Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic evidence of separate repressor and activator activities of the XylR regulator of the TOL plasmid, pWWO, of Pseudomonas putida

The XylR protein encoded by pWWO, the TOL (toluene biodegradation) plasmid of Pseudomonas putida, activates at a distance the transcription of Pu and Ps, which are the two σ54‐dependent promoters of the plasmid, but it also downregulates its own σ70‐promoter, Pr, which divergently overlaps the upstream activating sites of Ps. All regulatory elements that control Pr activity have been faithfully reproduced in Escherichia coli, and the basis of the autoregulation of XylR transcription has been examined by monitoring the activity in vivo of different combinations of mutant proteins and promoters in rpoN+ and rpoN‐ genetic backgrounds. By using PsIPr regions bearing deleted or offset binding sites for XylR and the σ54‐containing RNA polymerase, we could show that formation of a nucleoprotein complex involving the polymerase bound to the divergent promoter Ps is not required for downregulation of Pr. Mutant XylR proteins, G268N and A311V (mutated within the NTP‐binding region of XylR) or R453H (affected in multi‐merization), which are unable to activate (‐dependent transcription from Ps, were indistinguishable from the wild‐type XylR in their ability to repress a reporter Pr‐lacZ fusion. Autoregulation of XylR is therefore due exclusively to the binding of the protein to its target sites at the Pr promoter. This allows one to define sensu stricto XylR as a transcriptional repressor, independently of its activator role in other promoters.
Structured Stein Variational Inference for Continuous Graphical Models

We propose a novel distributed inference algorithm for continuous graphical models by extending Stein variational gradient descent (SVGD) to leverage the Markov dependency structure of the distribution of interest. The idea is to use a set of local kernel functions over the Markov blanket of each node, which alleviates the problem of the curse of high dimensionality and simultaneously yields a distributed algorithm for decentralized inference tasks. We justify our method with theoretical analysis and show that the use of local kernels can be viewed as a new type of localized approximation that matches the target distribution on the conditional distributions of each node over its Markov blanket. Our empirical results demonstrate that our method outperforms a variety of baselines including standard MCMC and particle message passing methods.
Impact of Filtering on Region of Interest Estimation from Diffusion Weighted Brain Images

For diffusion weighted imaging data there is no standardised pipeline for image preprocessing, especially in regard to filter application. Here, we demonstrate the impact of the Perona Malik Filter, an adaptive imaging filter, on derived fiber tracks with respect to their endvoxels. These end-voxels are an important outcome of tracking, for they are often taken as regions of interest for further investigations, i.e. when combining multiple investigation methods. The preliminary findings suggest that the application of the Perona Malik filter for corticospinal tracks (i.e. long superior/inferior tracks) has no distinct advantages with respect to region of interest estimation.
A comparative study of determinants of uxorilocal marriage in two counties of China

Abstract A strictly maintained patrilineal family system makes virilocal marriage almost universal and uxorilocal marriage rare in the history of rural China. Uxorilocal marriage can be divided into two types that may be termed, respectively, contingent and institutional. The former preserves family lineages in families without a son and occurs when uxorilocal marriage is uncommon. The latter serves practical economic purposes in families with sons and occurs when uxorilocal marriage is relatively prevalent. Using data from a survey in two counties of Shaanxi—Lueyang, where both kinds of uxorilocal marriage are prevalent, and Sanyuan, where uxorilocal marriage is rare and usually contingent—this paper employs logistic regression models in a quantitative comparative study of determinants of uxorilocal marriage in rural China. We show that the purposes and prevalence of the two types of uxorilocal marriage differ and that their determinants are also different in the two counties. In Sanyuan, the determinants are only a couple's sibling composition, membership in a large family clan, and educational level. In Lueyang, in addition to those determinants in Sanyuan, important contributions to the type of uxorilocal marriage include a couple's parental marriage type, age at marriage, adoption status, marriage arrangement, and their attitudes toward uxorilocal marriage. The results indicate the potential importance of encouraging uxorilocal marriage in rural areas as a means of mitigating demographic and social problems related to son preference, such as high sex ratio at birth and lack of old‐age security, which are projected for China's future.
Design of antennas for 3D wireless Network-on-Chip with micro-fluidic cooling layers

Recent trend in 3-D Network on a Chip (NoC) utilizing wireless interconnects to improve communication speeds have been successful. Liquid cooling channels introduced on top and bottom still leave the interior of the chip as a hot spot. In the present work, novel architecture of 3-D NoC is modeled in different configurations of embedded micro fluidic layers to address the interior heating. Wired interconnects through the fluidic layers is not possible, zig-zag antennas are implemented and placed in different configurations, to serve as wireless interconnects. The thermo-fluidic layers are modeled as channels of dielectric constant 1.75. Each antenna has been individually designed and successfully tuned to resonate at 60 GHz with a return loss (RL) less than -10dB, using ANSYS High Frequency System Simulator (HFSS). The paper also discusses the transmission coefficients and shows low noise up to 10 GHz.
The SIMCA algorithm for processing Ground Penetrating Radar data and its use in locating foundations in demolished buildings.

The main challenge of ground penetrating radar (GPR) based foundation detection is to have an accurate image analysis method. In order to solve the detection problem a system level analysis of the issues involved with the recognition of foundations using image reconstruction is required. The SIMCA (‘SIMulated Correlation Algorithm’) is a technique based on an area correlation between the trace that would be returned by an ideal point reflector in the soil conditions at the site and the actual trace. During an initialization phase, SIMCA carries out radar simulation using the design parameters of the radar and soil properties. Then SIMCA takes the raw data as the radar is scanned over the ground and in real-time uses a clutter removal technique to remove various clutter such as cross talk, initial ground reflection and antenna ringing. The trace which would be returned by a target under these conditions is then used to form a correlation kernel. The GPR b-scan is then correlated with the kernel using the Pearson correlation coefficient, resulting in a correlated image which is brightest at points most similar to the canonical target. This image is then raised to an odd power >2 to enhance the target/background separation. To validate and compare the algorithm, photographs of the building before it was demolished along with processed data using the REFLEXW package were used. The results produced by the SIMCA algorithm were very promising and were able to locate some features that the REFLEXW package were not able to identify.
Interaction of a common factor with ATF, Sp1, or TATAA promoter elements is required for these sequences to mediate transactivation by the adenoviral oncogene E1a

The adenovirus protein E1a stimulates transcription of both viral and cellular genes. Unlike most other transcription factors, it induces transactivation through several different promoter elements. The mechanism by which elements of diverse sequence mediate the effect of E1a is the focus of this study. Three E1a-responsive elements (an ATF site, an Sp1 site, and a TATA box containing the sequence TATAA) were studied to determine whether their interaction with a common factor is necessary for transactivation. In transfection assays, each element was used as a competitor against promoter constructs containing the other elements. The elements as competitors had no effect on basal transcription, but each competitor completely inhibited transactivation by E1a. Competitors that were not E1a responsive failed to inhibit transactivation. Therefore, either E1a itself or an E1a-inducible factor interacts with each of the elements to cause transactivation, most likely though an association with each element's specific binding protein.
Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites

Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening approach to identify all the metabolites in a given biological system is called metabolic fingerprinting. Using high‐resolution and high‐mass accuracy mass spectrometry, large metabolome coverage, sensitivity, and specificity can be attained. Although the theoretical concepts of this methodology are usually provided in life‐science programs, hands‐on laboratory experiments are not usually accessible to undergraduate students. Even if the instruments are available, there are not simple laboratory protocols created specifically for teaching metabolomics. We designed a straightforward hands‐on laboratory experiment to introduce students to this methodology, relating it to biochemical knowledge through metabolic pathway mapping of the identified metabolites. This study focuses on mitochondrial metabolomics since mitochondria have a well‐known, medium‐sized cellular sub‐metabolome. These features facilitate both data processing and pathway mapping. In this experiment, students isolate mitochondria from potatoes, extract the metabolites, and analyze them by high‐resolution mass spectrometry (using an FT‐ICR mass spectrometer). The resulting mass list is submitted to an online program for metabolite identification, and compounds associated with mitochondrial pathways can be highlighted in a metabolic network map. © 2015 by The International Union of Biochemistry and Molecular Biology, 44:38–54, 2016.
Cartographic analysis of woodlice fauna of the former USSR

Abstract An inventory of the woodlice fauna of the former USSR yielded 190 species, 64 of them were recorded from the territory of Russia. According to the cartographic analysis, the limits of distribution of epigean terrestrial isopods over the area, excluding mountains, is explained by temperature. No woodlice records were found outside the isocline of 120 days a year with the mean daily air temperature >10°C. The highest species diversity was found between the isoclines of 180 and 210 days. These areas correspond to forest-steppe and steppe zones.
Non-negativity constrained missing data estimation for high-dimensional and sparse matrices

Latent factor (LF) models have proven to be accurate and efficient in extracting hidden knowledge from high-dimensional and sparse (HiDS) matrices. However, most LF models fail to fulfill the non-negativity constraints that reflect the non-negative nature of industrial data. Yet existing non-negative LF models for HiDS matrices suffer from slow convergence leading to considerable time cost. An alternating direction method-based non-negative latent factor (ANLF) model decomposes a non-negative optimization process into small sub-tasks. It updates each LF non-negatively based on the latest state of those trained before, thereby achieving fast convergence and maintaining high prediction accuracy and scalability. This paper theoretically analyze the characteristics of an ANLF model, and presents detailed empirical study regarding its performance on several HiDS matrices arising from industrial applications currently in use. Therefore, its capability of addressing HiDS matrices is validated in both theory and practice.
Development of a Worry Questionnaire for Nursing Home Residents

ABSTRACT This paper describes a new measure, the Worry Questionnaire for Nursing Home Residents (WQNHR), designed to assess the frequency of specific worries. It was administered to 67 residents. Psychometric evaluation showed an average item-to-total correlation of 0.20 (range = 0.15 to 0.58), an internal consistency estimate of 0.79, and a test-re-test reliability coefficient of 0.80. The WQNHR showed good convergent validity with other measures of worry obtained from residents, good discriminant validity with measures of health, but poor discriminant validity with self-ratings of depression. Psychometric results also indicated that the WQNHR performed better for residents with higher cognitive functioning. In addition, a collateral form (WQNHR-C) was administered to family or friends; however, it was not significantly correlated with the WQNHR. Overall, the WQNHR is a promising screening instrument for assessing worry in nursing home residents. RÉSUMÉ Ce mémoire décrit un nouvel instrument de mesure, le Worry Questionnaire for Nursing Home Residents (WQNHR) (ou questionnaire des inquiétudes des pensionnaires d'établissements de soins infirmiers), qui sert à mesurer la fréquence de certains sujets d'inquiétude. Le questionnaire a été administré à 67 pensionnaires. L'évaluation psychométrique donne une corrélation item-score total moyenne de 0,20 (portée = 0,15 à 0,58), une cohérence interne estimative de 0,79, et un coefficient de fidélité au test-retest de 0,80. Le WQNHR a une bonne validité convergente avec d'autres mesures de l'inquiétude appliquées aux pensionnaires, une bonne validité discriminante avec les mesures de l'état de santé, mais une faible validité discriminante pour l'auto-évaluation de la dépression. Les résultats psychométriques indiquent aussi que le WQNHR donne de meilleurs résultats chez les pensionnaires ayant un fonctionnement cognitif supérieur. Un questionnaire annexe (WQNHR-C) avait également été administré aux familles ou amis des pensionnaires; mais la corrélation avec le WQNHR s'est avérée faible. Pour résumer, le WQNHR est un instrument de dépistage prometteur pour évaluer l'inquiétude des pensionnaires de maisons de soins infirmiers.
Aggressive periodontitis: 5-year follow-up of treatment.

BACKGROUND The hypothesis that in subjects with aggressive periodontitis, a long-term stability of periodontal health can be achieved following comprehensive mechanical/surgical and systemic antimicrobial therapy was tested in this prospective study. METHODS Thirteen patients (36.9+/-7.4 years) with aggressive periodontitis were monitored before and up to 5 years following periodontal therapy. Clinical attachment levels (CAL) were assessed pretherapy, and at 3 months following completion of active periodontal therapy supplemented by amoxicillin plus metronidazole. All subjects were subsequently enrolled in a maintenance program and provided with supportive periodontal therapy with 3 to 4 appointments annually. Reexaminations were performed after 6 months and 1, 2, 3, 4, and 5 years. The data were analyzed using the method of generalized estimating equations (GEE) for CAL changes from baseline to the 3-month visit, and from completion of periodontal therapy to each annual visit up to the 5-year follow-up reappointment. RESULTS During the 5-year study, all subjects strongly benefited from periodontal treatment. Between baseline and the 3-month reexamination, the CAL levels revealed a significant decrease of 2.23 mm (95% confidence interval [CI]: 1.77 to 2.69 mm; P < or =0.001). At the 5-year maintenance visit, the CAL changes ranged from -0.04 to +0.29 mm with no further statistically significant periodontal breakdown (P >0.05). Five years after surgery, 3.2% of the treated sites demonstrated a further CAL gain > or =3 mm. A stabilization (CAL -2 to +2 mm) occurred in 94.6% of the cases. The number of periodontal sites experiencing a breakdown varied from 5.3% at 6 months to 2.2% at 5 years. CONCLUSIONS In aggressive periodontitis, comprehensive mechanical/surgical and antimicrobial therapy is an appropriate treatment regimen for long-term stabilization of periodontal health. In this study, periodontal disease progression was successfully arrested in 95% of the initially compromised lesions, while 2% to 5% experienced discrete or recurrent episodes of loss of periodontal support.
Unaffordable housing and local employment growth: Evidence from California municipalities

It is widely believed that unaffordable housing could drive businesses away and thus impede job growth. However, there is little evidence to support this view. This paper presents a simple model to clarify how housing affordability is linked to employment growth and why unaffordable housing could negatively affect employment growth. The paper then investigates this effect empirically using data on California municipalities. For various reasons, a simple correlation between unaffordable housing and employment growth cannot be interpreted as causal. Several empirical strategies are employed to identify the causal effect of unaffordable housing on employment growth. The estimation results provide consistent evidence that unaffordable housing indeed slows local employment growth.
The Effect of Trail Pheromone and Path Confinement on Learning of Complex Routes in the Ant Lasius niger

Route learning is key to the survival of many central place foragers, such as bees and many ants. For ants which lay pheromone trails, the presence of a trail may act as an important source of information about whether an error has been made. The presence of trail pheromone has been demonstrated to support route learning, and the effect of pheromones on route choice have been reported to persist even after the pheromones have been removed. This could be explained in two ways: the pheromone may constrain the ants onto the correct route, thus preventing errors and aiding learning. Alternatively, the pheromones may act as a ‘reassurance’, signalling that the learner is on the right path and that learning the path is worthwhile. Here, we disentangle pheromone presence from route confinement in order to test these hypotheses, using the ant Lasius niger as a model. Unexpectedly, we did not find any evidence that pheromones support route learning. Indeed, there was no evidence that ants confined to the correct route learned at all. Thus, while we cannot support the ‘reassurance’ hypothesis, we can rule out the ‘confinement’ hypothesis. Other findings, such as a reduction in pheromone deposition in the presence of trail pheromones, are remarkably consistent with previous experiments. As previously reported, ants which make errors on their outward journey upregulate pheromone deposition on their return. Surprisingly, ants which would go on to make an error down-regulate pheromone deposition on their outward journey, hinting at a capacity for ants to gauge the quality of their own memories.
Chronic infection of Toxoplasma gondii downregulates miR-132 expression in multiple brain regions in a sex-dependent manner

SUMMARY MicroRNA-132 (miR-132) has been demonstrated to affect multiple neuronal functions and its dysregulation is linked to several neurological disorders. We previously showed that acute Toxoplasma gondii infection induces miR-132 expression both in vitro and in vivo. To investigate the impact of chronic infection on miR-132, we infected mice with T. gondii PRU strain and performed assessment 5 months later in six brain regions (cortex, hypothalamus, striatum, cerebellum, olfactory bulb and hippocampus) by qPCR. We found that while acute infection of T. gondii increases the expression of miR-132, chronic infection has the opposite effect. The effect varied amongst different regions of the brain and presented in a sex-dependent manner, with females exhibiting more susceptibility than males. MiR-132 and brain-derived neurotrophic factor (BDNF, an inducer of miR-132) were not co-varies in the brain areas of infected mice. T. gondii DNA/RNA was found in all tested brain regions and a selective tropism towards the hippocampus, based on bradyzoite density, was observed in both males and females. However, the expressions of miR-132 or BDNF were poorly reflected by the density of T. gondii in brain areas. Our findings highlight the importance of investigating the miR-132-mediated neuronal function in mice infected with T. gondii.
Patterns of disability related to diabetes mellitus in older women.

PURPOSE To identify pattern(s) of disability related to diabetes in older women and to determine the extent to which disability is mediated by selected diabetes complications. METHODS Cross-sectional analysis of data from a population-based study composed of a representative sample of 3570 noninstitutionalized women aged 65 years and older living in the Baltimore metropolitan area who agreed to be screened for the Women's Health and Aging Study. RESULTS 483 (13.5%) of the women reported physician-diagnosed diabetes. Compared to women without diabetes, women with diabetes were significantly more likely to report difficulty in 14 of 15 daily tasks, including walking 2-3 blocks, lifting 10 pounds, using the telephone, and bathing (range of odds ratios [OR] 1.5-2.8; all p <.01). After adjustment for age, race, and marital status, women with diabetes were about twice as likely to report difficulty in any one of four functioning groups (mobility, upper extremity, higher functioning tasks, or self-care) (OR 2.2; 95% confidence interval [CI] 1.8-2.7), and over three times as likely to report difficulty in a group combining higher functioning and self-care tasks (OR 3.2; 95% CI 2.4-4.1). Adjustment for self-reported heart disease, stroke, high blood pressure, and visual problems did not attenuate these associations. CONCLUSIONS Diabetes is strongly associated with a wide range of disabilities in older women. This association does not appear to be mediated by prevalent diabetes complications and risks, heart disease, high blood pressure, stroke, or eye disease. Other complications of diabetes (e.g., neuropathy, peripheral vascular disease) may mediate diabetes-associated disability in older adults.
Riluzole preserves motor function in a transgenic model of familial amyotrophic lateral sclerosis

Riluzole was tested in a dose-ranging study for preservation of motor function in a transgenic mouse model of familial ALS. The model is based on expression of mutant human Cu,Zn superoxide dismutase in mouse brain and spinal cord. In contrast with the human ALS trials, in the mouse model, riluzole significantly preserved motor function as assessed by nightly running in a wheel. The effect of riluzole on motor performance was greater earlier in disease than later, suggesting that riluzole may have benefit for"quality-of-life" measures in ALS. Treatment with riluzole was initiated earlier in the transgenic model than in the human ALS trials, which may account for the significantly better outcome.
Flow and Heat Transfer Characteristics of Supercritical Helium for Magnet Cooling

Supercritical Helium (SHe) is frequently used for the large-scale magnet cooling in many applications. In the present study, the flow and heat transfer characteristics of SHe in the mini-tubes of about 1.0-2.0 mm in diameters are numerically investigated to provide the useful information for the design of the cooling configuration of Cable-in-Conduits Conductors (CICCs) and the related. And a simplified equivalent model is also proposed to estimate the flow and heat transfer characteristics of SHe in the complicated configuration of CICCs.