Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and dynamics of a gene network model incorporating small RNAs

As advances in molecular biology continue to reveal additional layers of complexity in gene regulation, computational models need to incorporate additional features to explore the implications of new theories and hypotheses. It has recently been suggested that eukaryotic organisms owe their phenotypic complexity and diversity to the exploitation of small RNAs as signalling molecules. Previous models of genetic systems are, for several reasons, inadequate to investigate this theory. In this study, we present an artificial genome model of genetic regulatory networks based upon previous work by Torsten Reil, and demonstrate how this model generates networks with biologically plausible structural and dynamic properties. We also extend the model to explore the implications of incorporating regulation by small RNA molecules in a gene network. We demonstrate how, using these signals, highly connected networks can display dynamics that are more stable than expected given their level of connectivity.
Migratory Birds Reinforce Local Circulation of Avian Influenza Viruses

Migratory and resident hosts have been hypothesized to fulfil distinct roles in infectious disease dynamics. However, the contribution of resident and migratory hosts to wildlife infectious disease epidemiology, including that of low pathogenic avian influenza virus (LPAIV) in wild birds, has largely remained unstudied. During an autumn H3 LPAIV epizootic in free-living mallards (Anas platyrhynchos) — a partially migratory species — we identified resident and migratory host populations using stable hydrogen isotope analysis of flight feathers. We investigated the role of migratory and resident hosts separately in the introduction and maintenance of H3 LPAIV during the epizootic. To test this we analysed (i) H3 virus kinship, (ii) temporal patterns in H3 virus prevalence and shedding and (iii) H3-specific antibody prevalence in relation to host migratory strategy. We demonstrate that the H3 LPAIV strain causing the epizootic most likely originated from a single introduction, followed by local clonal expansion. The H3 LPAIV strain was genetically unrelated to H3 LPAIV detected both before and after the epizootic at the study site. During the LPAIV epizootic, migratory mallards were more often infected with H3 LPAIV than residents. Low titres of H3-specific antibodies were detected in only a few residents and migrants. Our results suggest that in this LPAIV epizootic, a single H3 virus was present in resident mallards prior to arrival of migratory mallards followed by a period of virus amplification, importantly associated with the influx of migratory mallards. Thus migrants are suggested to act as local amplifiers rather than the often suggested role as vectors importing novel strains from afar. Our study exemplifies that a multifaceted interdisciplinary approach offers promising opportunities to elucidate the role of migratory and resident hosts in infectious disease dynamics in wildlife.
Robust suboptimal control with disturbances compensation

This paper describes the robust suboptimal algorithm for a time-varying plant with unknown parameters and an uncontrollable disturbance. The algorithm provides minimization of a performance index with a given accuracy and transfers the plant from the known initial point to the known final point. Efficiency of the proposed scheme is illustrated by modeling.
The Entitativity of Social Group: Retrospect and Prospect

The entitativity of social groups refers to the degree to which groups are perceived to be a significantly substantive entity. Entitativity is influenced by percipient, social contexts and cultural factors. It has important consequences on intergroup relations; It affects ingroup identification, stereotypes, bias and group conflict. Group entitativity is not either a positive or a negative group attribute per se; rather, it depends on the context and the relationship between the perceiver and the group. The future researches should focus on how to enhance the positiveness of group entitativity, and how to strengthen entitativity studies in Chinese culture context, so as to achieve a harmonious society in China.
Query optimization for graph analytics on linked data using SPARQL

Triplestores that support query languages such as SPARQL are emerging as the preferred and scalable solution to represent data and meta-data as massive heterogeneous graphs using Semantic Web standards. With increasing adoption, the desire to conduct graph-theoretic mining and exploratory analysis has also increased. Addressing that desire, this paper presents a solution that is the marriage of Graph Theory and the Semantic Web. We present software that can analyze Linked Data using graph operations such as counting triangles, finding eccentricity, testing connectedness, and computing PageRank directly on triple stores via the SPARQL interface. We describe the process of optimizing performance of the SPARQL-based implementation of such popular graph algorithms by reducing the space-overhead, simplifying iterative complexity and removing redundant computations by understanding query plans. Our optimized approach shows significant performance gains on triplestores hosted on stand-alone workstations as well as hardware-optimized scalable supercomputers such as the Cray XMT.
PHYSICS IN THE BRAIN

The human body is a constant flux of thousands of chemical/biological interactions and processes connecting molecules, cells, organs, and fluids, throughout the brain, body, and nervous system. Up until recently it was thought that all these interactions operated in a linear sequence, passing on information much like a runner passing the baton to the next runner. However, the latest findings in quantum biology and biophysics have discovered that there is in fact a tremendous degree of coherence within all living systems.
Leakage-Delay Tradeoff in Wide-Bit Nanoscale CMOS

The scaling of nanometer technology has had a major impact on the power dissipation of CMOS circuits. As transistor size decreases it has become apparent that leakage power is becoming a dominant fighting force against future technology. In this paper the importance of static power consumption on the design of new and advanced CMOS technology is explored with the investigation of leakage power reduction techniques and their implementation on embedded CMOS adder circuits. Four different adder topologies of bit sizes 16, 32 and 64, were implemented using technology nodes 22nm, 32nm, and 45nm. To reduce the leakage power dissipation of these adders three different types of leakage reduction techniques were implemented and simulated using Hspice to determine the leakage and delay. The results were analyzed and the optimal leakage reduction technique(s) for each nanometer adder design was determined.
Working memory and developmental language impairments

Children with developmental language impairments (DLI) are often reported to show difficulties with working memory. This review describes the four components of the well-established working memory model, and considers whether there is convincing evidence for difficulties within each component in children with DLI. The emphasis is on the most demanding form of working memory that draws on central executive (CE) resources, requiring concurrent processing and storage of information. An evaluation of recent research evidence suggests that, not only are children with DLI impaired on verbal CE measures, but they also show difficulties on non-verbal CE tasks that cannot be assumed to tap language. Therefore, it seems increasingly likely that children with DLI show domain-general CE impairments, along with their more established impairments in verbal short-term memory. Implications for potential working memory interventions and classroom learning are discussed.
Semantic Relatedness Metric for Wikipedia Concepts Based on Link Analysis and its Application to Word Sense Disambiguation

Wikipedia has grown into a high quality up-todate knowledge base and can enable many knowledge-based applications, which rely on semantic information. One of the most general and quite powerful semantic tools is a measure of semantic relatedness between concepts. Moreover, the ability to efficiently produce a list of ranked similar concepts for a given concept is very important for a wide range of applications. We propose to use a simple measure of similarity between Wikipedia concepts, based on Dice’s measure, and provide very efficient heuristic methods to compute top k ranking results. Furthermore, since our heuristics are based on statistical properties of scale-free networks, we show that these heuristics are applicable to other complex ontologies. Finally, in order to evaluate the measure, we have used it to solve the problem of word-sense disambiguation. Our approach to word sense disambiguation is based solely on the similarity measure and produces results with high accuracy.
Designing Empathy: Ritual Respect

Design approaches have been developed to establish empathy between practitioners, researchers, collaborators, and participants in human-computer interaction (HCI) in the context of health, care, and wellbeing. Unpacking nuances of empathy, in this position paper we discuss our exploratory research into bereavement following miscarriage and consider how our visual practice has enhanced communication and comprehension within an interdisciplinary team. We propose that such accessible visualisations can stimulate a shared, compassionate understanding of user needs, and thus inform the development of empathic services, systems, and solutions.
An Analysis of Anthropometric Indicators and Modifiable Lifestyle Parameters Associated with Hypertensive Nephropathy

The surge in prevalence of chronic noncommunicable diseases like hypertension and chronic kidney disease has been linked with modifiable lifestyle practices and increased body fat. This study sought to compare the association between different modifiable lifestyle practices, adiposity indices, renal function parameters, and hypertension as well as the predictive implications for levels of these parameters in target cardiac organ damage among an urban Ghanaian hypertensive population. Using a hospital-based case-control study design, 241 Ghanaian indigenes from the Kumasi metropolis were recruited for this study. The case group was made up of 180 hypertensives and 61 normotensives served as controls. In addition to sociodemographic data, standard haemodynamic, anthropometric, renal function, and cardiac organ damage assessments were done. The prevalence of chronic kidney disease (CKD) ranged from 13.3% to 16.6% depending on the equation used in estimating the glomerular filtration rate (eGFR). Percentage cluster distribution by chronic kidney disease was observed to be significantly tilted toward the upper quartiles (3rd and 4th) of the haemodynamic parameters measured. Chronic kidney disease was significantly higher among self-reported smokers and alcoholic hypertensives. In this urban population, adiposity was associated with hypertension and renal insufficiency. Chronic kidney disease was associated with hypertension and cardiac abnormalities.
Intermediate phenotypes and biomarkers of treatment outcome in major depressive disorder

Major depressive disorder (MDD) is a pleomorphic illness originating from gene x environment interactions. Patients with differing symptom phenotypes receive the same diagnosis and similar treatment recommendations without regard to genomics, brain structure or function, or other physiologic or psychosocial factors. Using this present approach, only one third of patients enter remission with the first medication prescribed, and patients may take longer than 1 year to enter remission with repeated trials. Research to improve treatment effectiveness recently has focused on identification of intermediate phenotypes (IPs) that could parse the heterogeneous population of patients with MDD into subgroups with more homogeneous responses to treatment. Such IPs could be used to develop biomarkers that could be applied clinically to match patients with the treatment that would be most likely to lead to remission. Putative biomarkers include genetic polymorphisms, RNA and protein expression (transcriptome and proteome), neurotransmitter levels (metabolome), additional measures of signaling cascades, oscillatory synchrony, neuronal circuits and neural pathways (connectome), along with other possible physiologic measures. All of these measures represent components of a continuum that extends from proximity to the genome to proximity to the clinical phenotype of depression, and there are many levels along this continuum at which useful IPs may be defined. Because of the highly integrative nature of brain systems and the complex neurobiology of depression, the most useful biomarkers are likely to be those with intermediate proximity both to the genome and the clinical phenotype of MDD. Translation of findings across the spectrum from genotype to phenotype promises to better characterize the complex disruptions in signaling and neuroplasticity that accompany MDD, and ultimately to lead to greater understanding of the causes of depressive illness.
The NMDA Receptor M3 Segment Is a Conserved Transduction Element Coupling Ligand Binding to Channel Opening

Ion channels alternate stochastically between two functional states, open and closed. This gating behavior is controlled by membrane potential or by the binding of neurotransmitters in voltage- and ligand-gated channels, respectively. Although much progress has been made in defining the structure and function of the ligand-binding cores and the voltage sensors, how these domains couple to channel opening remains poorly understood. Here we show that the M3 transmembrane segments of the NMDA receptor allosterically interact with both the ligand-binding cores and the channel gate. It is proposed that M3 functions as a transduction element whose conformational change couples ligand binding with channel opening. Furthermore, amino acid homology between glutamate receptor M3 segments and the equivalent S6 or TM2 segments in K+ channels suggests that ion channel activation and gating are both structurally and functionally conserved.
Automatic floor segmentation for indoor robot navigation

Indoor autonomous robots can perform desired task in indoor environments without continuous human guidance, so navigation is indispensable for them. In the state of the art of vision-based navigation, one or more cameras are usually installed on a robot. This has led to a larger workload to deal with the data collected by cameras and arises the problem of delay. In the paper, we propose a novel vision-based navigation framework for indoor autonomous robots in which the camera is fixed on the ceiling. In the navigation scheme, a robot takes floor as their moving regions. So floor segmentation algorithm has to be designed to get floor regions in navigation images automatically. We adopted clustering analysis to implement automatic floor segmentation, and we also proposed a PCA based improved version of the algorithm to remove negative effect of shadow for segmented results.
The burden of diabetes (care).

Now that there is a plethora of clinical trial data with clinically meaningful end points proving that the burden of diabetes can be improved by a variety of interventions, including glycemic, blood pressure, and lipid control; the use of statins, ACE inhibitors, and aspirin; appropriately timed laser therapy for diabetic retinopathy; and screening of feet at high risk for neuropathic ulcers, it is now time to evaluate just how well we do with our current level of care. Over the past few years, there have been a variety of surveys indicating that despite our evidenced-based clinical trial data, diabetes care in the U.S. has been abysmal. Several of these reports have focused on levels of diabetes care comparing how providers of different specialties (and their patients) performed when compared with each other (1–4) in addition to the national standards. The ensuing discussions and controversies did not really address the major problem: all of the providers provided less-than-optimal care, and although there are many reasons for this, perhaps the most important one is the fact that our current systems of diabetes care make outstanding management for all difficult, if not impossible. Unfortunately, many providers confuse the “burden of diabetes,” which refers to diabetes-related morbidity and mortality issues, with the “burden of diabetes care. ” This latter concept is all too prevalent for too many physicians. These patients are complex, often do not take the best care of themselves, require multiple medications, and, importantly, often require follow-up between visits. For a primary care provider who may be allowed 10 or, at the most, 15 min to see this patient (an impossible task even with twice as much time), seeing many of these patients is truly …
Internet Resources for Radio Astronomy

A subjective overview of Internet resources for radio-astronomical information is presented. Basic observing techniques and their implications for the interpretation of publicly available radio data are described, followed by a discussion of existing radio surveys, their level of optical identification, and nomenclature of radio sources. Various collections of source catalogues and databases for integrated radio source parameters are reviewed and compared, as well as the web interfaces to interrogate the current and ongoing large-area surveys. Links to radio observatories with archives of raw (uv-) data are presented, as well as services providing images, both of individual objects or extracts (``cutouts'') from large-scale surveys. While the emphasis is on radio continuum data, a brief list of sites providing spectral line data, and atomic or molecular information is included. The major radio telescopes and surveys under construction or planning are outlined. A summary is given of a search for previously unknown optically bright radio sources, as performed by the students as an exercise, using Internet resources only. Over 200 different links are mentioned and were verified, but despite the attempt to make this report up-to-date, it can only provide a snapshot of the current situation.
Vitamin K Supplementation in Postmenopausal Women with Osteopenia (ECKO Trial): A Randomized Controlled Trial

Background Vitamin K has been widely promoted as a supplement for decreasing bone loss in postmenopausal women, but the long-term benefits and potential harms are unknown. This study was conducted to determine whether daily high-dose vitamin K1 supplementation safely reduces bone loss, bone turnover, and fractures. Methods and Findings This single-center study was designed as a 2-y randomized, placebo-controlled, double-blind trial, extended for earlier participants for up to an additional 2 y because of interest in long-term safety and fractures. A total of 440 postmenopausal women with osteopenia were randomized to either 5 mg of vitamin K1 or placebo daily. Primary outcomes were changes in BMD at the lumbar spine and total hip at 2 y. Secondary outcomes included changes in BMD at other sites and other time points, bone turnover markers, height, fractures, adverse effects, and health-related quality of life. This study has a power of 90% to detect 3% differences in BMD between the two groups. The women in this study were vitamin D replete, with a mean serum 25-hydroxyvitamin D level of 77 nmol/l at baseline. Over 2 y, BMD decreased by −1.28% and −1.22% (p = 0.84) (difference of −0.06%; 95% confidence interval [CI] −0.67% to 0.54%) at the lumbar spine and −0.69% and −0.88% (p = 0.51) (difference of 0.19%; 95% CI −0.37% to 0.75%) at the total hip in the vitamin K and placebo groups, respectively. There were no significant differences in changes in BMD at any site between the two groups over the 2- to 4-y period. Daily vitamin K1 supplementation increased serum vitamin K1 levels by 10-fold, and decreased the percentage of undercarboxylated osteocalcin and total osteocalcin levels (bone formation marker). However, C-telopeptide levels (bone resorption marker) were not significantly different between the two groups. Fewer women in the vitamin K group had clinical fractures (nine versus 20, p = 0.04) and fewer had cancers (three versus 12, p = 0.02). Vitamin K supplements were well-tolerated over the 4-y period. There were no significant differences in adverse effects or health-related quality of life between the two groups. The study was not powered to examine fractures or cancers, and their numbers were small. Conclusions Daily 5 mg of vitamin K1 supplementation for 2 to 4 y does not protect against age-related decline in BMD, but may protect against fractures and cancers in postmenopausal women with osteopenia. More studies are needed to further examine the effect of vitamin K on fractures and cancers. Trial registration: ClinicalTrials.gov (#NCT00150969) and Current Controlled Trials (#ISRCTN61708241)
Identifying and Modeling Financial Time Series : A Neural Network Approach

In this paper, a relatively new dynamic identification method using neural networks is developed for financial time series. Such method can capture homeostatic dynamics of the system under the influence of exogenous event. The results show that financial time series include both predictable deterministic and unpredictable random components. Neural networks can identify the properties of homeostatic dynamics and model the dynamic relation between endogenous and exogenous variables in financial time series input-output system. We also investigate the impact of the number of model inputs and the number of hidden layer neurons on forecasting.
Graphical user interface concepts for tactical augmented reality

Applied Research Associates and BAE Systems are working together to develop a wearable augmented reality system under the DARPA ULTRA-Vis program†. Our approach to achieve the objectives of ULTRAVis, called iLeader, incorporates a full color 40° field of view (FOV) see-thru holographic waveguide integrated with sensors for full position and head tracking to provide an unobtrusive information system for operational maneuvers. iLeader will enable warfighters to mark-up the 3D battle-space with symbologic identification of graphical control measures, friendly force positions and enemy/target locations. Our augmented reality display provides dynamic real-time painting of symbols on real objects, a pose-sensitive 360° representation of relevant object positions, and visual feedback for a variety of system activities. The iLeader user interface and situational awareness graphical representations are highly intuitive, nondisruptive, and always tactically relevant. We used best human-factors practices, system engineering expertise, and cognitive task analysis to design effective strategies for presenting real-time situational awareness to the military user without distorting their natural senses and perception. We present requirements identified for presenting information within a see-through display in combat environments, challenges in designing suitable visualization capabilities, and solutions that enable us to bring real-time iconic command and control to the tactical user community.