Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of free modeling targets in CASP11 and ROLL

We present an assessment of ‘template‐free modeling’ (FM) in CASP11and ROLL. Community‐wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256‐residue target (T0806‐D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837‐D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment‐based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites. Proteins 2016; 84(Suppl 1):51–66. © 2015 Wiley Periodicals, Inc.
An Essential Role for a Small Synaptic Vesicle-Associated Phosphatidylinositol 4-Kinase in Neurotransmitter Release

Glutamate release from nerve terminals is the consequence of Ca2+-triggered fusion of small synaptic vesicles with the presynaptic plasma membrane. ATP dependence of neurotransmitter release has been suggested to be founded, in part, on phosphorylation steps preceding membrane fusion. Here we present evidence for an essential role of phosphatidylinositol phosphorylation in stimulated release of neurotransmitter glutamate from isolated nerve terminals (synaptosomes). Specifically, we show that a phosphatidylinositol 4-kinase (PtdIns 4-kinase) activity resides on nerve terminal-derived small synaptic vesicles (SSVs) and that inhibition of the PtdIns 4-kinase activity in intact synaptosomes leads to attenuation of the evoked release of glutamate. The attenuation of transmitter release is reversible and correlates with respective changes in intrasynaptosomal PtdIns 4-kinase activity. Because only the Ca2+-dependent release of glutamate is affected, regulation appears to be at the level of exocytosis. Taken together, our data imply a mandatory role for PtdIns 4-kinase and phosphoinositide products in the regulated exocytosis of SSV in mammalian nerve terminals.
The Effects of the Urban Built Environment on Mental Health: A Cohort Study in a Large Northern Italian City

Mental health (MH) has a relevant burden on the health of populations. Common MH disorders (anxiety and non-psychotic depression) are well associated to socioeconomic individual and neighborhood characteristics, but little is known about the influence of urban structure. We analyzed among a Turin (Northwest Italy) urban population the association at area level of different urban structure characteristics (density, accessibility by public transport, accessibility to services, green and public spaces) and consumption of antidepressants. Estimates were adjusted by individual socio-demographic variables (education, housing tenure, employment) and contextual social environment (SE) variables (social and physical disorder, crime rates). Data was extracted from the Turin Longitudinal Study (TLS)—a census-based cohort study following up prospectively the mortality and morbidity of the population. As expected, individual characteristics show the strongest association with antidepressant drug consumption, while among built environment (BE) indicators accessibility by public transport and urban density only are associated to MH, being slightly protective factors. Results from this study, in agreement with previous literature, suggest that BE has a stronger effect on MH for people who spend more time in the neighborhood. Therefore, this research suggests that good accessibility to public transport, as well as a dense urban structure (versus sprawl), could contribute to reduced risk of depression, especially for women and elderly, by increasing opportunities to move around and have an active social life.
Psychological Debriefing for Road Traffic Accident Victims: Three-Year Follow-Up of a Randomised Controlled Trial

Background: Psychological debriefing is widely used for trauma victims, but there is uncertainty about its efficacy. We have previously reported a randomised controlled trial which concluded that at 4 months it was ineffective. Aims: To evaluate the 3-year outcome in a randomised controlled trial of debriefing for consecutive subjects admitted to hospital following a road traffic accident. Method: Patients were assessed in hospital by the Impact of Event Scale (IES), Brief Symptom Inventory (BSI) and questionnaire and re-assessed at 3 months and 3 years. The intervention was psychological debriefing as recommended and described in the literature. Results: The intervention group had a significantly worse outcome at 3 years in terms of general psychiatric symptoms (BSI), travel anxiety when being a passenger, pain, physical problems, overall level of functioning, and financial problems. Patients who initially had high intrusion and avoidance symptoms (IES) remained symptomatic if they had received the inter.
Intelligent Universal Transformer design and applications

Legacy transformers are passive, bulky, becoming expensive, and take longer time to deliver. They cannot provide the power quality or control which today's loads demand for proper functioning and the electric system needs for its survivability. Solid-state transformers have been promising technologies in recent years. EPRI is pursuing development of an innovative solution - the UTtrade (Intelligent Universal Transformer), based on R&D100 Award winner SGTO devices, advanced thermal- management technology and packaging concepts to provide flexible, precise quality and reliable power at affordable costs. The IUTtrade is a multi-function programmable power processing device ideal for Smart Grid and Sustainable Energy initiatives. This paper describes the design and application of this device.
Functional Fluorescent Ca2+ Indicator Proteins in Transgenic Mice under TET Control

Genetically encoded fluorescent calcium indicator proteins (FCIPs) are promising tools to study calcium dynamics in many activity-dependent molecular and cellular processes. Great hopes—for the measurement of population activity, in particular—have therefore been placed on calcium indicators derived from the green fluorescent protein and their expression in (selected) neuronal populations. Calcium transients can rise within milliseconds, making them suitable as reporters of fast neuronal activity. We here report the production of stable transgenic mouse lines with two different functional calcium indicators, inverse pericam and camgaroo-2, under the control of the tetracycline-inducible promoter. Using a variety of in vitro and in vivo assays, we find that stimuli known to increase intracellular calcium concentration (somatically triggered action potentials (APs) and synaptic and sensory stimulation) can cause substantial and rapid changes in FCIP fluorescence of inverse pericam and camgaroo-2.
Design and Evaluation of a Multi-Robot Control Interface

Abstract : Designing a human-machine interface for a semi-autonomous, mobile, multi-robot system is a challenging task. The requirements include operating in a real-time environment, facilitating asynchronous command execution, and supporting the operator in dividing his or her monitoring and control resources among multiple robots. This paper presents the results of two simulation-based, multi-robot experiments that were conducted to guide and support the development of a multi-robot control interface. The experiments were designed around a simple mission-independent task of navigating robots towards goal points. While working with an identical setup, the two experiments differed in the level of autonomy provided by the robots. In the first experiment, the robots' navigational capabilities were realized by a simple line-of-sight algorithm requiring the operator to explicitly specify a path. In the second experiment, a more elaborate path generation algorithm was used, reducing the operator's activity to the selection of a goal point. In separate trials, operators had to manage 2, 4, and 8 robots in the two different environments. Robot autonomy represents a requirement for a multi-robot system managed by a single operator. Understanding the impact of varying levels of robot autonomy on operator performance is important for the interface design process. (9 figures, 15 refs.)
Framing the Relationship Between Catalonia and Spain

The specific objective of this article is to analyze the different ways in which each of the four main political parties addresses the question of relations between Catalonia and Spain in its electoral messages. That is, we analyze whether and how each of the political parties represented in the Catalan Parliament confronts this question, how they define their starting position, the goals of the party, the goals of the country (whether Catalonia or Spain), and the means of meeting them.
The traditional ayurvedic medicine, Eugenia jambolana (Jamun fruit), decreases liver inflammation, injury and fibrosis during cholestasis

Cholestasis is a common disease of the liver. Chronic cholestasis eventually leads to hepatic cirrhosis and fibrosis, and rodent chronic cholestasis models are used to study aspects of fibrosis and cirrhosis. Cholestasis‐induced liver injury and fibrosis are associated with increased oxidative stress and inflammation. Few pharmacological therapies exist for treatment of cholestasis or cirrhosis, but it is known that humans with better nutritional intake are less likely to develop certain types of cirrhosis. Eugenia jambolana (Jamun) is a tropical berry fruit rich in antioxidant anthocyanin compounds.
Mindful Awareness, Mindsight, and Neural Integration

Mindful awareness has been demonstrated to alter brain function, mental activity, and interpersonal relationships toward well-being. This article hypothesizes that mindful awareness promotes these positive changes through a proposed “internal attunement” that catalyzes the fundamental process of integration. Integration—the linkage of differentiated elements of a system—leads to the flexible, adaptive, and coherent flow of energy and information in the brain, the mind, and relationships. This coherent flow enables the individual to attain an intentionally established state of mindfulness with practice in the moment and creates the experiential substrate for developing mindful traits in daily life. By freeing the individual from the top–down associations of memory, mindfulness also promotes an emergent sense of a vital and resilient self.
Autonomous Mobile Robot Control and Learning with the PELEA Architecture

In this paper we describe the integration of a robot control platform (Player/Stage) and a real robot (Pioneer P3DX) with PELEA (Planning, Execution and LEarning Architecture). PELEA is a general-purpose planning architecture suitable for a wide range of real world applications, from robotics to emergency management. It allows planning engineers to generate planning applications since it integrates planning, execution, replanning, monitoring and learning capabilities. We also present a relational learning approach for automatically modeling robot-action execution durations, with the purpose of improving the planning process of PELEA by refining domain definitions.
Dynamic analysis of a ZVS bidirectional isolated three-phase dc-dc converter using phase-shift control

This paper presents the dynamic analysis, simulation and experimental results on a ZVS (zero voltage switching) bidirectional isolated three-phase dc-dc converter. The topology uses a steady-state model based on fundamental components considering three possible control variables (dual phase-shift and duty cycle). The dynamic model of the converter using phase-shift (PS) control is developed employing the gyrator theory. Simulation results are presented to validate the plant model and test the digital control system. Implementation is performed in an FPGA (field-programmable gate array) device and closed-loop experimental results are discussed.
Optimal Flow Rate Control for SDN-Based Naval Systems

It is essential for a naval ship system (NSS) to transmit important information with very low delay for successful network-centric warfare under given time constraints. From this perspective, quality of service (QoS) control and low delay transmission are the most important components to improve efficient network utilization in NSSs. In general networks, conventional network algorithms have been optimized to manage network devices such as gateway, switch, bridge, hub, and router in a distributed manner for ease of plug-in and play operation, but which may not be optimal for the NSS. This is because, unlike the general network environment, the NSS is equipped with various nodes, which need to be operated through a centralized hierarchical network structure in accordance with their priorities. Thereby, it is difficult to apply new network algorithms to the NSS due to the closed network environment. To overcome this limitation, we propose a novel NSS employing software defined network (SDN) technology. A novel algorithm called real-time transmission via flow rate control (RTF) is proposed for the SDN-based NSS to optimize the specific environment of NSS. In the proposed algorithm, the optimal flow rates of nodes and network devices are obtained via dual decomposition in conjunction with requirements of delay and QoS. The proposed algorithm obtains the optimal solution iteratively while measuring the performance with traffic models based on real data measured in NSS. Through simulation using Floodlight, we demonstrate that RTF significantly contributes to improving throughput in real-time transmission compared with conventional algorithms. The proposed algorithm improves the average throughput by up to 11.8% while guaranteeing real-time transmission.
Glass-physics: using google glass to support high school physics experiments

We demonstrate how Smart Glasses can support high school science experiments. The vision is to (1) reduce the "technical" effort involved in conducting the experiments (measuring, generating plots etc.) and to (2) allow the students to interactively see/manipulate the theoretical representation of the relevant phenomena while at the same time interacting with them in the real world. As a use case, we have implemented a Google Glass app for a standard high school acoustics school experiment (determining the relationship between tone frequency that hitting a glass filled with water generates and the amount of water in the glass). We evaluated the system with a group of 36 high grade students split into a group using our application and a control group using an existing tablet based system. We show a statistically significant advantage in experiment execution speed, cognitive load, and curiosity.
Content, connectivity, and cloud: ingredients for the network of the future

A new network architecture for the Internet needs ingredients from three approaches: information- centric networking, cloud computing integrated with networking, and open connectivity. Information-centric networking considers pieces of information as first-class entities of a networking architecture, rather than only indirectly identifying and manipulating them via a node hosting that information; this way, information becomes independent from the devices they are stored in, enabling efficient and application- independent information caching in the network. Cloud networking offers a combination and integration of cloud computing and virtual networking. It is a solution that distributes the benefits of cloud computing more deeply into the network, and provides a tighter integration of virtualization features at computing and networking levels. To support these concepts, open connectivity services need to provide advanced transport and networking mechanisms, making use of network and path diversity (even leveraging direct optical paths) and encoding techniques, and dealing with ubiquitous mobility of user, content and information objects in a unified way.
[Design of an inverse planning system for radiotherapy using linear optimization].

Our approach shows that inverse planning for intensity-modulated beams in radiotherapy can be solved efficiently by the mathematical method of linear optimization. The completeness property of this method guarantees that calculated treatment plans fulfill the dose constraints given by the oncologist. Techniques developed by our group can also avoid the possible infeasibility caused by a physically impossible dose distribution. In contrast to other optimization methods, the simplex algorithm used for linear optimization allows a very high optimization speed, i.e., very short planning cycles. These preconditions were integrated in the development of the software system MIPART ("Munich Inverse Planning And Radiotherapy Treatment"). The object-oriented software architecture of MIPART achieves a maximum of extensibility and flexibility. Our clinical tests show that MIPART can be easily integrated in the clinical routine in spite of the complexity of data in the field of intensity-modulated radiotherapy. Moreover, qualitatively better treatment plans can be generated than in conventional treatment planning, especially in complicated cases.
Attentional modulation of visual processes in motion perception.

The present research examined the effects of spatially directed attention on the temporal characteristics of information transmission in the visual system. A two-stimulus, two-flash, long-range motion display was used. The results showed that attending to 1 of the 2 stimuli altered the perceived direction of motion, the pattern of motion and no-motion responses, and ratings of motion quality. The results were compared with predictions derived from 2 conceptual frameworks of attention: a temporal-profile model and an additive account. The results supported the temporal-profile model
KULEX: ADL power assistant robotic system for the elderly and the disabled (Abstract for video)

A new robotic system for upper-limb power assistance of the elderly and the disabled has been developed. It is composed of the three main modules, 1-DOF under-actuated hand module for the assistance of hand grasp motion, 3-DOF exoskeleton-type parallel wrist mechanism for wrist power assistance, and 6-DOF serial chain in order to assist an arbitrary movement of an operator's forearm. The operating capability of the proposed robot is observed from a demonstration of the robot performing some activities-of-daily-living (ADL) tasks such as picking up a pen with pinch grasp, gripping an object with power grasp, and brushing teeth.
Chronopharmacology and its impact on antihypertensive treatment.

Circadian rhythms have been documented throughout the plant and animal kingdom at every level of eukariotic organization. Circadian rhythms are endogenous in nature, driven by oscillators or clocks, and persist under free-running (e.g. constant darkness) conditions. The genes expressing the biological clock have been identified in various species. The important feature of endogeneous biological rhythms is their anticipatory character. Rhythmicity inherent to all living systems, allows them to adapt more easily and to better survive under changing environmental conditions during the 24 hours of a day as well as during changing seasons. Having this in mind it is easy to conceive that not only must the right amount of the right substance be at the right place, but also this must occur at the right time. Also in man nearly all functions of the body including those influencing pharmacokinetic parameters such as drug absorption and distribution, drug metabolism and renal elimination display significant daily variations. Also the onset and symptoms of diseases such as coronary infarction, angina pectoris, stroke, ventricular tachycardia are circadian phase dependent. Myocardial infarction and angina attacks as well as silent ischemias (ST-segment depression) in stable angina pectoris have an early morning peak between 8-12 h. In contrast, ECG abnormalities and angina attacks in variant angina mainly occur at night. Blood pressure and heart rate in normotensives and essential (primary) hypertensive patients display highest values during daytime followed by a nightly drop and an early morning rise. In about 70% of forms of secondary hypertension (e.g. renal disease, hyperthyroidisms, hormonal diseases, gestational hypertension), however, this rhythmic pattern is abolished or even reversed exhibiting nightly peaks in blood pressure. This form of hypertension is accompanied by increased end organ damages. Thus, different subtypes of a disease (angina pectoris, hypertension) can display different circadian patterns in symptoms. These observations are a challenge for basic and clinical research to get a better understanding on the underlying mechanisms of regulation. Moreover, they call for a circadian time-specified drug treatment. From above it is evident that pharmacokinetics may also not be constant within a day. Chronopharmacokinetics have been shown for several cardiovascular active drugs (propranolol, nifedipine, verapamil, enalapril, isosorbide-5-mononitrate, digoxin, etc.). Far more drugs were shown to display significant daily variations in their effects (chronopharmacodynamics, chronotoxicology) even after chronic application or constant infusion. In conclusion, there is clear evidence that the dose/concentration-response relationship of drugs can be significantly dependent on the time of day. Thus, circadian time has to be taken into account as an important variable influencing a drug's pharmacokinetics and/or its effects or side effects.
Monoclonality of normal human colonic crypts

The monoclonality of human colonic crypts was demonstrated by human androgen receptor (HUMARA) gene assay following application of the crypt isolation method. DNA was extracted from an isolated single crypt, Hpa II digestion was performed before polymerase chain reaction (PCR) by primers spanning the HUMARA exon 1 region. The PCR product of a single crypt clearly showed allelic exclusion based on methylation status, while PCR product from a mixture of 40 crypts or colonic mucosa as a whole that included epitheliums and interstitial connective tissue had two bands. This method will facilitate the non‐isotopic analysis not only of tumor clonality, but also of the nonnal structures derived from a single progenitor cell.