Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characterization of Community Acquired Staphylococcus aureus Bacteremia in Young Children in Southern Mozambique, 2001–2009

Background: The emergence of community-acquired Staphylococcus aureus infections is increasingly recognized as life threating problem worldwide. In Manhiça district, southern Mozambique, S. aureus is the leading cause of community-acquired bacteremia in neonates. Methods: Eighty-four S. aureus isolates from children less than 5 years admitted to Manhiça District Hospital from 2001 to 2009 were randomly selected and genetically characterized by DNA microarray and spa typing. Antimicrobial susceptibility was determined by VITEK 2. Results: Thirty-eight different spa types and 14 clonal complexes (CC) were identified. Spa-type t084 (n = 10; 12%) was the most predominant while CC8 (n = 18; 21%) and CC15 (n = 14; 16%) were the most frequent CCs. Mortality tended to be higher among children infected with CC45 (33.3%, 1/3) and CC8 (27.8%, 5/18). The majority of isolates possessed the accessory gene regulator I (45%) and belonged to either capsule type 8 (52%) or 5 (47%). Panton valentine leukocidin (PVL) encoding genes were detected in 30%. Antibiotic resistance was high for penicillin (89%), tetracycline (59%) and Trimethoprim Sulfamethoxazole (36%) while MRSA was uncommon (8%). Conclusions: Although MRSA were uncommon, we found high genetic diversity of methicillin susceptible S. aureus causing bacteremia in Mozambican children, associated with high resistance to the most available antibiotics in this community. Some CCs are likely to be more lethal indicating the need for prompt recognition and appropriate treatment.
Tetragonal-to-Tetragonal Phase Transition in Lead-Free (KxNa1−x)NbO3 (x = 0.11 and 0.17) Crystals

Lead free piezoelectric crystals of (KxNa1−x)NbO3 (x = 0.11 and 0.17) have been grown by the modified Bridgman method. The structure and chemical composition of the obtained crystals were determined by X-ray diffraction (XRD) and electron probe microanalysis (EPMA). The domain structure evolution with increasing temperature for (KxNa1−x)NbO3 (x = 0.11 and 0.17) crystals was observed using polarized light microscopy (PLM), where distinguished changes of the domain structures were found to occur at 400 °C and 412 °C respectively, corresponding to the tetragonal to tetragonal phase transition temperatures. Dielectric measurements performed on (K0.11Na0.89)NbO3 crystals exhibited tetragonal to tetragonal and tetragonal to cubic phase transitions temperatures at 405 °C and 496 °C, respectively.
Spatial channel properties and spectral efficiency of blast architecture

The Bell Labs Layered Space-Time (BLAST) architecture has been recently proposed as an extremely efficient tool for wireless communications in rich multipath environment [1-4]. Using multi-element antenna arrays and signal processing in the spatial dimension, this architecture achieves channel capacity as high as 10-100 times that of traditional architectures in certain applications (indoor communication, local-area networks, cellular systems in large cities etc.). Such a tremendous increase in the channel capacity will stimulate in future, without any doubts, widespread use of such communication systems. The main idea of the BLAST architecture is to exploit rather than suppress multipath propagation. For a classical communication architecture with multi-element antenna arrays, channel capacity (Shannon’s channel capacity limit) depends linearly on the logarithm of n (the number of array elements) and for the BLAST architecture – linearly on n (for uncorrelated spatial paths). Thus, it grows much faster in the latter case as n increases. An experimental setup was built to validate the new architecture and bit rates as high as 40 bits/s/Hz has been achieved for indoor communications [4].
A new global router for modern designs

In this paper, we present a new global router, NTHU-Route, for modern designs. NTHU-Route is based on iterative rip-ups and reroutes, and several techniques are proposed to enhance our global router. These techniques include (1) a history based cost function which helps to distribute overflow during iterative rip-ups and reroutes, (2) an adaptive multi-source multi-sink maze routing method to improve the wirelength of maze routing, (3) a congested region identification method to specify the order for nets to be ripped up and rerouted, and (4) a refinement process to further reduce overflow when iterative history based rip-ups and reroutes reach bottleneck. Compared with two state-of-the-art works on ISPD98 benchmarks, NTHU-Route outperforms them in both overflow and wirelength. For the much larger designs from the ISPD07 benchmark suite, our solution quality is better than or comparable to the best results reported in the ISPD07 routing contest.
Impaired Endothelial Function of the Retinal Vasculature in Hypertensive Patients

Background and Purpose— Arterial hypertension constitutes a central factor in the pathogenesis of stroke. We examined endothelial function of the retinal vasculature as a model of the cerebral circulation. Methods— Thirty-eight young subjects (19 hypertensive and 19 normotensive) were treated with the AT1-receptor blocker candesartan cilexetil and placebo, each over 7 days. Retinal capillary flow and blood flow velocity in the central retinal artery were assessed with scanning laser Doppler flowmetry and pulsed Doppler ultrasound, respectively. NG-mono-methyl-L-arginine (L-NMMA) was infused to inhibit nitric oxide (NO) synthesis. Diffuse luminance flicker was applied to stimulate NO release. Results— In normotensive subjects, L-NMMA decreased retinal capillary flow by 8.2%±13% (P < 0.05) and flickering light increased mean blood flow velocity in the central retinal artery by 19%±29% (P < 0.01). In contrast, no significant change to these provocative tests was seen in hypertensive subjects. Treatment with candesartan cilexetil restored a normal pattern of reactivity in retinal capillaries (L-NMMA: decrease in perfusion by 10%±17%, P < 0.05) and the central retinal artery (flicker: increase in mean blood flow velocity by 42%±31%, P < 0.001) in hypertensive patients. Conclusions— Endothelial function of the retinal vasculature is impaired in early essential hypertension but can be improved by AT1-receptor blockade.
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation

Transcriptional control is central to many cellular processes, and, consequently, much effort has been devoted to understanding its underlying mechanisms. The organization of nucleosomes along promoter regions is important for this process, since most transcription factors cannot bind nucleosomal sequences and thus compete with nucleosomes for DNA access. This competition is governed by the relative concentrations of nucleosomes and transcription factors and by their respective sequence binding preferences. However, despite its importance, a mechanistic understanding of the quantitative effects that the competition between nucleosomes and factors has on transcription is still missing. Here we use a thermodynamic framework based on fundamental principles of statistical mechanics to explore theoretically the effect that different nucleosome organizations along promoters have on the activation dynamics of promoters in response to varying concentrations of the regulating factors. We show that even simple landscapes of nucleosome organization reproduce experimental results regarding the effect of nucleosomes as general repressors and as generators of obligate binding cooperativity between factors. Our modeling framework also allows us to characterize the effects that various sequence elements of promoters have on the induction threshold and on the shape of the promoter activation curves. Finally, we show that using only sequence preferences for nucleosomes and transcription factors, our model can also predict expression behavior of real promoter sequences, thereby underscoring the importance of the interplay between nucleosomes and factors in determining expression kinetics.
A Reliable SVD-DWT Based Watermarking Scheme with Artificial Bee Colony Algorithm

A robust image watermarking scheme based on singular value decomposition (SVD) and discrete wavelet transform (DWT) with Artificial Bee Colony Algorithm is proposed in this paper. Previous SVD based watermarking algorithms have a major drawback of false positive detection. For solving this problem, the similarity measure of U matrix for ownership is checked. To achieve the highest possible robustness without losing the transparency, an adaptive scale factor is obtained by the artificial bee colony (ABC) algorithm. Experimental results demonstrate that the performance of the proposed approach outperforms the existing methods.
Genetic analysis of the stationary phase‐induced mcb operon promoter in Escherichia coli

A combination of deletion analysis and random mutagenesis was used to identify regulatory elements in Pmcb, the stationary phase‐induced promoter of the mcb operon. Our results indicate that Pmcb is controlled by at least three different factors, two previously identified and at least one unknown factor, which act at four different sites in the promoter. Sequences between −344 and −164 upstream of the transcriptional start site were required for wild‐type levels of mcb transcription in stationary phase. More dramatic reductions in both exponential and stationary phase expression were observed when sequences from −164 to −54 were deleted. Point mutations located between −105 and −138 decreased both exponential and stationary phase expression. All but one of these mutations decreased OmpR‐dependent activation of Pmcb transcription. EmrR, also known as MprA, acts directly or indirectly at sequences downstream of −54 to repress Pmcb. A minimal promoter containing sequences from −34 to +79 was still induced ≥10‐fold in stationary phase. Point mutations within this region identified sequences at −8, −11, −30, −31 and −32 as important for Pmcb activity. These bases are in the gearbox sequence, present in Pmcb and several other stationary phase‐induced Escherichia coli promoters.
Abstract B32: Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses

DNA methyltransferase inhibitors (DNMTis) upregulate immune attraction, including the interferon response, in solid tumors. We now define viral defense signaling as one mechanism for this. In epithelial ovarian cancer cells DNMTis upregulate viral defense by cytosolic sensing of double-stranded RNA (dsRNA), triggering a Type I Interferon response, upregulation of downstream interferon response genes, and increased apoptosis. Knockdown of the dsRNA sensors TLR3 and MAVS and inhibition of the interferon alpha/beta receptor blunt the DNMTi induced dsRNA response. DNMTis cause apoptosis of cancer cells, which is partially rescued by inhibiting the interferon alpha/beta receptor. We observe upregulation and demethylation of hypermethylated endogenous retroviruses (ERVs) and overexpression of individual ERVs whose sense and anti-sense transcripts may be key candidates for triggering the above signaling. Overexpression of ERVs alone is sufficient to trigger an interferon response in the absence of DNMTis. Basal levels of ERV and viral defense gene expression significantly correlate in primary OC and basal expression of the viral defense signature separates primary TCGA samples for multiple tumor types into low versus high expression groups. In melanoma patients treated with an immune checkpoint therapy, high viral defense signature expression in tumors significantly associates with durable clinical response and DNMTi treatment sensitizes to anti-CTLA4 therapy in a pre-clinical melanoma model. We thus define a major mechanism for how DNMTis may induce cancer cells to increase immune attraction and possibly sensitize patients to immunotherapy. Experiments determining which Aza-upregulated molecules on tumor cells are necessary for attraction and activation of host immune cells are ongoing. Citation Format: Katherine B. Chiappinelli, Pamela L. Strissel, Alexis Desrichard, Huili Li, Christine Henke, Benjamin Akman, Alexander Hein, Neal S. Rote, Leslie M. Cope, Alexandra Snyder, Vladimir Makarov, Sadna Budhu, Jedd Wolchok, Cynthia A. Zahnow, Taha Mergoub, Timothy A. Chan, Reiner Strick, Stephen B. Baylin. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B32.
ECOISLAND: A System for Persuading Users to Reduce CO2 Emissions

A significant portion of the carbon dioxide emissions that have been shown to cause global warming are due to household energy consumption and traffic. EcoIsland is a computer system aimed at persuading and assisting individual families in changing their lifestyle patterns in a way that reduces CO2 emissions. The system builds on our earlier work on persuasive ubiquitous computing applications and applies ideas from behaviorism, social psychology and emissions trading to attempt to motivate changes in users' behavior. In this paper, we briefly describe the concept and the theories behind it, and provide preliminary results from a user study measuring its effectiveness.
Detection of Drug-Drug Interactions by Modeling Interaction Profile Fingerprints

Drug-drug interactions (DDIs) constitute an important problem in postmarketing pharmacovigilance and in the development of new drugs. The effectiveness or toxicity of a medication could be affected by the co-administration of other drugs that share pharmacokinetic or pharmacodynamic pathways. For this reason, a great effort is being made to develop new methodologies to detect and assess DDIs. In this article, we present a novel method based on drug interaction profile fingerprints (IPFs) with successful application to DDI detection. IPFs were generated based on the DrugBank database, which provided 9,454 well-established DDIs as a primary source of interaction data. The model uses IPFs to measure the similarity of pairs of drugs and generates new putative DDIs from the non-intersecting interactions of a pair. We described as part of our analysis the pharmacological and biological effects associated with the putative interactions; for example, the interaction between haloperidol and dicyclomine can cause increased risk of psychosis and tardive dyskinesia. First, we evaluated the method through hold-out validation and then by using four independent test sets that did not overlap with DrugBank. Precision for the test sets ranged from 0.4–0.5 with more than two fold enrichment factor enhancement. In conclusion, we demonstrated the usefulness of the method in pharmacovigilance as a DDI predictor, and created a dataset of potential DDIs, highlighting the etiology or pharmacological effect of the DDI, and providing an exploratory tool to facilitate decision support in DDI detection and patient safety.
Synergism of Cefazolin-Gentamicin Against Enterococci

A miniaturized technique for detecting antibiotic synergy by using microliter volumes was perfected. With this microtiter serial dilution method, the effect of the previously untried combination of cefazolin and gentamicin on 10 strains of enterococci was evaluated. At clinically achievable concentrations, the combination of cefazolin and gentamicin was found to be synergistic against all 10 strains when the data were plotted in the form of an isobologram. These results were compared with the conventional method of detecting synergy in vitro, namely, the determination of the rate of killing of the microorganisms with the antibiotics, singly and in combination. Similar results were also observed. These findings indicate that the microtiter serial dilution technique is a useful method for the routine determination of drug synergy. Moreover, in a patient with penicillin hypersensitivity and enterococcal infection, the combination of cefazolin and gentamicin should be considered for possible therapy.
A mobile networking system based on Internet protocol

Users of portable computers would like to carry their laptops with them whenever they move from one place to another and yet maintain transparent network access through the wireless link. The existing set of network protocols do not meet this requirement since they were designed under the assumption of a stationary network topology in which hosts do not change their location over time. The authors' approach, which is based on the use of a natural model and an existing IP option, does not introduce any new protocol and achieves optimal routing. The solution is transparent to transport and higher layers, and does not require any changes to stationary hosts and routers. The model is natural, because the authors coordinate a collection of mobile hosts (MHs) as a new IP network. They route packets to the MHs by using a router. The router is special because once it receives a packet, it does special things to ensure its safe delivery to its destination (the MH). This special operation is invisible to existing hosts and routers, so all the routing difference due to movement of the hosts can be hidden and effected by mechanisms under the control of the special entities. The other part of the model, which is a very natural part of a physical wireless data communications system, is the transceiver (access point), which collects wireless packets from a MH for delivery to existing hosts along existing wired networks. This transceiver provides the reference point by which the location of the MH is known.
Implementing a business process management system using adept: A real-world case study

This article describes how the agent-based design of ADEPT (advanced decision environment for process tasks) and implementation philosophy was used to prototype a business process management system for a real-world application. The application illustrated is based on the British Telecom (BT) business process of providing a quote to a customer for installing a network to deliver a specified type of telecommunications service. Particular emphasis is placed upon the techniques developed for specifying services, allowing agents with heterogeneous information models to interoperate, allowing rich and exible interagent negotiation to occur, and on the issues related to interfacing agent-based systems and humans. This article builds upon the companion article (Applied Artificial Intelligence Vol. 14, no. 2, pgs. 145¨189) that provides details of the rationale and design of the ADEPT technology deployed in this application.
Chlamydia (uncomplicated, genital).

INTRODUCTION Genital chlamydia is the most commonly reported bacterial sexually transmitted infection in developed countries. The majority of infections affect young adults under the age of 25 years. METHODS AND OUTCOMES We conducted a systematic review and aimed to answer the following clinical questions: What are the effects of antibiotic treatment for men and non-pregnant women with uncomplicated genital chlamydial infection? What are the effects of antibiotic treatment for pregnant women with uncomplicated genital chlamydial infection? We searched: Medline, Embase, The Cochrane Library, and other important databases up to February 2014 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). RESULTS We found 26 studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. CONCLUSIONS In this systematic review we present information relating to the effectiveness and safety of the following interventions - for men and non-pregnant women: antibiotics (single-dose) and antibiotics (multiple-dose regimens); for pregnant women: antibiotics (single-dose), erythromycin or amoxicillin (multiple-dose regimens), and clindamycin (multiple-dose regimens).
Active speech level estimation in noisy signals with quadrature noise suppression

We present a noise-robust algorithm for estimating the active level of speech, which is the average speech power during intervals of speech activity. The proposed algorithm uses the clean speech phase to remove the quadrature noise component from the short-time power spectrum of the noisy speech, as well as SNR-dependent techniques to improve the estimation. The pitch of voiced speech frames is determined using a noise-robust pitch tracker and the speech level is estimated from the energy of the pitch harmonics using the harmonic summation principle. At low noise levels, the resultant active speech level estimate is combined with that from the standardized ITU-T P.56 algorithm to give a final composite estimate. The algorithm has been evaluated using a range of noise signals and gives consistently lower errors than previous methods and than the ITU-T P.56 algorithm, which is accurate for SNR levels of above 15 dB.
Social desirability bias and self-reports of motivation: a study of amazon mechanical turk in the US and India

In this study we extend research on online collaboration by examining motivation to do work on the crowdsoucing service Amazon Mechanical Turk (MTurk). We address a challenge to many existing studies of motivation in online contexts: they are based on survey self-reports, which are susceptible to effects such as social desirability bias. In addition we investigate a second challenge to the extant research on motivation in the context of MTurk: a failure to examine potential differences between MTurk workers (Turkers) from different parts of the world, especially those from the US and India, MTurk's two largest worker groups. Using a survey technique called the list experiment, we observe distinct profiles of motivation and patterns of social desirability effects among Turkers in the US and India. Among US Turkers, we find that social desirability encourages over-reporting of each of four motivating factors we examined. The over-reporting was particularly large in the case of money as a motivator. In contrast, among Turkers in India we find a more complex pattern of social desirability effects, with workers under-reporting "killing time" and "fun" as motivations, and drastically over-reporting "sense of purpose. " We conclude by discussing these results and proposing implications for future research and design.