Miracle-dz/UniFAR-FTUs huggingface dataset:
Tracing the Origin and Evolutionary Fate of Recent Gene Retrocopies in Natural Populations of the House Mouse

Abstract Although the contribution of retrogenes to the evolution of genes and genomes has long been recognized, the evolutionary patterns of very recently derived retrocopies that are still polymorphic within natural populations have not been much studied so far. We use here a set of 2,025 such retrocopies in nine house mouse populations from three subspecies (Mus musculus domesticus, M. m. musculus, and M. m. castaneus) to trace their origin and evolutionary fate. We find that ancient house-keeping genes are significantly more likely to generate retrocopies than younger genes and that the propensity to generate a retrocopy depends on its level of expression in the germline. Although most retrocopies are detrimental and quickly purged, we focus here on the subset that appears to be neutral or even adaptive. We show that retrocopies from X-chromosomal parental genes have a higher likelihood to reach elevated frequencies in the populations, confirming the notion of adaptive effects for “out-of-X” retrogenes. Also, retrocopies in intergenic regions are more likely to reach higher population frequencies than those in introns of genes, implying a more detrimental effect when they land within transcribed regions. For a small subset of retrocopies, we find signatures of positive selection, indicating they were involved in a recent adaptation process. We show that the population-specific distribution pattern of retrocopies is phylogenetically informative and can be used to infer population history with a better resolution than with SNP markers.
Structural insight on the liquid silk from the middle silk gland of non-mulberry silkworm Antheraea assamensis

Abstract This study highlights the preliminary characterization of liquid silk from the middle silk gland (MSG) along with the in-silico analysis of the sericin protein of a less explored non mulberry silkworm Antheraea assamensis which is endemic to the North Eastern region of India. Various biophysical methods have been applied to elucidate the conformational patterns of the liquid silk present inside the MSG without removing the sericin layer. This will help us to know the actual features of the in vivo transitional status of the silk in the MSG which travel towards the anterior silk gland (ASG) prior to spinning. The SDS PAGE analysis represented the existence of the both fibroin and sericin bands in the sample. The structural pattern of the MSG liquid silk as revealed by various methods denoted the occurrence of β-sheet component along with some random coil and β-turn components which in turn suggests the transitional state of the liquid silk attributed to the existence of both the crystalline and amorphous contents. The thermo gravimetric study and the aggregation behavior analysis results proposed the occurrence of intermolecular hydrogen bonding between the sericin and fibroin in the MSG. This study will sensitize the better understanding of the behavior of the liquid silk in the MSG of non-mulberry silkworm A. assamensis and will open avenues for various application-based studies of this silk. Communicated by Ramaswamy H. Sarma
Validating the use of U-tool as a novel method for measuring the corneal diameter in infants screened for congenital glaucoma

Purpose: The Castroviejo caliper is routinely used for measuring the corneal diameter in patients with primary congenital glaucoma, but needs an examination under anesthesia (EUA) or sedation. A simple U-shaped tool was devised to aid in the estimation of the corneal diameters of patients in settings where an ophthalmic caliper is not available or EUA is not feasible. Methods: Infants presenting to the congenital glaucoma clinic posted for EUA were recruited. The demographic details of the patients such as age, sex, and diagnosis were noted. A simple U-shaped tool was devised using three Schirmer strips or a printable ruler. Before the patient underwent a EUA, the corneal diameters were measured using the U-tool. During EUA, corneal diameters were measured using the Castroviejo caliper. Results: The mean age of infants was 6.7 ± 3.39 months (R = 1–12). The mean corneal diameter measured using the U-tool was 13.29 ± 1.33 mm and with Castroviejo caliper was 13.18 ± 1.39 mm. The difference between the corneal diameters measured using the two techniques was −0.114 mm with the Bland–Altman plot 95% Limits of agreement (LoA) from −0.965 to 0.737 mm. Corneal diameters measured with both instruments had a good correlation (Pearson's correlation coefficient = 0.95, P < 0.001). Conclusion: U-tool can be used for screening congenital glaucoma by first-contact physicians or optometrists. It can also be used by ophthalmologists when EUA is delayed.
Disease-Specific Imaging Utilizing Support Vector Machine Classification of H-Scan Parameters: Assessment of Steatosis in a Rat Model

In medical imaging, quantitative measurements have shown promise in identifying diseases by classifying normal versus pathological parameters from tissues. The support vector machine (SVM) has shown promise as a supervised classification algorithm and has been widely used. However, the classification results typically identify a category of abnormal tissues but do not necessarily differentiate progressive stages of a disease. Moreover, the classification result is typically provided independently as a supplement to medical images, which contributes to an overload of information sources in the clinic. Hence, we propose a new imaging method utilizing the SVM to integrate classification results into medical images. This framework is called disease-specific imaging (DSI) that produces a color overlaid highlight on B-mode ultrasound images indicating the type, location, and severity of pathology from different conditions. In this article, the SVM training was performed to construct hyperplanes that can differentiate normal, fibrosis, steatosis, and pancreatic ductal adenocarcinoma (PDAC) metastases in livers based on ultrasound echoes. Also, cluster centroids for specific diseases define unique disease axes, and the inner product between measured features and any disease axis selected by the SVM quantifies the disease progression. The features were measured from 2794 ultrasound frames using the H-scan analysis, attenuation estimation, and B-mode image analysis. The performance of our proposed DSI method was evaluated for a preclinical model of steatosis ( ${n} =400$ frames). The contribution of each feature was assessed, and the results were compared with ground truth from histology. Moreover, the images generated by our DSI were compared with earlier imaging methods of B-mode, H-scan, and histology. The comparisons demonstrate that DSI images yield higher sensitivity to monitor progressive steatosis than B-mode and H-scan and provide a comparable performance with the histology. For the parameter comparison, DSI and H-scan resulted in similar correlation with histology ( ${r}_{s} =0.83$ ) but higher than attenuation ( ${r}_{s} =0.73$ ) and B-mode ( ${r}_{s} =0.47$ ). Therefore, we conclude that DSI utilizing the SVM applied to steatosis can visually represent the classification results with color highlighting, which can simplify the interpretation of classification compared to the traditional SVM result. We expect that the proposed DSI can be used for any medical imaging modality that can estimate multiple quantitative parameters at high resolution.
A low-power, radiation-hard gigabit serializer for use in the CMS electromagnetic calorimeter

An integrated fiber-optic bit serializer and VCSEL driver has been constructed in radiation-hard complementary heterostructure GaAs FET (CHFET) technology. The serializer, which converts 20 parallel inputs into a high-speed serial output, consumes 60 mW at nominal supply voltage when operating at the Large Hadron Collider word rate of 40 MHz (0.8-GB/s serial rate). The integrated driver directly drives a VCSEL and provides 10-mA switched current and 5 mA of prebias. The complete digital optical link thus consumes 90 mW.
Improving Computational Efficiency of Bat-Inspired Algorithm in Optimal Structural Design

Bat-inspired (BI) algorithm is a recent metaheuristic optimization technique that simulates echolocation behavior of bats in seeking a design space. Along the same line with almost all metaheuristics, this algorithm also entails a large number of time-consuming structural analyses in structural design optimization applications. This study is focused on improving computational efficiency of the BI algorithm in optimum structural design. The number of structural analyses required by BI algorithm in the course of design optimization is reduced considerably by incorporating an upper bound strategy (UBS) into the solution procedure. The performance of the resulting algorithm, i.e. UBS integrated BI algorithm (UBI), is evaluated in discrete sizing optimization of large-scale steel skeletal structures designed for minimum weight according to American Institute of Steel Construction-Allowable Stress Design provisions. The numerical results verify that the UBI results in a significant gain in the computational efficiency of the standard algorithm.
Speech-in-Noise Audiometry in Adults: A Review of the Available Tests for French Speakers

Background: Difficulty understanding speech in background noise is the reason of consultation for most people who seek help for their hearing. With the increased use of speech-in-noise (SpIN) testing, audiologists and otologists are expected to evidence disabilities in a greater number of patients with sensorineural hearing loss. The purpose of this study is to list validated available SpIN tests for the French-speaking population. Summary: A review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. PubMed and Scopus databases were searched. Search strategies used a combination of 4 keywords: speech, audiometry, noise, and French. There were 10 validated SpIN tests dedicated to the Francophone adult population at the time of the review. Some tests use digits triplets as speech stimuli and were originally designed for hearing screening. The others were given a broader range of indications covering diagnostic or research purposes, determination of functional capacities and fitness for duty, as well as assessment of hearing amplification benefit. Key Messages: As there is a SpIN test for almost any type of clinical or rehabilitation needs, both the accuracy and duration should be considered for choosing one or the other. In an effort to meet the needs of a rapidly aging population, fast adaptive procedures can be favored to screen large groups in order to limit the risk of ignoring the early signs of forthcoming presbycusis and to provide appropriate audiological counseling.
Balance rehabilitation for postural control in children with Autism Spectrum Disorder: A two-case report study

ABSTRACT Objective:This study aimed to investigate the effect of balance rehabilitation on postural control in both low and increased cognitive load conditions in two children with Autism Spectrum Disorders (ASD). Methods: Two children diagnosed with ASD participated in a 4-week personalized balance rehabilitation program with two sessions per week. We assessed postural control in two single task (ST) conditions with low cognitive load: Eyes Closed (EC), Eyes Open (EO); and in five increased cognitive load conditions. Those dual task (DT) conditions consisted of presenting images representing a neutral condition, sadness, anger, happiness, and fear. Postural control parameters (surface, velocity, medio-lateral and antero-posterior sway amplitudes of the center of pressure (CoP)) were collected by a posturographic platform before and after the balance rehabilitation. Results: The rehabilitation program resulted in a 30–96% improvement of postural control parameters in the ST condition for both participants. In DT, participant 1 progressed on all conditions while participant 2 progressed on 3 of the 5 conditions (sadness, anger and fear). Conclusion: This suggests that these two children with ASD improved their balance control in both low and increased cognitive load conditions. These encouraging results need to be replicated before recommending balance rehabilitation as standard health rehabilitation in children with ASD.
Peer-Delivery of a Gender-Specific Smoking Cessation Intervention for Women Living in Disadvantaged Communities in Ireland We Can Quit2 (WCQ2)—A Pilot Cluster Randomized Controlled Trial

Abstract Introduction We Can Quit” (WCQ) is community-based stop-smoking program delivered by trained community facilitators, based on the socio-ecological framework and developed using a Community-based Participatory Research approach, targeting women living in socioeconomically disadvantaged (SED) areas of Ireland. Aims and Methods The We Can Quit2 (WCQ2) pilot trial assessed the feasibility of WCQ. A pragmatic cluster randomized controlled trial with a process evaluation WCQ2, was conducted in four matched pairs of SED districts (8–10 000 women per district). Districts were independently randomized to WCQ (group support + nicotine replacement therapy), or to individual support delivered by health professionals. Participants were adult women smokers interested in quitting, who were living or working in trial districts. Recruitment of districts and 194 women in four waves (49 women per wave); retention at 12 weeks and 6 months; fidelity to intervention delivery and acceptability of trial-related processes were assessed. Validated smoking abstinence at 12-week and 6-month post-intervention was recorded, missing data assumed as continued smoking. Results Eight districts were recruited. 125/188 (66.5%) eligible women consented. The 49 women target was reached in wave4. Retention at 12 weeks was (Intervention [I]: 55.4%; Control [C]: 51.7%), at 6 months (I: 47.7%; C: 46.7%). Smoking abstinence at 12 weeks was (I: 23.1%, [95% CI: 14.5 to 34.7]; C: 13%, [95% CI: 6.9 to 24.1]). 83.8% of session activities were delivered. Trial-related processes were acceptable to facilitators. Low literacy was highlighted as a barrier for participants’ acceptability. Conclusions WCQ was feasible to deliver by trained facilitators and indicated a positive direction in abstinence rates. Low literacy will need to be addressed in a future trial design. Implications This pilot trial showed that a stop-smoking intervention tailored to a group of women smokers living in SED areas which was delivered by trained local women within their local communities was feasible. Furthermore, although not formally compared, more WCQ women were abstinent from smoking at the end of treatment. The results are relevant to enhance the design of a fully powered effectiveness trial, and provide important evidence on the barriers to deliver a tailored smoking cessation service to SED women smokers in Ireland.
Contaminants of Emerging Concern in the Lower Volta River, Ghana, West Africa: The Agriculture, Aquaculture, and Urban Development Nexus

Contaminants of emerging concern (CECs) are ubiquitous in aquatic environments across all continents and are relatively well known in the developed world. However, few studies have investigated their presence and biological effects in low‐ and middle‐income countries. We provide a survey of CEC presence in the Volta River, Ghana, and examine the microbial consequences of anthropogenic activities along this economically and ecologically important African river. Water and sediment samples were taken by boat or from shore at 14 sites spanning 118 km of river course from the Volta estuary to the Akosombo dam. Sample extracts were prepared for targeted analysis of antimicrobial CECs, N,N‐diethyl‐meta‐toluamide, and per‐ and polyfluoroalkyl substances (PFAS; water only). Concurrent samples were extracted to characterize the microbial community and antibiotic‐resistant genes (ARGs). Antibiotics and PFAS (PFAS, 2–20 ng/L) were found in all water samples; however, their concentrations were usually in the low nanograms per liter range and lower than reported for other African, European, and North American studies. N,N‐Diethyl‐meta‐toluamide was present in all samples. The number of different genes detected (between one and 10) and total ARG concentrations varied in both water (9.1 × 10−6 to 8.2 × 10−3) and sediment (2.2 × 10−4 to 5.3 × 10−2), with increases in gene variety at sites linked to urban development, sand mining, agriculture, and shellfish processing. Total ARG concentration spikes in sediment samples were associated with agriculture. No correlations between water quality parameters, CEC presence, and/or ARGs were noted. The presence of CECs in the lower Volta River highlights their global reach. The overall low concentrations of CECs detected is encouraging and, coupled with mitigation measures, can stymie future CEC pollution in the Volta River. Environ Toxicol Chem 2022;41:369–381. © 2021 SETAC
Unique Physiological and Genetic Features of Ofloxacin-Resistant Streptomyces Mutants

The abuse or overuse of antibacterial agents for therapy and animal husbandry has caused an increased population of antimicrobial-resistant bacteria in the environment. Consequently, fewer effective antimicrobials are now available. ABSTRACT New antimicrobial agents are urgently needed to combat the emergence and spread of multidrug-resistant bacteria. Activating the cryptic biosynthetic gene clusters for actinomycete secondary metabolites can provide essential clues for research into new antimicrobial agents. An effective method for this purpose is based on drug resistance selection. This report describes interesting results for drug resistance selection using antibiotics that target DNA replication and can effectively potentiate secondary metabolite production by actinomycetes. Ofloxacin-resistant mutants were isolated from five different streptomycetes. Ofloxacin is an antibiotic that binds to DNA complexes and type II topoisomerase, causing double-stranded breaks in bacterial chromosomes. Physiological and genetic characterization of the mutants revealed that the development of ofloxacin resistance in streptomycetes leads to the emergence of various types of secondary metabolite-overproducing strains. In Streptomyces coelicolor A3(2), ofloxacin-resistant mutants that overproduced actinorhodin, undecylprodigiosin, or carotenoid were identified. An ofloxacin-resistant mutant that overproduces methylenomycin A, whose biosynthetic gene cluster is located on the endogenous plasmid, SCP1, also was isolated. These observations indicate that ofloxacin resistance activates biosynthetic genes on both chromosomes and endogenous plasmids. We also identified the mutations that are probably involved in the phenotype of ofloxacin resistance and secondary metabolite overproduction in S. coelicolor A3(2). Furthermore, we observed an interesting phenomenon in which several ofloxacin-resistant mutants overproduced antibiotics in the presence of ofloxacin. Based on these results, we present the unique physiological and genetic characteristics of ofloxacin-resistant Streptomyces mutants and discuss the importance and potential development of the new findings. IMPORTANCE The abuse or overuse of antibacterial agents for therapy and animal husbandry has caused an increased population of antimicrobial-resistant bacteria in the environment. Consequently, fewer effective antimicrobials are now available. Due to the depleted antibiotic pipeline, pandemic outbreaks caused by antimicrobial-resistant bacteria are deeply concerning, and the development of new antibiotics is now an urgent issue. Promising sources of antimicrobial agents include cryptic biosynthetic gene clusters for secondary metabolites in streptomycetes and rare actinomycetes. This study’s significance is the development of an unprecedented activation method to accelerate drug discovery research on a global scale. The technique developed in this study could allow for simultaneous drug discovery in different countries, maximizing the world’s microbial resources.
A Fast and Accurate Approach to Multiple-Vehicle Localization and Tracking from Monocular Aerial Images

In this work we present a novel end-to-end solution for tracking objects (i.e., vessels), using video streams from aerial drones, in dynamic maritime environments. Our method relies on deep features, which are learned using realistic simulation data, for robust object detection, segmentation and tracking. Furthermore, we propose the use of rotated bounding-box representations, which are computed by taking advantage of pixel-level object segmentation, for improved tracking accuracy, by reducing erroneous data associations during tracking, when combined with the appearance-based features. A thorough set of experiments and results obtained in a realistic shipyard simulation environment, demonstrate that our method can accurately, and fast detect and track dynamic objects seen from a top-view.
Multilevel metallization for large area point-contact solar cells

An analysis of the series resistances of different metallization schemes for large-area backside-contact (BC) solar cells is presented. The need for developing a multilevel metallization technology for such cells is demonstrated. The authors propose a new design for the metallization of BC cells that present a series resistance independent of the cell size. The particular features required for such a multilevel interconnection are studied, and a process using anodic oxidation of aluminum is presented. BC silicon solar cells of 0.64 cm/sup 2/ have been processed in this technology, resulting in 26.2% efficiencies at 10 W/cm/sup 2/ (100 suns AM1.5, 25.5 degrees C). Subsequent runs with a simplified process and a new cell design have given 27.3% efficiency cells. The cells have been soldered on alumina mounts. Results of thermal cycling are given. <<ETX>>
Research on point cloud wires detection method for helicopter avoidance

Helicopters are widely used due to their excellent low-altitude flight characteristics and convenient take-off and landing advantages. However, the densely distributed wires in the low-altitude environment have always been a huge threat to helicopters, and they are known as aerial "trips". Because of its ability to detect small obstacles in three dimensions, lidar has gradually become an important sensor to solve the problem of helicopter low-altitude line collision. This article first introduces the current lidar point cloud wire detection method, and then proposes a new point cloud wire detection method that can be used for helicopter obstacle avoidance. This method uses rough extraction, clustering, identification and fitting display steps. The symbolic prompts for wires and dangerous obstacles are realized. Experiments show that this method has high real-time characteristics on the basis of ensuring effective detection, and is suitable for wire detection in helicopter obstacle avoidance scenarios.
Decentralized neural-network sliding-mode robot controller

This paper develops a method for decentralized adaptive neural network control design with continuous sliding modes in which robustness is inherent. Neural network control is formulated to become a class of variable structure system control. Sliding modes are used to determine the best values for parameters in neural network learning rules; thereby, robustness in learning control can be improved. Derived equations of the decentralized neural network sliding-mode controller (DNNSMC) were verified on a real direct-drive 3-DOF PUMA mechanism. The new DNNSMC was successfully tested for adaptation capability of the algorithm for sudden changes in the manipulator dynamics (load).