Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular tools for studying HIV transmission in sexual networks

Purpose of reviewPhylogenetics is frequently used for studies of population-based HIV transmission. The purpose of this review is to highlight the current utilities and limitations of phylogenetics in HIV epidemiological research from sample collection through to data analysis. Recent findingsStudies of HIV phylogenies can provide critical information about HIV epidemics that are otherwise difficult to obtain through traditional study design such as transmission of drug-resistant virus, mixing between demographic groups, and rapidity of viral spread within populations. However, recent results from empirical and theoretical studies of HIV phylogenies challenge some of the key assumptions and interpretations from phylogenetic studies. Recent findings include lack of transmission bottlenecks in MSM and injection drug use epidemics, evidence for preferential transmission of HIV virus in heterosexual epidemics, and limited evidence that tree topologies correlate directly with underlying network structures. Other challenges include a lack of a standardized definition for a phylogenetic transmission cluster and biased or sparse sampling of HIV transmission networks. SummaryPhylogenetics is an important tool for HIV research, and offers opportunities to understand critical aspects of the HIV epidemic. Like all epidemiological research, the methods used and interpretation of results from phylogenetic studies should be made cautiously with careful consideration.
Track-Before-Detect Algorithms for Targets with Kinematic Constraints

We propose and assess new algorithms for adaptive detection and tracking based on space-time data. At design stage we take into account possible spillover of target energy to adjacent range cells and assume a target kinematic model. Then, resorting to the generalized likelihood ratio test (GLRT) we derive track-before-detect (TBD) algorithms that can operate in scan-to-scan varying scenarios and, more important, that ensure the constant false track acceptance rate (CFTAR) property with respect to the covariance matrix of the disturbance. Moreover, we also propose CFTAR versions of the maximum likelihood-probabilistic data association (ML-PDA) algorithm capable of working with data from an array of sensors. The preliminary performance assessment, conducted resorting to Monte Carlo simulation, shows that the proposed TBD structures outperform the ML-PDA implementations especially in terms of probability of track detection (and for low signal-to-noise ratio (SNR) values).
Associations between nucleus accumbens structural connectivity, brain function, and initiation of binge drinking

Adolescent alcohol use is associated with increased risk for alcohol use disorders later in life; therefore, identifying biomarkers for initiation of heavy alcohol use, such as individual differences in the development of white‐matter microstructure, may inform prevention strategies that improve public health. This prospective cohort study included 40 adolescents, ages 14 and 15, without substantial history of alcohol or drug use at baseline. Fractional anisotropy (FA), an index of white‐matter microstructure, was assessed in pathways connecting the nucleus accumbens (NAcc) to the rest of the brain using diffusion tensor imaging. Path analyses were conducted voxel‐wise within these pathways to examine direct effects of premorbid FA on number of months between baseline assessment and the onset of binge drinking and indirect effects mediated by NAcc activation during decision making assessed using functional magnetic resonance imaging. Adolescents with lower premorbid accumbofrontal FA began binge drinking sooner, an effect which was mediated by greater NAcc activation during decision making involving greater levels of risk and reward (P < .05 corrected). An additional direct effect of FA on duration to onset of binge drinking was observed in white matter near the ventral pallidum, as adolescents with lower premorbid FA in this region began binge drinking sooner (P < .05 corrected). Findings suggest that delayed maturation of prefrontal white matter is associated with less top‐down control over striatal sensitivity to reward. These factors, along with individual differences in white matter proximal to ventral pallidum, may represent premorbid risk factors for earlier initiation of heavy alcohol use.
Strain Monitoring of a Composite Drag Strut in Aircraft Landing Gear by Fiber Bragg Grating Sensors

This work reports on the use of Fiber Bragg Grating (FBG) sensors integrated with innovative composite items of aircraft landing gear for strain/stress monitoring. Recently, the introduction of innovative structures in aeronautical applications is appealing with two main goals: (i) to decrease the weight and cost of current items; and (ii) to increase the mechanical resistance, if possible. However, the introduction of novel structures in the aeronautical field demands experimentation and certification regarding their mechanical resistance. In this work, we successfully investigate the possibility to use Fiber Bragg Grating sensors for the structural health monitoring of innovative composite items for the landing gear. Several FBG strain sensors have been integrated in different locations of the composite item including region with high bending radius. To optimize the localization of the FBG sensors, load condition was studied by Finite Element Method (FEM) numerical analysis. Several experimental tests have been done in range 0–70 kN by means of a hydraulic press. Obtained results are in very good agreement with the numerical ones and demonstrate the great potentialities of FBG sensor technology to be employed for remote and real-time load measurements on aircraft landing gears and to act as early warning systems.
Blockage of glutamine-dependent anaplerosis affects mTORC1/2 activity and ultimately leads to cellular senescence-like response

ABSTRACT The purpose of study was to explore the role of glutamine-dependent anaplerosis in cell fate determination (proliferation and senescence) and the potential associated mechanism by employing a pharmacological inhibitor of glutamine-dependent anaplerosis, amino-oxyacetate (AOA). Using the WI38 normal human embryonic fibroblast cell line, we found that exposure to AOA induced mTORC1 inactivation−mTORC2 activation (within day 1), cell cycle arrest (day 2–6) and cellular senescence (day 4–6). These AOA effects were blocked by concomitantly providing anaplerotic factors [α-ketoglutarate (αKG), pyruvate or oxaloacetate], and not affected by ROS scavenger N-acetyl-cysteine (NAC). Moreover, AOA-induced cellular senescence in WI38 cells is associated with elevated protein levels of p53, p21CIP1 and p16INK4A and decreased Rb protein level, which was blocked by αKG supplementation. In p16INK4A-deficient U2OS human osteosarcoma cells and p16INK4A-knockdown WI38 cells, AOA exposure also induced similar effects on cell proliferation, and protein level of P-Rb-S807/811 and Rb. Interestingly, no AOA induction of cellular senescence was observed in U2OS cells, yet was still seen in p16INK4A-knockdown WI38 cells accompanied by the presence of p16 antibody-reactive p12. In summary, we disclose that glutamine-dependent anaplerosis is essential to cell growth and closely associated with mTORC1 activation and mTORC2 inactivation, and impedes cellular senescence particularly associated with p16INK4A. Summary: Glutamine-dependent anaplerosis is essential to cell growth and closely associated with mTORC1 activation and mTORC2 inactivation, and impedes cellular senescence particularly associated with p16INK4A.
Simple space-time coded SS-CDMA systems capable of perfect MUI/ISI elimination

In this letter we propose a very simple strategy for combining space-time block coding (STBC) with code division multiple access (CDMA) to be used in single-user links or in broadcasting over time-dispersive channels. The proposed system provides the desired space diversity gain and is capable of perfect cancellation of multiuser interference (MUI) and intersymbol interference (ISI), using a very simple receiver structure. The advantage is obtained by simply incorporating cyclic prefixes in the user codes. We provide a theoretical analysis, verified via simulation results, and a comparison between CDMA and OFDMA systems incorporating STBC.
Molecular cloning, expression, purification, and functional characterization of SP‐22 gene from Bombyx mori

Serine protease (SPs) is one of the immune enzyme's molecules that play a main role in the variation of a physiological process by controlling protease actions in vertebrates. For example, signaling cells, protector and improvement, which are included in melanization, are utilized to cascade with the meddling pathogens and defense the harmed tissue in insects. In this study, we explore the biochemical process of (SP‐22) from Bombyx mori. Reverse‐transcription polymerase chain reaction (RT‐PCR) discloses that BmSP‐22 is expressed in all tissues including the fat body. The formative expression profile of BmSP‐22 reveal that BmSP‐22 messenger RNA is expressed constitutively in larvae. Injection of recombinant BmSP‐22 into B. mori larvae reduces significantly the transcript levels of antimicrobial peptides in the fat body. Our results suggest that BmSP‐22 plays an important role in the innate immunity of B. mori and possibly in other insects.
Identification of a dimerization domain in the TMEM16A calcium-activated chloride channel (CaCC)

Transmembrane proteins with unknown function 16 (TMEM16A) is a calcium-activated chloride channel (CaCC) important for neuronal, exocrine, and smooth muscle functions. TMEM16A belongs to a family of integral membrane proteins that includes another CaCC, TMEM16B, responsible for controlling action potential waveform and synaptic efficacy, and a small-conductance calcium-activated nonselective cation channel, TMEM16F, linked to Scott syndrome. We find that these channels in the TMEM16 family share a homodimeric architecture facilitated by their cytoplasmic N termini. This dimerization domain is important for channel assembly in eukaryotic cells, and the in vitro association of peptides containing the dimerization domain is consistent with a homotypic protein–protein interaction. Amino acid substitutions in the dimerization domain affect functional TMEM16A-CaCC channel expression, as expected from its critical role in channel subunit assembly.
Relationship between Type D Personality and Anhedonia: A Dimensional Study of University Students

Type D personality—characterized by negative affectivity and social inhibition—and anhedonia have independently been found to be significantly associated with depression or suicidal ideation in the general population or in psychiatric subjects. The aim of the study was to evaluate the association between Type D personality and anhedonia in a population of 204 university students (102 men, 102 women) after controlling for depression as a confounding variable. Type D personality was evaluated using the Type D scale, anhedonia with the Snaith-Hamilton Pleasure Scale, and depression with the Beck Depression Inventory–II. Significant correlations were found between social inhibition and anhedonia before and after adjustment for depression. In women, a Sobel test indicated significant mediation by social inhibition of the relationship between anhedonia and depression. Results suggested that the social inhibition component of Type D personality could constitute a poor prognosis factor.
Fabrication of size-controllable human mesenchymal stromal cell spheroids from micro-scaled cell sheets

Recently, stromal cell spheroids have been actively studied for use in tissue regeneration. In this study, we report a method for the fabrication of size-controllable stromal cell spheroids in different sizes from micro-scaled cell sheets (μCS) using thermosensitive hydrogels and investigated their effects on stromal cell function. Mesenchymal stromal cells isolated from different tissues such as human turbinate tissue, bone marrow, and adipose tissue were adhered selectively to each micro-pattern (squares with widths of 100 and 400 μm) on the surface of the hydrogel and formed μCS. The diameters of the spheroids were modulated by the size of the patterns (45 ± 5 and 129 ± 4 μm in diameter for the 100 and 400 μm micro-patterns, respectively) and the seeding density (129 ± 4, 149 ± 6, and 163 ± 6 μm for 5.0, 10.0, and 15.0 × 104 cells cm−2, respectively, on 400 μm micro-pattern). In addition, the spheroids were successfully fabricated regardless of stromal cell origin, and the diameter of the spheroids was also affected by cell spreading area on a cell culture dish. Stemness markers were highly expressed in the spheroids regardless of the spheroid size. Furthermore, an increase in E-cadherin and decrease in N-cadherin gene expression showed the stable formation of spheroids of different sizes. Gene expression levels of hypoxia inducible factors and secretion of vascular endothelial growth factor were increased (13.2 ± 1.4, 325 ± 83.4 and 534.3 ± 121.5 pg ng−1 DNA in a monolayer, and 100 and 400 μm micro-patterned spheroids, respectively) proportional to the diameters of the spheroids. The size of spheroids were maintained even after injection, cryopreservation and 7 d of suspension culture with high viability (∼90%). In conclusion, this novel technique to fabricate spheroids with controlled size could be widely applied in various applications that require a controlled size in regenerative medicine.
Validation of the GARD™skin Assay for Assessment of Chemical Skin Sensitizers: Ring Trial Results of Predictive Performance and Reproducibility

Abstract Proactive identification of chemicals with skin sensitizing properties is a key toxicological endpoint within chemical safety assessment, as required by legislation for registration of chemicals. In order to meet demands of increased animal welfare and facilitate increased testing efficiency also in nonregulatory settings, considerable efforts have been made to develop nonanimal approaches to replace current animal testing. Genomic Allergen Rapid Detection (GARD™) is a state-of-the-art technology platform, the most advanced application of which is the assay for assessment of skin sensitizing chemicals, GARD™skin. The methodology is based on a dendritic cell (DC)-like cell line, thus mimicking the mechanistic events leading to initiation and modulation of downstream immunological responses. Induced transcriptional changes are measured following exposure to test chemicals, providing a detailed evaluation of cell activation. These changes are associated with the immunological decision-making role of DCs in vivo and include among other phenotypic modifications, up-regulation of co-stimulatory molecules, induction of cellular and oxidative stress pathways and xenobiotic responses, and provide a holistic readout of substance-induced DC activation. Here, results from an inter-laboratory ring trial of GARD™skin, conducted in compliance with OECD guidance documents and comprising a blinded chemical test set of 28 chemicals, are summarized. The assay was found to be transferable to naïve laboratories, with an inter-laboratory reproducibility of 92.0%. The within-laboratory reproducibility ranged between 82.1% and 88.9%, whereas the cumulative predictive accuracy across the 3 laboratories was 93.8%. It was concluded that GARD™skin is a robust and reliable method for the identification of skin sensitizing chemicals and suitable for stand-alone use or as a constituent of integrated testing. These data form the basis for the regulatory validation of GARD™skin.
Factors that may inluence the performance of wireless sensor networks

The Wireless Sensor Networks (WSNs) are penetrating more and more our daily life. They are used in a large type of applications as supervision, tracking and control in military, environmental, medical and several other domains. Therefore, new approaches and protocols are proposed every day in order to optimise the performance of the WSNs and to increase their reliability and quality of service. These new protocols take into consideration the challenges of the WSN and they are built up some key factors (parameters and concepts) to achieve their goals.
An influence model for factors in outsourced software maintenance

The rapid growth of the Internet in the recent past has encouraged global deployment of work by an increasing number of organizations around the world, and they are now in a better position to outsource their IT functions to specialist vendors. With the passage of time, we find more and more software systems moving into the maintenance phase. Such software systems have become an increasingly significant expenditure for businesses. Consequently, these are often potential candidates for outsourcing. Inadequate information regarding the size, complexity, reliability, maintainability, etc., of these systems often makes the task of estimating the maintenance effort a challenge. Other human and organizational factors, typical to maintenance activities, such as organization climate, customer attitude, engineers' attitude, the need for multi-location support teams, etc., make the situation even more complex. In this paper we present the results of an empirical study carried out to identify such factors and study their influence on the maintenance effort. We classify these factors in four categories, namely system baseline, maintenance team, customer's attitude and organizational climate. We also propose a model which can help a practitioner to predict and control the impact on maintenance effort, based on the strengths of these factors. Copyright © 2006 John Wiley & Sons, Ltd.
Comparative Analysis of Energy Efficient Secure MAC Protocols for Wireless Sensor Network

Wireless Sensor Networks (WSN) are practiced in many real life applications such as military, weather forecasting, medical, target spotting and tracking, etc. The sensor nodes are spread over the target area for the accumulation of data. The collected data further transmitted from one sensor node to other sensor node. WSN nodes have limited resources like energy, memory and processing capabilities. Efficient utilization of these resources is challenging task in WSN. MAC layer of wireless sensor nodes plays a vital role in WSN because most of the power is depleted at this layer due to collision in medium access and node synchronization. This paper presents a comparative analysis of all the existing WSN MAC protocol. The comparison is done on the basis of various parameters such as energy consumption, end to end latency, scalability, security from the outside attacker. Analysis of these MAC protocols will serve us in future detection as well as a selection of a protocol for a particular WSN application.
Multi-criteria Intelligent Algorithm for Supply Chain Management

In most societies, supply chain management and e-procurement processes, are one of the cornerstones of any economy and a primary influencer on people’s lives. Providing these communities with their different commodity needs depends on a wide range of suppliers. Due to supplier’s variety and diversity; the process of choosing the suitable supplier is considered the difficult and critical process, especially if this process is performed traditionally then decision making will be time and effort consuming to reach the desired results. To solve the problem of choosing the suitable supplier, this research suggests an intelligent algorithm, based on a given determinants that are specified by the decision maker or the customer. The proposed algorithm employs a set of intelligent formulas that will convert the predefined preferences into quantitative measurements. Quantitative measurements will be used to differentiate between different suppliers or between the set of given offers. The experimental results showed that D3S model employed the given preferences and succeeded in selecting the most appropriate offer among the many presented offers by the available suppliers. Keywords—Decision making; supplier; scoring; algorithms, supply chain management
Nanoscale Quantum Optics

Nanoscale quantum optics explores quantum phenomena in nanophotonics systems for advancing fundamental knowledge in nano and quantum optics and for harnessing the laws of quantum physics in the development of new photonics-based technologies. Here, we review recent progress in the field with emphasis on four main research areas: Generation, detection, manipulation and storage of quantum states of light at the nanoscale, Nonlinearities and ultrafast processes in nanostructured media, Nanoscale quantum coherence, Cooperative effects, correlations and many-body physics tailored by strongly confined optical fields. The focus is both on basic developments and technological implications, especially for what concerns information and communication technology, sensing and metrology, and energy efficiency.
Reading for pleasure and attainment in vocabulary and mathematics

This paper examines inequalities in attainment in vocabulary and mathematics at age 16 for a nationally representative cohort of people born in Britain in 1970 (the 1970 British Cohort Study). Our analytical sample is n=3, 583 cohort members who completed vocabulary and mathematics tests at age 16. We explore whether inequalities due to childhood social background are similar across the linguistic and mathematical domains, or whether they differ, and to what extent these inequalities are driven by families’ social class position, parents’ education and home reading resources. We examine the role of children’s own reading for pleasure controlling for all these background factors. As reading can be seen as an indicator of ‘cultural capital’, we also test the influence of an alternative indicator of cultural capital, playing a musical instrument. Our longitudinal analysis addresses the question of the extent to which differences in attainment are determined by age 10; and which factors are linked to a growth in differentials during adolescence. We show that childhood reading is linked to substantial cognitive progress between the ages of 10 and 16, whereas playing an instrument is not. Reading is most strongly linked to progress in vocabulary, with a weaker, but still substantial link to progress in maths. Strikingly, reading for pleasure is more strongly linked than parental education to cognitive progress in adolescence.
Teaching a black-box learner

One widely-studied model of teaching (Goldman & Kearns, 1995; Shinohara & Miyano, 1991; Anthony et al., 1992) calls for a teacher to provide the minimal set of labeled examples that uniquely speciﬁes a target concept. The assumption is that the teacher knows the learner’s hypothesis class, which is often not true of real-life teaching scenarios. We consider the problem of teaching a learner whose representation and hypothesis class are unknown : that is, the learner is a black box. We ﬁnd that a teacher who does not interact with the learner can do no better than providing random examples. However, by interacting with the black-box learner, a teacher can efﬁciently ﬁnd a set of teaching examples that is a provably good approximation to the optimal set. As an illustration, we show how this scheme can be used to shrink training sets for any family of classiﬁers: that is, to ﬁnd an approximately-minimal subset of training instances that yields the same classiﬁer as the entire set.