Miracle-dz/UniFAR-FTUs huggingface dataset:
TADOSS: computational estimation of tandem domain swap stability

Abstract Summary Proteins with highly similar tandem domains have shown an increased propensity for misfolding and aggregation. Several molecular explanations have been put forward, such as swapping of adjacent domains, but there is a lack of computational tools to systematically analyze them. We present the TAndem DOmain Swap Stability predictor (TADOSS), a method to computationally estimate the stability of tandem domain-swapped conformations from the structures of single domains, based on previous coarse-grained simulation studies. The tool is able to discriminate domains susceptible to domain swapping and to identify structural regions with high propensity to form hinge loops. TADOSS is a scalable method and suitable for large scale analyses. Availability and implementation Source code and documentation are freely available under an MIT license on GitHub at https://github.com/lafita/tadoss. Supplementary information Supplementary data are available at Bioinformatics online.
Finding the Right Way to Target EGFR in Glioblastomas; Lessons from Lung Adenocarcinomas

The EGFR gene is one of the most frequently mutated and/or amplified gene both in lung adenocarcinomas (LUAD) and in glioblastomas (GBMs). Although both tumor types depend on the mutation for growth, clinical benefit of EGFR tyrosine kinase inhibitors (TKIs) has only been observed in LUAD patients and, thus-far, not in GBM patients. Also in LUAD patients however, responses are restricted to specific EGFR mutations only and these ‘TKI-sensitive’ mutations hardly occur in GBMs. This argues for mutation-specific (as opposed to tumor-type specific) responses to EGFR-TKIs. We here discuss potential reasons for the differences in mutation spectrum and highlight recent evidence for specific functions of different EGFR mutations. These mutation-specific effects likely underlie the differential treatment response between LUAD and GBMs and provide new insights into how to target EGFR in GBM patients.
Loneliness and social isolation of military veterans: systematic narrative review.

Background Loneliness and social isolation are being increasingly recognized as influencing both physical and mental health. There is limited research carried out with military veterans and, to date, there is no review of existing evidence. Aims To synthesize and examine the evidence exploring aspects of social isolation and loneliness of military veterans, using a systematic narrative review strategy. Methods A database search was carried out utilizing relevant search criterion. Seven databases were searched for publications with no date restrictions. Articles were included if they involved veterans and either social isolation or loneliness. The initial search returned 484 papers, after exclusions, removal of duplications, and a reference/citation search, 17 papers remained and were included in this review. Results The retrieved papers examined four areas of loneliness and social isolation: prevalence of loneliness in the veteran population, experiences related to military service as impacting loneliness or social isolation, the relationship between mental health and loneliness or social isolation, and interventions to combat loneliness and social isolation. Differences between the experiences of younger and older veterans were also highlighted. Conclusions It is evident that military veterans present unique experiences of loneliness and social isolation, especially older veterans. This requires specific attention outside of campaigns targeted at the non-military population.
Epidemiology of lower respiratory tract infections in adults

ABSTRACT Introduction: Lower respiratory tract infections (LRTIs) are the leading infectious disease cause of death in the world and the fifth overall cause of death. From an epidemiological point of view, most consider pneumonia, influenza, bronchitis (including acute exacerbations in chronic obstructive pulmonary disease [AECOPD]), and bronchiolitis to be the most important LRTIs. Areas covered: This review will describe the epidemiology of LRTIs in adults focusing on community-acquired pneumonia, influenza, and AECOPD, utilizing data from the more recent literature. Expert commentary: LRTIs remain exceedingly common, although there have been significant changes in their epidemiology over recent years, both with regard to their frequency and the infecting pathogens. Part of the change in the epidemiology may relate to changing population demographics, the varying prevalence of smoking, and the introduction of the pneumococcal conjugate vaccine in children and patterns of vaccine usage. Furthermore, antigenic variations in the influenza viruses dictate the frequency and characteristics of the influenza epidemics and pandemics.
VC Syndication in the DACH Region: A Strategic Mean to Ensure Firm Survival.

This study proposes a new perspective to explain what drives venture capital (VC) firms located in the in the German-speaking countries of the EU, the so-called DACH region, to engage in syndication behaviour. By taking a context-sensitive approach, it postulates that these VC firms are driven to engage in syndication behaviour by the need to ensure future firm survival. Drawing upon resource dependence- , as well as signalling theory, a conceptual framework is developed to explain this reasoning, suggesting that in environments characterized by risk averse and inexperienced investors in respect to venture capital, VC firms face increased difficulties to collect sufficient capital for future firm existence. Especially those firms exhibiting unfavourable firm characteristics, alienating hesitant investors even more, face an accelerated risk of business failure. This study investigates which VC firm characteristics serve to explain that the syndication behaviour of VC firms in the DACH region is indeed need-driven. It proposes that a VC firm’s early stage- and dispersed industry focus, low access to financial resources, small HR capacity, as well as the opportunity to establish informal ties significantly influence a VC firm’s propensity to syndicate. Applying multiple linear regression, findings shows that a VC firm’s early stage- and dispersed industry focus, as well as its access to financial resources indeed have a positive influence, whereas its human resources capacity as well as alternative opportunities to establish ties have a negative influence on its decision to syndicate.
Contrasts between the cryoconite and ice-marginal bacterial communities of Svalbard glaciers

Cryoconite holes are foci of unusually high microbial diversity and activity on glacier surfaces worldwide, comprising melt-holes formed by the darkening of ice by biogenic granular debris. Despite recent studies linking cryoconite microbial community structure to the functionality of cryoconite habitats, little is known of the processes shaping the cryoconite bacterial community. In particular, the assertions that the community is strongly influenced by aeolian transfer of biota from ice-marginal habitats and the potential for cryoconite microbes to inoculate proglacial habitats are poorly quantified despite their longevity in the literature. Therefore, the bacterial community structures of cryoconite holes on three High-Arctic glaciers were compared to bacterial communities in adjacent moraines and tundra using terminal-restriction fragment length polymorphism. Distinct community structures for cryoconite and ice-marginal communities were observed. Only a minority of phylotypes are present in both habitat types, implying that cryoconite habitats comprise distinctive niches for bacterial taxa when compared to ice-marginal habitats. Curiously, phylotype abundance distributions for both cryoconite and ice-marginal sites best fit models relating to succession. Our analyses demonstrate clearly that cryoconites have their own, distinct functional microbial communities despite significant inputs of cells from other habitats.
Salt tolerance classification in wheat genotypes using reducing sugar accumulation and growth characteristics

The aim of the present study was to assess inter and intra-specific variations in Triticum groups. Local hexaploid bread wheat and Synthetic Elites and Durum where characterized based on growth abilities and amount of reducing sugar accumulated under 200 mM NaCl salinity. Further, the role of reducing sugar accumulation in adaptive process of different Triticum groups towards salinity was also measured. Identification of inter-specific and intra-specific variation with in the gene pool is of greater importance for breeding salt tolerant varieties. Salt tolerant genotypes tend to accumulate more carbohydrates under salt stress and prevent plants from oxidative damage. Wide differences observed between Triticum groups under salt stress for shoot length, shoot weight and reducing sugar content. Salt stress reduced shoot length and weight in both Local hexaploids and Synthetic elites but effect was more pronounced in Local hexaploid wheat. Kharchia and LU-26 were identified as salt tolerant standard genotypes which showed significant increase in reducing sugar content where as salt stress induced reduction in amount of reducing sugars of local hexaploid genotypes. Performance of salinity tester genotypes and synthetic elite and durum genotypes was less affected by salinity and prominent increase in reducing sugar content has been observed in comparison to local hexaploid genotypes. High values for salt tolerance indices were also observed for salinity tester set and synthetic elite and durum wheat genotypes. It may be concluded from the above findings that wheat genotypes like Kharchia, LU-26, Durum 155 and SE 88 with highest accumulation of reducing sugar content under stress could be used in breeding programs to develop salt tolerant germplasm and accumulation of reducing sugars under stress conditions could be a useful bio-marker for selecting tolerant wheat genotypes.
RELATIONSHIP BETWEEN INTELLECTUAL CAPITAL AND PERFORMANCE OF MICRO FINANCE INSTITUTIONS IN KENYA

Microfinance Institutions (MFIs) in kenya represent a vital part of the economy, being the source of various economic contributions through the generation of income via providing new job opportunities, introducing innovations, stimulating competition, and engine for employment, Intellectual capital appears as the most important and vital component of a knowledge-based eeconomy. Present economy is known as a knowledge-based economy where, knowledge, information and soft assets have more importance rather than the physical assets. The role and importance of MFIs in a knowledge-based economy has been highly appreciated and acknowledged. Moreover, in the present economy, MFIs are facing tremendous challenges and threats to survive in a competitive environment. In a competitive environment MFIs need to upgrade their intellectual capital including knowledge, database, technological advancement and innovation in order to stay in a competitive environment. The study examines the association between Intellectual Capital (IC) and performance of MFIs in Kenya. The study adopted descriptive research design. The finding of the study reveal that managerial skills of the owner/managers positively influence the performance of Small and Medium sized Enterprises in Kenya. The study found out that entrepreneurial skills have a great positive influence the performance of MFIs in Kenya. The findings of the study indicate that innovativeness influences the performance of MFIs in Kenya.
Long range measurements using a contactless low cost optical sensor

Length measurement is very common in many industrial applications and there is a number of instrumentation involved, mainly dependent on the range and accuracy requirements. In this work, a contactless optical measurement unit is developed. It is based on a mouse sensor and an external laser source. The system is calibrated using an optical board and an electronic distance measuring system. Accuracy and precision of the system is evaluated using the reference data from a total station. Values of 1 mm and 0.3 mm are respectively obtained. Length range during the experiment is 8.5 m. The data of the optical measurement unit are compared with those obtained from a commonly used wheel encoder. Results from the optical sensor of the mouse improve the encoder data.
Extended State Observer Based Adaptive Back-Stepping Sliding Mode Control of Electronic Throttle in Transportation Cyber-Physical Systems

Considering the high accuracy requirement of information exchange via vehicle-to-vehicle (V2V) communications, an extended state observer (ESO) is designed to estimate the opening angle change of an electronic throttle (ET), wherein the emphasis is placed on the nonlinear uncertainties of stick-slip friction and spring in the system as well as the existence of external disturbance. In addition, a back-stepping sliding mode controller incorporating an adaptive control law is presented, and the stability and robustness of the system are analyzed using Lyapunov technique. Finally, numerical experiments are conducted using simulation. The results show that, compared with back-stepping control (BSC), the proposed controller achieves superior performance in terms of the steady-state error and rising time.
Teacher characteristics and student performance: An analysis using hierarchical linear modelling

This research makes use of hierarchical linear modelling to investigate which teacher characteristics are significantly associated with student performance. Using data from the SACMEQ III study of 2007, an interesting and potentially important finding is that younger teachers are better able to improve the mean mathematics performance of their students. Furthermore, younger teachers themselves perform better on subject tests than do their older counterparts. Identical models are run for Sub Saharan countries bordering on South Africa, as well for Kenya and the strong relationship between teacher age and student performance is not observed. Similarly, the model is run for South Africa using data from SACMEQ II (conducted in 2002) and the relationship between teacher age and student performance is also not observed. It must be noted that South African teachers were not tested in SACMEQ II so it was not possible to observe differences in subject knowledge amongst teachers in different cohorts and it was not possible to control for teachers’ level of subject knowledge when observing the relationship between teacher age and student performance. Changes in teacher education in the late 1990s and early 2000s may explain the differences in the performance of younger teachers relative to their older counterparts observed in the later dataset.
Latitudinal and radial gradients of galactic cosmic ray protons in the inner heliosphere – PAMELA and Ulysses observations

Ulysses, launched on 6 October 1990, was placed in an elliptical, high inclined (80.2) orbit around the Sun, and was switched off in June 2009. It has been the only spacecraft exploring high-latitude regions of the inner heliosphere. The Kiel Electron Telescope (KET) aboard Ulysses measures electrons from 3 MeV to a few GeV and protons and helium in the energy range from 6 MeV/nucleon to above 2 GeV/nucleon. The PAMELA (Payload for Antimatter Matter Exploration and Light-nuclei Astrophysics) space borne experiment was launched on 15 June 2006 and is continuously collecting data since then. The apparatus measures electrons, positrons, protons, anti-protons and heavier nuclei from about 100 MeV to several hundreds of GeV. Thus the combination of Ulysses and PAMELA measurements is ideally suited to determine the spatial gradients during the extended minimum of solar cycle 23. For protons in the rigidity interval 1.6−1.8 GV we find a radial gradient of 2.7%/AU and a latitudinal gradient of −0.024%/degree. Although the latitudinal gradient is as expected negative, its value is much smaller than predicted by current particle propagation models. This result is of relevance for the study of propagation parameters in the inner heliosphere.
Impact of isoprene and HONO chemistry on ozone and OVOC formation in a semirural South Korean forest

Abstract. Rapid urbanization and economic development in East Asia in past decades has led to photochemical air pollution problems such as excess photochemical ozone and aerosol formation. Asian megacities such as Seoul, Tokyo, Shanghai, Guangzhou, and Beijing are surrounded by densely forested areas, and recent research has consistently demonstrated the importance of biogenic volatile organic compounds (VOCs) from vegetation in determining oxidation capacity in the suburban Asian megacity regions. Uncertainties in constraining tropospheric oxidation capacity, dominated by hydroxyl radical, undermine our ability to assess regional photochemical air pollution problems. We present an observational data set of CO, NOx, SO2, ozone, HONO, and VOCs (anthropogenic and biogenic) from Taehwa research forest (TRF) near the Seoul metropolitan area in early June 2012. The data show that TRF is influenced both by aged pollution and fresh biogenic volatile organic compound emissions. With the data set, we diagnose HOx (OH, HO2, and RO2) distributions calculated using the University of Washington chemical box model (UWCM v2.1) with near-explicit VOC oxidation mechanisms from MCM v3.2 (Master Chemical Mechanism). Uncertainty from unconstrained HONO sources and radical recycling processes highlighted in recent studies is examined using multiple model simulations with different model constraints. The results suggest that (1) different model simulation scenarios cause systematic differences in HOx distributions, especially OH levels (up to 2.5 times), and (2) radical destruction (HO2 + HO2 or HO2 + RO2) could be more efficient than radical recycling (RO2 + NO), especially in the afternoon. Implications of the uncertainties in radical chemistry are discussed with respect to ozone–VOC–NOx sensitivity and VOC oxidation product formation rates. Overall, the NOx limited regime is assessed except for the morning hours (8 a.m. to 12 p.m. local standard time), but the degree of sensitivity can significantly vary depending on the model scenarios. The model results also suggest that RO2 levels are positively correlated with oxygenated VOCs (OVOCs) production that is not routinely constrained by observations. These unconstrained OVOCs can cause higher-than-expected OH loss rates (missing OH reactivity) and secondary organic aerosol formation. The series of modeling experiments constrained by observations strongly urge observational constraint of the radical pool to enable precise understanding of regional photochemical pollution problems in the East Asian megacity region.
Short-term VHE variability in blazars: PKS 2155-304

Context. The γ-ray blazar PKS 2155-304 has attracted considerable attention because of its extreme TeV variability characteristics during an exceptional flaring period in 2006. Among the observed key findings are (i) a minimum variability timescale as short as ∼200 s and (ii) highly variable TeV emission, which in the frequency interval [10−4 Hz, 10−2 Hz] can be described by a log-normal distribution and suggests an underlying multiplicative (and not additive) process. Aims. Simultaneously accounting for these findings appears difficult within conventional approaches. Following earlier suggestions for the TeV blazar Mkn 501, we explore a possible scenario where PKS 2155-304 is supposed to harbor a supermassive binary black hole system and where the observed TeV variability is dominated by emission from the less massive black hole. Methods. We analyze the constraints on the very high energy (VHE) source imposed by the observed variability characteristics and the integrated VHE luminosity output, and discuss its implications for a binary black hole system. Results. We show that for a secondary mass of mBH ∼ 107 M , fluctuations in the disk accretion rate that feed the jet could account for the observed red-noise type variability process down to frequencies of ∼10−2 Hz. Jet curvature induced by orbital motion, on the other hand, could further relax constraints on the intrinsic jet speeds. Conclusions. Because a binary system can lead to different (yet not independent) periodicities in different energy bands, a longterm (quasi-) periodicity analysis could offer important insights into the real nature of the central engine of PKS 2155-304.
Insights into Gene Expression of Activated Pathogenic Autoimmune T Cells - Studies in Experimental Multiple Sclerosis-like Model

Multiple Sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE), are autoimmune diseases driven by pathogenic memory T cells. Using myelin oligodendrocyte glycoprotein (MOG) 35-55-specific encephalitogenic T cells (TMOG) isolated from MOG35-55-immunized EAE mice we describe here their gene expression profile following antigen specific activation. A vast number of pro-inflammatory genes including cytokines, chemokines and growth factors (e.g., Csf2, Il3, Ccl1, Ccl3) as well as signaling pathways (e.g., iNOS, MAPK, JAK/STAT, NFκβ) were dramatically upregulated following MOG35-55 stimulation of TMOG cells. A number of Th17-related pathways were induced confirming potent Th17-like activation of TMOG. Interestingly, genes known for their anti-inflammatory role (Sit1, Hsd11b1, Pias3, Pparg, Lgmn, Klk3, Tnfaip8l2) were down-regulated in response to MOG35-55 suggesting that silencing of intrinsic suppressory mechanisms may underlie the hyperactivation of memory T cells. MOG35-55 activation led to lower transcription of pro-apoptotic/autophagic genes (Ddit4, Bbc3, Dapk2, Wbp1) and to enhanced level of anti-apoptotic transcripts (Bcl2l1). Transcripts related to toll-like receptors and MyD88-signaling were induced, revealing the involvement of innate immunity pathways in T cell driven autoimmunity. This study reveals the transcriptional events that lead to enhanced cytotoxicity, proliferation and resistance to apoptosis of activated autoimmune T cells. We suggest that encephalitogenic T cells may serve as a reliable in vitro model for screening for possible therapeutics against T cell driven autoimmune diseases.
The effect of leading edge serrations on dynamic stall

An investigation into the effects of dynamic stall was carried out on six aerofoil profiles with sinusoidal leading edges having two amplitudes and three different wavelengths. The study also investigated the effect of wavelength on the static performance of the aerofoil as well as the static hysteresis performance of these profiles. Compared to a baseline model, it was found that a reduction in wavelength increased the maximum lift and the static stall angle. The maximum baseline lift was not reached in any of the cases. The static hysteresis performance of the sinusoidal leading edge profiles was found to be significantly better than the baseline with virtually no static hysteresis recorded. The dynamic study revealed that the sinusoidal profiles improved the performance of the aerofoil by increasing the maximum percentage of lift generated as well as by reducing the size of the hysteresis loop.