Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characteristics and antibiotic resistance profiles of Escherichia coli strains isolated from urinary tract infections in children admitted to children's referral hospital of Qom, Iran.

BACKGROUND Urinary tract infections (UTIs) are a highly prevalent infection among children and Escherichia coli is one of the most important pathogens causing pediatric UTIs. Production of extended spectrum b-lactamase (ESBL) enzymes is an important factor in the emergence of antibiotic resistance among these bacteria. This study aimed to determine the resistance patterns, the frequency of ESBL-encoding genes and the genetic diversity of E. coli strains isolated from children with UTIs who were admitted to children's referral hospital of Hazrat Masoumeh, Qom, Iran. METHODS A total of 102 consecutive non-duplicative strains of E.coli that were isolated from children with UTIs were included into the study. Antibiotic susceptibility of the isolates was determined by disk diffusion method according to the CLSI guidelines. The ability of the isolates to produce ESBLs was phenotypically determined by both combined disk test and double disk synergy test. The ESBL encoding genes (bla CTX-M, bla SHV, and bla TEM) in phenotypically confirmed ESBL-positive isolates was detected by PCR method. The genetic relatedness of the isolates was designated by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). RESULTS Eighty-three percent (n=85) of the children were female. Most of the infected boys (88%, n=15) were less than 1 year of age and most of the infected girls (48%, n=41) aged 1 to 6 years old. The highest sensitivity was observed to nitrofurantoin (8%, n=8), followed by amikacin (12%, n=12) and piperacillin-tazobactam (17%, n=17). In contrast, the highest resistance rate was seen to ampicillin (94%, n=96) and cefazolin (93%, n=95). Eighty-eight percent (90 out of 102) of the strains were multidrug-resistant (MDR). Fifty-eight percent (n=59) of the strains were ESBL-positive and results of the combined disk test was in concordance with PCR. The blaCTX-M was the most frequent ESBL encoding gene (88%, n=52), followed by blaTEM (54%, n=32), and blaSHV (15%, n=9). Based on the ERIC-PCR technique, isolates were clustered in 13 different types. There was no relationship between different ERIC types and origin of the isolates (i.e. hospitalized or outpatients), ESBL-producing ability, and antibiotic resistance patterns. CONCLUSIONS High prevalence of ESBL-positive isolates of E. coli (58%) was found in our study and all of them were MDR. In addition, there were statistically significant differences in the resistance rates of ESBL-producers, and non-producers to some antibiotics, which result in limiting their therapeutic options. Continuous surveillance of the emergence of ESBL-producing isolates and their antibiotic resistance profiles as well as using appropriate typing methods is needed for reducing their spread, selecting appropriate treatment regimens and finding hospital outbreaks.
Optimal code size reduction for software-pipelined loops on DSP applications

Code size expansion of software-pipelined loops is a critical problem for DSP systems with strict code size constraint. Some ad-hoc code size reduction techniques were used to try to reduce the prologue/epilogue produced by software pipelining. We present the fundamental understanding of the relationship between code size expansion and software pipelining. Based on the retiming concept, we present a powerful Code-size REDuction (CRED) technique and its application on various kinds of processors. We also provide CRED algorithms integrated with the software pipelining process. One advantage of our algorithms is that it can explore the trade-off space between "perfect" software pipelining and constrained code size. That is, the software pipelining process can be controlled to generate a schedule concerned with code size requirement. The experiment results show the effectiveness of our algorithms in both reducing the code size for software-pipelined loops and exploring the code size/performance trade-off space.
A Quick Emergency Response Model for Micro-blog Public Opinion Crisis Based on Text Sentiment Intensity

On the basis of discussing the information spreading mechanism under Internet environment, we have studied on how to build a public opinion monitoring model according to the semantic content or text mining in recent years. A micro-blog public opinion corpus named MPO Corpus on the content of micro-blog information as a test data set has been constructed by our research team. In this paper, it proposes a quick emergency response model (QREM) for micro-blog public opinion crisis oriented to Mobile Internet services. Firstly, it describes the micro-blog cases and emergency response plan library using web ontology language (OWL), which makes the transitive logical reason capacity among micro-blog subjects, micro-blog cases and emergency plans. Secondly, it proposes an algorithm to calculate the sentiment intensity of micro-blogs from three levels on words, sentences and documents based on HowNet Knowledge-base respectively. Thirdly, we continue to study on how to update cases under the subjects and quick response processes for micro-blog case base. Finally, we design a test experiment which shows some merits of QREM in time, which basically meets the quick emergency response demand on the micro-blog public opinions crisis under Mobile Internet environment. Thus, it will provide more efficient support to the government and related monitoring departments involved with the public opinions crisis.
Combining Speak-Up with DefCOM for Improved DDoS Defense

This work combines two existing defenses against distributed denial-of-service (DDoS) attacks - DefCOM and speak-up - resulting in a synergistic improvement. DefCOM defense organizes existing source-end, victim-end and core defenses into a collaborative overlay to filter DDoS floods. Source networks that do not participate in DefCOM often receive poor service and their traffic is severely rate-limited. This is because core nodes in DefCOM that perform filtering lack cheap algorithms to differentiate legitimate from attack traffic at line speed - they must conservatively assume all high-rate traffic from legacy networks to be attack. Thus, in its attempt to mitigate DDoS, DefCOM ends up denying service during attacks to legitimate hosts that reside in legacy networks. Speak-up is a recently proposed defense, which invites all clients of the DDoS victim to send additional payment traffic, with the assumption that attack machines are already sending close to their full capacity. Clients that send a lot of payment traffic are considered legitimate and whitelisted. Speak-up is relatively cheap to deploy at the clients and the DDoS victim, but since payment traffic needs to be sent continuously, this creates additional congestion at the victim, which is undesirable. We combine speak-up and DefCOM into a synergistic defense that addresses the shortcomings of the individual defenses and confirms the success of collaborative protection against DDoS attacks. Speak-up is integrated with core defenses in DefCOM and whitelists clients based on their payment traffic. Legitimate clients in legacy networks can thus be detected and served. Further, since Speak-up is implemented in the core, payment and attack traffic do not reach the victim and any undesirable congestion effects are localized to the vicinity of legacy networking.
Cost Inefficiency, Size of Firms and Takeovers

This study, using the Cox proportional hazards model, finds that the risk of takeover rises with cost inefficiency. It also finds that a firm faces a significantly higher risk of takeover if its cost performance lags behind its industry benchmark. Moreover, these findings appear to be remarkably stable over the nearly two decades spanned by the sample. The effect of the variables used to measure the risk-size relationship, however, indicates temporal changes. Lastly, the study presents evidence from fixed-effects models of ex post cost efficiency improvements that support the hypothesis that takeover targets are selected based on the potential for improvement.
An anomaly detection framework for BGP

Abnormal events such as large scale power outages, misconfigurations, and worm attacks can affect the global routing infrastructure and consequently create regional or global Internet service interruptions. As a result, early detection of abnormal events is of critical importance. In this study we present a framework based on data mining algorithms that are applied to anomaly detection on global routing infrastructure. To show the applicability of our framework, we conduct extensive experiments with a variety of abnormal events and classification algorithms. Our results demonstrate that when we train our system with abnormal events including worm attacks, power supply outages, submarine cable cuts, and misconfigurations, we can detect a similar type of event as it happens.
Fuzzy Logic Based Sliding Mode Controlled For Active Clamp SEPIC Converter

In this paper a modified design of a sliding mode controller based on fuzzy logic for a soft switching sepic converter is introduced. Here a proportional integral (PI)-type current mode control is employed and a sliding mode controller is designed utilizing fuzzy algorithm. Sliding mode controller ensures robustness against all variations and fuzzy logic helps to reduce chattering phenomenon introduced by sliding controller. Therefore error, voltage and current ripples decrease. One of the advantages of proposed controller is better performance in comparison with conventional sliding mode controller in soft switching sepic converter The proposed system is simulated by MATLAB / SIMULINK. The simulation results verify the good performance of proposed controller against variation of input and reference voltages.
Agent Interaction in Ambient Intelligent Environments

Most of the research on ambient intelligence focusses on how to integrate smart objects into our real environment without considering how users interact with these objects and make use of their functionality. In this paper, we discuss interaction design methods in an ambient intelligent environment in order to develop a model for interaction design between the user who resides in the real world and the software components that are working behind the scenes.
Environmental Toxicology and Chemistry

Carbonaceous nanomaterials, such as fullerenes (C60, C70) and the derivative phenyl‐C61‐butyric acid methyl ester (PCBM), have promising application in solar energy technologies. Although the acute ecotoxicity of C60 has been reported widely in the literature, ecotoxicity assays for different fullerene forms and broader ecosystem impact studies remain scarce. To address these knowledge gaps, acute, chronic, and life stage exposure studies with freshwater zooplankton, Daphnia magna and Daphnia pulex, were performed for each material. Experimental results indicated that C60 and PCBM are not acutely toxic at estimated environmentally relevant concentrations; however, C70 had significant acute effects. All forms of fullerene caused a gradual elevation in heart rate over time and visual darkening of the Daphnia spp. carapace. The impact of fullerenes on susceptibility to predation was then assessed experimentally by presenting D. pulex to the visual predator Lepomis macrochirus (bluegill). Predation risk was significantly increased in fullerene‐exposed D. pulex. The present study underscores the need to broaden the scope of traditional ecotoxicity for emerging materials: studies are required that evaluate portfolios of related nanomaterials and that capture chronic and cascading ecosystem‐level effects. Environ Toxicol Chem 2019;38:1714‒1723. © 2019 SETAC
The Effect of Morphology on the Spinal Engine Driven Locomotion in a Quadruped Robot

The biological hypothesis of spinal engine states that the locomotion is mainly achieved by the spine, while legs only serve as assistance. Inspired by this spinal engine hypothesis, a compliant, multi-DOF, biologically inspired spine has been developed and embedded into a quadruped robot without actuation on legs. The experimental results support this spinal engine hypothesis and reveal that this kind of robot can achieve rapid, stable, and even dynamical locomotion by appropriately tuning the spine’s morphological parameters, e.g., rearranging the silicone blocks.
Optimizing IPTV video delivery using SVC spatial scalability

This paper focuses on two typical constraints present in current video delivery platforms such as IPTV: accommodating the diversity of consumer end-devices and coping with various bandwidth constraints of the deployed network access technologies. We propose the use of the Scalable Video Coding (SVC) extension of H.264/AVC to cope with these two constraints: three different techniques to combine SD and HD versions of a video sequence in one SVC stream are presented and we assess how quality scalability compares to spatial scalability in producing video streams that can be tailored to various bandwidth constraints. The results show that the three proposed techniques for combining SD and HD perform equally good and that, under certain conditions, spatial scalability outperforms quality scalability to cope with various bandwidth constraints.
Gait analysis and body composition after treatment of quadriceps tendon ruptures showed equal results independent of suture anchor or transosseus repair technique used: a pilot study

Abstract Purpose: Suture anchor repair is a fairly new surgical technique for quadriceps tendon ruptures. It is supposed to be superior to the standard transosseus sutures because of biomechanical superiority and – due to a less invasive surgery – earlier rehabilitation onset. This study focused on analyzing functionality of the quadriceps muscle during gait as well as body composition between a suture anchor and a transosseus suture repair group and is the first study that undertook systematic gait analyses in this patient population. Materials and methods: Seventeen patients who underwent either suture anchor (9 subjects) or transosseus suture repair surgery (8 subjects) at two different trauma surgery centers between 2010 and 2015 were included. Gait analysis was performed with a three dimensional motion capture system (Vicon) and body composition was assessed with bioelectrical impedance analysis (Nutribox). Parametrical statistical analyses were conducted using independent t-tests. Results: No statistically significant differences were found in any outcome parameter of gait analysis or body composition measurement. Conclusion: Suture anchor repair shows equal results to transosseus suture repair technique regarding gait quality and body composition. Implications for rehabilitation In a long term follow-up suture anchor repair shows similar results to the transosseus suture technique regarding body composition and musculus quadriceps function in gait. Without the implementation of an appropriate rehabilitation protocol incorporating the earlier load-carrying capacity, early biomechanical advantages of suture anchor technique over transosseus sutures might vanish over time. The decision which surgery technique might be best for the individual patient, should not be based on the expectation that suture anchor repair alone without considering appropriate rehabilitation would lead to long term functional advantages over transosseus suture technique.
Phylogeny Predicts Future Habitat Shifts Due to Climate Change

Background Taxa may respond differently to climatic changes, depending on phylogenetic or ecological effects, but studies that discern among these alternatives are scarce. Here, we use two species pairs from globally distributed spider clades, each pair representing two lifestyles (generalist, specialist) to test the relative importance of phylogeny versus ecology in predicted responses to climate change. Methodology We used a recent phylogenetic hypothesis for nephilid spiders to select four species from two genera (Nephilingis and Nephilengys) that match the above criteria, are fully allopatric but combined occupy all subtropical-tropical regions. Based on their records, we modeled each species niche spaces and predicted their ecological shifts 20, 40, 60, and 80 years into the future using customized GIS tools and projected climatic changes. Conclusions Phylogeny better predicts the species current ecological preferences than do lifestyles. By 2080 all species face dramatic reductions in suitable habitat (54.8–77.1%) and adapt by moving towards higher altitudes and latitudes, although at different tempos. Phylogeny and life style explain simulated habitat shifts in altitude, but phylogeny is the sole best predictor of latitudinal shifts. Models incorporating phylogenetic relatedness are an important additional tool to predict accurately biotic responses to global change.
Gamma Oscillations in the Temporal Pole in Response to Eyes

The eyes of an individual act as an indispensable communication medium during human social interactions. Functional neuroimaging studies have revealed that several brain regions are activated in response to eyes and eye gaze direction changes. However, it remains unclear whether the temporal pole is one of these regions. Furthermore, if the temporal pole is activated by these stimuli, the timing and manner in which it is activated also remain unclear. To investigate these issues, we analyzed intracranial electroencephalographic data from the temporal pole that were obtained during the presentation of eyes and mosaics in averted or straight directions and their directional changes. Time–frequency statistical parametric mapping analyses revealed that the bilateral temporal poles exhibited greater gamma-band activation beginning at 215 ms in response to eyes compared with mosaics, irrespective of the direction. Additionally, the right temporal pole showed greater gamma-band activation beginning at 197 ms in response to directional changes of the eyes compared with mosaics. These results suggest that gamma-band oscillations in the temporal pole were involved in the processing of the presence of eyes and changes in eye gaze direction at a relatively late temporal stage compared with the posterior cortices.
In Vivo Live Imaging of Oncolytic Mammalian Orthoreovirus Expressing NanoLuc Luciferase in Tumor Xenograft Mice

Engineering of recombinant MRV for improved oncolytic activity has not yet been achieved due to difficulty in generating autonomous replicating MRV harboring transgenes. Here, we constructed a reporter MRV that can be used to monitor cancer-selective infection by oncolytic MRV in a mouse model. Among the numerous oncolytic viruses, MRV has an advantage in that the wild-type virus shows marked oncolytic activity in patients without any notable adverse effects. The reporter MRV developed herein will open avenues to the development of recombinant MRV vectors armed with anticancer transgenes. ABSTRACT Wild-type mammalian reoviruses (MRVs) have been evaluated as oncolytic agents against various cancers; however, genetic modification methods for improving MRV agents have not been exploited fully. In the present study, using MRV strain T1L, we generated a reporter MRV that expresses a NanoLuc luciferase (NLuc) gene and used it for noninvasive imaging of MRV infection in tumor xenograft mice. NLuc and a P2A self-cleaving peptide gene cassette were placed upstream of the L1 gene open reading frame to enable bicistronic expression of NLuc and the L1 gene product. BALB/c nude mice intranasally infected with MRV expressing NLuc (rsT1L-NLuc) displayed bioluminescent signals in the chest area at 4 days postinfection (dpi), which is consistent with natural MRV infection in the lung. Furthermore, to monitor tumor-selective infection by MRV, nude mice bearing human cancer xenografts were infected intravenously with rsT1L-NLuc. Bioluminescent signals were detected in tumors as early as 3 dpi and persisted for 2 months. The results demonstrate the utility of an autonomous replicating reporter MRV for noninvasive live imaging of replicating oncolytic MRV agents. IMPORTANCE Engineering of recombinant MRV for improved oncolytic activity has not yet been achieved due to difficulty in generating autonomous replicating MRV harboring transgenes. Here, we constructed a reporter MRV that can be used to monitor cancer-selective infection by oncolytic MRV in a mouse model. Among the numerous oncolytic viruses, MRV has an advantage in that the wild-type virus shows marked oncolytic activity in patients without any notable adverse effects. The reporter MRV developed herein will open avenues to the development of recombinant MRV vectors armed with anticancer transgenes.
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes

Abstract Summary G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data and repeat finders. G-OnRamp can be used to visualize large genomics datasets and to perform collaborative genome annotation projects in both research and educational settings. Availability and implementation The virtual machine images and tutorials are available on the G-OnRamp web site (http://g-onramp.org/deployments). The source code is available under an Academic Free License version 3.0 through the goeckslab GitHub repository (https://github.com/goeckslab). Supplementary information Supplementary data are available at Bioinformatics online.
Decidable Fragments of First-Order Language Under Stable Model Semantics and Circumscription

The stable model semantics was recently generalized by Ferraris, Lee and Lifschitz to the full first-order language with a syntax translation approach that is very similar to McCarthy's circumscription. In this paper, we investigate the decidability and undecidability of various fragments of first-order language under both semantics of stable models and circumscription. Some maximally decidable classes and undecidable classes are identified. The results obtained in the paper show that the boundaries between decidability and undecidability for these two semantics are very different in spite of the similarity of definition. Moreover, for all fragments considered in the paper, decidability under the semantics of circumscription coincides with that in classical first-order logic. This seems rather counterintuitive due to the second-order definition of circumscription and the high undecidability of first-order circumscription.
The Piezo-resistive MC Sensor is a Fast and Accurate Sensor for the Measurement of Mechanical Muscle Activity

A piezo-resistive muscle contraction (MC) sensor was used to assess the contractile properties of seven human skeletal muscles (vastus medialis, rectus femoris, vastus lateralis, gastrocnemius medialis, biceps femoris, erector spinae) during electrically stimulated isometric contraction. The sensor was affixed to the skin directly above the muscle centre. The length of the adjustable sensor tip (3, 4.5 and 6 mm) determined the depth of the tip in the tissue and thus the initial pressure on the skin, fatty and muscle tissue. The depth of the tip increased the signal amplitude and slightly sped up the time course of the signal by shortening the delay time. The MC sensor readings were compared to tensiomyographic (TMG) measurements. The signals obtained by MC only partially matched the TMG measurements, largely due to the faster response time of the MC sensor.