Miracle-dz/UniFAR-FTUs huggingface dataset:
Distributed delayed stochastic optimization

We analyze the convergence of gradient-based optimization algorithms that base their updates on delayed stochastic gradient information. The main application of our results is to gradient-based distributed optimization algorithms where a master node performs parameter updates while worker nodes compute stochastic gradients based on local information in parallel, which may give rise to delays due to asynchrony. We take motivation from statistical problems where the size of the data is so large that it cannot fit on one computer; with the advent of huge datasets in biology, astronomy, and the internet, such problems are now common. Our main contribution is to show that for smooth stochastic problems, the delays are asymptotically negligible and we can achieve order-optimal convergence results. We show n-node architectures whose optimization error in stochastic problems-in spite of asynchronous delays-scales asymptotically as O(1/√nT) after T iterations. This rate is known to be optimal for a distributed system with n nodes even in the absence of delays. We additionally complement our theoretical results with numerical experiments on a logistic regression task.
LDA topics: Representation and evaluation

In recent years many automated topic coherence formulas (using the top-m words of a topic inferred by latent Dirichlet allocation) based on word similarities have been proposed and evaluated against human ratings. We treat a wordy topic as an object and quantitatively describe it via normalized mean values of pair-wise word similarities. Two types of word similarities, thesaurus and local corpus-based, are used as the descriptive features of a topic. We perform topic classification using represented topics as input and bi-level human ratings about topic coherence as class labels. Classification results (precision, recall and accuracy) based on two datasets and three supervised classification algorithms suggest that the novel topic representation is consistent with human ratings. Corpus-based word similarities are positively correlated with human ratings whereas thesaurus-based similarities have negative relations. The proposed representation of topics opens a window for us to investigate the utilization of topics with different perspectives.
Alan Turing and Enigmatic Statistics

Caros leitores, gostaria de dar boas vindas ao Victor Fossaluza (UFSCar) e também agradecê-lo por ter aceito a tarefa de ser o editor deste boletim para o biênio 2013-2014. Ele, em seu primeiro boletim, nos traz um excelente texto de K. V. Mardia e S. B. Cooper sobre o trabalho de Alan Turing. Sendo assim, esperamos muito mais dele para os próximos boletins! Gostaria também de informá-los que o volume com os anais do EBEB 2012 está dispońıvel em XI Brazilian Meeting on Bayesian Statistics (2012). Editores: J. M. Stern, M. de S. Lauretto, A. Polpo and M. A. Diniz. AIP Conference Proceedings, volume 1490, editora AIP. http://scitation.aip. org/dbt/dbt.jsp? KEY=APCPC S&Volume=1490&Issue=1. Boa leitura!
Spectroscopy of B-type emission-line stars with compact dusty envelopes: HD 85567, Hen 3-140, and Hen 3-1398

We report the results of our spectroscopic observations (3600{5900 A, R' 16 000 and 5750{8750 A, R' 11 000) of three southern emission-line B{type stars associated with IRAS sources, HD 85567, Hen 3{140, and Hen 3{1398, whose nature and evolutionary state are not well-established yet. We also obtained new multicolour photometry of HD 85567 (UBV(RI)cJHKL) and Hen 3{140 (JHKLM). A large near-IR excess is found in Hen 3{ 140 for the rst time. All three objects show double-peaked Fe ii lines in emission. The Balmer emission lines are double-peaked in HD 85567 and Hen 3{140, while the He i lines are found in absorption. Hen 3{1398 displays triple-peaked Balmer lines as well as single-peaked He i and He ii lines in emission. Fundamental parameters of the stars are estimated on the basis of both photometric and spectroscopic data. The whole set of their properties resemble that of a recently dened group of Be stars with warm dust (Sheikina et al. 2000).
Inhibitors of RecA Activity Discovered by High-Throughput Screening: Cell-Permeable Small Molecules Attenuate the SOS Response in Escherichia coli

The phenomenon of antibiotic resistance has created a need for the development of novel antibiotic classes with nonclassical cellular targets. Unfortunately, target-based drug discovery against proteins considered essential for in vitro bacterial viability has yielded few new therapeutic classes of antibiotics. Targeting the large proportion of genes considered nonessential that have yet to be explored by high-throughput screening, for example, RecA, can complement these efforts. Recent evidence suggests that RecA-controlled processes are responsible for tolerance to antibiotic chemotherapy and are involved in pathways that ultimately lead to full-fledged antibiotic resistance. Therefore inhibitors of RecA may serve as therapeutic adjuvants in combination chemotherapy of bacterial infectious diseases. Toward the goal of validating RecA as a novel target in the chemotherapy of bacterial infections, the authors have screened 35,780 small molecules against RecA. In total, 80 small molecules were identified as primary hits and could be clustered in 6 distinct chemotype clades. The most potent class of hits was further examined, and 1 member compound was found to inhibit RecA-mediated strand exchange and prevent ciprofloxacin-induced SOS expression in Escherichia coli. This compound represents the first small molecule demonstrating an ability to inhibit the bacterial SOS response in live bacterial cell cultures. (Journal of Biomolecular Screening 2009:1092-1101)
Evolutionary dynamics of group formation

Group formation is a quite ubiquitous phenomenon across different animal species, whose individuals cluster together forming communities of diverse size. Previous investigations suggest that, in general, this phenomenon might have similar underlying reasons across the interested species, despite genetic and behavioral differences. For instance improving the individual safety (e.g. from predators), and increasing the probability to get food resources. Remarkably, the group size might strongly vary from species to species, e.g. shoals of fishes and herds of lions, and sometimes even within the same species, e.g. tribes and families in human societies. Here we build on previous theories stating that the dynamics of group formation may have evolutionary roots, and we explore this fascinating hypothesis from a purely theoretical perspective, with a model using the framework of Evolutionary Game Theory. In our model we hypothesize that homogeneity constitutes a fundamental ingredient in these dynamics. Accordingly, we study a population that tries to form homogeneous groups, i.e. composed of similar agents. The formation of a group can be interpreted as a strategy. Notably, agents can form a group (receiving a ‘group payoff’), or can act individually (receiving an ‘individual payoff’). The phase diagram of the modeled population shows a sharp transition between the ‘group phase’ and the ‘individual phase’, characterized by a critical ‘individual payoff’. Our results then support the hypothesis that the phenomenon of group formation has evolutionary roots.
Trends towards Lower Antimicrobial Susceptibility and Characterization of Acquired Resistance among Clinical Isolates of Brachyspira hyodysenteriae in Spain

ABSTRACT The antimicrobial susceptibility of clinical isolates of Brachyspira hyodysenteriae in Spain was monitored, and the underlying molecular mechanisms of resistance were investigated. MICs of tylosin, tiamulin, valnemulin, lincomycin, and tylvalosin were determined for 87 B. hyodysenteriae isolates recovered from 2008 to 2009 by broth dilution. Domain V of the 23S rRNA gene and the ribosomal protein L3 gene were sequenced in 20 isolates for which the tiamulin MIC was ≥4 μg/ml, presenting decreased susceptibility, and in 18 tiamulin-susceptible isolates (MIC ≤ 0.125 μg/ml), and all isolates were typed by multiple-locus variable-number tandem repeats analysis. A comparison with antimicrobial susceptibility data from 2000 to 2007 showed an increase in pleuromutilin resistance over time, doubling the number of isolates with decreased susceptibility to tiamulin. No alteration in susceptibility was detected for lincomycin, and the MIC of tylosin remained high (MIC50 > 128 μg/ml). The decreased susceptibility to tylosin and lincomycin can be explained by mutations at position A2058 of the 23S rRNA gene (Escherichia coli numbering). A2058T was the predominant mutation, but A2058G also was found together with a change of the neighboring base pair at positions 2057 to 2611. The role of additional point mutations in the vicinity of the peptidyl transferase center and mutations in the L3 at amino acids 148 and 149 and their possible involvement in antimicrobial susceptibility are considered. An association between G2032A and high levels of tiamulin and lincomycin MICs was found, suggesting an increasing importance of this mutation in antimicrobial resistance of clinical isolates of B. hyodysenteriae.
Calibration of Direct-Conversion Transceivers

Due to its architectural simplicity, the direct conversion scheme is attractive for low-cost, low-complexity and/or reconfigurable transceiver design. Unfortunately, this scheme comes with moderate performance due to its sensitivity to circuit impairments such as transmitter and receiver quadrature imbalance, carrier feedthrough and receiver dc-offset. In this paper, a calibration method is presented to estimate and compensate for these circuit impairments such that their distortions at the transmitter and receiver output are eliminated. The proposed method is noniterative and enables calibration during normal transmit operation. The calibration is directly applicable on most direct-conversion transceivers embedding two frequency synthesizers as the increase of complexity is concentrated in the digital domain only. The performance has been evaluated based on measurements of three different systems operating on frequencies corresponding to major wireless interface standards, namely WLAN, WiMAX, WiFi, DVB-T/H, and even 60-GHz multi-gigabit wireless. The calibration improved the system performance significantly, exceeding standard compliancy.
Identification of Secretion Determinants of the Bordetella pertussis BrkA Autotransporter

ABSTRACT The autotransporters comprise a functionally diverse family of gram-negative proteins that mediate their own export across the bacterial outer membrane. They consist of an amino-terminal passenger region called the “α-domain” and the structural hallmark of the autotransporter family, a carboxy-terminal transporter region usually referred to as the “β-domain. ” The passenger region can be quite diverse and constitutes the effector functions of these proteins, whereas the C-terminal region is conserved and is responsible for translocating the passenger moiety across the outer membrane. BrkA is the 103-kDa autotransporter protein in Bordetella pertussis that is cleaved to yield a 73-kDa N-terminal α-domain and a 30-kDa C-terminal β-domain. We have previously shown that a recombinant form of the β-domain of BrkA is capable of forming channels in artificial membranes. Here, we define two additional secretion determinants of BrkA. N-terminal sequencing of the 73-kDa BrkA passenger from B. pertussis and Escherichia coli revealed that BrkA has a 42-amino-acid signal peptide. In addition, deletion analysis of BrkA identified a 31- to 39-amino-acid region found immediately upstream of the β-domain that was essential for surface expression. This 31- to 39-amino-acid linker region, together with the β-domain, defines the minimal BrkA translocation unit. The linker region may also serve to anchor the BrkA passenger to the bacterial surface.
Milk protein synthesis is regulated by T1R1/T1R3, a G protein-coupled taste receptor, through the mTOR pathway in the mouse mammary gland.

SCOPE Understanding the regulatory mechanism of milk protein synthesis is important to develop strategies to improve milk protein and enhance lactation performance. The mammalian target of rapamycin (mTOR) pathway is a crucial modulator of protein synthesis. In this study, we want to investigate if T1R1/T1R3 can regulate milk protein synthesis and mediate the mTOR pathway in the mice mammary gland in vivo. METHODS AND RESULTS T1R1 knockout mice, WT mice, and mammary explants were used. The weigh-suckle-weigh method was used to quantify the milk yield. The expression level of β-casein and AA transporter mRNA were analyzed by qPCR. Western blot was used to analyze protein abundance of members of the mTOR pathway. As expected, the knockout of T1R1 not only reduced the total milk yield in the mice mammary glands, but also repressed β-casein synthesis. Additionally, the phosphorylation of 4EBP1 and S6K was significantly decreased in T1R1 knockout mice. The T1R1 knockout also increased the protein abundance of the AA transporter SLC3A2 and mRNA expression of SLC7A5/SLC3A2 and SLC1A5. Activation of the mTOR pathway was repressed by inhibition of T1R3 or T1R1 knockout in mammary gland explants. CONCLUSION T1R1/T1R3 modulates the mTOR pathway to regulate milk protein synthesis in the mouse mammary gland in vivo.
A Randomized Pilot Study of L-Arginine Infusion in Severe Falciparum Malaria: Preliminary Safety, Efficacy and Pharmacokinetics

Background Decreased nitric oxide (NO) and hypoargininemia are associated with severe falciparum malaria and may contribute to severe disease. Intravenous L-arginine increases endothelial NO in moderately-severe malaria (MSM) without adverse effects. The safety, efficacy and pharmacokinetics of L-arginine or other agents to improve NO bioavailability in severe malaria have not been assessed. Methods In an open-label pilot study of L-arginine in adults with severe malaria (ARGISM-1 Study), patients were randomized to 12 g L-arginine hydrochloride or saline over 8 hours together with intravenous artesunate. Vital signs, selected biochemical measures (including blood lactate and L-arginine) and endothelial NO bioavailability (using reactive hyperemia peripheral arterial tonometry [RH-PAT]) were assessed serially. Pharmacokinetic analyses of L-arginine concentrations were performed using NONMEM. Results Six patients received L-arginine and two saline infusions. There were no deaths in either group. There were no changes in mean systolic (SBP) and diastolic blood pressure (DBP) or other vital signs with L-arginine, although a transient but clinically unimportant mean maximal decrease in SBP of 14 mmHg was noted. No significant changes in mean potassium, glucose, bicarbonate, or pH were seen, with transient mean maximal increases in plasma potassium of 0.3 mmol/L, and mean maximal decreases in blood glucose of 0.8 mmol/L and bicarbonate of 2.3 mEq/L following L-arginine administration. There was no effect on lactate clearance or RH-PAT index. Pharmacokinetic modelling (n = 4) showed L-arginine concentrations 40% lower than predicted from models developed in MSM. Conclusion In the first clinical trial of an adjunctive treatment aimed at increasing NO bioavailability in severe malaria, L-arginine infused at 12 g over 8 hours was safe, but did not improve lactate clearance or endothelial NO bioavailability. Future studies may require increased doses of L-arginine. Trial Registration ClinicalTrials.gov NTC00616304
Community Participation as a Tool for Tourism and Environmental Conservation: A Case of Bang Ta Boon Village, Phetchaburi, Thailand

Within a wide body of literature, it has been debated that community participation in tourism development is advantageous in terms of the sustainability and effectiveness of the conservation policies adopted. As tourism is frequently cited as a tool by which Thais can strengthen the economies of their cultural and natural resources, thriving tourism development stands in need of citizen participation in the planning and development process. The main purpose of this study is to investigate the characteristic of community participation expected by various interest groups with special references to a fishing village destination in Thailand. Field research was designed and applied through a case study approach. The fishing village of Bang Ta Boon, located in a bay off the Gulf of Thailand in Phetchaburi province has proved to be a practicable community to undertake community participation in tourism and environmental conservation. Findings show that the expected nature of community participation by interest groups varies from non-participation to one form of spontaneous participation, even though politically Thailand has been considered unstable towards community participation. Possible success factors are discussed and suggestions for conducting similar future research on Thailand’s destinations are advanced for consideration.
Psychological Trauma Symptom Improvement in Veterans Using Emotional Freedom Techniques: A Randomized Controlled Trial

Abstract This study examined the effect of Emotional Freedom Techniques (EFT), a brief exposure therapy combining cognitive and somatic elements, on posttraumatic stress disorder (PTSD) and psychological distress symptoms in veterans receiving mental health services. Veterans meeting the clinical criteria for PTSD were randomized to EFT (n = 30) or standard of care wait list (SOC/WL; n = 29). The EFT intervention consisted of 6-hour–long EFT coaching sessions concurrent with standard care. The SOC/WL and EFT groups were compared before and after the intervention (at 1 month for the SOC/WL group and after six sessions for the EFT group). The EFT subjects had significantly reduced psychological distress (p < 0.0012) and PTSD symptom levels (p < 0.0001) after the test. In addition, 90% of the EFT group no longer met PTSD clinical criteria, compared with 4% in the SOC/WL group. After the wait period, the SOC/WL subjects received EFT. In a within-subjects longitudinal analysis, 60% no longer met the PTSD clinical criteria after three sessions. This increased to 86% after six sessions for the 49 subjects who ultimately received EFT and remained at 86% at 3 months and at 80% at 6 months. The results are consistent with that of other published reports showing EFT’s efficacy in treating PTSD and comorbid symptoms and its long-term effects.
Reducing energy consumption in mobile ad-hoc sensor networks

Recent rapid development of wireless communication technologies and portable mobile devices such as tablets, smartphones and wireless sensors bring the best out of mobile computing, particularly Mobile Ad-hoc Sensor Networks (MASNETs). MASNETs are types of Mobile Ad-hoc Networks (MANETs) that are designed to consider energy in mind because they have severe resource constraints due to their lack of processing power, limited memory, and bandwidth as in Wireless Sensor Networks (WSNs). Hence, they have the characteristics, requirements, and limitations of both MANETs and WSNs. There are many potential applications of MASNETs such as a real-time target tracking and an ocean temperature monitoring. In these applications, mobility is the fundamental characteristic of the sensor nodes, and it poses many challenges to the routing algorithm. One of the greatest challenge is to provide a routing algorithm that is capable of dynamically changing its topology in the mobile environment with minimal consumption of energy. In MASNETs, the main reason of the topology change is because of the movement of mobile sensor nodes and not the node failure due to energy depletion. Since these sensor nodes are limited in power supply and have low radio frequency coverage, they easily lose their connection with neighbours, and face difficulties in updating their routing tables. The switching process from one coverage area to another consumes more energy. This network must be able to adaptively alter the routing paths to minimize the effects of variable wireless link quality, topological changes, and transmission power levels on energy consumption of the network. Hence, nodes prefer to use as little transmission power as necessary and transmit control packets as infrequently as possible in energy constrained MASNETs. Therefore, in this thesis we propose a new dynamic energy-aware routing algorithm based on the transmission power control (TPC). This method effectively decreases the average percentage of packet loss and reduces the average total energy consumption which indirectly prolong the network lifetime of MASNETs. To validate the proposed protocol, we ran the simulation on the Avrora simulator and varied speed, density, and route update interval of mobile nodes. Finally, the performance of the proposed routing algorithm was measured and compared against the basic Ad-hoc On-demand Distance Vector (AODV) routing algorithm in MASNETs.
R-PM2 : Milk Quality in the 21 st Century

High quality raw milk is free of undesirable flavors, chemical or antibiotic residues, is low in somatic cells and bacteria, and contains a minimum of 3.5% butterfat, 3.1% protein, and 4.8% lactose. However, from a veterinary perspective SCC (somatic cell count) has become the "gold standard" measure of milk quality. The herd SCC level is dependent on the number and duration of infections present plus rate of new infections. Since mammary gland infection is multi-factorial, the epidemiological principle of "sufficient cause" has bearing on whether or not exposure to mastitis pathogens will cause mammary gland infection. For example, in order for a new mammary gland infection to occur, there not only must be teat exposure to a mastitis pathogen but also a circumstance (i.e., air slips) that results in the pathogen penetrating the teat canal. Even then, the pathogen must be of sufficient dose and virulence to overwhelm the cow's immune system allowing establishment of an infection. The sum of all these factors results in "sufficient cause" for an infection to occur. The whole thrust of mastitis control has been to identify those critical factors necessary for infection to occur and block them by strategic intervention (i.e., teat dipping) so that infection does not occur. By consistent application of control practices, high quality, low SCC, low bacteria count, and antibiotic and chemical free wholesome safe milk can be produced.