Miracle-dz/UniFAR-FTUs huggingface dataset:
M. tuberculosis AlkX Encoded by rv3249c Regulates a Conserved Alkane Hydroxylase System That Is Important for Replication in Macrophages and Biofilm Formation

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is the leading cause of death worldwide due to a single infectious agent. It is important to understand how M. tuberculosis adapts to and replicates in the intracellular environment of the host. ABSTRACT Mycobacterium tuberculosis is a highly specialized human pathogen. The success of M. tuberculosis is due to its ability to replicate within host macrophages, resist host immune responses, and ultimately enter a persistent state during a latent tuberculosis infection. Understanding how M. tuberculosis adapts to and replicates in the intracellular environment of the host is crucial for the development of novel, targeted therapeutics. We report the characterization of an M. tuberculosis mutant lacking Rv3249c, a TetR transcriptional regulator. We show that Rv3249c directly represses the adjacent alkB-rubA-rubB operon encoding an alkane hydroxylase/rubredoxin system. For consistency with related systems, we have named the rv3249c gene alkX. The alkX mutant survived better than wild-type M. tuberculosis inside macrophages. This could be phenocopied by overexpression of the alkB-rubA-rubB locus. We hypothesized that the improved intracellular survival phenotype is a result of increased fitness of the mutant; however, we found that the alkX mutant had a defect when grown on some host-associated carbon sources in vitro. We also found that the alkX mutant had a defect in biofilm formation, also linked to the overexpression of the alkB-rubAB genes. Combined, these results define the primary role of AlkX as a transcriptional repressor of the alkB-rubAB operon and suggest the operon contributes to intracellular survival of the pathogen. IMPORTANCE Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is the leading cause of death worldwide due to a single infectious agent. It is important to understand how M. tuberculosis adapts to and replicates in the intracellular environment of the host. In this study, we characterized the TetR transcriptional regulator Rv3249c and show that it regulates a highly conserved alkane hydroxylase/rubredoxin system. Our data demonstrate that the AlkBRubAB system contributes to the success of the bacterium in host macrophages.
Preventive potential of Bacillus sonorensis exopolysaccharide upon hepatocellular carcinoma and quantitation of tumor suppressor protein p53

Background Exopolysaccharide, a carbohydrate polymer, is known to possess several biological activities. This approach was designed to clarify the cytotoxic mechanism of Bacillus sonorensis exopolysaccharide (EPS-1) on Huh7, HepG2 and BNL cells besides exploring its influence on the expression of the tumor suppressor protein p53. p53 is the biomarker of the prognosis and occurrence of severe stages of the tumor and activation of both cell-cycle arrest and apoptosis in cancer cells which are the most targeted cellular processes for the therapy of tumor patients. Methods The cytotoxic impact of EPS-1 was quantified via neutral red uptake assay and the results were confirmed by a morphology study. The expression level of p53 was analyzed using quantitative real-time PCR. Results The outcomes of the present study explicated that EPS-1 with IC50 = 164 and 398 µg ml-1 exhibited an inhibitory influence on Huh7 and HepG2 cells growth after 48 h incubation time respectively. EPS-1 showed no influence on normal BNL cells. Furthermore, the molecular genetic analysis revealed that EPS-1 provoked significant upregulation in the expression level of the p53 gene in the treated Huh7 cell line more than that in HepG2, whereas no significant gene expression was noticed in BNL cells (P = 0.006, 0.65 and 0.83), respectively. Conclusion The antitumor activity displayed by this compound may be of interest for further studies of its structure-activity relationship. Before application in phase 1 of the clinical study, in-vivo studies would be needed to confirm the results obtained in the hope of finding more active and selective anticancer agents for drug development in the future.
Women's Agency as Reason for Life Threats Among the Pashtuns in Pakistan: Narratives of Women Fleeing Honor Killing and Masculine Domination

This article uses the narratives of survivors of honor killing to show that women's agency is the reason for life threats because it undermines masculine domination. The findings show that life threats are made against women engaging in behaviors not aligned to cultural norms as perceived by male members of their family, to escape shame and gossip, and it is a manifestation of men losing control over women. These survivors of honor-based violence have undermined masculine domination by acting in unanticipated ways and by fleeing to a shelter home in the face of overwhelming cultural sanctions and structural inequalities.
Energy expenditure of red-footed tortoises (Chelonoidis carbonaria) fed kibble diets with high levels of fibre, starch, or fat

ABSTRACT Knowledge of energy requirements is necessary to optimise the nutritional management of animals. For tortoises, very little is known about their nutrient and energy requirements. Data on substrate oxidation and the implications of starch or fat intake on the energy metabolism are lacking. The present study compared the daily energy expenditures (DEE) of red-footed tortoises (Chelonoidis carbonaria) that were fed three extruded diets: a control diet high in fibre and two test diets, one with high starch content and another with high fat content. A total of 18 tortoises (5.5 ± 1.18 kg) were used in a completely randomised design, with 6 animals per diet. After 14 months of experimental diet intake and 48 h of preliminary fasting, the animals were kept for 12 h in 70-l respiratory chambers. An open “push mode” system was used to determine the carbon dioxide production and oxygen consumption levels for the subsequent calculations of DEE. The data were analysed with ANOVA, and the means were compared by using Tukey’s test (p < 0.05). The body weights, chamber temperatures and food intakes of the tortoises were similar among the treatments (p > 0.05). There were no significant differences in oxygen consumption (21.7 ± 3.16 ml · kg−1 · h−1), carbon dioxide production (18.1 ± 1.96 ml · kg−1 · h−1), or DEE (9.7 ± 1.04 kJ · kg−1 d−1) between diets or sex (p > 0.05). The respiratory quotients (0.84 ± 0.11) were also similar among the diets (p > 0.05). The DEE of red footed tortoises did not differ after a long-term starch or fat intake.
‘They Sent Me Out to School, and I Came Back with a Baby’: Perinatal Women’s Experiences of Biographical Disruption and Nonfatal Suicidal Behaviour

Exploring perinatal women’s experience of nonfatal suicidal behaviour (NFSB) could help illuminate the contexts in which perinatal suicide occurs and new ways to conceptualise maternal suicide prevention. Our aim was to explore perinatal women’s subjective experience of NFSB in South Africa. Data were collected via in-depth interviews with seven perinatal women hospitalised following NFSB. Thematic analysis showed how poverty and gender norms shape experiences of pregnancy and highlighted the need for eco-systemic interventions for perinatal women in resource scarce environments to increase social support, assist with childcare, improve educational retention, challenge gender norms and increase paternal involvement. Pregnancy can precipitate biographical disruption by disturbing women’s view of themselves and their futures. An inability to reconstruct a coherent narrative and re-imagine the future impedes the transition to motherhood and provides a context for suicide. Using the concept of biographical disruption to frame perinatal suicide, could identify novel approaches to suicide prevention.
Permanent Magnet and Electromechanical Devices: Materials, Analysis, and Applications

Preface 1. Materials Introduction Units Classification of Materials Atomic Magnetic Moments Single electron atoms Multielectron atoms Paramagnetism Ferromagnetism Magnetostatic Energy Demagnetization Field Anisotropy Magnetocrystalline Anisotropy Shape Anisotropy Domains Hysteresis Soft Magnetic Materials Hard Magnetic Materials Ferrites Alnico Samarium-Cobalt Neodymium-iron-boron Bonded Magnets Magnetization Stability 2. Review of Maxwell's Equations Introduction Maxwell's Equations Constitutive Relations Integral Equations Boundary Conditions Force and Torque Potentials Quasi-static Theory Static Theory Magnetostatic Theory Electrostatic Theory Summary 3. Field Analysis Introduction Magnetostatic Analysis Vector Potential Force and Torque Maxwell Stress Tensor Energy Inductance The Current Model The Charge Model Force Torque Magnetic Circuit Analysis Current Sources Magnet Sources Boundary-Value Problems Cartesian Coordinates Cylindrical Coordinates Spherical Coordinates Method of Images Finite Element Analysis Finite Difference Method 4. Permanent Magnet Applications Introduction Magnet Structures Rectangular Structures Cylindrical Structures High Field Structures Magnetic Latching Magnetic Suspension Magnetic Gears Magnetic Couplings Magnetic Resonance Imaging Electrophotography Magneto-Optical Recording Free-Electron Lasers 5. Electromechanical Devices Introduction Device Basics Quasi-static Field Theory Stationary Reference Frame Moving Reference Frames Electrical Equations Stationary Circuits Moving Coils Mechanical Equations Electromechanical Equations Stationary Circuits Moving Coils Energy Analysis Magnetic Circuit Actuators Axial-Field Actuators Resonant Actuators Magneto-Optical Bias Field Actuator Linear Actuators Axial-Field Motors Stepper Motors Hybrid Analytical-FEM Analysis Magnetic MEMS Vector Analysis Cartesian Coordinates Cylindrical Coordinates Spherical Coordinates Integrals of Vector Functions Theorems and Identities Coordinate Transformations Green's Function Systems of Equations Euler's Method Improved Euler Method Runge-Kutta Methods Units
An Ultrasonic Adaptive Beamforming Method and Its Application for Trans-Skull Imaging of Certain Types of Head Injuries; Part II: Reception Mode and Adaptive Imaging

Objective: Background theory and a new algorithm for single-point adaptive focusing in transmission mode through ultrasonic barriers via one-dimensional phased arrays were reported in part I. In this paper the algorithm is further extended and implemented into a full adaptive beamforming process, including complete transmission and reception modes. Methods: Corrected time delay patterns, adapted to the local acoustical and geometrical properties of the barrier, are calculated and applied in both modes. Further, an adaptive imaging process is also developed that implements the proposed beamforming process for two-dimensional imaging through randomly shaped multilayered phase-aberrating structures. The method is optimized for the case of human skull as the ultrasound barrier and its application for transcranial imaging is discussed. Results: Laboratory results of adaptive imaging through realistic skull-mimicking phantoms are presented. The algorithms are implemented on a 64-channel ultrasound open-source phased array platform controlling a standard 128-element biomedical phased array. Irregularly shaped reflectors with characteristic dimensions of the order of ∼0.5 mm to ∼4.5 mm were used as targets behind the skull phantoms in our experiments. Minimum and maximum distortional target displacements of 2.2 mm and 25.3 mm (in 12 cm depth) were observed in sonograms when uncompensated time delays were used. By contrast, the positioning errors ranged from 0.0 to 0.9 mm when our algorithm was employed. Conclusion and Significance: The adaptive imaging results demonstrate strong potential of the proposed technique for diagnostic imaging of acoustically reflective head injuries directly through intact human skull.
Dietary In ﬂ ammatory Index and Risk of Colorectal Cancer in the Iowa Women's Health Study Epidemiology,Biomarkers&Prevention

Background: Colorectalcancer,thethirdmostcommoncancerintheUnitedStates,hasanaturalhistorythat usually encompasses several decades. Dietary components have been implicated in the etiology of colorectal cancer, perhaps through their effect on inﬂammation. Methods: We examined the ability of the dietary inﬂammatory index (DII) to predict colorectal cancer in the Iowa Women’s Health Study. The DII was computed based on dietary intake assessed by a 121-item food frequency questionnaire in this cohort of 34,703 women, ages 55 to 69 years, free of any self-reported prior malignancy at enrollment in 1986. Incident colorectal cancer cases were identiﬁed through linkage with the State Health Registry of Iowa (a Surveillance, Epidemiology, and End Results program member). Cox proportional hazards regression was used to estimate HRs. Through the end of 2010, 1,636 incident colorectal cancers were identiﬁed, including 1,329 colon and 325 rectal cancers. Results: Multivariable analysis, adjusting for body mass index, smoking status, pack-years of smoking, hormone replacement therapy, education, diabetes, and total energy intake, revealed positive associations between higher DII and colorectal cancer risk [HR for DII continuous : 1.07 per unit increase in DII (corresponding to 0.5 SD unit increase); 95% conﬁdence interval (CI), 1.01–1.13; HR for DII quintiles : Q5 vs. Q1 ¼ 1.20; 95% CI, 1.01–1.43]. HRs for DII were similar for colon cancer and rectal cancer, though not statistically signiﬁcant for rectal cancer. Conclusions: These results indicate that a proinﬂammatory diet, as indicated by higher DII scores, was associated with higher risk of developing colorectal cancer. Impact: Proinﬂammatory diets are associated with increased risk of colorectal cancer. Cancer Epidemiol Biomarkers Prev; 23(11); 1–10. (cid:1) 2014 AACR.
Delay Testing in Nanoscale Technology under Process Variations

In modern CMOS technology, process variations have significantly increased impact on the circuit behavior with continuously scaled transistor sizes. Manufactured devices tend to have different performances due to parameter variations during manufacturing and in the operating context. Conventional tests generated regardless of variations could fail to rule out devices with low performance and even functional failure caused by extreme variations; the unreliability in shipped products is in turn raised. To tackle the problem, many existing test approaches have focused on identifying and testing a number of critical paths in the circuit, and aimed at the efficiency of the searching process. However, the statistical circuit model, which better describes the circuit timing behavior under variations, is not yet sufficiently investigated and employed by existing testing methodologies. This thesis work proposes Opt-KLPG and MIRID, which can be utilized by a statistical delay testing flow. Opt-KLPG—a K Longest Paths Generation (KLPG) algorithm for optimal solutions under memory constraints—can pin-pointedly generate tests for small delay defects, which are common small timing deviations under process variations, based on the traditional KLPG algorithm. In contrast to KLPG, Opt-KLPG guarantees the optimality of the solution (the K longest sensitizable paths indeed). MIRID is a mixed-mode timing-aware simulator, incorporating effects of power-supply noise and combining an event-driven logic simulation engine with interfaces to provided electrical models. MIRID aims at evaluating delay tests in presence of process variations efficiently yet accurately, by performing logic simulation at the gate level while determining the gate delays using simplified electrical modes. The electrical models applied by the simulator focus on the IR drop effect. Electrical parameters mainly contributing to the effect are incorporated into the model. The simulator is generic and flexible to be adapted by modifying the interfaces with minor effort. Both applications were verified in various aspects by experiments for academical/industrial circuits, and turned out to have satisfiable effectiveness and performance.
Suppression of annexin A1 and its receptor reduces herpes simplex virus 1 lethality in mice

Herpes simplex virus 1 (HSV-1)-induced encephalitis is the most common cause of sporadic, fatal encephalitis in humans. HSV-1 has at least 10 different envelope glycoproteins, which can promote virus infection. The ligands for most of the envelope glycoproteins and the significance of these ligands in virus-induced encephalitis remain elusive. Here, we show that glycoprotein E (gE) binds to the cellular protein, annexin A1 (Anx-A1) to enhance infection. Anx-A1 can be detected on the surface of cells permissive for HSV-1 before infection and on virions. Suppression of Anx-A1 or its receptor, formyl peptide receptor 2 (FPR2), on the cell surface and gE or Anx-A1 on HSV-1 envelopes reduced virus binding to cells. Importantly, Anx-A1 knockout, Anx-A1 knockdown, or treatments with the FPR2 antagonist reduced the mortality and tissue viral loads of infected mice. Our results show that Anx-A1 is a novel enhancing factor of HSV-1 infection. Anx-A1-deficient mice displayed no evident physiology and behavior changes. Hence, targeting Anx-A1 and FPR2 could be a promising prophylaxis or adjuvant therapy to decrease HSV-1 lethality.
Noise Characteristics Modeled Unsupervised Network for Robust CT Image Reconstruction

Deep learning (DL)-based methods show great potential in computed tomography (CT) imaging field. The DL-based reconstruction methods are usually evaluated on the training and testing datasets which are obtained from the same distribution, i.e., the same CT scan protocol (i.e., the region setting, kVp, mAs, etc.). In this work, we focus on analyzing the robustness of the DL-based methods against protocol-specific distribution shifts (i.e., the training and testing datasets are from different region settings, different kVp settings, or different mAs settings, respectively). The results show that the DL-based reconstruction methods are sensitive to the protocol-specific perturbations which can be attributed to the noise distribution shift between the training and testing datasets. Based on these findings, we presented a low-dose CT reconstruction method using an unsupervised strategy with the consideration of noise distribution to address the issue of protocol-specific perturbations. Specifically, unpaired sinogram data is enrolled into the network training, which represents unique information for specific imaging protocol, and a Gaussian mixture model (GMM) is introduced to characterize the noise distribution in CT images. It can be termed as GMM based unsupervised CT reconstruction network (GMM-unNet) method. Moreover, an expectation-maximization algorithm is designed to optimize the presented GMM-unNet method. Extensive experiments are performed on three datasets from different scan protocols, which demonstrate that the presented GMM-unNet method outperforms the competing methods both qualitatively and quantitatively.
The roles of mixing, geothermal heating, and surface buoyancy forcing in ocean meridional overturning dynamics

The dynamics of the oceanic large-scale meridional overturning circulation are investigated through a series of numerical experiments using an idealized single-hemisphere general circulation model. In addition to the system's scaling behavior, the consequences of diapycnal mixing location, the impact of deep buoyancy fluxes, and the importance of the surface restoring timescale are considered. As required by advective-diffusive balance, upwelling across isopycnals in low latitudes occurs where diapycnal mixing is specified. Downward mass transport into the abyss is relatively buoyant; the abyssal heat budget is such that this flow is subsequently cooled through deep convective mixing and re-warmed by diapycnal heat fluxes. Thus, mixing below the thermocline affects the abyssal stratification and upwelling profile, but does not contribute significantly to the zonally averaged circulation through the thermocline or the meridional oceanic heat transport. Boundary mixing is more efficient than interior mixing at driving the meridional overturning circulation; with interior mixing, the planetary vorticity constraint interferes with the communication of interior water mass properties and the eastern boundary. The results are consistent with thermodynamic considerations that suggest the strength of the overturning is a function of the vertical heat fluxes through the thermocline. Accordingly, diapycnal mixing must result in surface heat input to influence the portion of largescale overturning that effects the meridional heat transport. When a buoyancy flux (e.g., geothermal heating) is applied to the ocean floor, a perturbation deep meridional overturning cell on the order of several Sv is produced. The surface flow is also perturbed at high latitudes, allowing the additional heat to be released to the atmosphere. Rising motion is concentrated near the equator. The upward penetration of the deep cell is limited by the thermocline, analogous to the role of the stratosphere in limiting the upward penetration of convective plumes in the atmosphere. The magnitude of the advective response is inversely proportional to the deep stratification; with a weaker meridional overturning circulation and hence a less stratified abyss, the overturning maximum of the deep cell is increased. These results suggest that geothermal heat fluxes, typically ignored in general circulation models, might play a more significant role than thought in the determining the abyssal circulation. For the lowest two decades of changes to diapycnal mixing diffusivity (K), the system's response is largely "self-similar", but experiences a transition to a different regime at very high values of diffusivity. The maximum in overturning circulation obeys an approximate 2/3 power scaling law over both regimes. In contrast, given changes in the imposed equator-to-
Reduction of broadcast storm in urban VANETs using network science

VANETs is very interesting research area. Development of an efficient routing protocol in urban VANETs is a very challenging task that can support communication between vehicles with minimum overhead and maximum reachability. The main overhead in urban network is redundant reception of safety or warning messages. Sometimes we call this broadcast storm. In urban VANETs most of message dissemination protocols use broadcast approach to send messages. Broadcast storm is a major problem in high vehicle density area mainly at cross points. In this paper we reduce broadcast storm or communication overhead by using some techniques developed with help of study of network science. In this paper we study various network parameters of VANETs like node degree distribution, clustering coefficient, average shortest path length, network reachability, mobility pattern, road topology, penetration rate and network overhead. We then show how this information can be used to reduce communication overhead in urban vehicular broadcasting protocol (UVCAST) with no major reduction in performance of existing protocol.
Complete Genome Sequence of the Gordonia Bacteriophage BiggityBass

Here, we characterized the complete genome of the Siphoviridae BiggityBass, a lytic subcluster DR bacteriophage infecting Gordonia terrae CAG3. Its 63.2-kb genome contains 84 protein-coding genes, of which 40 could be assigned a putative function. BiggityBass is related most closely to AnClar and Yago84 with 90.61% and 90.52% nucleotide identity, respectively. ABSTRACT Here, we characterized the complete genome of the Siphoviridae BiggityBass, a lytic subcluster DR bacteriophage infecting Gordonia terrae CAG3. Its 63.2-kb genome contains 84 protein-coding genes, of which 40 could be assigned a putative function. BiggityBass is related most closely to AnClar and Yago84 with 90.61% and 90.52% nucleotide identity, respectively.