Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of pathogenicity islands in Salmonella spp

We investigated the phylogenetic distribution of the SPI-1 and SPI-2 pathogenicity islands in Salmonella spp. SPI-1 was present in representatives of all eight subspecific groups, but no SPI-2-hybridizing sequences were detected in group V (S. bongori). Our data suggest that SPI-2 was acquired by S. enterica after its split from S. bongori.
Assessment of TCP Parameters for Mobile Devices Concerning Performance and Energy Consumption

Mobile devices have become quite popular, and they are responsible for a significant part of Internet traffic. In these devices, multimedia services, such as video streaming over HTTP, are commonly adopted, and TCP protocol is the standard to assure reliable data transmission. To deal with applications that require higher bandwidth, several modifications were made on TCP, and they are called extensions for high performance. For instance, these extensions allow a better utilization of network bandwidth offered by high-speed network technologies, such as WCDMA (3G) and LTE (4G). Changes in network technologies and TCP parameters may solve performance issues, but this modification may increase energy consumption (which considerably impacts mobile devices). This paper presents a performance and energy consumption evaluation of network technology and TCP/IP parameters for mobile devices. We utilize video streaming over HTTP as the workload, and results indicate some TCP parameters may influence energy consumption as well as performance.
Influence of autochthonous lactic acid bacteria and enzymatic yeast extracts on the microbiological, biochemical and sensorial properties of Lben generic products.

In this study we identified Lactococcus lactis subsp. lactis, Lc. lactis subsp. lactis biovar diacetylactis, Kluyveromices lactis and Saccharomyces cerevisiae as the dominant microorganisms of traditional Moroccan acid-alcoholic fermented milk named Lben. The low pH (3·8±0·3), lactose (16·8±3·4 mg/l) and lactic acid (8·16±0·6 mg/l) content indicated that a strong fermentation occurred in the traditional product which was also characterised by the substantial presence of ethanol and typical volatile carbonyl compounds (i.e., acetoin, diacetyl and acetaldehyde). Microbiological analyses of experimental Lben manufactured with selected strains (isolated from the traditional product) of Lc. lactis subsp. lactis and Lc. lactis subsp. lactis biovar. diacetylactis alone (batch A) and in combination with enzymatic extract of a K. lactis strain (batch B) indicated a good effectiveness of the starters employed (∼1010 CFU/g of lactococci after 8 h of incubation) and a significant effect of the yeast enzyme extract on lactococci viability. Despite slight changes in the physicochemical characteristics of the two Lben during the 15 d storage period, volatile compounds (i.e. ethanol, acetaldehyde, diacetyl and acetoin) were consistently higher in batch B. Moreover, sensorial analysis performed after 15 d of storage, highlighted higher odour and flavour intensity, vegetable odour and viscosity in batch B while batch A displayed higher astringency.
Hepatitis C virus (HCV) infection & risk factors for HCV positivity in injecting & non-injecting drug users attending a de-addiction centre in northern India

Background & objectives: Injecting drug use is a major route of hepatitis C virus (HCV) infection in India, but there may be other risk factors also. This study was carried out to determine the seroprevalence of anti-HCV antibody in injecting drug users (IDUs) vs. non-IDUs (NIDUs), and to study the risk estimates for HCV seropositivity in the total sample of substance users with regard to various demographic, clinical, behavioural and personality factors. Methods: The IDUs (n = 201) and NIDUs (n = 219) were assessed for demographic, clinical and behavioural information, and were rated on instruments for severity of dependence, risk behaviour and personality profiles. Anti-HCV antibody was tested by ELISA and confirmed by recombinant immunoblot assay (RIBA) test. Results: Almost one-third of the IDUs (64 of 201; 31.8%) were positive for anti-HCV antibody, as opposed to only seven (3.2%) of the NIDUs. The four risk factors strongly associated with HCV positivity in multivariate analysis were sharing syringe [Exp(B) 75.04; 95%CI 18.28-307.96; P<0.001], reuse of injection accessories (16.39; 3.51-76.92; P<0.001), blood transfusion (5.88; 1.63-21.23; P=0.007) and IDU status (3.60; 1.26-10.31; P=0.017). Other variables less strongly but significantly associated with HCV positivity were multiple sex partners, opioid dependence, risk behaviour scores, impulsivity, and lower age of onset of drug use. Interpretation & conclusions: Our study showed a high seroprevalence of anti-HCV antibody in IDUs. In the substance users, HCV positivity was significantly and independently associated with several clinical, behavioural, and personality risk factors.
Electric Measurement of Cultured Myoblast Oriented on Scaffold with Micro-pattern

The electric impedance of cultured myoblasts oriented on the scaffold with micro pattern has been measured between surface electrodes in vitro. Several parallel lines of micro rectangular ridges (0.001 mm height, 0.003 mm width, and 0.003 mm interval) have been made between a pair of the surface titanium electrodes at the surface of the scaffold of glass by the photolithography technique. C2C12 (mouse myoblast cell line) was cultured for 4 days on the micro-patterned scaffold in the medium of D-MEM (Dulbecco’s Modified Eagle Medium). The electric impedance between electrodes was measured once a day with the sinusoidal electric waves (frequency, 1 Hz < f < 1 MHz; amplitude, ±0.1 V < V1 < ±5 V). The experimental result shows that electric impedance has frequency characteristic and that the impedance of the capacitance component increases with proliferation of myoblasts. The orientation of myoblasts is detected by the impedance between the surface electrodes, when the orientation is varied by the direction of micro ridges of the scaffold.
What causes the decrease in haematocrit during egg production

Summary 1. Anaemia has been reported in wild animals, typically associated with traumatic events or ill health. However, female birds routinely become ‘anaemic’ during egglaying; we sought to determine the causes of this reduction in haematocrit. 2. Haematocrit in female European Starlings ( Sturnus vulgaris Linnaeus) decreased between pre-breeding and egg-laying in 3 out of 4 years (the decrease was marginally non-significant in the fourth year). This was independent of changes in ambient temperature altering the metabolic requirements for thermoregulation. 3. There was a positive relationship between haematocrit and plasma levels of the yolk precursor vitellogenin among egg-laying birds, supporting the hypothesis that the initial reduction in haematocrit is caused by increased blood volume associated with osmoregulatory adjustments to elevated levels of yolk precursors. 4 . H owever, haematocrit did not always recover upon cessation of egg production, remaining low at clutch completion (2 of 4 years), incubation (1 of 2 years) and chick rearing (1 of 4 years), suggesting an additional cause of the prolonged reduction in haematocrit. 5. Given the magnitude and prolonged nature of the changes in haematocrit we report, and the interannual variation in haematocrit even during chick-rearing (47‐54%), we suggest that ‘anaemia’ associated with egg production might have implications for aerobic performance during later stages of breeding.
c-myc regulation during retinoic acid-induced differentiation of F9 cells is posttranscriptional and associated with growth arrest

We have shown that c-myc mRNA levels decrease more than 20-fold when F9 teratocarcinoma stem cells are induced to arrest growth and terminally differentiate to parietal endoderm after exposure to retinoic acid and cyclic AMP (Campisi et al., Cell 36:241-247, 1984). Here, we demonstrate that although growth arrest and full expression of the differentiated phenotype required about 3 days, c-myc mRNA declined abruptly between 8 and 16 h after the addition of retinoic acid and cyclic AMP. The decline was independent of cyclic AMP. We found little or no change in the level of c-myc transcription during differentiation, although two other genes showed marked transcriptional regulation. Thus, decreased c-myc mRNA is a consequence of very early posttranscriptional regulation directed by retinoic acid. Differentiation was not fundamental to this regulation. We have shown that sodium butyrate blocks expression of the differentiated phenotype if added within 8 h of retinoic acid and cyclic AMP (Levine et al., Dev. Biol. 105:443-450, 1984). However, butyrate did not inhibit the decrease in c-myc mRNA. Furthermore, F9 cells partially arrested growth without differentiating when grown in isoleucine-deficient medium. Under these conditions, c-myc mRNA levels also declined. Our results suggest that induction of differentiation-specific genes may be under retinoic acid-mediated control dissimilar from that responsible for the decay of c-myc mRNA. In addition, they raise the possibility that growth arrest may be initiated by reduced c-myc expression.
Microtubule-associated Protein 1S (MAP1S) Bridges Autophagic Components with Microtubules and Mitochondria to Affect Autophagosomal Biogenesis and Degradation*

The ubiquitously distributed MAP1S is a homologue of the exclusively neuronal distributed microtubule-associated protein 1A and 1B (MAP1A/B). They give rise to multiple isoforms through similar post-translational modification. Isoforms of MAP1S have been implicated in microtubule dynamics and mitotic abnormalities and mitotic cell death. Here we show that ablation of the Map1s gene in mice caused reduction in the B-cell CLL/lymphoma 2 or xL (Bcl-2/xL) and cyclin-dependent kinase inhibitor 1B (P27) protein levels, accumulation of defective mitochondria, and severe defects in response to nutritive stress, suggesting defects in autophagosomal biogenesis and clearance. Furthermore, MAP1S isoforms interacted with the autophagosome-associated light chain 3 of MAP1A/B (LC3), a homologue of yeast autophagy-related gene 8 (ATG8), and recruited it to stable microtubules in a MAP1S and LC3 isoform-dependent mode. In addition, MAP1S interacted with mitochondrion-associated leucine-rich PPR-motif containing protein (LRPPRC) that interacts with the mitophagy initiator and Parkinson disease-related protein Parkin. The three-way interactions of MAP1S isoforms with LC3 and microtubules as well as the interaction of MAP1S with LRPPRC suggest that MAP1S isoforms may play positive roles in integration of autophagic components with microtubules and mitochondria in both autophagosomal biogenesis and degradation. For the first time, our results clarify roles of MAP1S in bridging microtubules and mitochondria with autophagic and mitophagic initiation, maturation, trafficking, and lysosomal clearance. Defects in the MAP1S-regulated autophagy may impact heart disease, cancers, neurodegenerative diseases, and a wide range of other diseases.
Existence and Uniqueness of Solutions to Dynamic Models with Occasionally Binding Constraints

Abstract Occasionally binding constraints (OBCs) like the zero lower bound (ZLB) can lead to multiple equilibria, and so to belief-driven recessions. To aid in finding policies that avoid this, we derive existence and uniqueness conditions for otherwise linear models with OBCs. Our main result gives necessary and sufficient conditions for such models to have a unique (“determinate”) perfect foresight solution returning to a given steady state, for any initial condition. While standard New Keynesian models have multiple perfect-foresight paths eventually escaping the ZLB, price level targeting restores uniqueness. We also derive equilibrium existence conditions under rational expectations for arbitrary nonlinear models.
Quantifying the dielectric constant of thick insulators by electrostatic force microscopy: effects of the microscopic parts of the probe

We present a systematic analysis of the effects that the microscopic parts of electrostatic force microscopy probes (the cone and cantilever) have on the electrostatic interaction between the tip apex and thick insulating substrates (thickness > 100 μm). We discuss how these effects can influence the measurement and quantification of the local dielectric constant of the substrates. We propose and experimentally validate a general methodology that takes into account the influence of the cone and the cantilever, thus enabling us to obtain very accurate values of the dielectric constants of thick insulators.
Effective Mechanical Advantage About the Ankle Joint and the Effect of Achilles Tendon Curvature During Toe-Walking

Aim: To study the causes of locomotor dysfunction, estimate muscle forces, or understand the influence of altered sarcomere and muscle properties and behaviours on whole body function, it is necessary to examine the leverage with which contractile forces operate. At the ankle joint, current methods to quantify this leverage for the plantarflexors do not account for curvature of the Achilles tendon, and so may not be appropriate when studying equinus gait. Thus, novel methodologies need to be developed and implemented to quantify the Achilles tendon moment arm length during locomotion. Methods: Plantarflexor internal moment arm length and effective mechanical advantage of 11 typically developed young adults were calculated throughout stance, while heel-toe walking and voluntarily toe-walking on an instrumented treadmill. Achilles tendon moment arm was defined in two-ways: (1) assuming a straight tendon, defined between the gastrocnemius medialis myotendinous junction and Achilles tendon insertion point, and (2) accounting for tendon curvature, by tracking the initial path of the Achilles tendon from the calcaneal insertion. Results: When accounting for tendon curvature, Achilles tendon moment arm length and plantarflexor effective mechanical advantage did not differ between walking conditions (p > 0.05). In contrast, when assuming a straight tendon, Achilles tendon moment arm length (p = 0.043) and plantarflexor effective mechanical advantage (p = 0.007) were significantly greater when voluntary toe-walking than heel-toe walking in late stance. Discussion: Assuming a straight Achilles tendon led to a greater Achilles tendon moment arm length and plantarflexor effective mechanical advantage during late stance, compared to accounting for tendon curvature. Consequently, plantarflexor muscle force would appear smaller when assuming a straight tendon. This could lead to erroneous interpretations of muscular function and fascicle force-length-velocity behaviour in vivo, and potentially inappropriate and ineffective clinical interventions for equinus gait.
Phasic dopamine release in the medial prefrontal cortex enhances stimulus discrimination

Significance Much of our knowledge about the role of dopamine (DA) during learning comes from studying the ventral tegmental area (VTA)-to-striatum pathway, and considerably less is known about the function of phasic DA release in other regions, such as the medial prefrontal cortex (mPFC). By pairing auditory conditioned stimuli (CSs) with optogenetically activated VTA-to-mPFC projections, we show that mice learn faster a subsequent task that involves discrimination of the same CSs against unpaired stimuli. During and after CS-DA pairing, mPFC neurons specifically increase firing in response to the paired CSs, and blocking DA receptors in mPFC during learning impairs stimulus discrimination. Thus, phasic DA acts in mPFC to enhance discrimination of behaviorally relevant stimuli during learning. Phasic dopamine (DA) release is believed to guide associative learning. Most studies have focused on projections from the ventral tegmental area (VTA) to the striatum, and the action of DA in other VTA target regions remains unclear. Using optogenetic activation of VTA projections, we examined DA function in the medial prefrontal cortex (mPFC). We found that mice perceived optogenetically induced DA release in mPFC as neither rewarding nor aversive, and did not change their previously learned behavior in response to DA transients. However, repetitive temporal pairing of an auditory conditioned stimulus (CS) with mPFC DA release resulted in faster learning of a subsequent task involving discrimination of the same CS against unpaired stimuli. Similar results were obtained using both appetitive and aversive unconditioned stimuli, supporting the notion that DA transients in mPFC do not represent valence. Using extracellular recordings, we found that CS-DA pairings increased firing of mPFC neurons in response to CSs, and administration of D1 or D2 DA-receptor antagonists in mPFC during learning impaired stimulus discrimination. We conclude that DA transients tune mPFC neurons for the recognition of behaviorally relevant events during learning.
The Female Sex Work Industry in a District of India in the Context of HIV Prevention

HIV prevalence in India remains high among female sex workers. This paper presents the main findings of a qualitative study of the modes of operation of female sex work in Belgaum district, Karnataka, India, incorporating fifty interviews with sex workers. Thirteen sex work settings (distinguished by sex workers' main places of solicitation and sex) are identified. In addition to previously documented brothel, lodge, street, dhaba (highway restaurant), and highway-based sex workers, under-researched or newly emerging sex worker categories are identified, including phone-based sex workers, parlour girls, and agricultural workers. Women working in brothels, lodges, dhabas, and on highways describe factors that put them at high HIV risk. Of these, dhaba and highway-based sex workers are poorly covered by existing interventions. The paper examines the HIV-related vulnerability factors specific to each sex work setting. The modes of operation and HIV-vulnerabilities of sex work settings identified in this paper have important implications for the local programme.
Improving Glycerol Photoreforming Hydrogen Production Over Ag2O-TiO2 Catalysts by Enhanced Colloidal Dispersion Stability

Solar-driven photocatalytic reforming of biomass-derived resources for hydrogen production offers a sustainable route toward the generation of clean and renewable fuels. However, the dispersion stability of the catalyst particles in the aqueous phase hinders the efficiency of hydrogen production. In this work, a novel method of mixing Ag2O-TiO2 photocatalysts with different morphologies was implemented to promote colloidal dispersion stability, thereby improving hydrogen production performance. A series of Ag2O-TiO2 nanoparticles with different morphologies were synthesized, and their dispersion stabilities in aqueous phase were investigated individually. Two types of Ag2O-TiO2 particles with different morphologies under certain proportions were mixed and suspended in glycerol aqueous solution without adding any dispersant for enhancing dispersion stability while reacting. From the results, photocatalytic hydrogen production was found to be strongly correlated to colloidal dispersion stability. The mixed suspension of Ag2O-TiO2 nanosphere and nanoplate achieved an excellent colloidal dispersion stability without employing any additives or external energy input, and the photoreforming hydrogen production obtained from this binary component system was around 1.1–2.3 times higher than that of the single-component system. From the calculated hydrogen production rate constants between continuous stirring and the binary system, there was only <6% difference, suggesting an efficient mass transfer of the binary system for photoreforming hydrogen production. The proposed method could provide some inspiration to a more energy-efficient heterogeneous catalytic hydrogen production process.
Evaluation of Somatic Hypermutation Status in Chronic Lymphocytic Leukemia (CLL) in the Era of Next Generation Sequencing

Somatic hypermutation (SHM) status provides an important prognostic indicator for chronic lymphocytic leukemia (CLL), a very common type of mature B-cell leukemia. Owing to the adverse prognosis associated with an unmutated immunoglobulin heavy chain variable (IGHV) status, SHM testing is performed as a standard of care in CLL. Conventionally, SHM testing has been performed using labor intensive and primarily analog Sanger sequencing method following PCR amplification of the clonal immunoglobulin heavy chain gene rearrangements in CLL cells. In comparison, recent availability of next generation sequencing (NGS) allows more versatile detection and direct identification of clonal immunoglobulin gene rearrangements in neoplastic B-cell populations. The ability to identify specific clonal IGHV signature(s) in both baseline (diagnostic) and post-treatment settings enables unique clinical applications of NGS such as determination of SHM status, minimal residual disease (MRD) monitoring, clonal heterogeneity and B cell receptor IG stereotypy. We provide a review of current practices and recommendations for SHM determination using NGS including examples of difficult cases.
1 GENDER DIFFERENCES IN BULLYING AND THE SOCIAL CONSTRUCTION OF MASCULINITY

In the past ten years considerable attention has been devoted in the literature to violence in schools, especially, bullying behaviour. Research has established that this form of violent behaviour is an endemic problem as school students seek to develop a system of attitudes and values based on mixed social messages from today’s society. The inconsistent models and images they receive from their peers, teachers, parents and the media help to perpetuate and to a certain extent, condone, this state of almost institutionalised violence. While research has established that bullying behaviour is widespread (Byrne, 1994; Maslin, 1994; Olweus, 1978; Rigby & Slee, 1989) of particular interest to this proposed study is the issue of gender differences in the nature, extent and attitudes towards bullying behaviour. While it is true that boys bully more often than girls and are more often the victims of bullying behaviour girls are picked on or teased more frequently by boys than other girls (Tulloch, 1995). The issue of gender and violence focuses on the social construction of masculinity and femininity and how it underlies the nature and extent of bullying behaviour in schools. Research into gendered violence in schools (Askew, 1989; Maslin, 1994; O’Doherty, 1994; Ollis & Tomaszewski, 1993; Roland, 1989; Tulloch, 1995) highlights the imbalance in the power relationship between males and females and needs further investigation as it is reasonable to suggest that in many cases cross sex bullying constitutes sexual harassment. Studies have established that intervention programs designed to address violence in schools are effective in reducing the level of bullying behaviour in schools. The O’Doherty (1994) Report in NSW goes further by suggesting schools adopt strategies to address gender equity issues in relation to violence in schools, in particular, boys’ education. On this basis cross gender bullying deserves a closer look with regards sex role perceptions and attitudes of students and the extent of cross sex victimisation experienced. DEFINITIONS OF AND HISTORICAL PERSPECTIVES ON BULLYING. Bullying is a phenomenon that has been described in literary works for a very long time and most adults would have experienced it from their own school days. While there has been concern in the media and in schools for some time the authorities did not involve themselves (Maslin, 1994) until fairly recently in the form of research attention. A number of researchers have reported on the phenomenon of bullying behaviour in society in general and schools in particular. It is with reference to this behaviour in schools that the present review is interested. Scandinavian researchers are considered to have pioneered studies into bullying behaviour (Besag, 1989; Olweus, 1978, 1993). One definition of bullying/victimisation is described as follows:“ A