Miracle-dz/UniFAR-FTUs huggingface dataset:
A SRS2 homolog from Arabidopsis thaliana disrupts recombinogenic DNA intermediates and facilitates single strand annealing

Genetic and biochemical analyses of SRS2 homologs in fungi indicate a function in the processing of homologous recombination (HR) intermediates. To date, no SRS2 homologs have been described and analyzed in higher eukaryotes. Here, we report the first biochemical characterization of an SRS2 homolog from a multicellular eukaryote, the plant Arabidopsis thaliana. We studied the basic properties of AtSRS2 and were able to show that it is a functional 3′- to 5′-helicase. Furthermore, we characterized its biochemical function on recombinogenic intermediates and were able to show the unwinding of nicked Holliday junctions (HJs) and partial HJs (PX junctions). For the first time, we demonstrated strand annealing activity for an SRS2 homolog and characterized its strand pairing activity in detail. Our results indicate that AtSRS2 has properties that enable it to be involved in different steps during the processing of recombination intermediates. On the one hand, it could be involved in the unwinding of an elongating invading strand from a donor strand, while on the other hand, it could be involved in the annealing of the elongated strand at a later step.
Augmenting the Field-of-View of Head-Mounted Displays with Sparse Peripheral Displays

In this paper, we explore the concept of a sparse peripheral display, which augments the field-of-view of a head-mounted display with a lightweight, low-resolution, inexpensively produced array of LEDs surrounding the central high-resolution display. We show that sparse peripheral displays expand the available field-of-view up to 190º horizontal, nearly filling the human field-of-view. We prototyped two proof-of-concept implementations of sparse peripheral displays: a virtual reality headset, dubbed SparseLightVR, and an augmented reality headset, called SparseLightAR. Using SparseLightVR, we conducted a user study to evaluate the utility of our implementation, and a second user study to assess different visualization schemes in the periphery and their effect on simulator sickness. Our findings show that sparse peripheral displays are useful in conveying peripheral information and improving situational awareness, are generally preferred, and can help reduce motion sickness in nausea-susceptible people.
A Novel Transgenic Rat Model for Spinocerebellar Ataxia Type 17 Recapitulates Neuropathological Changes and Supplies In Vivo Imaging Biomarkers

Spinocerebellar ataxia 17 (SCA17) is an autosomal-dominant, late-onset neurodegenerative disorder caused by an expanded polyglutamine (polyQ) repeat in the TATA-box-binding protein (TBP). To further investigate this devastating disease, we sought to create a first transgenic rat model for SCA17 that carries a full human cDNA fragment of the TBP gene with 64 CAA/CAG repeats (TBPQ64). In line with previous observations in mouse models for SCA17, TBPQ64 rats show a severe neurological phenotype including ataxia, impairment of postural reflexes, and hyperactivity in early stages followed by reduced activity, loss of body weight, and early death. Neuropathologically, the severe phenotype of SCA17 rats was associated with neuronal loss, particularly in the cerebellum. Degeneration of Purkinje, basket, and stellate cells, changes in the morphology of the dendrites, nuclear TBP-positive immunoreactivity, and axonal torpedos were readily found by light and electron microscopy. While some of these changes are well recapitulated in existing mouse models for SCA17, we provide evidence that some crucial characteristics of SCA17 are better mirrored in TBPQ64 rats. Thus, this SCA17 model represents a valuable tool to pursue experimentation and therapeutic approaches that may be difficult or impossible to perform with SCA17 transgenic mice. We show for the first time positron emission tomography (PET) and diffusion tensor imaging (DTI) data of a SCA animal model that replicate recent PET studies in human SCA17 patients. Our results also confirm that DTI are potentially useful correlates of neuropathological changes in TBPQ64 rats and raise hope that DTI imaging could provide a biomarker for SCA17 patients.
Characterization of a factor that promotes neurite outgrowth: evidence linking activity to a heparan sulfate proteoglycan

Rat sympathetic neurons, plated onto extracellular matrix produced by cultured bovine corneal endothelial cells, rapidly extended neurites in the absence of nerve growth factor (NGF). The response was unaffected by antiserum to NGF. Rapid outgrowth also occurred when sympathetic neurons were plated onto polylysine-coated surfaces that had been exposed to serum-free medium conditioned by corneal endothelial cells (CMSF). A response was seen even when the neurons were cultured without serum. When plated onto a polylysine-coated dish treated with CMSF over half its surface, only the neurons on the treated half extended neurites. The active factor in CMSF was destroyed by trypsin, acid (pH 1.6), base (pH 12.7), or heating to 80 degrees C; it was stable to heating to 60 degrees C, collagenase, deoxyribonuclease, and neuraminidase. The factor elutes just after the void volume of a Sepharose 6B column. In associative cesium chloride gradients, it sediments as a peak centered at a density of 1.36-1.37, corresponding to a peak of material that can be biosynthetically labeled with [35S]sulfate or [3H]leucine. Material from this fraction was inactivated by heparinase, but not chondroitinase ABC, implying that a heparin sulfate proteoglycan is essential for the factor's activity. Inactivation by contaminants in the heparinase preparation was ruled out. Further purification indicated that the active factor may exist as an aggregate containing a heparin sulfate proteoglycan and other molecules. CMSF also promoted neurite outgrowth by other types of neurons. Furthermore, a variety of cell types were shown to produce factors similar to that in CMSF.
EMG-based control of an exoskeleton robot for human forearm and wrist motion assist

We have been developing exoskeleton robots for assisting the motion of physically weak individuals such as elderly or slightly disabled in daily life. In this paper we propose an EMG-based control of a three degree of freedom (3-DOF) exoskeleton robot for the forearm pronation/supination motion, wrist flexion/extension motion and ulnar/radial deviation. The paper describes the hardware design of the exoskeleton robot and the control method. The skin surface electromyographic (EMG) signals of muscles in forearm of the exoskeleton's user and the hand force/forearm torque are used as input information for the proposed controller. By applying the skin surface EMG signals as main input signals to the controller, automatic control of the robot can be realized without manipulating any other equipment. Fuzzy control method has been applied to realize the natural and flexible motion assist. An experiment has been performed to evaluate the proposed exoskeleton robot.
Diffraction modeling for interactive virtual acoustical environments

Since the dimensions of many of the objects/surfaces encountered in our daily lives are within an order of magnitude of the wavelength of audible sounds, diffraction is an elementary means of sound propagation. Despite its importance in the real-world, diffraction effects are often overlooked by acoustical modeling methods leading to a degredation in immersion or presence. This paper describes an acoustical diffraction method based on the Huygens-Fresnel principle. The method is simple and efficient allowing it to be incorporated in interactive acoustical environments including virtual environments. Experimental results are presented that illustrate the performance and effectiveness of the method and its conformance to theoretical diffraction models.
Controlling for localised spatio-temporal autocorrelation in long-term air pollution and health studies

Estimating the long-term health impact of air pollution using an ecological spatio-temporal study design is a challenging task, due to the presence of residual spatio-temporal autocorrelation in the health counts after adjusting for the covariate effects. This autocorrelation is commonly modelled by a set of random effects represented by a Gaussian Markov random field (GMRF) prior distribution, as part of a hierarchical Bayesian model. However, GMRF models typically assume the random effects are globally smooth in space and time, and thus are likely to be collinear to any spatially and temporally smooth covariates such as air pollution. Such collinearity leads to poor estimation performance of the estimated fixed effects, and motivated by this epidemiological problem, this paper proposes new GMRF methodology to allow for localised spatio-temporal smoothing. This means random effects that are either geographically or temporally adjacent are allowed to be autocorrelated or conditionally independent, which allows more flexible autocorrelation structures to be represented. This increased flexibility results in improved fixed effects estimation compared with global smoothing models, which is evidenced by our simulation study. The methodology is then applied to the motivating study investigating the long-term effects of air pollution on respiratory ill health in Greater Glasgow, Scotland between 2007 and 2011.
Corporate Fraud, Governance and Auditing

We analyze corporate fraud in a model in which managers have superior information but are biased against liquidation, because of their private benefits from empire building. This may induce them to misreport information and even bribe auditors when liquidation would be value-increasing. To curb fraud, shareholders optimally choose auditing quality and the performance sensitivity of managerial pay, taking external corporate governance and auditing regulation into account. For given managerial pay, it is optimal to rely on auditing when external governance is in an intermediate range. When both auditing and incentive pay are used, worse external governance must be balanced by heavier reliance on both of those incentive mechanisms. In designing managerial pay, equity can improve managerial incentives while stock options worsen them.
Exome Capture Sequencing of Adenoma Reveals Genetic Alterations in Multiple Cellular Pathways at the Early Stage of Colorectal Tumorigenesis

Most of colorectal adenocarcinomas are believed to arise from adenomas, which are premalignant lesions. Sequencing the whole exome of the adenoma will help identifying molecular biomarkers that can predict the occurrence of adenocarcinoma more precisely and help understanding the molecular pathways underlying the initial stage of colorectal tumorigenesis. We performed the exome capture sequencing of the normal mucosa, adenoma and adenocarcinoma tissues from the same patient and sequenced the identified mutations in additional 73 adenomas and 288 adenocarcinomas. Somatic single nucleotide variations (SNVs) were identified in both the adenoma and adenocarcinoma by comparing with the normal control from the same patient. We identified 12 nonsynonymous somatic SNVs in the adenoma and 42 nonsynonymous somatic SNVs in the adenocarcinoma. Most of these mutations including OR6X1, SLC15A3, KRTHB4, RBFOX1, LAMA3, CDH20, BIRC6, NMBR, GLCCI1, EFR3A, and FTHL17 were newly reported in colorectal adenomas. Functional annotation of these mutated genes showed that multiple cellular pathways including Wnt, cell adhesion and ubiquitin mediated proteolysis pathways were altered genetically in the adenoma and that the genetic alterations in the same pathways persist in the adenocarcinoma. CDH20 and LAMA3 were mutated in the adenoma while NRXN3 and COL4A6 were mutated in the adenocarcinoma from the same patient, suggesting for the first time that genetic alterations in the cell adhesion pathway occur as early as in the adenoma. Thus, the comparison of genomic mutations between adenoma and adenocarcinoma provides us a new insight into the molecular events governing the early step of colorectal tumorigenesis.
Common biological networks underlie genetic risk for alcoholism in African‐ and European‐American populations

Alcohol dependence (AD) is a heritable substance addiction with adverse physical and psychological consequences, representing a major health and economic burden on societies worldwide. Genes thus far implicated via linkage, candidate gene and genome‐wide association studies (GWAS) account for only a small fraction of its overall risk, with effects varying across ethnic groups. Here we investigate the genetic architecture of alcoholism and report on the extent to which common, genome‐wide SNPs collectively account for risk of AD in two US populations, African‐Americans (AAs) and European‐Americans (EAs). Analyzing GWAS data for two independent case–control sample sets, we compute polymarker scores that are significantly associated with alcoholism (P = 1.64 × 10–3 and 2.08 × 10–4 for EAs and AAs, respectively), reflecting the small individual effects of thousands of variants derived from patterns of allelic architecture that are population specific. Simulations show that disease models based on rare and uncommon causal variants (MAF < 0.05) best fit the observed distribution of polymarker signals. When scoring bins were annotated for gene location and examined for constituent biological networks, gene enrichment is observed for several cellular processes and functions in both EA and AA populations, transcending their underlying allelic differences. Our results reveal key insights into the complex etiology of AD, raising the possibility of an important role for rare and uncommon variants, and identify polygenic mechanisms that encompass a spectrum of disease liability, with some, such as chloride transporters and glycine metabolism genes, displaying subtle, modifying effects that are likely to escape detection in most GWAS designs.
COPING TRENDS OF PARENTS HAVING CHILDREN WITH DEVELOPMENTAL DISABILITIES: A LITERATURE REVIEW

Having to take care of children with developmental disabilities can affect parents not only in their psychological well-being but also affect physical well-being. Taking care of a child with special needs can be a growing experience or it can become stressful depending on how a parent perceives the event. Depending on the cognitive appraisal and the person-environment interaction, parents can either engage in positive behaviours of dealing with the disability or indulge in poor coping behaviour which will have adverse impact physically as well as psychologically. The present article attempts to highlight the various ways of coping used by parents to deal with their children’s disabilities. Review of research papers suggests some clear differences between affected parents and non-affected parents on use of different types of coping strategies along with various moderating factors like education, income, social support available, socio-economic conditions, and type of coping used. There were also findings on how mothers differ from the fathers in their coping behaviours when dealing with disabilities. Article visualizations:
Determinants of Industrial Embeddedness: Evidence from African Manufacturing Firms

Recent developments in policy initiatives as well as some current practical events have combined to put the spotlight on the issue of industrial embeddedness in sub-Saharan Africa. Though extant research documents, some stylized facts, as determinants of its manifestations of their relevance to realities in the sub-continent, have until now been overlooked. Yet, it is difficult to ignore the fact that its constituent economies possess some peculiar attributes with potentially significant implications for embeddedness behaviour. Using data for the country of Lesotho, a probit model is estimated to ascertain the veracity of some of the widely acclaimed explanatory factors. We find, as we argue, that among all, the issue of supply potentials appears the most important.
CMOS transconductance multipliers: a tutorial

Real time analog multiplication of two signals is one of the most important operations in analog signal processing. The multiplier is used not only as a computational building block but also as a programming element in systems such as filters, neural networks, and as mixers and modulators in a communication system. Although high performance bipolar junction transistor multipliers have been available for some time, the CMOS multiplier implementation is still a challenging subject especially for low-voltage and low-power circuit design. Despite the large number of papers proposing new CMOS multiplier structures, they can be roughly grouped into a few categories. This tutorial provides a complete survey of CMOS multipliers, presents a unified generation of multiplier architectures, and proposes the most recommended MOS multiplier structure. This tutorial could serve as a starting reference point (and metric) for comparison of new CMOS multiplier circuit configurations. An illustrative CMOS chip prototype verifying theoretical results is presented.
High-Performance Spatial Join Processing on GPGPUs with Applications to Large-Scale Taxi Trip Data

Spatially joining GPS recorded locations with infrastructure data, such as points of interests, road network, land cover and different types of zones, and assigning a point with its nearest polyline or polygon is a prerequisite for trip related analysis, which is becoming increasingly important in ubiquitous computing. However, existing spatial databases and GIS are incapable of handling large-scale data. The poor performance of these systems that takes tens of hours to dozens of days to complete such a commonly used spatial join query is undesirable. By leveraging several high-performance techniques, including massive data parallel General Purpose computing on Graphics Processing Units (GPGPU) technologies and cache friendly main-memory data structures, we are able to design an efficient spatial join query processing system. The experiments using a commodity workstation equipped with a Nvidia GPU device and real NYC taxi trip location data show that our system can join 170 million points with nearly a million polygons based on the nearest neighbor principle in about 33 seconds The performance represents a 3-4 orders of speedup when compared with an optimized serial CPU implementation using two leading open source packages for spatial indexing and spatial data management, respectively. We report our designs and implementations of GPU based filtering and refinement in spatial join processing and discuss the implications of modern hardware architectures for spatial databases and GIS.
SCALING LAWS FOR DARK MATTER HALOS IN LATE-TYPE AND DWARF SPHEROIDAL GALAXIES

Dark matter (DM) halos of Sc–Im and dwarf spheroidal (dSph) galaxies satisfy scaling laws: halos in lower-luminosity galaxies have smaller core radii, higher central densities, and smaller velocity dispersions. These results are based on maximum-disk rotation curve decompositions for giant galaxies and Jeans equation analysis for dwarfs. (1) We show that spiral, Im, and Sph galaxies with absolute magnitudes MV > −18 form a sequence of decreasing baryon-to-DM surface density with decreasing luminosity. We suggest that this is a sequence of decreasing baryon retention versus supernova-driven losses or decreasing baryon capture after cosmological reionization. (2) The structural differences between S+Im and Sph galaxies are small. Both are affected mostly by the physics that controls baryon depletion. (3) There is a linear correlation between the maximum rotation velocities of baryonic disks and the outer circular velocities Vcirc of test particles in their DM halos. Baryons become unimportant at Vcirc = 42 ± 4 km s−1. Smaller galaxies are dim or dark. (4) We find that, absent baryon “depletion” and with all baryons converted into stars, dSph galaxies would be brighter by ∼4.6 mag and dIm galaxies would be brighter by ∼3.5 mag. Both have DM halos that are massive enough to help to solve the “too big to fail” problem with DM galaxy formation. (5) We suggest that there exist many galaxies that are too dark to be discovered by current techniques, as required by cold DM theory. (6) Central surface densities of DM halos are constant from MB ∼ −5 to −22. This implies a Faber–Jackson law with halo mass M ∝ (halo dispersion)4.
Developmental Neurobiology of the Rat Attachment System and Its Modulation by Stress

Stress is a powerful modulator of brain structure and function. While stress is beneficial for survival, inappropriate stress dramatically increases the risk of physical and mental health problems, particularly when experienced during early developmental periods. Here we focus on the neurobiology of the infant rat’s odor learning system that enables neonates to learn and approach the maternal odor and describe the unique role of the stress hormone corticosterone in modulating this odor approach learning across development. During the first nine postnatal days, this odor approach learning of infant rats is supported by a wide range of sensory stimuli and ensures attachment to the mother’s odor, even when interactions with her are occasionally associated with pain. With maturation and the emergence of a stress- or pain-induced corticosterone response, this odor approach learning terminates and a more adult-like amygdala-dependent fear/avoidance learning emerges. Strikingly, the odor approach and attenuated fear learning of older pups can be re-established by the presence of the mother, due to her ability to suppress her pups’ corticosterone release and amygdala activity. This suggests that developmental changes in stress responsiveness and the stimuli that produce a stress response might be critically involved in optimally adapting the pup’s attachment system to its respective ecological niche.
Write-aware random page initialization for non-volatile memory systems

Due to the high scalability and low power leakage, emerging non-volatile memories (NVMs) are promising to be integrated into memory hierarchy. However, NVMs have write issues, such as limited write endurance and high write energy. This paper observes that a large fraction of writes are caused by memory page initialization in the OS kernel stack. Thus, this paper proposes a write-aware random page initialization technique (WRPI) to reduce writes without sacrificing system security. Instead of initializing all bits of an allocated page, WRPI randomly initializes part bits. Moreover, WRPI sets the values of initialized bits to zeros or ones that require writing the least number of bits. The evaluation results show that WRPI can reduce writing bits to NVM memory by up to 21.0% and 11.3% on average, compared to the conventional page initialization. WRPI can also reduce the write energy consumption and the total energy consumption of NVM memory system by 14.0% and 5.8% on average, respectively.