Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplementary Information for " Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-equilibrium Simulations "

Model System Setup. The model system (Fig. 2 in the paper) used to illustrate transition path theory, has been set up in the following manner. First, a potential function was set up as: V (x, y) = x 2 + y 2 − 50 cos s " x − 25 1.7 « 2 + " y − 25 1.7 « 2 with Gaussian-type energy basins defined as N (x, y, µx, µy, σx, σy) = exp " − (x − µx) 2 σ 2 x − (y − µy) 2 σ 2 y « The potential V (x, y) was then evaluated on a lattice of x, y integer values in the range 0,. ,49. On this lattice, a jump process was defined by a transition matrix with each row corresponds to one coordinate x, y and is defined by where z is chosen such that the transition matrix row sums up to 1. Entries that would go across the 0,. ,49 boundary, such as T0,0→0,−1 are forced to zero. This dynamics is a Monte Carlo jump process on a discrete lattice with potential defined by V (x, y). The sets A and B were defined by all lattice points that are inside a radius of 6 and outside a radius of 16 from the center at (25,25). Since the dynamics is Markovian by definition, the application of transition path theory consisting of computation of the stationary probability, the committor probabilities, the folding flux and the coarse-grained folding flux, is exact. PinWW Simulation Setup. All simulations were carried out with the 3.2. 1 version of the GROMACS engine [1] using the GROMOS-96 43a1 force field. LINCS constraints [2] of order 4 using a tolerance of 10 −4 nm were applied to all bond lengths (see also [14]) and masses of heavy atoms were redistributed such as to increase the masses of covalently bound hydrogen atoms to 4 atomic mass units [15]. This permitted an integration time step of 4 fs [16]. Van der Waals interactions were considered within a twin range cutoff of 0.8 and 1.4 nm without inclusion of long-range dispersion corrections so as to be consistent with the way the force field was parametrized [17]. The reaction field method was chosen to calculate electrostatic interactions. The Coulomb potential was cutoff at 1.4 nm. The dielectric constant of the continuum was set to 54 so as to be consistent with the SPC …
Atherosclerosis at arterial bifurcations: evidence for the role of haemodynamics and geometry

Summary Atherosclerotic plaques are found at distinct locations in the arterial system, despite the exposure to systemic risk factors of the entire vascular tree. From the study of arterial bifurcation regions, emerges ample evidence that haemodynamics are involved in the local onset and progression of the atherosclerotic disease. This observed co-localisation of disturbed flow regions and lesion prevalence at geometrically predisposed districts such as arterial bifurcations has led to the formulation of a ‘haemodynamic hypothesis’, that in this review is grounded to the most current research concerning localising factors of vascular disease. In particular, this review focuses on carotid and coronary bifurcations because of their primary relevance to stroke and heart attack. We highlight reported relationships between atherosclerotic plaque location, progression and composition, and fluid forces at vessel’s wall, in particular shear stress and its ‘easier-tomeasure’ surrogates, i.e. vascular geometric attributes (because geometry shapes the flow) and intravascular flow features (because they mediate disturbed shear stress), in order to give more insight in plaque initiation and destabilisation. Analogous to Virchow’s triad for thrombosis, atherosclerosis must be thought of as subject to a triad of, and especially interactions among, haemodynamic forces, systemic risk factors, and the biological response of the wall.
Vitamin D, vitamin A, the primary melanoma transcriptome and survival

Survival from melanoma is influenced by several, well‐established clinical and histopathological factors, e.g. age, Breslow thickness and microscopic ulceration. We (the Section of Epidemiology and Biostatistics, University of Leeds) have carried out research to better understand the biological basis for these observations. Preliminary results indicated a protective role for vitamin D in melanoma relapse and that higher vitamin D was associated with thinner primary melanomas.
The early acquisition of word meaning

ABSTRACT The development of the meaning of shoe in one pre-lingual child, plus additional examples drawn from the literature, support a notion that word meanings start out very narrow and only become overextended later, though sometimes before the word is spoken. This appears to contradict the course of development of meaning hypothesized by Clark (1973). It is argued that the early development of word meaning is simply a special case of a much more general learning process.
Personalized identification of altered pathways in cancer using accumulated normal tissue data

Motivation: Identifying altered pathways in an individual is important for understanding disease mechanisms and for the future application of custom therapeutic decisions. Existing pathway analysis techniques are mainly focused on discovering altered pathways between normal and cancer groups and are not suitable for identifying the pathway aberrance that may occur in an individual sample. A simple way to identify individual’s pathway aberrance is to compare normal and tumor data from the same individual. However, the matched normal data from the same individual are often unavailable in clinical situation. Therefore, we suggest a new approach for the personalized identification of altered pathways, making special use of accumulated normal data in cases when a patient’s matched normal data are unavailable. The philosophy behind our method is to quantify the aberrance of an individual sample's pathway by comparing it with accumulated normal samples. We propose and examine personalized extensions of pathway statistics, overrepresentation analysis and functional class scoring, to generate individualized pathway aberrance score. Results: Collected microarray data of normal tissue of lung and colon mucosa are served as reference to investigate a number of cancer individuals of lung adenocarcinoma (LUAD) and colon cancer, respectively. Our method concurrently captures known facts of cancer survival pathways and identifies the pathway aberrances that represent cancer differentiation status and survival. It also provides more improved validation rate of survival-related pathways than when a single cancer sample is interpreted in the context of cancer-only cohort. In addition, our method is useful in classifying unknown samples into cancer or normal groups. Particularly, we identified ‘amino acid synthesis and interconversion’ pathway is a good indicator of LUAD (Area Under the Curve (AUC) 0.982 at independent validation). Clinical importance of the method is providing pathway interpretation of single cancer, even though its matched normal data are unavailable. Availability and implementation: The method was implemented using the R software, available at our Web site: http://bibs.snu. ac.kr/ipas. Contact: tspark@stat.snu. ac.kr or namhuh@samsung.com Supplementary information: Supplementary data are available at Bioinformatics online.
Comparative Validity Analysis of Multiple Measures of Violence Risk in a Sample of Criminal Offenders

This study compared the predictive validity of multiple indices of violence risk among 188 general population criminal offenders: Historical-Clinical-Risk Management-20 (HCR-20) Violence Risk Assessment Scheme, Violence Risk Appraisal Guide (VRAG), Violent Offender Risk Assessment Scale (VORAS), Hare Psychopathy Checklist-Revised (PCL-R), and Screening Version (PCL:SV). Several indices were related to violent recidivism with large statistical effect sizes: HCR-20 (Total, Clinical and Risk Management scales, structured risk judgments), VRAG, and behavioral scales of psychopathy measures. Multivariate analyses showed that HCR-20 indices were consistently related to violence and that the VRAG entered some analyses. Findings are inconsistent with a position of strict actuarial superiority, as HCR-20 structured risk judgments—an index of structured professional or clinical judgment—were as strongly related to violence.
A2C: Anti-Attack Counters for Traffic Measurement

Flow-level sampling methods have been widely studied and extensively employed in network traffic measurement systems. However, traffic anomalies are becoming more prevalent and severe in the Internet, which pose great challenges to the traffic measurement. Existing solutions targeted at such scenario have either low accuracy or high memory usage. In this paper, we propose a two-stage sampling approach-Anti Attack Counters (A2C) and an efficient parameter adapting method to solve the problem. The proposed sampling mechanism can adapt to the network condition automatically and collect more information even under severe traffic attacks. Theoretical analysis on accuracy and resource requirement is presented in our work. Furthermore, we validate our approach using both synthetic and real traces. The experimental results demonstrate that A2C is of high resilience while providing significantly improved measurement accuracy with reduced memory occupation comparing with other existing anti-attack countermeasures.
The Role of Experience in Inter-Racial Recognition

Anecdotal evidence abounds with respect to the notion that to members of a given ethnic group, those members of different ethnic groups all look alike. The Black poet Langston Hughes, in his last book, &dquo;Misery Is&dquo; (1969) cites as an example of Black misery, &dquo;Misery is when your friends see Harry Belafonte walking down the street and say &dquo;There goes Sidney Poitier. &dquo; The recent Angela Davis trial in California broached the related question of the reliability of White witnesses testifying under oath that they recognized Miss Davis at the site of the crime for which she was accused. In every instance, these White witnesses contended that they could recognize members of the Black race. While considerable research in perceptual psychology (Gibson 1969) indicates that continuous exposure to unfamiliar stimuli results in improvement in recognition performance, recent studies of inter-race recognition appeared to be in conflict with perceptual psychology. The basic question of the effects of experience on &dquo;other-race&dquo; recognition has not yet been condlusively answered. Two studies (Seeleman 1940, and Malpass and Kravitz 1969) found that both White and Black S’s displayed the own-race phenomenon. However, both the Malpass and Kravitz study and a more recent study by Galper (1973) suggest that there is no necessary relationship between reported other-race experience and recognition of members of that particular race. Galper attempts to explain the lack of
Fast object approximation for real-time 3D obstacle avoidance with biped robots

In order to achieve fully autonomous humanoid navigation, environment perception must be both fast enough for real-time planning in dynamic environments and robust against previously unknown scenarios. We present an open source, flexible and efficient vision system that represents dynamic environments using simple geometries. Based only on onboard sensing and 3D point cloud processing, it approximates objects using swept-sphere-volumes while the robot is moving. It does not rely on color or any previous models or information. We demonstrate the viability of our approach by testing it on our human-sized biped robot Lola, which is able to avoid moving obstacles in real-time while walking at a set speed of 0.4m/s and performing whole-body collision avoidance.
What constitutes the sovereign state?

One might try to determine just what constitutes a sovereign state empirically, by examining the characteristics of states whose sovereignty is indisputable. All sovereign states, it might be observed, have territory, people, and a government. Curiously, however, cogent standards do not seem to exist either in law or in practice for the dimensions, number of people, or form of government that might be required of a sovereign state. Indeed, a United Nations General Assembly Resolution declared that neither small size, nor remote geographical location, nor limited resources constitutes a valid objection to sovereign statehood.
Happiness Quantified: A Satisfaction Calculus Approach

How do we measure happiness? Focusing on subjective measures as a proxy for welfare and well-being, this book finds ways to do that. Subjective measures have been used by psychologists, sociologists, political scientists, and, more recently, economists to answer a variety of scientifically and politically relevant questions. Van Praag, a pioneer in this field since 1971, and Ferrer-i-Carbonell present in this book a generally applicable methodology for the analysis of subjective satisfaction. Drawing on a range of surveys on people's satisfaction with their jobs, income, housing, marriages, and government policy, among other areas of life, this book shows how satisfaction with life "as a whole" is an aggregate of these domain satisfactions. Using German, British, Dutch, and Russian data, the authors cover a wide range of topics. This groundbreaking book presents a new and fruitful methodology that constitutes a welcome addition to the social sciences. The paperback edition has been revised to bring the literature review up-to-date and the chapter on poverty has been revised and extended to take account of new research.
Poverty, migration and sex work: youth transitions in Ethiopia

Despite an emerging body of work on youth transitions, research has yet to explore the often unconventional routes to adulthood for young people marginalised through poverty. By drawing on interviews with 60 young commercial sex workers in Ethiopia, this paper explores the connections between poverty, migration and sex work and demonstrates that sex work provides a risky alternative, but often successful, path to independence for some rural-urban migrants. The paper concludes by offering recommendations for policies that seek to support young sex workers by enabling them to maintain their independence while seeking different employment.
Is Mislocalization during Saccades Related to the Position of the Saccade Target within the Image or to the Gaze Position at the End of the Saccade?

A stimulus that is flashed around the time of a saccade tends to be mislocalized in the direction of the saccade target. Our question is whether the mislocalization is related to the position of the saccade target within the image or to the gaze position at the end of the saccade. We separated the two with a visual illusion that influences the perceived distance to the target of the saccade and thus saccade endpoint without affecting the perceived position of the saccade target within the image. We asked participants to make horizontal saccades from the left to the right end of the shaft of a Müller-Lyer figure. Around the time of the saccade, we flashed a bar at one of five possible positions and asked participants to indicate its location by touching the screen. As expected, participants made shorter saccades along the fins-in (<–>) configuration than along the fins-out (>–<) configuration of the figure. The illusion also influenced the mislocalization pattern during saccades, with flashes presented with the fins-out configuration being perceived beyond flashes presented with the fins-in configuration. The difference between the patterns of mislocalization for bars flashed during the saccade for the two configurations corresponded quantitatively with a prediction based on compression towards the saccade endpoint considering the magnitude of the effect of the illusion on saccade amplitude. We conclude that mislocalization is related to the eye position at the end of the saccade, rather than to the position of the saccade target within the image.
Music, emotion and dementia: Insight from neuroscientific and clinical research

Music has an important meaning in the lives of many elderly persons. Its capacity to evoke emotions and influence mood and arousal is often relatively well preserved also in dementia. Neuroscientific and clinical research has increased our understanding about the mechanisms underlying music enjoyment and its therapeutic effects. This article reviews previous studies that address the neural basis of music cognition and emotion. We also introduce the effects of varying music interventions on emotional and cognitive functioning in dementia. Findings suggest that both traditional music therapy and caregiver-implemented music activities may have the capacity to reduce emotional and behavioral disturbances in dementia, although firm conclusions about the long- term effects of music still remain elusive. The rapid growth of dementia warrants study in the rehabilitative effects of everyday musical leisure activities or hobbies, such as music listening and singing, on well-being in dementia, especially in its early stages.
Optimization of Experimental Model Parameter Identification for Energy Storage Systems

The smart grid approach is envisioned to take advantage of all available modern technologies in transforming the current power system to provide benefits to all stakeholders in the fields of efficient energy utilisation and of wide integration of renewable sources. Energy storage systems could help to solve some issues that stem from renewable energy usage in terms of stabilizing the intermittent energy production, power quality and power peak mitigation. With the integration of energy storage systems into the smart grids, their accurate modeling becomes a necessity, in order to gain robust real-time control on the network, in terms of stability and energy supply forecasting. In this framework, this paper proposes a procedure to identify the values of the battery model parameters in order to best fit experimental data and integrate it, along with models of energy sources and electrical loads, in a complete framework which represents a real time smart grid management system. The proposed method is based on a hybrid optimisation technique, which makes combined use of a stochastic and a deterministic algorithm, with low computational burden and can therefore be repeated over time in order to account for parameter variations due to the battery’s age and usage.
A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergent Salmonella enterica serovar Infantis strain.

Of all known Salmonella enterica serovars, S. Infantis is one of the most commonly isolated and has been recently emerging worldwide. To understand the recent emergence of S. Infantis in Israel, we performed extensive comparative analyses between pre-emergent and the clonal emergent S. Infantis populations. We demonstrate the fixation of adaptive mutations in the DNA gyrase (gyrA) and nitroreductase (nfsA) genes, conferring resistance to quinolones and nitrofurans, respectively, and the carriage of an emergent-specific plasmid, designated pESI. This self-transferred episome is a mosaic megaplasmid (∼280 kb), which increases bacterial tolerance to environmental mercury (mer operon) and oxidative stress, and provides further resistance to tetracycline, sulfamethoxazole and trimethoprim, most likely due to the presence of tetRA, sulI and dfrA genes respectively. Moreover, pESI carries the yersiniabactin siderophore system and two novel chaperone-usher fimbriae. In vitro studies established that pESI conjugation into a plasmidless S. Infantis strain results in superior biofilm formation, adhesion and invasion into avian and mammalian host cells. In vivo mouse infections demonstrated higher pathogenicity and increased intestinal inflammation caused by an S. Infantis strain harboring pESI compared with the plasmidless parental strain. Our results indicate that the presence of pESI that was found only in the emergent population of S. Infantis in Israel contributes significantly to antimicrobials tolerance and pathogenicity of its carrier. It is highly likely that pESI plays a key role in the successful spread of the emergent clone that replaced the local S. Infantis community in the short time of only 2-3 years.
Assessing Torso Deformity in Scoliosis Using Self-Organizing Neural Networks (SNN)

This paper presents a novel technique for parameterizing malformation of the torso in scoliosis. Scoliosis is complex 3 dimensional deformity of the spine in which the trunk distorts because of the internal spinal deformity. Thus monitoring the distortion in the external torso would be beneficial in tracking important changes and possibly predicting the underlying changes in the internal spine. The technique proposed in this paper, facilitates torso surface assessment and it consists of three stages of digitizing, parameterizing and mapping. Self-organizing neural networks (SNN) is used to parameterize the torso malformation. The orientation and position of the neuron in the SNN provides detailed insight regarding significant changes in the torso model. Preliminary results are presented to further illustrate the capability of the technique.
From Dutch Dispersal to Ethnic Enclaves in the UK

Since 2000, a considerable number of Somalis with Dutch passports have started to move from cities and small towns in the Netherlands, which were relatively mixed, to residential environments in the UK with much higher concentrations of Somalis and other immigrants. This paper examines experiences of integration and segregation in the Netherlands and the UK by interviewing some of these Somalis. What do their experiences teach us about segregation and integration? It was found that current understandings of segregation and integration are too focused on cultural aspects, and overlook structural factors that obstruct immigrantsâ€™ integration. They also give rise to an inability to imagine immigrantsâ€™ own feelings of belonging and their transnational orientations.
Th17 Cells as Potential Probiotic Therapeutic Targets in Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBD) are characterized by wasting and chronic intestinal inflammation triggered by various cytokine-mediated pathways. In recent years, it was shown that T helper 17 (Th17) cells are involved in the pathogenesis of IBD, which makes them an attractive therapeutic target. Th17 cells preferentially produce interleukin (IL)-17A–F as signature cytokines. The role of the interplay between host genetics and intestinal microbiota in the pathogenesis of IBD was demonstrated. Probiotics are live microorganisms that when orally ingested in adequate amounts, confer a health benefit to the host by modulating the enteric flora or by stimulating the local immune system. Several studies indicated the effectiveness of probiotics in preventing and treating IBD (ulcerative colitis, and Crohn’s disease). Furthermore, there is mounting evidence of probiotics selectively targeting the Th17 lineage in the prevention and management of inflammatory and autoimmune diseases such as IBD. This review highlights critical roles of Th17 cells in the pathogenesis of IBD and the rationale for using probiotics as a novel therapeutic approach for IBD through manipulation of Th17 cells. The potential molecular mechanisms by which probiotics modulate Th17 cells differentiation and production are also discussed.