Miracle-dz/UniFAR-FTUs huggingface dataset:
Roles of Serine Accumulation and Catabolism in the Colonization of the Murine Urinary Tract by Escherichia coli CFT073

ABSTRACT A d-serine deaminase (DsdA) mutant of uropathogenic Escherichia coli strain CFT073 has a hypercolonization phenotype in a murine model of urinary tract infection (UTI) due to increased virulence gene expression by an unknown mechanism (B. J. Haugen et al., Infect. Immun. 75:278-289, 2007). DsdC is a d-serine-dependent activator of dsdXA transcription. DsdC may regulate the virulence genes responsible for hypercolonization. The loss of DsdA leads to increased intracellular accumulation of d-serine. In this study we show that deletion of the genes encoding l-serine deaminases SdaA and SdaB resulted in a mutant that accumulates higher intracellular levels of l-serine than CFT073. CFT073 sdaA sdaB has a mild competitive colonization defect whereas a CFT073 dsdA sdaA sdaB triple mutant shows a greater loss in competitive colonization ability. Thus, the inability to generate serine-specific catabolic products does not result in hypercolonization and the ability to catabolize serine represents a positive physiological trait during murine UTI. CFT073 dsdC and CFT073 dsdC dsdA mutants continue to outcompete the wild type in the UTI model. These results confirm that loss of DsdA activity results in the hypercolonization phenotype and that DsdC does not play a direct role in the elevated-colonization phenotype. Interestingly, a CFT073 dsdA mutant with deletions of d-serine transporter genes dsdX and cycA shows wild-type colonization levels of the bladder but is attenuated for kidney colonization. Thus, d-serine acts as a signal for hypercolonization and virulence gene expression by CFT073 dsdA, whereas overall catabolism of serine represents a positive Escherichia coli fitness trait during UTI.
A Contribution to the Selection of Emission‐Line Galaxies Using Narrowband Filters in the Optical Airglow Windows

Emission‐line galaxies are an invaluable tool for understanding the evolution of galaxies in the universe. Imaging deep fields with narrowband filters allows not only the selection of these objects, but also inferences about the line flux and the equivalent width of the emission line, with some assumptions. The narrowband filter technique provides homogeneous samples of galaxies in small comoving volumes in the sky. We present an analysis of the selection of emission‐line galaxies using narrowband filters. Different methods of observation are considered: broadband−narrowband filters, two narrowband filters, and two broadband and one narrowband filter. We also study the effect of several lines simultaneously entering the filters (as in the case of Hα). In each case, the equations used to obtain the equivalent width and line flux from the photometry are obtained. Candidate emission‐line objects are selected by their color excess in a color‐magnitude diagram. For different narrowband filters, we compute the mean colors of stars and galaxies, showing that in addition to galaxies, some types of stars can be selected with certain filter sets. We show how to compute the standard deviation of the colors of the objects, even in the usual case in which there are not enough objects to determine the standard deviation from the data. We also present helpful equations to compute the narrow‐ and broadband exposure times in order to obtain minimal dispersion in the flux ratios of both bands, with a minimum total exposure time.
The Unified Protocol for Transdiagnostic Treatment of Emotional Disorders Compared With Diagnosis-Specific Protocols for Anxiety Disorders: A Randomized Clinical Trial

Importance Transdiagnostic interventions have been developed to address barriers to the dissemination of evidence-based psychological treatments, but only a few preliminary studies have compared these approaches with existing evidence-based psychological treatments. Objective To determine whether the Unified Protocol for Transdiagnostic Treatment of Emotional Disorders (UP) is at least as efficacious as single-disorder protocols (SDPs) in the treatment of anxiety disorders. Design, Setting, and Participants From June 23, 2011, to March 5, 2015, a total of 223 patients at an outpatient treatment center with a principal diagnosis of panic disorder with or without agoraphobia, generalized anxiety disorder, obsessive-compulsive disorder, or social anxiety disorder were randomly assigned by principal diagnosis to the UP, an SDP, or a waitlist control condition. Patients received up to 16 sessions of the UP or an SDP for 16 to 21 weeks. Outcomes were assessed at baseline, after treatment, and at 6-month follow-up. Analysis in this equivalence trial was based on intention to treat. Interventions The UP or SDPs. Main Outcomes and Measures Blinded evaluations of principal diagnosis clinical severity rating were used to evaluate an a priori hypothesis of equivalence between the UP and SDPs. Results Among the 223 patients (124 women and 99 men; mean [SD] age, 31.1 [11.0] years), 88 were randomized to receive the UP, 91 to receive an SDP, and 44 to the waitlist control condition. Patients were more likely to complete treatment with the UP than with SDPs (odds ratio, 3.11; 95% CI, 1.44-6.74). Both the UP (Cohen d, −0.93; 95% CI, −1.29 to −0.57) and SDPs (Cohen d, −1.08; 95% CI, −1.43 to −0.73) were superior to the waitlist control condition at acute outcome. Reductions in clinical severity rating from baseline to the end of treatment (&bgr;, 0.25; 95% CI, −0.26 to 0.75) and from baseline to the 6-month follow-up (&bgr;, 0.16; 95% CI, −0.39 to 0.70) indicated statistical equivalence between the UP and SDPs. Conclusions and Relevance The UP produces symptom reduction equivalent to criterion standard evidence-based psychological treatments for anxiety disorders with less attrition. Thus, it may be possible to use 1 protocol instead of multiple SDPs to more efficiently treat the most commonly occurring anxiety and depressive disorders. Trial Registration clinicaltrials.gov Identifier: NCT01243606
Mapping landslide susceptibility and types using Random Forest

ABSTRACT Landslides are one of the most destructive natural hazards; they can drastically alter landscape morphology, destroy man-made structures, and endanger people’s life. Landslide susceptibility maps (LSMs), which show the spatial likelihood of landslide occurrence, are crucial for environmental management, urban planning, and minimizing economic losses. To date, the majority of research into data mining LSM uses small-scale case studies focusing on a single type of landslide. This paper presents a data mining approach to producing LSM for a large, heterogeneous region that is susceptible to multiple types of landslides. Using a case study of Piedmont, Italy, a Random Forest algorithm is applied to produce both susceptibility maps and classification maps. These maps are combined to give a highly accurate (over 85% classification accuracy) LSM which contains a large amount of information and is easy to interpret. This novel method of mapping landslide susceptibility demonstrates the efficacy of Random Forest to produce highly accurate susceptibility maps for a large heterogeneous region without the need for multiple susceptibility assessments.
Development of an RF-CMOS Surface Acoustic wave (SAW) resonator

Surface Acoustic wave resonators serve as essential components in Radio Frequency (RF) electronics and transceiver circuits. SAW resonators are traditionally discrete components, fabricated on piezoelectric substrates making it incompatible with CMOS technology processes. This work proposes modeling and simulation of SAW resonators which are integrated in RF-CMOS technology. An equivalent circuit model developed specifically for RF-CMOS resonator is presented. Three design examples of these resonators are shown to demonstrate the characteristics of the resonators at different resonant frequencies. The comparison between the simulated and fabricated resonators have been presented.
Traceability recovery by modeling programmer behavior

When a system evolves, while the source code is changed, documentation and traceability links are barely ever updated: maintaining traceability information between software artifacts is a costly and tedious activity, which is frequently sacrificed during development and maintenance due to market pressure. The paper presents a new method to recovery traceability links between high level and low level artifacts. The method is based on the partial knowledge of a subset of tracability links. It can be fully automated and the human intervention is only required to confirm or confute recovered traceability links. The method has been applied to software written in Java, to trace classes onto functional requirements. Experimental results demonstrate the superiority of the novel method over previously published results on the same system.
Wikipedia Missing Link Discovery: A Comparative Study

In this paper, we describe our work on discovering missing links in Wikipedia articles. This task is important for both readers and authors of Wikipedia. The readers will benefit from the increased article quality with better navigation support. On the other hand, the system can be employed to support the authors during editing. This study combines the strengths of different approaches previously applied for the task, and adds its own techniques to reach satisfactory results. Because of the subjectivity in the nature of the task; automatic evaluation is hard to apply. Comparing approaches seems to be the best method to evaluate new techniques, and we offer a semi-automatized method for evaluation of the results. The recall is calculated automatically using existing links in Wikipedia. The precision is calculated according to manual evaluations of human assessors. Comparative results for different techniques are presented, showing the success of our improvements. We employ Turkish Wikipedia, we are the first to study on it, to examine whether a small instance is scalable enough for such purposes.
Lattice-Reduction Aided Multi-User STBC Decoding with Resource Constraints

Lattice-reduction aided decoders have been proposed in MIMO system to achieve near maximum likelihood decoder performance while maintaining reasonable complexity. This paper studies the implementation of lattice-reduction aided linear decoders on a programmable device for multi-user space-time block coding (MU-STBC). By reloading software, the device can be configured to use different decoding schemes according to the amount of resources available, which is an important feature of cognitive radio. In this paper, two different lattice-reduction aided linear decoding methods namely SQRD-LR and AQRD-LR for MU-STBC are evaluated based on their BER performance and computational complexity. Furthermore, the effect of deadline constraint on LR is evaluated and based on the evaluation, a new method namely adaptive decoding is proposed by us to allow mode-switching of the decoder according to the environment parameters, so that the best decoder performance can always be achieved while fulfiling the resource constraints.
Estimation of Design Flood Hydrographs for Osun River at Iwo Control Station in Osun State, Nigeria

The unit and storm hydrographs for the catchment of Osun River at Iwo station Osun State, Nigeria were developed. Soil Conservation Service (SCS) and Snyder’s unit hydrograph methods were used to develop synthetic hydrographs for the catchment, while the SCS Curve Number method was used to estimate excess rainfall values from rainfall depth of different return periods. The peak storm flows obtained based on the unit hydrograph ordinates using convolution procedures determined by SCS for rainfall events of 10yr, 20yr, 50yr, 100yr and 200yr return periods for the catchment vary from 819.87 m 3 /s to 1681.34 m 3 /s, while those based on Snyder’s method for the catchment vary from 551.41m 3 /s to 1134.86 m 3 /s . The statistical analysis at 5% level of significance indicated that there were significant differences in the two methods. The analysis showed that the total peak flows for different return periods obtained from SCS method is higher than that of Snyder’s method by 33.16%. SCS method was recommended for use on the watershed since it incorporates most major hydrological and morphological characteristics of the basins like the watershed area, main channel length, river channel slope and watershed slope.
Strain differences in susceptibility to murine respiratory mycoplasmosis in C57BL/6 and C3H/HeN mice

Not only is murine respiratory mycoplasmosis, due to Mycoplasma pulmonis, a complication of biomedical research, it provides excellent animal models to study the development of a naturally occurring respiratory disease induced by an infectious agent. The understanding of pathogenic mechanisms of disease can be greatly facilitated by studying genetic differences in susceptibility. Five strains of mice with various H-2K haplotypes were examined for their susceptibility to murine respiratory mycoplasmosis; of these, C57BL/6 and C3H/HeN mice were chosen for additional study. There were no significant differences in the incidence of infection in either the upper or lower respiratory tract or in the severity of upper respiratory tract lesions in the two strains as determined at 14 days postinfection. In striking contrast, the C57BL/6 mice were significantly more resistant to the development of gross and microscopic lung lesions and to death due to pneumonia as shown by an almost 100-fold difference in the 50% lethal dose, 50% gross pneumonia dose, and 50% microscopic lesion dose. The most apparent differences in lung lesions between the two strains were in the severity of acute lesions of the bronchial epithelium, the amount of mixed inflammatory response in the alveoli, and the amount of lymphoid infiltrates. All were significantly more severe in C3H/HeN mice. In addition, more C3H/HeN mice developed antibody responses to M. pulmonis. The amount of antibody correlated with lesion severity in both strains.
Flight to Quality, Flight to Liquidity, and the Pricing of Risk

We propose a dynamic equilibrium model of a multi-asset market with stochastic volatility and transaction costs. Our key assumption is that investors are fund managers, subject to withdrawals when fund performance falls below a threshold. This generates a preference for liquidity that is time-varying and increasing with volatility. We show that during volatile times, assets' liquidity premia increase, investors become more risk averse, assets become more negatively correlated with volatility, assets' pairwise correlations can increase, and illiquid assets' market betas increase. Moreover, an unconditional CAPM can understate the risk of illiquid assets because these assets become riskier when investors are the most risk averse.
Limiting DNA replication to once and only once

In Escherichia coli cells, the origin of chromosomal replication is temporarily inactivated after initiation has occurred. Origin sequestration is the first line of defence against over‐initiation, providing a time window during which the initiation potential can be reduced by: (i) titration of DnaA proteins to newly replicated chromosomal elements; (ii) regulation of the activity of the DnaA initiator protein; and (iii) sequestration of the dnaA gene promoter. This review represents the first attempt to consider together older and more recent data on such inactivation mechanisms in order to analyze their contributions to the overall tight replication control observed in vivo. All cells have developed mechanisms for origin inactivation, but those of other bacteria and eukaryotic cells are clearly distinct from those of E. coli. Possible differences and similarities are discussed.
SMAD Signaling Is Required for Structural Integrity of the Female Reproductive Tract and Uterine Function During Early Pregnancy in Mice

ABSTRACT Pregnancy is a complex physiological process tightly controlled by the interplay among hormones, morphogens, transcription factors, and signaling pathways. Although recent studies using genetically engineered mouse models have revealed that ligands and receptors of transforming growth factor beta (TGFbeta) and bone morphogenetic protein (BMP) signaling pathways are essential for multiple reproductive events during pregnancy, the functional role of SMAD transcription factors, which serve as the canonical signaling platform for the TGFbeta/BMP pathways, in the oviduct and uterus is undefined. Here, we used a mouse model containing triple conditional deletion of the BMP receptor signaling Smads (Smad1 and Smad5) and Smad4, the central mediator of both TGFbeta and BMP signaling, to investigate the role of the SMADs in reproductive tract structure and function in cells from the Amhr2 lineage. Unlike the respective single- or double-knockouts, female Smad1flox/flox Smad5flox/flox Smad4flox/flox Amhr2cre/+conditional knockout (i.e., Smad1/5/4-Amhr2-cre KO) mice are sterile. We discovered that Smad1/5/4-Amhr2-cre KO females have malformed oviducts that subsequently develop oviductal diverticuli. These oviducts showed dysregulation of multiple genes essential for oviduct and smooth muscle development. In addition, uteri from Smad1/5/4-Amhr2-cre KO females exhibit multiple defects in stroma, epithelium, and smooth muscle layers and fail to assemble a closed uterine lumen upon embryo implantation, with defective uterine decidualization that led to pregnancy loss at early to mid-gestation. Taken together, our study uncovers a new role for the SMAD transcription factors in maintaining the structural and functional integrity of oviduct and uterus, required for establishment and maintenance of pregnancy.
Parsimonious sediment transport equations based on Bagnold's stream power approach

It is increasingly recognized that effective river management requires a catchment scale approach. Sediment transport processes are relevant to a number of river functions but quantifying sediment fluxes at network scales is hampered by the difficulty of measuring the variables required for most sediment transport equations (e.g. shear stress, velocity, and flow depth). We develop new bedload and total load sediment transport equations based on specific stream power. These equations use data that are relatively easy to collect or estimate throughout stream networks using remote sensing and other available data: slope, discharge, channel width, and grain size. The new equations are parsimonious yet have similar accuracy to other, more established, alternatives. We further confirm previous findings that the dimensionless critical specific stream power for incipient particle motion is generally consistent across datasets, and that the uncertainty in this parameter has only a minor impact on calculated sediment transport rates. Finally, we test the new bedload transport equation by applying it in a simple channel incision model. Our model results are in close agreement to flume observations and can predict incision rates more accurately than a more complicated morphodynamic model. These new sediment transport equations are well suited for use at stream network scales, allowing quantification of this important process for river management applications. Copyright © 2017 John Wiley & Sons, Ltd.
Angiotensin-converting enzyme inhibition and free-radical scavenging properties of cationic peptides derived from soybean protein hydrolysates

Soybean protein isolate was hydrolyzed consecutively with pepsin and pancreatin followed by separation of the digest on a SP-Sepharose column to obtain angiotensin-converting enzyme (ACE)-inhibitory fractions. Three of the five fractions obtained inhibited ACE activity, with values of the concentration of hydrolysate fraction that inhibited 50% of ACE activity of 1.09, 0.42, and 0.25 mg/ml for fractions 2, 3, and 4, respectively. Kinetic analysis showed that fractions 2, 3, and 4 are non-competitive, competitive and mixed inhibitors of ACE, respectively. Fluorescence emission of ACE was quenched along with a red shift in wavelength of emission maxima in the presence of the protein hydrolysate fractions. Fraction 3 was the most potent free-radical scavenger, while fraction 4 had almost no scavenging effect. We concluded that fraction 3 had the most potential to be used as a bioactive ingredient because of its strong ACE-inhibitory and free-radical scavenging properties.
Personalized video composition method based on user intention learning

In this paper we present a personalized video composition method based on user intention learning. The proposed system generates video clips by choosing user's assets such as still images and video clips based on pre-designed templates. The search-and-suggestion technique plays an important role for providing appropriate templates. We mainly focus on the learning mechanism which will be gradually improving through repeated template recommendations. Our prototype demonstrates the feasibility of the proposed approach.
Mycobacterial toxin MazF-mt6 inhibits translation through cleavage of 23S rRNA at the ribosomal A site

The Mycobacterium tuberculosis genome contains an unusually high number of toxin–antitoxin modules, some of which have been suggested to play a role in the establishment and maintenance of latent tuberculosis. Nine of these toxin–antitoxin loci belong to the mazEF family, encoding the intracellular toxin MazF and its antitoxin inhibitor MazE. Nearly every MazF ortholog recognizes a unique three- or five-base RNA sequence and cleaves mRNA. As a result, these toxins selectively target a subset of the transcriptome for degradation and are known as “mRNA interferases. ” Here we demonstrate that a MazF family member from M. tuberculosis, MazF-mt6, has an additional role—inhibiting translation through targeted cleavage of 23S rRNA in the evolutionarily conserved helix/loop 70. We first determined that MazF-mt6 cleaves mRNA at 5′UU↓CCU3′ sequences. We then discovered that MazF-mt6 also cleaves M. tuberculosis 23S rRNA at a single UUCCU in the ribosomal A site that contacts tRNA and ribosome recycling factor. To gain further mechanistic insight, we demonstrated that MazF-mt6–mediated cleavage of rRNA can inhibit protein synthesis in the absence of mRNA cleavage. Finally, consistent with the position of 23S rRNA cleavage, MazF-mt6 destabilized 50S–30S ribosomal subunit association. Collectively, these results show that MazF toxins do not universally act as mRNA interferases, because MazF-mt6 inhibits protein synthesis by cleaving 23S rRNA in the ribosome active center.
Image Segmentation by Hybrid Active Contour Model Using Harmonic Mean

Edge-based models can identify the objects having solid borderline effectively, however, these models cannot appropriately segment the images with weak object borderline. On the other hand, region-based models perform better for images with unclear object borderline, however, these models cannot accurately segment images with intensity inhomogeneity. In this study, we propose a hybrid Active Contour Model (ACM) that can overcome these limitations. It is formed by substituting the edge information into region-based level set with a harmonic mean based signed pressure force function HSPF. Due to the utilization of harmonic mean intensities of the image in HSPF, the new data fitting energy can better uphold the subtle difference among the desired object intensities and that of its background that results in the effective segmentation of low contrast images. Since our proposed model has both, the region and edge information, so in comparison to traditional models, it performs better in the segmentation of images with regions of interest (ROI) having noise, indistinct borders, and intensity inhomogeneity. The proposed model is tested on noisy, real and medical images to exhibit its correctness, efficiency, and robustness. The experimental results validate that our proposed model is more efficient, rapid and correct as compared to the other related models.