Miracle-dz/UniFAR-FTUs huggingface dataset:
A toolkit to quantify the sampling quality of molecular dynamics trajectories: studying highly flexible biomolecules

In this computational work, we investigate the sampling of molecular dynamics (MD) simulations of the two highly flexible biomolecules: Methionine-enkephalin (Met-Enkephalin) and the third variable loop (V3) of the glycoprotein 120 (gp120) from the human immunodeficiency virus type-1 (HIV-1). The conformational dynamics of the three-dimensional (3D) protein structures are of central importance for the biomolecular function. A common possibility to obtain these dynamics at atomic resolution are MD simulations. But reaching a converged MD sampling in adequate time is limited by the huge conformational space of flexible systems. Moreover, an automatic sampling validation is still not established as settled protocol in today's MD studies. Furthermore, existing tools aim primarily to investigate single trajectory convergence which is not always practical for flexible molecules. But in fact, a universal assessment is necessary to classify, whether the sampling is sufficient or not. Otherwise the extracted thermodynamic results are completely meaningless. The aim of this work is to develop a toolkit to quantitatively assess the MD sampling quality for flexible systems. This toolkit is freely available at https://github.com/MikeN12/PySamplingQuality. We use diverse sets of trajectories with different initial conformations along with enhanced sampling techniques such as accelerated MD (aMD) and scaled MD (sMD). These distort the energy landscape to ease conformational transitions. The sampling is assessed by two new quantities, the conformational Oconf and density overlap Odens, including also the cluster number Nc and cluster distribution entropy Sc. These new overlap quantities measure the self-consistency of sampling as a necessary condition for complete sampling. We use Met-Enkephalin as benchmarking system because of its small size but non-trivial dynamics. Our tool reveals that the MD sampling of already such a small molecule converges in a microsecond regime. Furthermore, we can show that aMD is the most efficient algorithm to assess the convergence and also to detect wrong sampling. However, Odens analysis comparing MD with aMD/sMD reveals that we have not completely corrected the bias from enhanced sampling. Therefore, Odens can also be used to compare different methods. On the other hand, V3 demonstrates that much more resources must be spent to achieve convergence compared to those generally invested today. The results highlight the necessity of a multi-trajectory approach to detect incomplete sampling. Altogether, we are able to generate a universally and easily applicable toolkit to assess the MD sampling quality of any kinds of multi-trajectory experiments using certain error estimates and decide, whether the extracted thermodynamic properties are correct or not.
Genotypic variation in induced resistance and induced susceptibility in the peach/Myzus persicae aphid system

In response to herbivore damage or stress, plants may express physiological or morphological changes known as induced responses. We tested whether previous herbivory by the aphid Myzus persicae differentially altered the expression of resistance and susceptibility among five genotypes of peach that differ in their resistance phenotype (avoidance resistance, antibiosis resistance or susceptibility). We measured behavioural and performance parameters of aphid success on plants previously infested by conspecifics as compared to uninfested controls. Significant variation was found both among genotypes and among resistance phenotype, including between genotypes showing a same resistance phenotype. Genotypes with avoidance resistance showed either induced resistance to aphid settling or no response. Genotypes with antibiosis resistance showed induced susceptibility to aphid settling, but the effects of previous herbivory on aphid development were either positive or negative depending on the genotype. In the susceptible genotype, most parameters of aphid settlement and performance, including reproduction, were positively influenced by previous herbivory. Using electronic recording, the aphid probing behaviour was examined to tentatively identify host plant tissues most likely to play a role in induced defenses. Probing behaviour was significantly affected by plant genotype, previous herbivory, and their interaction, indicating complex relations between the two factors. In the genotypes with avoidance resistance, aphids were deterred before they reach the phloem. In the genotypes expressing susceptibility or antibiosis resistance, previous herbivory triggered instead the induction of a phloem-mediated response, that however diverged depending on the resistance status (facilitation or reduction of phloem sap uptake respectively). Genotypic variation in induction found in the peach-M. persicae system establishes a useful framework to improve our knowledge of the ecological role of induced plant responses to aphids.
American Sign Language Recognition Using Machine Learning and Computer Vision

1 2 3 Speech impairment is a disability which affects an individual’s ability to communicate 4 using speech and hearing. People who are affected by this use other media of 5 communication such as sign language. Although sign language is ubiquitous in recent 6 times, there remains a challenge for non-sign language speakers to communicate with 7 sign language speakers or signers. With recent advances in deep learning and computer 8 vision there has been promising progress in the fields of motion and gesture recognition 9 using deep learning and computer vision-based techniques. The focus of this work is to 10 create a vision-based application which offers sign language translation to text thus 11 aiding communication between signers and non-signers. The proposed model takes video 12 sequences and extracts temporal and spatial features from them. We then use Inception, a 13 CNN (Convolutional Neural Network) for recognizing spatial features. We then use an 14 RNN (Recurrent Neural Network) to train on temporal features. The dataset used is the 15 American Sign Language Dataset. 16 17
New Approaches to Duals of Fourier-like Systems

The sequences of the form {Embgn}m,n∈Z, where Emb is the modulation operator, b > 0 and gn is the window function in L2(R), construct Fourier-like systems. We try to consider some sufficient conditions on the window functions of Fourier-like systems, to make a frame and find a dual frame with the same structure. We also extend the given two Bessel Fourier-like systems to make a pair of dual frames and prove that the window functions of Fourier-like Bessel sequences share the compactly supported property with their extensions. But for polynomials windows, a result of this type does not happen.
Meta-Attitudinal Similarity and Relationship Closeness1

This study investigated a possible mediation between attitudinal similarity and closeness of relationship by similarities in the meta-attitudinal prioritization of attitudinal issues. Members of 22 romantic couples rated their positions on 22 issues and then rank-ordered their priority. Rank-order correlations were higher for couples than noncouple pairs and, when analyses were restricted to couples’ high-priority attitudes, attitude dissimilarity correlated with closeness of relationship. Results suggest that emotional closeness may require some attitudinal friction in otherwise interdependent couples.
Associations between smoking and extra-axial manifestations and disease severity in axial spondyloarthritis: results from the British Society for Rheumatology Biologics Register for Ankylosing Spondylitis (BSRBR-AS)

Objective. The effects of smoking on disease manifestations in axial spondyloarthritis (axSpA) are inadequately described. Utilising a large and well-characterised cohort, we investigated the association between smoking and (i) extra-axial manifestations (EAM) and (ii) disease severity measures. Methods. Baseline data from the British Society for Rheumatology Biologics Register for Ankylosing Spondylitis were explored. Our analyses focused on EAMs and other disease severity measures, including scales for fatigue, sleep, anxiety and depression. Logistic and linear models were used to quantify associations between disease characteristics according to smoking status (current/ex/never) and quantity (heavy/light), adjusting for age, gender, BMI, education, deprivation, comorbidities, symptom duration and alcohol status. Results. A total of 2031 participants were eligible for the current analysis (68% male, mean age 49 years). 24% were current and 32% ex-smokers. When compared to non-smokers, current smokers had lower odds of uveitis (ORadj 0.7, 95%CI 0.5 to 0.9) and higher odds of psoriasis (ORadj 1.6, 95%CI 1.1 to 2.3). Exand current smokers had incrementally more severe disease than never smokers, with higher BASDAI (β=0.3, 95%CI 0.1 to 0.6; β=0.9, 95%CI 0.6 to 1.2) and BASFI (β=0.5, 95%CI 0.2 to 0.8; β=1.3, 95%CI 1.0 to 1.6); similar associations were observed for fatigue, sleep, anxiety and depression. Conclusions. In this large cross-sectional study, we observed that smoking is independently associated with an adverse disease profile in axSpA, including worse fatigue, sleep, anxiety, depression and higher odds of psoriasis. The paradoxical association between current smoking and reduced odds of uveitis is interesting and warrants further investigation.
Communication descending

Systematic examination of the role theory has played in the major associational journals in communication shows an exponential growth in the number of theories appearing in these journals. The sheer number and short lifespan of these theories as well as their limited impact on society suggest that they have little epistemological value but are, rather, the product of a closed system of discourse, symptomatic of a community speaking to itself.
The disappearance of oysters from the Wadden Sea: a cautionary tale for no-take zones

1. The question as to whether no-take zones, as reference areas in the Wadden Sea (eastern North Sea), may develop within a few years or decades towards an ecological situation similar to the one which may have existed in earlier times is examined. 2. It is argued that the driving forces behind changes in species and habitats in the Wadden Sea are natural long-term variability of abiotic factors and area-wide anthropogenic impact (coastal engineering). 3. Fisheries in the Wadden Sea are shown to be of minor importance, and it is proposed that establishment of no-take zones here will not result in the recovery and recolonization of missing species and habitats. The examples of species include European oysters (Ostrea edulis), sabellarian reefs (Sabellaria spinulosa) and white weed (Sertularia cupressina, Hydrallmania falcata). Copyright © 2004 John Wiley & Sons, Ltd.
Overview of Seizure and Epilepsy Syndromes and Their Multidisciplinary Management

Abnormal hyperexcitable electrical discharges of the cerebral cortex lead to the disturbance between the inhibitory and excitatory balance of the neural network. Seizure is caused by four main mechanisms, including metabolic, structural, inflammatory, and infectious mechanisms. Seizures are classified as partial and generalized based on the isolation in a specific area in one brain hemisphere or passing through the nerve fibers and spreading to the other hemisphere as well. Epilepsy is defined as the occurrence of more than two unprovoked and unpredicted repeated seizures. Epilepsy affects more than three million individuals in the United States and approximately 50 million individuals worldwide. Epilepsy may be of an unknown origin, while it could also be associated with certain syndromes. General and specific approaches to seizure treatment encompass a wide range of factors. The general approach should be focused on reassurance and raising the awareness of the patients and their family, and the specific treatment is focused on utilizing pharmacological and surgical approaches. In general, the surgical approaches used for medication-refractory seizures are both palliative and curative, showing promising results if the epileptogenic area is localized using a multidisciplinary approach via live video-electroencephalography monitoring or direct intracranial electrode placement. In addition, the utilization of live modern imaging modalities coupled with surgical approaches could enhance the success rate of the treatment and increase the seizure-free duration.
Book reviews

In About to Die: How News Images Move the Public, Barbie Zelizer develops a rich and compelling argument about the functions and consequences of impending death photographs in contemporary journalism. In this visual trope, the camera focuses with anticipation on an impending event or outcome, freezing a moment and opening it up to the speculative possibilities of the viewer’s imagination and emotions. Included within this trope are images of people falling or jumping to their deaths, of assassinations, violent suppression of protesters, tsunami devastation, military targets, and campaigns of genocide. Death is news, whether local, national, or global, and whether the result of accident, natural forces, or human design. But picturing death, the already dead, is often problematic, posing ethical, political, commercial, and aesthetic challenges. Images of impending death implicate us in the most consequential phenomenon in human experience, whether they focus on the intimacy of a single life about to be extinguished or reveal the spectacular scope of carnage or devastation. At the heart of this project, Zelizer questions the longstanding assumption that visual representation is a mere adjunct to the written word, a supplement to the power of language to describe in detail and explicate complexity. Her success in this project is demonstrating how news images serve purposes far beyond information relay. But this is not a struggle of more-or-less between the word and the image. Rather, as Zelizer argues, the image takes on special significance and power in matters that are contested, murky, unresolved, or discomfiting. Particularly when news covers tragedy, disaster, and atrocity, events are often remembered more for the visual image that freezes a moment, than for the text that describes, unpacks, and elucidates the complex issues that comprise the story. As the subtitle of Zelizer’s book suggests, images may have less to do with informing readers about events than with moving readers, with shaping readers’ impressions and feelings about those events, and about themselves in relation to those events. This is the subjunctive voice of the visual and the domain of the ‘about-to-die’ image. In contrast to the indicative voice that describes the world ‘as is’, the voice of the impending death image is motivated by ‘as if’. Regardless of its scope or source, the ‘about-to-die’ image freezes a moment immediately prior to death, or a moment in which death might have occurred, or might yet occur. 436777 JOU10.1177/1464884912436777Book ReviewJournalism 2012
Body Mass Index and Risk of Hypertension: 8-Year Prospective Findings From a Nationwide Thai Cohort Study

OBJECTIVE: As Thailand modernizes an ensuing health risk transition associates with rising chronic non-communicable diseases, especially hypertension. This is a driving force for emerging vascular disease, especially stroke and hypertension. Studies in other countries have shown hypertension is associated with obesity. Longitudinal information is needed forthailand and here we present our cohort data collected over 8 years And recording incidence of hypertension and exposure to elevated abnormal BMI. DESIGN & METHODS: BMI effects on incident hypertension were investigated prospectively in a nationwide Thai Cohort Study (TCS) from 2005 to 2013. Data were derived from 42 785 off-campus Sukhothai Thammathirat Open University students returning mail-based questionnaire surveys in both 2005 and 2013. Participants analysed were normotensive at the start (40 548). Multivariable regression estimated adjusted relative risks estimate linking obesity (measured by BMI) and hypertension (self-reported) among Thai men and women. RESULTS: In Thailand from 2005 to 2013 the TCS 8-Year Incidence of hypertension was 5.1% (men 7.1%, women 3.6%), which meant 1958 participants developed hypertension. BMI was directly associated with an increased risk of hypertension. Compared to participants with a normal BMI (18.5-22.9 Kg/M2), The relative risks (95% confidence interval) of developing hypertension with a BMI of ≤ 18.5. 23.0–24.9, 25-29.9 and >30 Kg/m2 were 0.54 (0.3-0.97), 1.8(1.49-2.18), 3.27 (2.73-3.91) and 6.73 (5.1-8.97) for men and 0.65 (0.45-0.95), 2.28 (1.81-2.88), 3.71 (2.96-4.64) and 9.72 (7.09-13.32) for women respectively (p-trend <0.0001). CONCLUSION: Our data confirmed the adverse effects of long-term high bmi on an increased risk of hypertension in Thai people. Therefore, Ministry of Public Health should develop a national program to encourage people to remain healthy with a normal BMI. There are many health gains from such a program and the information presented here shows clearly that decreased hypertension would be one of the expected benefits for the Thai population.
Performance of non-uniform functionally graded piezoelectric energy harvester beams

The appearance of functionally graded piezoelectric materials has solved the lamination problem of the conventional piezoelectric structures. Functionally graded piezoelectric materials are the new materials with unexplored capabilities. This article theoretically investigates the effects of non-uniformity on the performance of the functionally graded piezoelectric material cantilever beams subjected to harmonic excitation. The governing equations are derived based on Timoshenko and Euler–Bernoulli beam theories. The finite element method with the application of superconvergent element is employed here for the discretization and the vibration analysis of the system. This model is validated by comparing the numerical results with the experimental results of piezoelectric energy harvesters of conventional shapes available in the open literature. Parametric studies are carried out with respect to the effects of tapering ratios, the degree of non-uniformity, load resistance, and the volume fraction parameter on the electrical output power and the fundamental resonance frequency. It was observed that the application of diverging beams noticeably enhances the power output per mass of piezoelectric element extracted while decreases the natural frequency which is advantageous for scavenging energy from ambient surroundings. The results reveal that there is an optimal value for the non-homogeneous parameter leading to the maximized harvested energy under different operating conditions.
Estimation of the total fish biomass in the Baltic Sea during the 20th century

Catch composition and yield data are used to estimate the evolution of fish biomass. These results are compared with the catch rates of Polish and Swedish fisheries. Both series, estimated biomasses and catch rates, suggest that biomass was low during the first half of this century. Subsequently, it increased to over 8 million tonnes in the 1970s. The yield shows essentially the same picture. Peak catches of almost 1 million tonnes were achieved at the end of the 1970s. Fishing mortality increased between 1900 and 1945. After this time, yield increased because of growing biomass (1940‐1950, 1965‐1970) or because of growing fishing eVort (1950‐1965, 1970‐1975). There is evidence to indicate that eutrophication has caused the increase in biomass of Baltic fish stocks.
Characteristics of modern triticale quality: commercially significant flour traits and cookie quality

Abstract. Triticale (Triticosecale × Wittmack) is a high yielding cereal crop with the potential to increase grain production for human food in the coming decades. The quality of triticale flour is usually intermediate between its progenitor species; however, there are considerable differences in quality and response to agronomic conditions among cultivars. The aim of this research was to quantify existing genetic variation to provide preliminary data for classification of triticale cultivars for a milling market. Eleven triticale cultivars from three growing environments were compared with five wheat cultivars bred for various end users. Average protein content, milling yield, thousand-kernel weight, test weight, hardness, colour and ash content supported previous reports. One cultivar was identified with grain hardness and milling yield equivalent to durum wheat, suggesting a null allele at the rye softness protein locus. Ash content was higher than wheat, particularly in the flour despite lower extraction rates, suggesting triticale naturally stores more minerals in its endosperm and the benchmark for milling-grade triticale should be higher than the standard for wheat. Cookie dough weight of triticale was significantly lower per unit volume, indicating current baking processes must be altered to deal with the generally poor water retention of triticale. Significant differences were observed among cultivars for cookie quality and some produced cookies equivalent to soft wheat. There is a clear need to classify cultivars into suitability for various end users to facilitate production and marketing of quality triticale.