruzi

Introduction: Phylogenetic relationships between different lineages of Trypanosoma cruzi, the agent of Chagas disease, have been controversial for several years. However, recent phylogenetic and phylogenomic analyses clarified the nuclear relationships among such lineages. However, incongruence between nuclear and kinetoplast DNA phylogenies has emerged as a new challenge. This incongruence implies several events of mitochondrial introgression at evolutionary level. However, the mechanism that gave origin to introgressed lineages is unknown. Here, I will review and discuss how maxicircles of the kinetoplast were horizontally and vertically transferred between different lineages of T. cruzi. Conclusion: Finally, I will discuss what we know - and what we don't - about the kDNA transference and inheritance in the context of sexual reproduction in this parasite.
Beating heart motion prediction using iterative optimal sine filtering

A novel motion prediction algorithm is proposed to robustly track heart beat in minimally invasive surgery. To model the movement of Points of Interest (POI) on heart tissue, the Dual Time-Varying Fourier Series (DTVFS) is employed. The Fourier coefficients and the frequencies of the DTVFS model are estimated separately using the dual Kalman filtering. An iterative optimal sine filtering algorithm is developed, which can accurately measure the instantaneous frequencies of breathing circle and heart beating from the motion curves of the POI. The proposed method is verified on the simulated dataset and the real-measured datasets captured by the daVinci surgical system.
Habitat selection by the Northern Long-eared Myotis ( Myotis septentrionalis ) in the Midwestern United States: Life in a shredded farmscape

Populations of the Northern Long-Eared Myotis (Myotis septentrionalis) have declined dramatically in recent years in eastern North America due to white-nose syndrome. Although M. septentrionalis was once common in parts of eastern North America, few studies have examined habitat selection of this species in an agricultural landscape. We used acoustical methods to quantify bat activity and construct a habitat model of M. septentrionalis in an intensively farmed area in the Midwestern United States, where mortality from white-nose syndrome has not yet been observed. Our study confirms that M. septentrionalis prefers forest and avoids open habitats in this agricultural region. The best landscape variable for predicting activity in woodland sites was the proportion of forest coverage within a radius of 2000 meters. Our analysis indicates that bat activity increased exponentially as forest coverage increased. There is no evidence that M. septentrionalis preferred open areas at the edge of forest (within 5 m of forest edge), or that once in the woods, the distance to the forest edge had any impact on activity.
Efficacy and safety of Oxalobacter formigenes to reduce urinary oxalate in primary hyperoxaluria.

BACKGROUND Primary hyperoxaluria (PH) is a rare genetic disease, in which high urinary oxalate (Uox) cause recurrent kidney stones and/or progressive nephrocalcinosis, often followed by early end-stage renal disease, as well as extremely high plasma oxalate, systemic oxalosis and premature death. Oxalobacter formigenes, an anaerobic oxalate degrading bacterium, naturally colonizes the colon of most humans. Orally administered O. formigenes (Oxabact) was found to significantly reduce urine and plasma oxalate. We aimed to evaluate its effect and safety in a randomized, double-blind, placebo-controlled multicenter study. METHODS Oral Oxabact was given to PH patients (>5 years old, Uox > 1.0 mmol/1.73 m(2)/day, glomerular filtration rate (GFR) > 50 mL/min) at nine PH referral sites worldwide. Primary endpoint was the change from baseline in Uox (mmol/1.73 m(2)/day) after 24 weeks of treatment (>20% reduction). RESULTS Of the 43 subjects randomized, 42 patients received either placebo (23 subjects) or Oxabact (19 subjects). The change in Uox was <20% and not different between groups (P = 0.616). Ad hoc analysis was performed in 37 patients compliant with medication and urine processing. Change in Uox was -19% in subjects given Oxabact and -10% in placebo, (P = 0.288), but -21 and -7% with Uox expressed as molar creatinine ratio (Ox:Cr, mmol/mol, P = 0.06). Reduction of Ox:Cr was more obvious for patients with higher baseline values (>160 mmol/mol, Oxabact -28%, placebo -6%; P < 0.082). No serious adverse events were reported. CONCLUSION Oxabact was safe and well tolerated. However, as no significant change in Uox was seen, further studies to evaluate the efficacy of Oxabact treatment are needed.
Subconcussive Blows to the Head: A Formative Review of Short-term Clinical Outcomes

Background:Given questions about “lower thresholds” for concussion, as well as possible effects of repetitive concussion and chronic traumatic encephalopathy (CTE), and associated controversy, there is increasing interest in “subconcussive” blows and their potential significance. Objective:A formative review with critical examination of the developing literature on subconcussive blows in athletes with an emphasis on clinical outcomes. Methods:Studies of biomechanical, performance and/or symptom-based, and neuroimaging data were identified via PubMed search and critically reviewed. Five studies of symptom reporting/performance and 4 studies of neuroimaging were included. Results:The relation between biomechanical parameters and diagnosed concussion is not straightforward (ie, it is not the case that greater and more force leads to more severe injury or cognitive/behavioral sequelae). Neuropsychological studies of subconcussive blows within a single athletic season have failed to demonstrate any strong and consistent relations between number and severity of subconcussive events and cognitive change. Recent studies using neuroimaging have demonstrated a potential cumulative effect of subconcussive blows, at least in a subset of individuals. Conclusion:Human studies of the neurological/neuropsychological impact of subconcussive blows are currently quite limited. Subconcussive blows, in the short-term, have not been shown to cause significant clinical effects. To date, findings suggest that any effect of subconcussive blows is likely to be small or nonexistent, perhaps evident in a subset of individuals on select measures, and maybe even beneficial in some cases. Longer-term prospective studies are needed to determine if there is a cumulative dose effect.
Cascaded convolutional neural networks for object detection

Recent advances in object detection depend on region proposal algorithms or networks to predict object locations. The pipeline of region proposal-based object detection can be decomposed into two cascaded sub-tasks: 1) region proposals generation from input image, 2) proposals classification into various object categories. In this paper, we propose cascaded convolutional neural networks to make improvement for two sub-tasks respectively. For the region proposals generation stage, we add a RefineNet after the original region proposal network(RPN) to make the proposals more compact and better located. For the classification stage, we integrate a binary classifier for each object class into the network which makes the feature representation capture more intra-class variance. Experiments on PASCAL VOC dataset demonstrate that our approach can achieve considerable improvement over state-of-the-art object detectors.
Assessing Top-Down and Bottom-Up Contributions to Auditory Stream Segregation and Integration With Polyphonic Music

Polyphonic music listening well exemplifies processes typically involved in daily auditory scene analysis situations, relying on an interactive interplay between bottom-up and top-down processes. Most studies investigating scene analysis have used elementary auditory scenes, however real-world scene analysis is far more complex. In particular, music, contrary to most other natural auditory scenes, can be perceived by either integrating or, under attentive control, segregating sound streams, often carried by different instruments. One of the prominent bottom-up cues contributing to multi-instrument music perception is their timbre difference. In this work, we introduce and validate a novel paradigm designed to investigate, within naturalistic musical auditory scenes, attentive modulation as well as its interaction with bottom-up processes. Two psychophysical experiments are described, employing custom-composed two-voice polyphonic music pieces within a framework implementing a behavioral performance metric to validate listener instructions requiring either integration or segregation of scene elements. In Experiment 1, the listeners' locus of attention was switched between individual instruments or the aggregate (i.e., both instruments together), via a task requiring the detection of temporal modulations (i.e., triplets) incorporated within or across instruments. Subjects responded post-stimulus whether triplets were present in the to-be-attended instrument(s). Experiment 2 introduced the bottom-up manipulation by adding a three-level morphing of instrument timbre distance to the attentional framework. The task was designed to be used within neuroimaging paradigms; Experiment 2 was additionally validated behaviorally in the functional Magnetic Resonance Imaging (fMRI) environment. Experiment 1 subjects (N = 29, non-musicians) completed the task at high levels of accuracy, showing no group differences between any experimental conditions. Nineteen listeners also participated in Experiment 2, showing a main effect of instrument timbre distance, even though within attention-condition timbre-distance contrasts did not demonstrate any timbre effect. Correlation of overall scores with morph-distance effects, computed by subtracting the largest from the smallest timbre distance scores, showed an influence of general task difficulty on the timbre distance effect. Comparison of laboratory and fMRI data showed scanner noise had no adverse effect on task performance. These Experimental paradigms enable to study both bottom-up and top-down contributions to auditory stream segregation and integration within psychophysical and neuroimaging experiments.
Electromyographical Comparison of a Traditional, Suspension Device, and Towel Pull-Up

Abstract Strengthening muscles of the back may have various implications for improving functions of daily living, aiding in the transfer of power in throwing, and assist in injury prevention of the shoulder complex. While several versions of the pull-up exist, there is currently no literature comparing their differences. The purpose of this investigation was to compare the electromyographical activity of the latissimus dorsi, posterior deltoid, middle trapezius, and biceps brachii while performing three variations of the pull-up. Resistance-trained men and women (n =15, age = 24.87 ± 6.52 years) participated in this study by performing traditional pull-ups, suspension device pull-ups, and towel pull-ups in a randomized fashion. Each pull-up was performed for three repetitions with a 1.5 bi-acromial grip-width for each participant. Normalized (%MVC) electromyographical values were recorded for each muscle group during each pull-up variation. No significant differences existed within the latissimus dorsi, biceps brachii or posterior deltoid between any of the exercises. For the middle trapezius, towel pull-ups provided significantly lower muscle activity than the traditional pull-up, while no differences between suspension pull-ups and the other variations occurred. In conclusion, only one muscular difference existed between the exercise variations and all versions examined provided electromyographical values, determined by current literature, to invoke a sufficient stimulus to promote increases in muscle strength and hypertrophy. Although further research is needed, practitioners can be confident when programming any of the movement variations examined when attempting to elicit adaptations of muscular strength and hypertrophy.
Help Resources in Games: Gamers' Opinions and Preliminary Design Remarks

Help resources are available in many ways and required in many applications. However, in the digital game context, little has been investigated and discussed about why, how and when to offer help in order to not jeopardize the gameplay. In this work, we present an exploratory research on gamers' preferences and opinions about help in games, conducted by means of an online survey. We found out gamers prefer help resources to be fast, discreet, and relevant, capable of fostering learning, so they can evolve by themselves. We also observed that gamers need these resources in specific moments, and they must be perceived as necessary in order to avoid disturbing the gameplay. Finally, we make available some design remarks to support designers to better understand gamers' needs and improve design in what concerns to help resources in games.
On Developers' Personality in Large-Scale Distributed Projects: The Case of the Apache Ecosystem

Large-scale distributed projects are typically the results of collective efforts performed by multiple developers, each one having a different personality. The study of developers' personalities has the potential of explaining their' behavior in various contexts. For example, the propensity to trust others, a critical factor to the success of global software engineering – has been found to influence positively the result of code reviews in distributed projects. In this paper, we perform a quantitative analysis of developers' personality in open source software projects, intended as an extreme form of distributed projects in which no single organization controls the project. We mine ecosystem-level data from the code commits and email messages contributed by the developers working on the Apache Software Foundation (ASF) projects, as representative of large scale-distributed projects. We find that developers become over time more conscientious, agreeable, and neurotic. Moreover, personality traits do not vary with their role, membership, and extent of contribution to the projects. We also find evidence that more open and more agreeable developers are more likely to become project contributors.
Lack of Agreement Between Gross Visual and Histological Assessment of Burn Reepithelialization in a Porcine Burn Model

One of the most important and earliest measures of burn healing is wound reepithelialization. Reepithelialization is a vital determinant of wound infection and scarring. Reepithelialization is generally based on gross visual assessment; however, histological assessment remains the criterion standard. We hypothesized that there would be poor agreement (r < .4) between gross visual and histological assessments of burn reepithelialization in a porcine model. The study design was prospective observational using three anesthetized female pigs (20–25 kg). Forty-eight 2.5- × 2.5-cm burns were created on the flanks of pig's using an aluminum bar (150 g) preheated to 80°C for 20 seconds. Burns were treated with an occlusive or antimicrobial dressing and photographed at day 10 for determination of gross percentage reepithelialization in a 1-cm diameter circle in the center of the burn by two experienced clinicians masked to each other's measurements. A 10-mm full-thickness punch biopsy was taken from the center of the burns and evaluated by a board-certified dermatopathologist masked to clinical assessments. One clinician and the dermatopathologist repeated the assessments 1 month apart. The outcome was percentage wound reepithelialization at 10 days. The criterion standard was the histological assessment. Intraobserver and interobserver agreements were calculated with Pearson's correlation coefficients. A coefficient less than . 4 was considered poor. Sixteen burns were created on each of three animals. Six wounds were excluded because of the presence of a thick eschar covering the burn, making the gross determination of reepithelialization impossible. Intraobserver agreement for histological reepithelialization was 0.96 (P < .001). Intraobserver agreement for gross visual assessment of reepithelialization was 0.75 (P < .001). Interobserver agreement for gross visual assessment of reepithelialization was 0.60 (P < .001). The agreement between gross visual and histological assessment of burn reepithelialization was −0.25. Although there was a good interobserver agreement for gross visual assessments, there was a poor agreement between gross visual and histological assessments of burn reepithelialization. Care should be used when determining burn reepithelialization based on gross visual assessments alone.
Diurnal fluctuations in chloroplast GSH redox state regulate susceptibility to oxidative stress and cell fate in a bloom‐forming diatom

Diatoms are one of the key phytoplankton groups in the ocean, forming vast oceanic blooms and playing a significant part in global primary production. To shed light on the role of redox metabolism in diatom's acclimation to light–dark transition and its interplay with cell fate regulation, we generated transgenic lines of the diatom Thalassiosira pseudonana that express the redox‐sensitive green fluorescent protein targeted to various subcellular organelles. We detected organelle‐specific redox patterns in response to oxidative stress, indicating compartmentalized antioxidant capacities. Monitoring the GSH redox potential (EGSH) in the chloroplast over diurnal cycles revealed distinct rhythmic patterns. Intriguingly, in the dark, cells exhibited reduced basal chloroplast EGSH but higher sensitivity to oxidative stress than cells in the light. This dark‐dependent sensitivity to oxidative stress was a result of a depleted pool of reduced glutathione which accumulated during the light period. Interestingly, reduction in the chloroplast EGSH was observed in the light phase prior to the transition to darkness, suggesting an anticipatory phase. Rapid chloroplast EGSH re‐oxidation was observed upon re‐illumination, signifying an induction of an oxidative signaling during transition to light that may regulate downstream metabolic processes. Since light–dark transitions can dictate metabolic capabilities and susceptibility to a range of environmental stress conditions, deepening our understanding of the molecular components mediating the light‐dependent redox signals may provide novel insights into cell fate regulation and its impact on oceanic bloom successions.
Inborn Errors of Bile Acid Metabolism

Bile acids are synthesized by the liver from cholesterol through a complex series of reactions involving at least 14 enzymatic steps. A failure to perform any of these reactions will block bile acid production with failure to produce "normal bile acids" and, instead, result in the accumulation of unusual bile acids and intermediary metabolites. Failure to synthesize bile acids leads to reduced bile flow and decreased intraluminal solubilization of fat and fat-soluble vitamins. In some circumstances, the intermediates created because of blockade in the bile acid biosynthetic pathway may be toxic to hepatocytes. Nine recognized inborn errors of bile acid metabolism have been identified that lead to enzyme deficiencies and impaired bile acid synthesis in infants, children, and adults. Patients may present with neonatal cholestasis, neurologic disease, or fat and fat-soluble vitamin malabsorption. If untreated, progressive liver disease may develop or reduced intestinal bile acid concentrations may lead to serious morbidity or mortality. This review focuses on a description of the disorders of bile acid synthesis that are directly related to single defects in the metabolic pathway, their proposed pathogenesis, treatment, and prognosis.