Miracle-dz/UniFAR-FTUs huggingface dataset:
Autosomal recessive congenital cataract, intellectual disability phenotype linked to STX3 in a consanguineous Tunisian family

The aim of this study is to investigate the genetic basis of autosomal recessive congenital cataract and intellectual disability phenotype in a consanguineous Tunisian family. The whole genome scan of the studied family was performed with single nucleotide polymorphisms (SNPs). The resulted runs of homozygosity (ROH) were analyzed through the integrated Systems Tool for Eye gene discovery (iSyTE) in order to prioritize candidate genes associated with congenital cataract. Selected genes were amplified and sequenced. Bioinformatic analysis was conducted to predict the function of the mutant gene. We identified a new specific lens gene named syntaxin 3 linked to the studied phenotype. The direct sequencing of this gene revealed a novel missense mutation c.122A>G which results in p.E41G. Bioinformatic analysis suggested a deleterious effect of this mutation on protein structure and function. Here, we report for the first time a missense mutation of a novel lens specific gene STX3 in a phenotype associating autosomal recessive congenital cataract and intellectual disability.
Living at risk

The current research examined whether the associations between attachment orientations and support provision are mediated by personal distress, and whether these mediation paths are moderated by exposure to geopolitical stress. One-hundred and thirty-three married couples, who were exposed to different levels of geopolitical stress, participated in the study. We found that personal distress mediated the link between attachment anxiety and support provision, and that this effect was stronger among people in high-risk areas than in low-risk areas. Personal distress mediated the link between attachment avoidance and support provision, but only among people living in high-risk areas. Our results highlight the importance of considering personal, interpersonal, and contextual factors when studying marital support processes.
Interference-aware Incoming Message Detection for MPI Threaded Progression

To enable overlap of computation and communication with non-blocking collective communication, it is required to progress asynchronously a sequence of communications. One of the naive implementation is to use a separate thread for communitation and run it in back of computation thread. However if the total number of threads is greater than the number of physical cores, context switches cause performance degradation of the computation thread. Simultaneous MultiThread (SMT) can be used to avoid this problem. However, commonly-used busy polling for incoming message detection also causes performance degradation of the computation thread. In this paper, we propose incoming message detection method using MONITOR/MWAIT instructions to reduce the performance degradation. Experiment results show that the performance of computation thread is improved largely compared to the busy polling method while latency is suppressed by a small increase.
The potential for climate-driven bathymetric range shifts: sustained temperature and pressure exposures on a marine ectotherm, Palaemonetes varians

Range shifts are of great importance as a response for species facing climate change. In the light of current ocean-surface warming, many studies have focused on the capacity of marine ectotherms to shift their ranges latitudinally. Bathymetric range shifts offer an important alternative, and may be the sole option for species already at high latitudes or those within enclosed seas; yet relevant data are scant. Hydrostatic pressure (HP) and temperature have wide ranging effects on physiology, importantly acting in synergy thermodynamically, and therefore represent key environmental constraints to bathymetric migration. We present data on transcriptional regulation in a shallow-water marine crustacean (Palaemonetes varians) at atmospheric and high HP following 168-h exposures at three temperatures across the organisms’ thermal scope, to establish the potential physiological limit to bathymetric migration by neritic fauna. We observe changes in gene expression indicative of cellular macromolecular damage, disturbances in metabolic pathways and a lack of acclimation after prolonged exposure to high HP. Importantly, these effects are ameliorated (less deleterious) at higher temperatures, and exacerbated at lower temperatures. These data, alongside previously published behavioural and heat-shock analyses, have important implications for our understanding of the potential for climate-driven bathymetric range shifts
Electrical Activity of Single Fibers of the Atrioventricular Node

The mechanism of atrioventricular delay has been studied in isolated rabbit hearts. Multiple intracellular microelectrodes have been employed to obtain simultaneous records from single fibers of atrium, A-V node and His bundle. An appreciable delay in the transmission of excitation has been found only in the atrial portion of the A-V node. Action potentials recorded from single fibers in this area show a low resting potential, slow diastolic depolarization, slow upstroke and low amplitude. These action potentials frequently show one or more notches or steps on the rising phase. Action potentials recorded from fibers of the His bundle are similar in shape and amplitude to those of peripheral Purkinje fibers. Records obtained at several sites between the atrial portion of the node and the His bundle show a gradual transition in action potential shape. The mechanism of slow transmission across the A-V node is discussed in relation to the electrical activity of fibers at the atrial end of this structure.
The UOT system

We present the UOT Machine Translation System that was used in the IWSLT-09 evaluation campaign. This year, we participated in the BTEC track for Chinese-to-English translation. Our system is based on a string-to-tree framework. To integrate deep syntactic information, we propose the use of parse trees and semantic dependencies on English sentences described respectively by Head-driven Phrase Structure Grammar and Predicate-Argument Structures. We report the results of our system on both the development and test sets.
Ethical Concerns Related to Developing Pharmacogenomic Treatment Strategies for Addiction

Pharmacogenomics (PGx) research is poised to enable physicians to identify optimally effective treatments for individual substance abusers based on their genetic profiles. This paper addresses ethical issues related to PGx treatment strategies for addiction, focusing especially on the use of race variables in genomics research and ensuring equitable access to novel PGx treatments. Unless the field addresses the ethical challenges posed by these issues, PGx treatment innovations for addiction threaten to exacerbate already dramatic disparities in the burden of drug dependence for minority and other underserved populations.
Sensation-seeking, performance genres and substance use among musicians

Popular cultural imagery has long assumed that musicians routinely use both licit and illicit substances for recreational purposes, to enhance creativity or to cope with the vicissitudes of an artistic lifestyle. To date, however, there has been little empirical examination of the presumed links between drugs and musical performance. In this analysis, we examined relationships among personality, musical performance genres, and the use of substances both licit (tobacco and alcohol) and illicit (marijuana and other drugs). Drawing on self-report survey data from a sample of 226 Western New York professional and amateur musicians, we used hierarchical regression analyses to test the simultaneous effects of sensation-seeking and performance genres on eight substance use outcomes, controlling for gender, age, race, and ethnicity. All forms of substance use were positively associated with sensation-seeking. Substance use outcomes were positively associated with Intense/Rebellious genres (e.g., rock) and to a lesser extent with Energetic/Rhythmic genres (e.g., rap/hip-hop), but negatively associated with Upbeat/Conventional genres (e.g., pop) and Reflective/Complex genres (e.g., jazz). The relationships between performance genres and both smoking and alcohol use were gender-specific.
Cognitive tuning of corticospinal excitability during human gait: adaptation to the phase

The aim of this study was to investigate how the cognitive tuning of corticospinal (CS) excitability adapts to the type of evoked‐movement (Flexion vs. Extension) during human gait. Transcranial magnetic stimulation (TMS) was used both as a central perturbation evoking a movement and as a tool for quantifying the CS excitability of the muscles under study (RF/BF). In the first condition (Dst), the TMS occurred at mid‐stance, inducing hip extension, whereas in the second condition (Dsw), the TMS occurred at the beginning of the swing phase, inducing hip flexion. In both conditions, the subjects were asked to cognitively prepare to either not intervene (NINT) or to compensate (COMP) for the evoked‐movements. The results showed that, regardless of the type of evoked‐movement, preparing to compensate resulted in a selective increase in the CS excitability to those muscles that would be involved in counteracting the possible central perturbation, i.e. the hip extensor muscle (BF) to compensate for an evoked flexion during the swing phase or the hip flexor muscle (RF) to compensate for an evoked extension during the stance phase. This latter result offers the first evidence of a modulation in CS excitability to the proximal muscles during the stance phase. In conclusion, the cognitive tuning of CS excitability was found to adapt to the gait phases. Moreover, the same selective preparation strategy was observed whether the central perturbation occurred during the stance or the swing phase of the step cycle.
Changes in conserved region 2 of Escherichia coli sigma 70 affecting promoter recognition.

We describe a mutation in rpoD, the gene encoding the sigma 70 subunit of RNA polymerase, which alters the promoter specificity of the holoenzyme in vivo. The mutant sigma causes a substantial and specific increase in the activity of mutant ant and lac promoters with a T.A to C.G substitution at position -12, the first position of the -10 hexamer. The rpoD mutation is a single base-pair substitution causing a Gln----His change at position 437, which is in a domain of conserved region 2.4 that is predicted to form an alpha-helix. Gln437 would lie one turn of the alpha-helix away from Thr440, which was previously implicated in recognition of position -12. The rpoD-QH437 mutation described here lends further support to the model that region 2.4 of sigma is involved in recognition of the 5' end of the -10 hexamer. In addition, two rpoD mutations with non-specific effects on promoter recognition are described.
Quality by design in formulation and process development for a freeze-dried, small molecule parenteral product: a case study

A case study has been developed to illustrate one way of incorporating a Quality by Design approach into formulation and process development for a small molecule, freeze-dried parenteral product. Sodium ethacrynate was chosen as the model compound. Principal degradation products of sodium ethacrynate result from hydrolysis of the unsaturated ketone in aqueous solution, and dimer formation from a Diels–Alder condensation in the freeze-dried solid state. When the drug crystallizes in a frozen solution, the eutectic melting temperature is above −5°C. Crystallization in the frozen system is affected by pH in the range of pH 6–8 and buffer concentration in the range of 5–50 mM, where higher pH and lower buffer concentration favor crystallization. Physical state of the drug is critical to solid state stability, given the relative instability of amorphous drug. Stability was shown to vary considerably over the ranges of pH and buffer concentration examined, and vial-to-vial variability in degree of crystallinity is a potential concern. The formulation design space was constructed in terms of pH and drug concentration, and assuming a constant 5 mM concentration of buffer. The process design space is constructed to take into account limitations on the process imposed by the product and by equipment capability.
Synchronous Optical Hierarchy

We introduce and describe the problems and challenges for the SOH (synchronous optical hierarchy), which is a form of WRON (wavelength routed optical network) where the signals occupy fractions of a wavelength through the use of timeslots in frames. Using timeslots for transparent optical networks will solve the capacity granularity problem which is present in the WRON. We define the problem of assigning wavelengths and timeslots to traffic demands by mathematical formulations in integer linear programming. By solving the integer linear programs for networks with static traffic assumptions we compare efficiency of SOH networks with WRONs measured in wavelength usage. Further, the influence of the timeslot and frame parameters describing SOH networks is studied. The effect of timeslot and wavelength conversion in SOH networks are also studied, as well as the presence of delay of timeslots.
Statistical modelling in the investigation of stranger rape

A sample of stranger rape offences (n = 271) registered in the Dutch Violence Crime Linkage Analysis System database in the Netherlands between 1997 and 2007 was studied with the objective of developing statistical models, which give an indication of the probability of basic offender characteristics. Observable crime characteristics concerning the modus operandi, interaction between the offender and the victim, violence, precautionary measures, and sexual behaviours were selected in the dataset. Offender characteristics were selected based on their usefulness for the police organisation in narrowing the scope of a criminal investigation. Spatial behaviour, criminal history, and living situation of the offender were selected. From the predictive models, four out of five achieved a correct rate of over 70%, and all models predicted better than the best guess method. The proposed models for distance and prior convictions for violence seem particularly promising. Both these models show an improvement of correctly predicted offender characteristics of more than 20 percentile points compared with that which could have been estimated based on the average in the total sample. The predictive value of the models needs to be tested further with ‘new offences’, which were not used to construct the model. In general, the current study supports the finding that crime characteristics can be used to get an indication of the probability of certain offender characteristics. Nevertheless, for an understanding of the relationship between the crime characteristics and offender characteristics, a further development of a theoretical framework is urgently necessary. Copyright © 2009 John Wiley & Sons, Ltd.
Trickle-D: High Fairness and Low Transmission Load With Dynamic Redundancy

Embedded devices of the Internet of Things form the so-called low-power and lossy networks. In these networks, nodes are constrained in terms of energy, memory, and processing. Links are lossy and exhibit a transient behavior. From the point of view of energy expenditure, governing control overhead emission is crucial and is the role of the Trickle algorithm. We address Trickle’s fairness problem to evenly distribute the transmission load across the network, while keeping the total message count low. First, we analytically analyze two underlying causes of unfairness in Trickle networks: 1) desynchronization among nodes and 2) nonuniform topologies. Based on our analysis, we propose a first algorithm whose performance and parameters we study in an emulated environment. From this feedback, we design a second algorithm Trickle-D that adapts the redundancy parameter to achieve high fairness while keeping the transmission load low. We validate Trickle-D in real-life conditions using a large scale experimental testbed. Trickle-D requires minimal changes to Trickle, zero user input, emits 17.7% less messages than state-of-the-art and 37.2% less messages than state-of-practice, while guaranteeing high fairness across the network.
Inhibition of the replication of hepatitis B virus by the carbocyclic analogue of 2'-deoxyguanosine.

We report that treatment of 2.2. 15, a human hepatoblastoma-derived cell line in which hepatitis B virus is actively replicating, with the carbocyclic analogue of 2'-deoxyguanosine [Shealy, Y. F. , O'Dell, C. A. , Shannon, W. M. & Arnett, G. (1984) J. Med. Chem. 27, 1416-1421] resulted in the nearly complete cessation of viral replication, as monitored by the absence of both intracellular episomal and secreted viral DNAs and by the absence of viral DNA polymerase activity. The drug was nontoxic in concentrations up to 200 times the minimum effective inhibitory concentration.
Signal Detection Using Ica: Application to Chat Room Topic Spotting

Signal detection and pattern recognition for online grouping huge amounts of data and retrospective analysis is becoming increasingly important as knowledge based standards, such as XML and advanced MPEG, gain popularity. Independent component analysis (ICA) can be used to both cluster and detect signals with weak a priori assumptions in multimedia contexts. ICA of real world data is typically performed without knowledge of the number of non-trivial independent components, hence, it is of interest to test hypotheses concerning the number of components or simply to test whether a given set of components is significant relative to a “white noise” null hypothesis. It was recently proposed to use the so-called Bayesian information criterion (BIC) approximation, for estimation of such probabilities of competing hypotheses. Here, we apply this approach to the understanding of chat. We show that ICA can detect meaningful context structures in a chat room log file.
Drunk and (Dis) Orderly: the Role of Alcohol in Supporting Liminality

This paper examines the use of alcohol consumption to provide support for students during transitions at a key liminal stage. We explore some of the positive experiences and rituals surrounding alcohol consumption via student-led focus groups. Our findings suggest that this extended period of liminality is often experienced positively, lending students ‘permission’ to behave in ways they might otherwise consider unacceptable. Liminality helps us to understand this context of students ‘betwixt and between’ different important life stages, whereby alcohol assumes an important facilitating role enabling them to play with their identity.
The impact of electrode area, contact impedance and boundary shape on EIT images

Electrical impedance tomography (EIT) measures the conductivity distribution within an object based on the current applied and voltage measured at surface electrodes. Thus, EIT images are sensitive to electrode properties (i.e. contact impedance, electrode area and boundary shape under the electrode). While some of these electrode properties have been investigated individually, this paper investigates these properties and their interaction using finite element method simulations and the complete electrode model (CEM). The effect of conformal deformations on image reconstruction when using the CEM was of specific interest. Observed artefacts were quantified using a measure that compared an ideal image to the reconstructed image, in this case a no-noise reconstruction that isolated the electrodes’ effects. For electrode contact impedance and electrode area, uniform reductions to all electrodes resulted in ringing artefacts in the reconstructed images when the CEM was used, while parameter variations that were not correlated amongst electrodes resulted in artefacts distributed throughout the image. When the boundary shape changed under the electrode, as with non-symmetric conformal deformations, using the CEM resulted in structured distortions within the reconstructed image. Mean electrode contact impedance increases, independent of inter-electrode variation, did not result in artefacts in the reconstructed image.
ASN-FWD: Shrinking the IPv4 Share on the Forwarding Information Base

This paper presents a proposal for shrinking the number of IPv4 FIB (Forwarding Information Base) entries required on routers. Traffic forwarding under the proposed mechanism is based on the current ASNs (Autonomous System Numbers), and can be gradually adopted by ISPs.We find that, at the cost of adding 8 bytes per packet, the proposed ASN-FWD technique is capable of providing full IPv4 traffic forwarding based on ASN information, which is correspondent to 10% of the current number of IPv4 prefixes present on FIB of routers. Among its main benefits, the proposed approach alleviates the pressure on the amount of FIB shipped on routers, and paves the way for a worldwide adoption of IPv6.
The relationship between qualitative and quantitative research: Lessons from feminist psychology

The dominant methodological approach in psychological research has involved the use of quantitative methods within a positivist framework. In this article we argue that both qualitative and quantitative methods have their strengths and limitations, depending on the research question under investigation. We examine some of the advantages of qualitative methods, paying particular attention to the value of such methods for feminist researchers. We challenge the positivist assumption that all research should be apolitical and value-free, arguing that the political context in which all research studies take place plays an important role in decisions about the appropriate research methods to use. Despite the value attached to qualitative methods by feminist researchers, there may be projects for which quantitative methods, or a combination of qualitative and quantitative techniques, are more suitable. We draw on examples from our research on the transition from school to the job market for young people, and a study of 16- to 19-year-old first time mothers to illustrate these points, examining the practical implications of our arguments for applied social psychology research
Maximizing Production of Human Interferon-γ in HCDC of Recombinant E. coli

Tuning recombinant protein expression is an approach which can be successfully employed for increasing the yield of recombinant protein production in high cell density cultures. On the other hand, most of the previous results reported the optimization induction conditions during batch and continuous culture of recombinant E. coli, and consequently fed-batch culture have received less attention. Hence, in this research induction conditions for the over-production of recombinant interferon-γ including the amount of inducer, induction time and post-induction duration during chemical induction were optimized. E. coli BL21 (DE3) (pET3a-hifnγ) was used to over-express human interferon-gamma (hIFN-γ) in an exponential fed-batch procedure with a maximum attainable specific growth rate of 0.55 h-1 at the beginning of feeding and 0.4 h-1 in induction time. The factors were considered as the amount of inducer (IPTG) in the range of 0.565-22 mg g-1 L-1 at seven levels, cell density at induction time as 53, 65 and 75 g (dry cell weight) L-1, induction duration at different intervals of 3, 4, and 5 h after induction time. The final concentration of biomass and interferon gamma reached to 127 g L-1 (DCW) and 51 g (hIFN-γ) L-1 after 17 h, and also the final specific yield and overall productivity were obtained 0.4 g (hIFN-γ) g-1 DCW and 3 g (hIFN-γ) L-1 h-1, respectively, which are the highest amounts of reported specific yield and productivity for recombinant proteins production.