Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites

Abstract Genome-wide association studies have discovered a large number of genetic variants in human patients with the disease. Thus, predicting the impact of these variants is important for sorting disease-associated variants (DVs) from neutral variants. Current methods to predict the mutational impacts depend on evolutionary conservation at the mutation site, which is determined using homologous sequences and based on the assumption that variants at well-conserved sites have high impacts. However, many DVs at less-conserved but functionally important sites cannot be predicted by the current methods. Here, we present a method to find DVs at less-conserved sites by predicting the mutational impacts using evolutionary coupling analysis. Functionally important and evolutionarily coupled sites often have compensatory variants on cooperative sites to avoid loss of function. We found that our method identified known intolerant variants in a diverse group of proteins. Furthermore, at less-conserved sites, we identified DVs that were not identified using conservation-based methods. These newly identified DVs were frequently found at protein interaction interfaces, where species-specific mutations often alter interaction specificity. This work presents a means to identify less-conserved DVs and provides insight into the relationship between evolutionarily coupled sites and human DVs.
Multi-component Decomposition of Cosmic Infrared Background Fluctuations

The near-infrared background between 0.5 and 2 μm contains a wealth of information related to radiative processes in the universe. Infrared background anisotropies encode the redshift-weighted total emission over cosmic history, including any spatially diffuse and extended contributions. The anisotropy power spectrum is dominated by undetected galaxies at small angular scales and a diffuse background of Galactic emission at large angular scales. In addition to these known sources, the infrared background also arises from intrahalo light (IHL) at z < 3 associated with tidally stripped stars during galaxy mergers. Moreover, it contains information on the very first galaxies from the epoch of reionization (EoR). The EoR signal has a spectral energy distribution (SED) that goes to zero near optical wavelengths due to Lyman absorption, while other signals have spectra that vary smoothly with frequency. Due to differences in SEDs and spatial clustering, these components may be separated in a multi-wavelength-fluctuation experiment. To study the extent to which EoR fluctuations can be separated in the presence of IHL, and extragalactic and Galactic foregrounds, we develop a maximum likelihood technique that incorporates a full covariance matrix among all the frequencies at different angular scales. We apply this technique to simulated deep imaging data over a 2 × 45 deg2 sky area from 0.75 to 5 μm in 9 bands and find that such a “frequency tomography” can successfully reconstruct both the amplitude and spectral shape for representative EoR, IHL, and the foreground signals.
The Impact of Institutional Characteristics on Latino Male Graduation Rates in Community Colleges

This study examined the impact of select institutional characteristics (e.g., attendance intensity, degree of urbanization, institutional size, governance type) on Latino male graduation rates in public, two-year institutions. Data were collected from the Integrated Postsecondary Education Data System (IPEDS) and included the 2008 completion rates of degree/certificate-seeking Hispanic male students from 254 public two-year, degreegranting institutions. Findings from this study revealed that select institutional characteristics do in fact result in differential graduation rates for these students. Specifically, findings indicated that Latino males are more likely to achieve at institutions with higher full-time enrollment and at suburban colleges. Implications for practice and further research are extended.
Investigation of moisture sorption behavior of soluble sodium caseinate

Casein is a potential food protein, used in a number of food applications. In this work, moisture sorption isotherms of casein were determined at 10, 20 and 30 o C under different relative humidity in the range of 12 to 98 percent using gravimetric method. The equilibrium moisture uptake data were interpreted with the help of three well-known sorption isotherm models namely, (GAB, Halsey and Oswin models) using non-linear least square method. The experimental moisture uptake data were best interpreted by GAB model. The monolayer moisture content X m was found to vary from 54.08 x 10 -3 to 10.48 x10 -3 kg kg -1 (db) for a temperature rise from 10 to 30 o C, thus indicating negative temperature dependence. The Clausius-Clapeyron equation was used to determine the isosteric heat of sorption (q st ). The uptake data was also used to determine isokinetic temperature T β (315.9 K) and harmonic mean temperature T hm (292.8 K). The enthalpy-entropy compensation theory indicated that moisture sorption process was enthalpy driven.
Environmental analysis of present and future fuels in 2D simple model marine gas tubines

Increased worldwide concerns about fossil fuel costs and effects on the environment lead many governments and scientific societies to consider the hydrogen as the fuel of the future. Many researches have been made to assess the suitability of using the hydrogen gas as fuel for internal combustion engines and gas turbines; this suitability was assessed from several viewpoints including the combustion characteristics, the fuel production and storage and also the thermodynamic cycle changes with the application of hydrogen instead of ordinary fossil fuels. This paper introduces the basic environmental differences happening when changing the fuel of a marine gas turbine from marine diesel fuel to gaseous hydrogen for the same power output. Environmentally, the hydrogen is the best when the CO2 emissions are considered, zero carbon dioxide emissions can be theoretically attained. But when the NOx emissions are considered, the hydrogen is not the best based on the unit heat input. The hydrogen produces 270% more NOx than the diesel case without any control measures. This is primarily due to the increased air flow rate bringing more nitrogen into the combustion chamber and the increased combustion temperature (10% more than the diesel case). Efficient and of course expensive NOx control measures are a must to control these emissions levels.
A Modular Percussion Synthesis Environment

The construction of new virtual instruments is one long-ter m goal of physical modeling synthesis; a common strategy across va rious different physical modeling methodologies, including lum ped network models, modal synthesis and scattering based methods, is to provide a canonical set of basic elements, and allow the user to build an instrument via certain specified connection rules. Such an environment may be described as modular. Percussion instruments form a good test-bed for the development of modular synthesis techniques—the basic componen ts are bars and plates, and may be accompanied by connection elements, with a nonlinear character. Modular synthesis has b een approached using all of the techniques mentioned above, but time domain finite difference schemes are an alternative, allowi ng many problems inherent in the above methods, including computab ility, large memory and precomputation requirements, and lack of e xtensibility to more complex systems, to be circumvented. One such network model is presented here along with the associated difference schemes, followed by a discussion of impl e entation details, the issues of excitation and output, and a de scription of various instrument configurations. The article conclude s with a presentation of simulation results, generated in the Matla b prototyping language.
The Distribution of Firm Size and Aggregate Investment

We investigate empirically how the distributional dynamics of firm investment rates and firm size affect aggregate US investment during the period 1962-2006. We find that the cross-sectional covariation between firms’ investment rates and their relative size accounts on average for about half of aggregate investment rate. The negative sign of this covariance implies that a mean-preserving increase in the cross-sectional dispersion of investment rates and/or relative size reduces aggregate investment rate. We investigate the implications of firm-level conditional convergence in corporate investment rates on the dynamics of aggregate investment. We identify the cross-sectional variance of firm relative size as being particularly relevant to explain aggregate investment dynamics. With aggregate NIPA investment data, the cross-sectional variance of firm size fits the investment equation better than the traditional measure of Tobin’s Q and it drives out cash flow.
Floristic diversity and vegetation analysis of Wadi Al-Noman, Mecca, Saudi Arabia

Wadi Al-Noman in Mecca is one of the most important wadis. It was included among the most important water sources where the springs and wells of Zobida run and it provides drinking water for the holy places in Mecca and visitors to the Kaaba and Arafat regions. The present study provides an analysis of floristic composition, vegetation types, and structure and species distribution at 20 sites, emphasising the environmental factors that affect species distribution. A total of 126 species representing 39 families of vascular plants are recorded. Fabaceae, Poaceae, and Boraginaceae are the largest families, and therophytes and chamaephytes are the most frequent, indicating a typical desert life-form spectrum. The floristic composition of the different geomorphologic landscape units shows differences in species richness. The highest species richness value (23 species stand1) is recorded in the wadi bed. The lowest species richness value (18 species stand1) is recorded in the wadi plateau and fissures. Chorological analysis revealed that 52% of the studied species are bioregional, native to the Saharo-ArabianSudano-Zambezian region. After application of the TWINSPAN, DCA, and CCA programs 4 vegetation groups were identified, and they were named after the characteristic species as follows: (I) Aristolochia bracteolata-Cucumis prophetarum; (II) Calotropis procera-Acacia hamulosa-Caralluma russeliana; (III) Acacia abyssinica-Acacia hamulosa-Tephrosia desertorum; and (IV) Argemone ochroleuca-Senna italica. The associations and speciation of these Wadi Al-Noman plants demonstrate significant variation in pH, electrical conductivity, soil mineral contents, and human impact.
Determination of Some Quality Criteria of Cold Storaged Marinated Anchovy under Vacuum and Modified Atmosphere Conditions

This study was performed to determine the effects of vacuum packaging (VP) and modified-atmosphere packaging (MAP) by different gas mixtures (70% CO2 / 30% N2 = M1, 50% CO2 / 50% N2 = M2) on the potential quality index, shelflife and histamine formation in marinated anchovies during the storage at 2±2°C. Results showed that thiobarbituric acid (TBA) values marinated anchovies under M1 and M2 exceeded the limit given by Turkish Food Codex and the sensoric qualities were reduced from “first quality” to “not consumed” on month 11 of storage at 2±2°C as compared to vacuum packaging (7 th month). The levels of TVB-N, histamine and microbial load in the samples from both of the packaging methods were under the limits given in Turkish Food Codex. It was concluded that TBA values depending on the level of fatty oxidation and sensory evaluation determined the shelf life of marinated anchovies under vacuum and MAP conditions during storage at 2±2°C. Marinated anchovies under MAP conditions were edible until the 11 th month of storage. The shelflifes of marinated anchovies could be extended 4 months by MAP, as compared to vacuum packaging (7 th month), and the two different gas mixture (M1 and M2) in MAP had same effect on taking to this shelf lifes.
A Seven-Month Practicum: Collaborating Teachers' Response.

In this study, we interviewed collaborating teachers who had participated in our field experience program to examine collaborating teachersi perceptions of a long-term, onsite teacher-education program and to define their role as teacher educators. Collaborating teachers stated that this long-term, preservice field experience effectively socialised teacher candidates into the teaching profession, both in the classroom and the school. They describe the strategies they used to scaffold teacher candidates into teaching. Successful scaffolding techniques are situated within the context of an extended field experience.
Paths to Scaling-up through Replication: An Educational Perspective

Replication is found to be an essential approach to consider when scaling-up. This dissertation argues that while there is no one universally applicable path through which to achieve success, more can be done to support educational non-government organisations in choosing the best path to follow. This path is found to depend on the specific, individual circumstances and the context within which it operates. With the aid of diagrams, four known paths to replication are dissected to explore their advantages and disadvantages in the light of current development thinking. A definition and an exemplar for each are also provided. As a result of this discussion the importance of introducing a new path is highlighted, and the term ‘Network replication’ is coined. A further outcome is the notion of a Portfolio of replicable concepts which is introduced alongside arguments for its potential application for the wider development sector. The Portfolio criteria are then applied to one specific initiative, which is then used to illustrate how an organisation might choose which path is most likely to bring them scaling-up success. By introducing these new themes to the scaling-up debate, this dissertation brings the discourse forward and indicates a number of avenues for future research.
ACF Based Region Proposal Extraction for YOLOv3 Network Towards High-Performance Cyclist Detection in High Resolution Images

You Only Look Once (YOLO) deep network can detect objects quickly with high precision and has been successfully applied in many detection problems. The main shortcoming of YOLO network is that YOLO network usually cannot achieve high precision when dealing with small-size object detection in high resolution images. To overcome this problem, we propose an effective region proposal extraction method for YOLO network to constitute an entire detection structure named ACF-PR-YOLO, and take the cyclist detection problem to show our methods. Instead of directly using the generated region proposals for classification or regression like most region proposal methods do, we generate large-size potential regions containing objects for the following deep network. The proposed ACF-PR-YOLO structure includes three main parts. Firstly, a region proposal extraction method based on aggregated channel feature (ACF) is proposed, called ACF based region proposal (ACF-PR) method. In ACF-PR, ACF is firstly utilized to fast extract candidates and then a bounding boxes merging and extending method is designed to merge the bounding boxes into correct region proposals for the following YOLO net. Secondly, we design suitable YOLO net for fine detection in the region proposals generated by ACF-PR. Lastly, we design a post-processing step, in which the results of YOLO net are mapped into the original image outputting the detection and localization results. Experiments performed on the Tsinghua-Daimler Cyclist Benchmark with high resolution images and complex scenes show that the proposed method outperforms the other tested representative detection methods in average precision, and that it outperforms YOLOv3 by 13.69% average precision and outperforms SSD by 25.27% average precision.
Screening and treatment of trauma-related symptoms in youth with autism spectrum disorder among community providers in the United States

Using a cross-sectional survey of 673 multidisciplinary autism spectrum disorder providers recruited from five different sites in the United States, we examined the frequency with which community-based providers inquire about, screen, and treat trauma-related symptoms in their patients/students and assessed their perceptions regarding the need for and barriers to providing these services. Univariate and bivariate frequencies of self-reported trauma service provision, training needs, and barriers were estimated. Multivariable logistic regressions identified provider and patient-related factors associated with trauma-related symptoms screening and treatment. Over 50% of providers reported some screening and treatment of trauma-related symptoms in youth with autism spectrum disorder. Over 70% informally inquired about trauma-related symptoms; only 10% universally screened. Screening and treatment varied by provider discipline, setting, amount of interaction, and years of experience with autism spectrum disorder, as well as by patient/student sex, ethnicity, and socioeconomic status. Most providers agreed that trauma screening is a needed service impeded by inadequate provider training in trauma identification and treatment. The findings indicate that community providers in the United States of varied disciplines are assessing and treating trauma-related symptoms in youth with autism spectrum disorder, and that evidence-based approaches are needed to inform and maximize these efforts.
Commentary on Lifestyle Interventions Are Feasible in Patients with Colorectal Cancer with Potential Short-Term Health Benefits

Purpose Lifestyle interventions have been proposed to improve cancer survivorship in patients with colorectal cancer (CRC), but with treatment pathways becoming increasingly multi-modal and prolonged, opportunities for interventions may be limited. This systematic review assessed the evidence for the feasibility of performing lifestyle interventions in CRC patients and evaluated any short- and long-term health benefits. Methods Using PRISMA Guidelines, selected keywords identified randomised controlled studies (RCTs) of lifestyle interventions [smoking, alcohol, physical activity (PA) and diet/excess body weight] in CRC patients. These electronic databases were searched in June 2015: Dynamed, Cochrane Database, OVID MEDLINE, OVID EMBASE, and PEDro. Results Fourteen RCTs were identified: PA RCTs ( n = 10) consisted mainly of telephone-prompted walking or cycling interventions of varied durations, predominately in adjuvant setting; dietary/excess weight interventions RCTs ( n = 4) focused on low-fat and/or high-fibre diets within a multimodal lifestyle intervention. There were no reported RCTs in smoking or alcohol cessation/reduction. PA and/or die-tary/excess weight interventions reported variable recruitment rates, but good adherence and retention/follow-up rates, leading to short-term improvements in dietary quality, physical, psychological and quality-of-life parameters. Only one study assessed long-term follow-up, finding significantly improved cancer-specific survival after dietary intervention. Conclusions This is the first systematic review on lifestyle interventions in patients with CRC finding these interventions to be feasible with improvements in short-term health. Future work should focus on defining the optimal type of intervention (type, duration, timing and intensity) that not only leads to improved short-term outcomes but also assesses long-term survival. randomised factors, overall
Assessment of the life experiences of visually impaired adults in the Empangeni region of Kwazulu

The purpose of the study was to assess how visual impairment influenced the experiences of daily living of blind adults in a rural community in KwaZulu, Information was elicited through semi-structured interviews with 16 people (eight men and eight women) between the ages of 21 and 55 years who had been visually impaired from one to more than 20 years. Such visual impairment ranged from inability to perform some of the activities that require the use of eyesight to inability to see at all.
PTPN3 acts as a tumor suppressor and boosts TGF‐β signaling independent of its phosphatase activity

TGF‐β controls a variety of cellular functions during development. Abnormal TGF‐β responses are commonly found in human diseases such as cancer, suggesting that TGF‐β signaling must be tightly regulated. Here, we report that protein tyrosine phosphatase non‐receptor 3 (PTPN3) profoundly potentiates TGF‐β signaling independent of its phosphatase activity. PTPN3 stabilizes TGF‐β type I receptor (TβRI) through attenuating the interaction between Smurf2 and TβRI. Consequently, PTPN3 facilitates TGF‐β‐induced R‐Smad phosphorylation, transcriptional responses, and subsequent physiological responses. Importantly, the leucine‐to‐arginine substitution at amino acid residue 232 (L232R) of PTPN3, a frequent mutation found in intrahepatic cholangiocarcinoma (ICC), disables its role in enhancing TGF‐β signaling and abolishes its tumor‐suppressive function. Our findings have revealed a vital role of PTPN3 in regulating TGF‐β signaling during normal physiology and pathogenesis.
Accelerating Recovery from Exercise-Induced Muscle Injuries in Triathletes: Considerations for Olympic Distance Races

The triathlon is one of the fastest developing sports in the world due to expanding participation and media attention. The fundamental change in Olympic triathlon races from a single to a multistart event is highly demanding in terms of recovery from and prevention of exercise-induced muscle injures. In elite and competitive sports, ultrastructural muscle injuries, including delayed onset muscle soreness (DOMS), are responsible for impaired muscle performance capacities. Prevention and treatment of these conditions have become key in regaining muscular performance levels and to guarantee performance and economy of motion in swimming, cycling and running. The aim of this review is to provide an overview of the current findings on the pathophysiology, as well as treatment and prevention of, these conditions in compliance with clinical implications for elite triathletes. In the context of DOMS, the majority of recovery interventions have focused on different protocols of compression, cold or heat therapy, active regeneration, nutritional interventions, or sleep. The authors agree that there is a compelling need for further studies, including high-quality randomized trials, to completely evaluate the effectiveness of existing therapeutic approaches, particularly in triathletes. The given recommendations must be updated and adjusted, as further evidence emerges.