Miracle-dz/UniFAR-FTUs huggingface dataset:
Responses of Wild-Type and Resistant Strains of the Hyperthermophilic Bacterium Thermotoga maritima to Chloramphenicol Challenge

ABSTRACT Transcriptomes and growth physiologies of the hyperthermophile Thermotoga maritima and an antibiotic-resistant spontaneous mutant were compared prior to and following exposure to chloramphenicol. While the wild-type response was similar to that of mesophilic bacteria, reduced susceptibility of the mutant was attributed to five mutations in 23S rRNA and phenotypic preconditioning to chloramphenicol.
LDL cholesterol and apolipoprotein B are associated with ascending aorta dilatation in bicuspid aortic valve patients.

BACKGROUND The factors related to ascending aorta dilation (AAD) in patients with bicuspid aortic valve (BAV) are not completely understood. In addition, the role of cholesterol metabolism in AAD has not been studied. METHODS We analyzed the relationship between different lipid parameters and the ascending aorta diameter/presence of aortic dilatation in 91 consecutive patients with BAV. RESULTS We observed a positive linear correlation between the total cholesterol, low-density lipoprotein (LDL) cholesterol and apolipoprotein B (ApoB) levels and the ascending aorta diameter. The patients with AAD had higher LDL cholesterol and ApoB levels. Whereas LDL cholesterol and ApoB were identified as independent factors predictors of the aortic root diameter, only ApoB predicted the diameter of the ascending aorta. On the other hand, the levels of ApoB were an independent factor related to the dilatation of the aortic root. CONCLUSIONS We have observed that cholesterol is associated with ascending aorta diameter and dilation in BAV patients. Further experimental and clinical studies are needed to explain the pathobiology of this association.
Early use of TIPS in patients with cirrhosis and variceal bleeding.

BACKGROUND Patients with cirrhosis in Child-Pugh class C or those in class B who have persistent bleeding at endoscopy are at high risk for treatment failure and a poor prognosis, even if they have undergone rescue treatment with a transjugular intrahepatic portosystemic shunt (TIPS). This study evaluated the earlier use of TIPS in such patients. METHODS We randomly assigned, within 24 hours after admission, a total of 63 patients with cirrhosis and acute variceal bleeding who had been treated with vasoactive drugs plus endoscopic therapy to treatment with a polytetrafluoroethylene-covered stent within 72 hours after randomization (early-TIPS group, 32 patients) or continuation of vasoactive-drug therapy, followed after 3 to 5 days by treatment with propranolol or nadolol and long-term endoscopic band ligation (EBL), with insertion of a TIPS if needed as rescue therapy (pharmacotherapy-EBL group, 31 patients). RESULTS During a median follow-up of 16 months, rebleeding or failure to control bleeding occurred in 14 patients in the pharmacotherapy-EBL group as compared with 1 patient in the early-TIPS group (P=0.001). The 1-year actuarial probability of remaining free of this composite end point was 50% in the pharmacotherapy-EBL group versus 97% in the early-TIPS group (P<0.001). Sixteen patients died (12 in the pharmacotherapy-EBL group and 4 in the early-TIPS group, P=0.01). The 1-year actuarial survival was 61% in the pharmacotherapy-EBL group versus 86% in the early-TIPS group (P<0.001). Seven patients in the pharmacotherapy-EBL group received TIPS as rescue therapy, but four died. The number of days in the intensive care unit and the percentage of time in the hospital during follow-up were significantly higher in the pharmacotherapy-EBL group than in the early-TIPS group. No significant differences were observed between the two treatment groups with respect to serious adverse events. CONCLUSIONS In these patients with cirrhosis who were hospitalized for acute variceal bleeding and at high risk for treatment failure, the early use of TIPS was associated with significant reductions in treatment failure and in mortality. (Current Controlled Trials number, ISRCTN58150114.)
Using technology and structured peer reviews to enhance students’ writing

This article reports an initiative to improve student writing by incorporating technology-based structured peer review in the revision process. Although the most important step of writing, the revision step, is overlooked by students for several reasons. We describe a successful 10-week long intervention with students from upper-level undergraduate courses. Effectiveness was assessed by means of a pre- and post-test design, student feedback, and student performance scores. Areas where the intervention was found to have most significant impact were the following: students’ overall ability to make revisions, overall English writing, and feedback skills. Educators would find technology-based peer review helpful by having students learn and apply revision efforts in their written assignments. Benefits and trade-offs of the innovative pedagogy are discussed and directions for future study indicated.
Minimal basilar membrane motion in low-frequency hearing

Significance To perceive speech, the brain relies on inputs from sensory cells located near the top of the spiral-shaped cochlea. This low-frequency region of the inner ear is anatomically difficult to access, and it has not previously been possible to study its mechanical response to sound in intact preparations. Here, we used optical coherence tomography to image sound-evoked vibration inside the intact cochlea. We show that low-frequency sound moves a small portion of the basilar membrane, and that the motion declines in an exponential manner across the basilar membrane. Hence, the response of the hearing organ to speech-frequency sounds is different from the one evident in high-frequency cochlear regions. Low-frequency hearing is critically important for speech and music perception, but no mechanical measurements have previously been available from inner ears with intact low-frequency parts. These regions of the cochlea may function in ways different from the extensively studied high-frequency regions, where the sensory outer hair cells produce force that greatly increases the sound-evoked vibrations of the basilar membrane. We used laser interferometry in vitro and optical coherence tomography in vivo to study the low-frequency part of the guinea pig cochlea, and found that sound stimulation caused motion of a minimal portion of the basilar membrane. Outside the region of peak movement, an exponential decline in motion amplitude occurred across the basilar membrane. The moving region had different dependence on stimulus frequency than the vibrations measured near the mechanosensitive stereocilia. This behavior differs substantially from the behavior found in the extensively studied high-frequency regions of the cochlea.
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article, we use a large and diverse benchmark to prove that is possible to improve consistently the cross-docking performance against a single receptor conformation, using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and our method predicted the top-ranked near native ligand poses 20% more efficiently than using a single receptor. The multiple conformations were derived from the collective variable space defined by all heavy-atom elastic network normal modes, including backbone and side chains. We have found that the binding site displacements for best positioning of the ligand seem rather independent from the global collective motions of the protein. We also found that the number of binding site conformations needed to represent nonredundant flexibility was < 100. The ensemble of receptor conformations can be generated at our Web site at http://abagyan.scripps. edu/MRC.
Semantic Contexts and Fisher Vectors for the ImageCLEF 2011 Photo Annotation Task

This paper describes the participation of UNI- CAEN/GREYC to the ImageCLEF 2011 photo annotation task. The proposed approach uses visual image features and binary annota- tions of concepts only. In this approach, the annotations are predicted by SVM classiers trained separately for each concept. The classiers take Bag-of-Words histograms and sher vectors representations as inputs, both being combined at the decision level. Furthermore, contextual information is also embedded into the Bag-of-Words histograms to enhance their performance. The experimental results show that the combination of Bag-of-Words histograms and Fisher vectors brings signicant performance increase (e.g. 4% for Mean Average Precision). Furthermore, the results of our best-run rank in top 3 for both concept and image level evaluations.
Cholesterol Oxidase Is Indispensable in the Pathogenesis of Mycobacterium tuberculosis

Despite considerable research effort, the molecular mechanisms of Mycobacterium tuberculosis (Mtb) virulence remain unclear. Cholesterol oxidase (ChoD), an extracellular enzyme capable of converting cholesterol to its 3-keto-4-ene derivative, cholestenone, has been proposed to play a role in the virulence of Mtb. Here, we verified the hypothesis that ChoD is capable of modifying the bactericidal and pro-inflammatory activity of human macrophages. We also sought to determine the contribution of complement receptor 3 (CR3)- and Toll-like receptor 2 (TLR2)-mediated signaling pathways in the development of macrophage responses to Mtb. We found that intracellular replication of an Mtb mutant lacking a functional choD gene (ΔchoD) was less efficient in macrophages than that of the wild-type strain. Blocking CR3 and TLR2 with monoclonal antibodies enhanced survival of ΔchoD inside macrophages. We also showed that, in contrast to wild-type Mtb, the ΔchoD strain induced nitric oxide production in macrophages, an action that depended on the TLR2, but not the CR3, signaling pathway. Both wild-type and mutant strains inhibited the production of reactive oxygen species (ROS), but the ΔchoD strain did so to a significantly lesser extent. Blocking TLR2-mediated signaling abolished the inhibitory effect of wild-type Mtb on ROS production by macrophages. Wild-type Mtb, but not the ΔchoD strain, decreased phorbol myristate acetate-induced phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), which are involved in both TLR2- and CR3-mediated signaling pathways. Our finding also revealed that the production of interleukin 10 by macrophages was significantly lower in ΔchoD-infected macrophages than in wild-type Mtb-infected macrophages. However, tumor necrosis factor-α production by macrophages was the same after infection with mutant or wild-type strains. In summary, we demonstrate here that ChoD is required for Mtb interference with the TLR2-mediated signaling pathway and subsequent intracellular growth and survival of the pathogen in human macrophages.
One Integrated Energy Efficiency Proposal for 5G IoT Communications

To further enhance the energy efficiency (EE) performance of fifth generation (5G) Internet of Things systems, an integrated structure is proposed in this paper. That is, other than prior studies that separately study the wireless and wired parts, the wireless and wired parts are holistically combined together to comprehensively optimize the EE of the whole system. The integrated system structure is introduced beforehand with the proposed unified control center components for better deployment of the select-and-sleep mechanism. In addition, in the wireless part, one cellular partition zooming (CPZ) mechanism is proposed. In contrast, in the wired part, a precaching mechanism is introduced. With these proposals, the proposed system EE performance is investigated. Comprehensive computer-based simulation results demonstrate that the proposed schemes display better EE performance. This is due to the fact that system power consumption is further reduced with these schemes as compared to the prior work.
Energy-Aware Backbone Networks: A Case Study

Power consumption of ICT is becoming more and more a sensible problem, which is of interest for both the research community, for ISPs and for the general public. In this paper we consider a real IP backbone network and a real traffic profile. We evaluate the energy cost of running it, and, speculating on the possibility of selectively turning off spare devices whose capacity is not required to transport off-peak traffic, we show that it is possible to easily achieve more than 23% of energy saving per year, i.e., to save about 3GWh/year considering today's power footprint of real network devices.
Symbiotic routing in future data centers

Building distributed applications that run in data centers is hard. The CamCube project explores the design of a shipping container sized data center with the goal of building an easier platform on which to build these applications. CamCube replaces the traditional switch-based network with a 3D torus topology, with each server directly connected to six other servers. As in other proposals, e.g. DCell and BCube, multi-hop routing in CamCube requires servers to participate in packet forwarding. To date, as in existing data centers, these approaches have all provided a single routing protocol for the applications. In this paper we explore if allowing applications to implement their own routing services is advantageous, and if we can support it efficiently. This is based on the observation that, due to the flexibility offered by the CamCube API, many applications implemented their own routing protocol in order to achieve specific application-level characteristics, such as trading off higher-latency for better path convergence. Using large-scale simulations we demonstrate the benefits and network-level impact of running multiple routing protocols. We demonstrate that applications are more efficient and do not generate additional control traffic overhead. This motivates us to design an extended routing service allowing easy implementation of application-specific routing protocols on CamCube. Finally, we demonstrate that the additional performance overhead incurred when using the extended routing service on a prototype CamCube is very low.
Low cost reorder buffer for MDF FFT with reduced memory size

This paper presents a general low cost architecture of reorder buffer for multipath delay feedback (MDF) FFT processor. Because of its high throughput, the MDF FFT is widely adopted in communication systems such as ultra-wideband (UWB), wireless personal area network (WPAN) and long term evolution-advanced (LTE-A). However, as its parallel nonstop output is in bit-reversed order, an output reorder buffer is always required to change it to normal order. The memory of the traditional ping-pong buffer scheme, whose size is twice of the FFT length, takes up the most area of the reorder buffer. To save memory, a new addressing method is proposed where the simultaneous read and write operation use the same set of address. So that only a single RAM bank is required and the total memory size is reduced to 50% of the ping-pong buffer. Mathematical derivation of the single-RAM-bank reorder algorithm and a quantitative express of the area of memory saved by this technique are given. To demonstrate the benefits of this approach, this paper presents a realization of a reorder buffer designed for an 8-path 512-point MDF FFT processor using Silterra 0.13 um process. The core area of the whole output reorder buffer is 0.1 mm2, 95% of which is occupied by RAMs, and 32% of that is saved by this new reorder architecture.
Representation of stable social dominance relations by human infants

What are the origins of humans’ capacity to represent social relations? We approached this question by studying human infants’ understanding of social dominance as a stable relation. We presented infants with interactions between animated agents in conflict situations. Studies 1 and 2 targeted expectations of stability of social dominance. They revealed that 15-mo-olds (and, to a lesser extent, 12-mo-olds) expect an asymmetric relationship between two agents to remain stable from one conflict to another. To do so, infants need to infer that one of the agents (the dominant) will consistently prevail when her goals conflict with those of the other (the subordinate). Study 3 and 4 targeted the format of infants’ representation of social dominance. In these studies, we found that 12- and 15-mo-olds did not extend their expectations of dominance to unobserved relationships, even when they could have been established by transitive inference. These results suggest that infants' expectation of stability originates from their representation of social dominance as a relationship between two agents rather than as an individual property. Infants’ demonstrated understanding of social dominance reflects the cognitive underpinning of humans’ capacity to represent social relations, which may be evolutionarily ancient, and may be shared with nonhuman species.
EM-based on-chip aging sensor for detection and prevention of counterfeit and recycled ICs

The counterfeiting and recycled integrated circuits (ICs) has become a major security threat for commercial and military systems. In addition to the huge economic impacts, they post significant security and safety threats on those systems. In this paper, we propose a new lightweight on-chip aging sensor, which is based on the electromigration (EM)-induced aging effects for fast detection and prevention of recycled ICs. Our new EM-based aging sensor exploits the natural aging/failure mechanism of interconnect wires to time the aging of the chip. Compared with existing aging sensor, the new aging sensor can provide more accurate prediction of the chip usage time at smaller area footprints due to its simple structure. The new sensor is based on a newly proposed physics-based stress evolution model of EM effects for accurate prediction of the EM failure. As a result, we can design the interconnect wire structures based on copper interconnect technology so that the resulting wires will have detectable EM failure at a specific time with sufficient accuracy. In order to mitigate the problem of the inherent variations in the metal grain sizes and assess its impacts on the nucleation time of metal wires, a number of parallel properly structured wires are used in the sensor. The parameters of the wires are optimized using the new EM model. Our statistical and variational analysis shows that the proposed aging sensor can accurately predict the targeted failure times in the presence of both inherent uncertainties. Our study also shows that more parallel wires will lead to more accurate statistical predictions at costs of more areas.
Reduced QT variability and increased QT/RR slope in ECG signals of depressed patients with suicidal ideation

Major depressive disorder (MDD) is associated with a number of comorbidities including cardiovascular disease (CVD), with an increased risk of death after myocardial. The aim of this study was to investigate if parameters for ventricular repolarization variability and dynamics in ECG signals are different in MDD patients with/without suicidal ideation and healthy volunteers. Sixty-one ECG recordings (10 minutes) were acquired and analysed from control subjects (44 CONT), 20 MDD subjects with (MDDSI+) and 21 without suicidal ideation [SI] (MDDSI-) for a case-control analysis at a psychiatric clinic in the UAE. The Mini-International Neuropsychiatric Interview (MINI) made diagnoses of MDD and the subscale for was used to evaluate the patients' suicidal intensions [0 to 38]. The subscale for SI consists of 19 items, which was used to evaluate the patients' suicidal intensions [0 to 38]. Then heart rate-corrected QT interval (QTc), QT/RR slope, QT variability (QTV), Median T-wave amplitudes and T-wave variability were estimated. MDD patients with suicidal ideation displayed increased QT/RR slope and reduced QTV, which may reflect abnormal ventricular repolarization liability and lead to higher risk of cardiac arrhythmia and future cardiovascular diseases.
Detecting Dynamic Traffic Assignment Capacity Paradoxes in Saturated Networks

Creation of a new link or increase in capacity of an existing link can reduce the efficiency of a congested network as measured by the total travel cost. This phenomenon, of which an extreme example is given by Braess paradox, has been examined in conventional studies within the framework of static assignment. For dynamic traffic assignment, which makes account of the effect of congestion through explicit representation of queues, Akamatsu (2000) gave a simple example of the occurrence of this paradox. The present paper extends that result to a more general network. We first present a necessary and sufficient condition for the paradox to occur in a general network in which there is a queue on each link. We then give a graph-theoretic interpretation of the condition, which gives us a convenient method to test whether or not the paradox will occur by performing certain tests on information that describes the network structure. Finally, as an application of this theory, we examine several example networks and queueing patterns where occurrence of this paradox is inevitable.
Tadpole Analysis of Orientifolded Plane-Waves

We study orientifolds of type-IIB string theory in the plane-wave background supported by null RR 3-form flux F(3). We describe how to extract the RR tadpoles in the Green-Schwarz formalism in a general setting. Two models with orientifold groups {1, Ω} and {1, Ω I4}, which are T-dual to each other, are considered. Consistency of these backgrounds requires 32 D9 branes for the first model and 32 D5 branes for the second one. We study the spectra and comment on the heterotic duals of our models.
A Simulation Optimization Approach to Epidemic Forecasting

Reliable forecasts of influenza can aid in the control of both seasonal and pandemic outbreaks. We introduce a simulation optimization (SIMOP) approach for forecasting the influenza epidemic curve. This study represents the final step of a project aimed at using a combination of simulation, classification, statistical and optimization techniques to forecast the epidemic curve and infer underlying model parameters during an influenza outbreak. The SIMOP procedure combines an individual-based model and the Nelder-Mead simplex optimization method. The method is used to forecast epidemics simulated over synthetic social networks representing Montgomery County in Virginia, Miami, Seattle and surrounding metropolitan regions. The results are presented for the first four weeks. Depending on the synthetic network, the peak time could be predicted within a 95% CI as early as seven weeks before the actual peak. The peak infected and total infected were also accurately forecasted for Montgomery County in Virginia within the forecasting period. Forecasting of the epidemic curve for both seasonal and pandemic influenza outbreaks is a complex problem, however this is a preliminary step and the results suggest that more can be achieved in this area.