Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression, Autoregulation, and DNA Binding Properties of the Mycobacterium tuberculosis TrcR Response Regulator

ABSTRACT The TrcRS two-component system of Mycobacterium tuberculosis is comprised of the TrcS histidine kinase and the TrcR response regulator, which is homologous to the OmpR class of DNA binding response regulators. Reverse transcription-PCRs with total RNA showed that the trcR and trcS two-component system genes are transcribed in broth-grown M. tuberculosis. Analysis of the trcR and trcS genes using various SCOTS (selective capture of transcribed sequences) probes also confirmed that these genes are expressed in broth-grown cultures and after 18 h of M. tuberculosis growth in cultured human primary macrophages. To determine if the TrcR response regulator is autoregulated, a trcR-lacZ fusion plasmid and a TrcR expression plasmid were cotransformed into Escherichia coli. Upon induction of the TrcR protein, there was a >500-fold increase in β-galactosidase activity from the trcR-lacZ fusion, indicating that TrcR is involved in transcriptional autoactivation. Gel mobility shift assays with the trcR promoter and TrcR established that the response regulator was autoregulating via direct binding. By use of a delimiting series of overlapping trcR PCR fragments in gel mobility shift assays with TrcR, an AT-rich region of the trcR promoter was shown to be essential for TrcR binding. Additionally, this AT-rich sequence was protected by TrcR in DNase I protection assays. To further analyze the role of the AT-rich region in TrcR autoregulation, the trcR promoter was mutated and analyzed in lacZ transcriptional fusions in the presence of TrcR. Alteration of the AT-rich sequence in the trcR promoter resulted in the loss of trcR transcriptional activation in the presence of TrcR. This report indicates that the M. tuberculosis TrcR response regulator activates its own expression by interacting with the AT-rich sequence of the trcR promoter.
Local Oestrogen for Pelvic Floor Disorders: A Systematic Review

Objective The decline in available oestrogen after menopause is a possible etiological factor in pelvic floor disorders like vaginal atrophy (VA), urinary incontinence (UI), overactive bladder (OAB) and pelvic organ prolapse (POP). This systematic review will examine the evidence for local oestrogen therapy in the treatment of these pelvic floor disorders. Evidence Acquisition We performed a systematic search in MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials and the non-MEDLINE subset of PubMed from inception to May 2014. We searched for local oestrogens and VA (I), UI/OAB (II) and POP (III). Part I was combined with broad methodological filters for randomized controlled trials (RCTs) and secondary evidence. For part I and II two reviewers independently selected RCTs evaluating the effect of topical oestrogens on symptoms and signs of VA and UI/OAB. In part III all studies of topical oestrogen therapy in the treatment of POP were selected. Data extraction and the assessment of risk of bias using the Cochrane Risk of Bias Tool was undertaken independently by two reviewers. Evidence Synthesis The included studies varied in ways of topical application, types of oestrogen, dosage and treatment durations. Objective and subjective outcomes were assessed by a variety of measures. Overall, subjective and urodynamic outcomes, vaginal maturation and vaginal pH changed in favor of vaginal oestrogens compared to placebo. No obvious differences between different application methods were revealed. Low doses already seemed to have a beneficial effect. Studies evaluating the effect of topical oestrogen in women with POP are scarce and mainly assessed symptoms and signs associated with VA instead of POP symptoms. Conclusion Topical oestrogen administration is effective for the treatment of VA and seems to decrease complaints of OAB and UI. The potential for local oestrogens in the prevention as well as treatment of POP needs further research.
Immune Inspired Approach for Securing Wireless Ad hoc Networks

Summary New computational techniques are being developed based on the immune system concepts, seeking to solve several engineering problems. Moreover, mobile ad hoc networks (MANETs) have no clear line of defense and no fixed infrastructure; therefore, the known security techniques used for cabled networks might not work perfectly. A security approach based on immune inspired properties and features is presented. Mobile agent system has been used so as to map different immune components that collaborate to defend the human body against different kinds of diseases. Distributed detection, first response, second response, self recovery, adaptability, and danger theory representation are the hallmarks of the proposed security approach which places emphasis on infrastructure less and high nodes mobility capabilities.
TRACKING OF DOUBTFUL REAL ESTATE TRANSACTIONS BY OUTLIER DETECTION METHODS: A COMPARATIVE STUDY

Doubtful real estate transactions, with the prices far away from the market prices, appear because of non commercial transactions or efforts in order to hide the taxes. To estimate the right values of parameters, such data must be removed from a data set or robust methods of parameters estimation are to be used, while developing a mass appraisal model. Such transactions are outlying observations, which can be detected and removed by outlier detection methods. The purpose of the work is to review outlier detection methods and to test the possibility of using them to solve the task. An overview of real estate market value, valuation methods and process of mass appraisal is made to introduce to real estate mass valuation. Overview of outlier detection method contains scaling and such methods: resampling by half means, the smallest half volume, the closest distance to the center, ellipsoidal multivariate trim- ming, minimum volume ellipsoid, minimum scatter determinant, analysis of projection matrix, principal components and residuals, also influence measures, robust regression, and classification methods. The reviewed methods were categorized; commonly used methods were selected and tested experimentally aiming to compare the effectiveness. Best results were achieved using the multilayer perceptron and the principal component analysis based technique.
Redundancy, redundancy, redundancy: the three keys to highly robust anatomical parsing in medical images

Although redundancy reduction is the key for visual coding in the mammalian visual system [1,2], at a higher level, the visual understanding step, a central component of intelligence, achieves high robustness by exploiting redundancies in the images, in order to resolve uncertainty, ambiguity, or contradiction [3,4]. In this paper, an algorithmic framework, Learning Ensembles of Anatomical Patterns (LEAP), is presented for the purpose of automatic localization and parsing of human anatomy from medical images. It achieves high robustness by exploiting statistical redundancies at three levels: the anatomical level, the parts-whole level, and the voxel level in the scale space. The recognition-by-parts intuition is formulated in a more principled way as a spatial ensemble, with added redundancy and less parameter tuning for medical imaging applications. Different use cases were tested using 2D and 3D medical images, including X-ray, CT, and MRI images, for different purposes such as view identication, organ and body parts localization, and MR imaging plane detection. LEAP is shown to significantly outperform existing methods or its "non-redundant" counterparts.
Budgeted region sampling (BeeRS): do not separate sampling from warm-up, and then spend wisely your simulation budget

While the recent surge of research articles on sampling started with rather large sample sizes, it has later shifted to very small intervals, and it is now converging to intermediate sizes, and even to varying sizes. With 100M samples, warm-up is not an issue, at least with current cache sizes. However, with significantly smaller samples, warm-up becomes critical, especially when the sampling target accuracy is of the order of a few percent. However, in most sampling research works, warm-up has largely been treated as a separate issue. In this article, we advocate for an integrated approach at (simulator-based) warm-up and sampling. Instead of separating warm-up and sampling, we take exactly the opposite approach, provide a common instruction budget for warm-up and sampling, and we attempt to spend it as wisely as possible on either one. This budget and integrated approach at warm-up and sampling achieves an average CPI error of 1.68% on the 26 Spec benchmarks with an average sampling size of 288 millions instructions, and at the same time, it relieves the user from any delicate decision such as setting the sampling or warm-up sizes, thanks to the integrated warm-up+sampling and the region partitioning approaches
Brief report: sleep in parents of children with autism spectrum disorders.

OBJECTIVE To examine sleep quality and sleep-wake patterns in parents of children with autism spectrum disorders (ASDs) and parents of typically developing (TD) children. METHODS Thirty-five mothers and 22 fathers completed the Pittsburgh Sleep Quality Index, a 7-day sleep diary, and wore an actigraph for 1 week. RESULTS Parents of children with ASDs reported poorer sleep quality compared to the TD group. In addition, parents of children with ASDs had objectively different sleep patterns, with an earlier wake time and shorter total sleep time than parents of TD children. Finally, regardless of group, fathers had significantly shorter sleep time compared to mothers. CONCLUSIONS This study is one of the first to demonstrate poorer sleep quality and shorter sleep quantity in parents of children with ASDs using validated measures of sleep. Future studies should examine the relationship between chronic sleep loss and stress in parents of children with ASDs.
A New Radiation Hydrodynamics Code and Application to the Calculation of Type IA Supernovae Light Curves and Continuum Spectra

A new, fully dynamic and self-consistent radiation hydrodynamics code, suitable for the calculation of supernovae light curves and continuum spectra, is described. It is a multigroup (frequency-dependent) code and includes all important $O(v/c)$ effects. It is applied to the model W7 of Nomoto, Thielemann, \& Yokoi (1984) for supernovae of type Ia. Radioactive energy deposition is incorporated through use of tables based upon Monte Carlo results. Effects of line opacity (both static or line blanketing and expansion or line blocking) are neglected, although these may prove to be important. At maximum light, models based upon different treatments of the opacity lead to values for $M_{B,max}$ in the range of -19.0 to -19.4. This range falls between the values for observed supernova claimed by Leibundgut \& Tammann (1990) and by Pierce, Ressler, \& Shure (1992).
Distributed and decentralized multi-camera tracking: a survey

In recent years the decreasing cost of cameras and advances in miniaturization have favoured the deployment of largescale camera networks. This growing number of cameras enables new signal processing applications that use cooperatively multiple sensors over wide areas. In particular, object tracking is an important step in many applications related to security, traffic monitoring and event recognition. Such applications require the optimal trade-off between accuracy, communication and computing across the network. The costs associated to communication and computing depend on the type and amount of cooperation performed among cameras for information gathering, sharing and processing to validate decisions as well as to rectify (or to reduce) estimation errors and uncertainties. In this survey we discuss data fusion and tracking methods for camera networks and compare their performance. In particular we cover decentralized and distributed trackers and the challenges to be addressed for the design of accurate and energy-efficient algorithms.
A Structured Contextual Approach to Design for All

Although a variety of concepts have been published to implement the design principles for user interfaces for all, there is still a lack of techniques applicable for structured development of this type of user interfaces. This paper deals with an approach that has been developed in the course of an industrial design project. It suggests to gather design options and structure the design process through a formal decision making procedure, hence increasing the maintainability of deign solutions and products this way.
Drumming to a New Beat: A Group Therapeutic Drumming and Talking Intervention to Improve Mental Health and Behaviour of Disadvantaged Adolescent Boys

Background: This research examined the impact of a programme integrating therapeutic music and group discussions (Holyoake's DRUMBEAT programme) on disadvantaged adolescents’ mental wellbeing, psychological distress, post-traumatic stress symptoms and antisocial behaviour. Method: Students displaying antisocial behaviours in grades eight to ten at three socio-economically disadvantaged secondary schools in Perth, Western Australia were invited to participate in a 10-week DRUMBEAT programme (incorporating drumming with djembes, therapeutic discussions and a final performance). Eight DRUMBEAT programmes were held in 2014. Pre- and post-intervention questionnaires measured mental wellbeing (Warwick–Edinburgh Mental Wellbeing Scale), psychological distress (Kessler-5), post-traumatic stress symptoms (Abbreviated Post-Traumatic Stress Disorder Checklist- Civilian Version) and antisocial behaviours (Adapted Self-Reported Delinquency Scale). Results: Of the 62 students completing DRUMBEAT, 41 completed pre- and post-questionnaires. Post-programme boys scored an average 7.6% higher mental wellbeing (WEMWBS) (p = .05), 19.3% lower post-traumatic stress symptoms (A PCL-C) (p = .05) and 23.9% lower antisocial behaviour (ARSDC) (p = .02). These changes were not evident for girls. No significant differences were detected for differences in psychological distress for either gender. Conclusion: This research highlights the potential of the DRUMBEAT programme as an effective, targeted strategy to reduce post-traumatic stress symptoms and antisocial behaviour and increase mental wellbeing in socio-economically disadvantaged adolescent boys.
Dual-axis Cellular Force Microscope for mechanical characterization of living plant cells

Understanding the mechanisms of plant growth and morphogenesis is of importance, not only to the field of plant sciences but also in a broader agricultural and economical context, as plants provide important raw materials such as food, fiber, wood and fuel. Mathematical modeling and simulation can provide insights into intricate biomechanical growth mechanisms. Mechanical characterization at single cellular level is essential for providing quantitative model parameters. The dual-axis Cellular Force Microscope (CFM) provide many of these desired parameters by micro-indentation measurements. The dual-axis CFM integrates a MEMS force sensing technology with a piezoelectric nano-positioning system. The dual force feedback from the MEMS sensor allows the system to be used for arbitrary indentation angles and to accurately measure biological samples despite their curved surfaces. The accuracy of the dual-axis CFM is verified by measuring a force-standard with a certified stiffness of 15.15 N/m at indentation angles of 90° and 60°. The obtained stiffness measurements are 15.60 N/m and 14.63 N/m and differ from the calibrated value by 2.97% and 3.63%, respectively. Additionally, the dual-axis CFM offers topographic imaging which was used to visualize two hemispherical structures fabricated using two-photon photopolymerization with radii of 5 μm and 7.5 μm. The potential of the system to study plant cell mechanics at a single cell level is shown by indenting a Lilium longiflorum pollen tube along its axis at the tip. The topographical information combined with the recorded force feedback in axial and lateral directions show promising results for further mechanical characterization of plant cells using the dual-axis CFM.
Anatomy of the Ophthalmic Artery: A Review concerning Its Modern Surgical and Clinical Applications

Anatomy of ophthalmic artery has been thoroughly studied and reviewed in many anatomical and surgical textbooks and papers. Issues of interest are its intracranial and extracranial course, its branches, its importance for vision, and its interaction with various intracranial pathologies. Improvement of our understanding about pathophysiology of certain diseases like aneurysm formation, central retinal artery occlusion, and retinoblastoma and also invention of new therapeutic modalities like superselective catheterization, intra-arterial fibrinolysis, and intra-arterial chemotherapy necessitate a reappraisal of its anatomy from a clinical point of view. The aim of this review is to examine clinical anatomy of ophthalmic artery and correlate it with new diagnostic and therapeutic applications.
Instrument timbre chroma contours and psycho-visual human analysis

Chroma is considered as a powerful representation that is widely used in musical information retrieval applications and assumed to convey essentially the tonal information. In this paper, a new music timbre description based only on chroma contours is investigated allowing the identification of both tonal content and particularly the timbre instrument. Instrument recognition performance obtained by an automatic system, based on popular vector features and models, is compared to psycho-visual human analysis exploiting only the chroma contours. Results are very promising and the graphical analysis demonstrates that contours are dependent of the instrument and will be useful for timbre characterization.
Methods for Counting High-Frequency Repeat Victimizations in the National Crime Victimization Survey. Technical Series Report. NCJ 237308.

Executive Summary As part of ongoing research efforts associated with the redesign of the National Crime Victimization Survey (NCVS), the Bureau of Justice Statistics (BJS) has investigated ways to include high-frequency repeat victimizations, or series victimizations, in estimates of criminal victimization. Including series victimizations would obtain a more accurate estimate of victimization. This report summarizes the research results and describes changes in BJS's enumeration practices regarding the treatment of series victimizations when estimating annual victimization rates. The NCVS's primary purpose is to accurately estimate the number and type of criminal victimizations that occur each year in the United States. To enumerate and classify victimizations, the NCVS employs an interview procedure that asks respondents to recall specific types of criminal events that occurred over the previous 6 months. Repeatedly victimized persons have experiences that present considerable challenges for the accurate counting and description of criminal events. These experiences involve multiple crimes that are often indistinguishable to victims, making it difficult for them to separate the details of each event. Such experiences may include intimate partner violence or bullying by schoolmates. To handle these repeated victimizations, the NCVS employs a series victimization protocol. Currently, the NCVS records a series victimization when the respondent reported experiencing six or more similar crimes during the 6-month reference period and was unable to recall or describe each event in detail. If all of these conditions are met, the NCVS interviewer records the victim's report of the number of times this type of victimization occurred and collects detailed information only for the most recent victimization. Although information about series victimizations is collected in the NCVS, BJS typically excludes series victimizations from annual estimates of crime. This enumeration practice resulted from concerns about the accuracy of the victimization count, whether each victimization in the series occurred within the reference period, and whether characteristics of the most recent victimization (such as whether an injury occurred) would apply to the other victimizations in the series. To assess the strengths and weaknesses for enumerating and classifying series victimizations into national victimization estimates, this report examined the extent and the nature of series victimization in the NCVS and reviewed the general patterns and statistical properties of victims' responses to being asked how many times the incident occurred. Series victimization analyses also examined how different treatments would affect conclusions about the victimization level and annual rate of change for various crime types and …
Transformation Invariant Autoassociation with Application to Handwritten Character Recognition

When training neural networks by the classical backpropagation algorithm the whole problem to learn must be expressed by a set of inputs and desired outputs. However, we often have high-level knowledge about the learning problem. In optical character recognition (OCR), for instance, we know that the classification should be invariant under a set of transformations like rotation or translation. We propose a new modular classification system based on several autoassociative multilayer perceptrons which allows the efficient incorporation of such knowledge. Results are reported on the NIST database of upper case handwritten letters and compared to other approaches to the invariance problem.
Sustained Neurog3 expression in hormone-expressing islet cells is required for endocrine maturation and function

Neurog3 (Neurogenin 3 or Ngn3) is both necessary and sufficient to induce endocrine islet cell differentiation from embryonic pancreatic progenitors. Since robust Neurog3 expression has not been detected in hormone-expressing cells, Neurog3 is used as an endocrine progenitor marker and regarded as dispensable for the function of differentiated islet cells. Here we used 3 independent lines of Neurog3 knock-in reporter mice and mRNA/protein-based assays to examine Neurog3 expression in hormone-expressing islet cells. Neurog3 mRNA and protein are detected in hormone-producing cells at both embryonic and adult stages. Significantly, inactivating Neurog3 in insulin-expressing β cells at embryonic stages or in Pdx1-expressing islet cells in adults impairs endocrine function, a phenotype that is accompanied by reduced expression of several Neurog3 target genes that are essential for islet cell differentiation, maturation, and function. These findings demonstrate that Neurog3 is required not only for initiating endocrine cell differentiation, but also for promoting islet cell maturation and maintaining islet function.