Miracle-dz/UniFAR-FTUs huggingface dataset:
Six1 is required for the early organogenesis of mammalian kidney

The murine Six gene family, homologous to Drosophila sine oculis (so) which encodes a homeodomain transcription factor, is composed of six members (Six1-6). Among the six members, only the Six2 gene has been previously shown to be expressed early in kidney development, but its function is unknown. We have recently found that the Six1 gene is also expressed in the kidney. In the developing kidney, Six1 is expressed in the uninduced metanephric mesenchyme at E10.5 and in the induced mesenchyme around the ureteric bud at E11.5. At E17.5 to P0, Six1 expression became restricted to a subpopulation of collecting tubule epithelial cells. To study its in vivo function, we have recently generated Six1 mutant mice. Loss of Six1 leads to a failure of ureteric bud invasion into the mesenchyme and subsequent apoptosis of the mesenchyme. These results indicate that Six1 plays an essential role in early kidney development. In Six1-/- kidney development, we have found that Pax2, Six2 and Sall1 expression was markedly reduced in the metanephric mesenchyme at E10.5, indicating that Six1 is required for the expression of these genes in the metanephric mesenchyme. In contrast, Eya1 expression was unaffected in Six1-/- metanephric mesenchyme at E10.5, indicating that Eya1 may function upstream of Six1. Moreover, our results show that both Eya1 and Six1 expression in the metanephric mesenchyme is preserved in Pax2-/- embryos at E10.5, further indicating that Pax2 functions downstream of Eya1 and Six1 in the metanephric mesenchyme. Thus, the epistatic relationship between Pax, Eya and Six genes in the metanephric mesenchyme during early kidney development is distinct from a genetic pathway elucidated in the Drosophila eye imaginal disc. Finally, our results show that Eya1 and Six1 genetically interact during mammalian kidney development, because most compound heterozygous embryos show hypoplastic kidneys. These analyses establish a role for Six1 in the initial inductive step for metanephric development.
Molecular Diagnostic and Pathogenesis of Hereditary Hemochromatosis

Hereditary hemochromatosis (HH) is an autosomal recessive disorder characterized by enhanced intestinal absorption of dietary iron. Without therapeutic intervention, iron overload leads to multiple organ damage such as liver cirrhosis, cardiomyopathy, diabetes, arthritis, hypogonadism and skin pigmentation. Most HH patients carry HFE mutant genotypes: homozygosity for p.Cys282Tyr or p.Cys282Tyr/p.His63Asp compound heterozygosity. In addition to HFE gene, mutations in the genes that encode hemojuvelin (HJV), hepcidin (HAMP), transferrin receptor 2 (TFR2) and ferroportin (SLC40A1) have been associated with regulation of iron homeostasis and development of HH. The aim of this review was to identify the main gene mutations involved in the pathogenesis of type 1, 2, 3 and 4 HH and their genetic testing indication. HFE testing for the two main mutations (p.Cys282Tyr and p.His63Asp) should be performed in all patients with primary iron overload and unexplained increased transferrin saturation and/or serum ferritin values. The evaluation of the HJV p.Gly320Val mutation must be the molecular test of choice in suspected patients with juvenile hemochromatosis with less than 30 years and cardiac or endocrine manifestations. In conclusion, HH is an example that genetic testing can, in addition to performing the differential diagnostic with secondary iron overload, lead to more adequate and faster treatment.
Soft decoding of variable-length codes

We present the results of two methods for soft decoding of variable-length codes. We first show that maximum likelihood (ML) sequential decoding and maximum a posteriori (MAP) sequence estimation gives significant decoding improvements over hard decisions alone, then we show that further improvements can be gained by additional transmission of the symbol length. Finally, we show that it is possible to make use of the inherent meaning of the codewords without additional transmission of side information which results in a further gain.
Near infrared operation of femtosecond laser micro-machined in-fiber Mach Zehnder interferometers for refractive index sensing

This paper discusses refractive index (n) measurement capabilities of interferometers based on micro-cavities of various diameters (d = 50 and 60 μm) fabricated in optical fibers by a femtosecond laser. In comparison to previously presented structures, the reported sensor operates in the near-infrared spectral range. Bottom of the cavity intersected the fiber’s core (5.2 μm in diameter), which induced the Mach-Zehnder interferometer effect. After filling the cavity, a set of minima can be observed in the transmission spectrum, and they shift in wavelength with a change in n. The fabricated sensors exhibit high and linear sensitivity and can measure sub-nanoliter volumes of liquids, what make this sensor perfect for various diagnostic medical or biochemical applications.
Modeling Failure Modes for Residual Life Prediction Using Stochastic Filtering Theory

This paper reports on a theoretical Bayesian modeling development for residual life prediction in the context of condition-based maintenance. At each monitoring point during a components lifetime, the stochastic filter is used to establish a posterior conditional probability density function (PDF) for the residual life. The PDF can then be used in the evaluation of maintenance and replacement decisions. The research documented in this paper extends the modeling principles in accordance with a practical consideration recognized in a number of previous case applications. Many monitoring scenarios provide evidence that the operational components involved may potentially be subject to a number of individual distinct failure modes, rather than a single dominant failure mode as modeled previously. The modeling procedure proposed to handle this scenario is based on the assumption that an individual monitored component will fail according to one of a number of predefined failure modes. Individual stochastic filters are constructed to facilitate the residual life prediction under the influence of each potential failure mode, and the output from each filter is weighted according to the probability that the particular failure mode is the true underlying (unknown) failure mode. The probabilities associated with each failure mode are recursively derived using a Bayesian model, and the condition monitoring information obtained to date. The modeling process is applied to a set of simulated condition monitoring histories incorporating two potential failure modes, and the results are compared with those obtained using a general model with no failure mode assumptions. The results indicate that, when individual failure modes are identifiable using historical data, the modeling process described in the paper could greatly improve residual life prediction capabilities, and prevent the occurrence of costly component failures.
The media as messenger.

Staff at Media Processing Services Unit: Carol Briggs – Processing Center Librarian Barbara Cavanaugh – Instructional Materials Asst I Jeff Hawkins – Materials Property Assistant Teresa Riner – Instructional Materials Assistant II Mary Werner – Processing Center Librarian (PT) Pinkie (Natasha) Pamnani – Buyer II & Supervisor Please return videos and DVDs as scheduled so that other schools can place orders for those items. Family Life will be starting soon and you are requested to place your orders on Web Max as soon as possible.
Frequency dependent deformation reversibility during cyclic loading

ABSTRACT High-frequency testing (HFT) is useful for accelerated fatigue testing of conventional materials that typically serve under low-frequency loading conditions, as well as for the assessment of the robustness of microelectromechanical systems which typically experience high-frequency service conditions. Using discrete dislocation dynamics, we attempt to elucidate the effect of loading frequency on the reversibility of cyclic deformation. We demonstrate that the HFT induces a higher fraction of reversible cyclic deformation because of a larger portion of elastic/anelastic deformation due to limited dislocation mobility, and a higher degree of reversibility in plastic deformation owing to the less occurrence of cross-slip. IMPACT STATEMENT Dislocation-based frequency effects on high-cycle deformation reversibility in metals are elucidated. Hysteresis energy is shown to dissipate even under ideal, damage-free conditions, contrary to popular assumptions of energy-based fatigue models. GRAPHICAL ABSTRACT
ARIEL and AMELIA: Testing for an Accumulation of Rare Variants Using Next-Generation Sequencing Data

Objectives: There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. Here, we propose two locus-based methods that incorporate variant quality scores: a regression-based collapsing approach and an allele-matching method. Methods: Using simulated sequencing data we compare 4 locus-based tests of trait association under different scenarios of data quality. We test two collapsing-based approaches and two allele-matching-based approaches, taking into account variant quality scores and ignoring variant quality scores. We implement the collapsing and allele-matching approaches accounting for variant quality in the freely available ARIEL and AMELIA software. Results: The incorporation of variant quality scores in locus-based association tests has power advantages over weighting each variant equally. The allele-matching methods are robust to the presence of both protective and risk variants in a locus, while collapsing methods exhibit a dramatic loss of power in this scenario. Conclusions: The incorporation of variant quality scores should be a standard protocol when performing locus-based association analysis on sequencing data. The ARIEL and AMELIA software implement collapsing and allele-matching locus association analysis methods, respectively, that allow the incorporation of variant quality scores.
The psychosocial impact of lymphedema‐related distress among breast cancer survivors in the WHEL Study

Lymphedema is a distressing and chronic condition affecting up to 30% of breast cancer survivors. Using a cross‐sectional study design, we examined the impact of self‐reported lymphedema‐related distress on psychosocial functioning among breast cancer survivors in the Women's Healthy Eating and Living Study. The Women's Healthy Eating and Living Study has a dataset that includes self‐report data on lymphedema status, symptoms, and distress.
Structural and Functional Adaptations to Extreme Temperatures in Psychrophilic, Mesophilic, and Thermophilic DNA Ligases*

Psychrophiles, host of permanently cold habitats, display metabolic fluxes comparable to those exhibited by mesophilic organisms at moderate temperatures. These organisms have evolved by producing, among other peculiarities, cold-active enzymes that have the properties to cope with the reduction of chemical reaction rates induced by low temperatures. The emerging picture suggests that these enzymes display a high catalytic efficiency at low temperatures through an improved flexibility of the structural components involved in the catalytic cycle, whereas other protein regions, if not implicated in catalysis, may be even more rigid than their mesophilic counterparts. In return, the increased flexibility leads to a decreased stability of psychrophilic enzymes. In order to gain further advances in the analysis of the activity/flexibility/stability concept, psychrophilic, mesophilic, and thermophilic DNA ligases have been compared by three-dimensional-modeling studies, as well as regards their activity, surface hydrophobicity, structural permeability, conformational stabilities, and irreversible thermal unfolding. These data show that the cold-adapted DNA ligase is characterized by an increased activity at low and moderate temperatures, an overall destabilization of the molecular edifice, especially at the active site, and a high conformational flexibility. The opposite trend is observed in the mesophilic and thermophilic counterparts, the latter being characterized by a reduced low temperature activity, high stability and reduced flexibility. These results strongly suggest a complex relationship between activity, flexibility and stability. In addition, they also indicate that in cold-adapted enzymes, the driving force for denaturation is a large entropy change.
Review: The potential for estrogens in preventing Alzheimer's disease and vascular dementia

Estrogens are the best-studied class of drugs for potential use in the prevention of Alzheimer's disease (AD). These steroids have been shown to be potent neuroprotectants both in vitro and in vivo, and to exert effects that are consistent with their potential use in prevention of AD. These include the prevention of the processing of amyloid precursor protein (APP) into beta-amyloid (Aβ), the reduction in tau hyperphosphorylation, and the elimination of catastrophic attempts at neuronal mitosis. Further, epidemiological data support the efficacy of early postmenopausal use of estrogens for the delay or prevention of AD. Collectively, this evidence supports the further development of estrogen-like compounds for prevention of AD. Several approaches to enhance brain specificity of estrogen action are now underway in an attempt to reduce the side effects of chronic estrogen therapy in AD.
Performance optimization using template mapping for datapath-intensive high-level synthesis

This paper introduces a new approach to performance-driven template mapping for high-level synthesis. Template mapping, the process of mapping high-level algorithmic descriptions to specialized hardware libraries or instruction sets, involves template matching, template selection, and clock selection. Efficient algorithms for each are presented, and novel issues such as partial matching are addressed. The paper focuses on datapath-intensive ASIC design, though the concepts are also highly applicable to compiler development. Experimental results on examples from real applications show significant improvements in throughput with limited area overhead.
Bax-inhibiting peptide attenuates bleomycin-induced lung injury in mice

ABSTRACT Bax is a pro-apoptotic member of the Bcl-2 family of proteins, and plays a central role in mitochondria-dependent apoptosis. Several lines of evidence have implied that Bax is involved in both epithelial apoptosis and fibroblast proliferation in idiopathic pulmonary fibrosis; however, the mechanisms remain unknown. Bax-inhibiting peptide V5 (BIP-V5) exhibits membrane permeability and inhibits the activation of Bax. The purpose of this study was to investigate whether the control of Bax activity by BIP-V5 reduces the degree of bleomycin-induced lung injury. C57BL/6J mice were administered bleomycin and BIP-V5 intratracheally on day 0. Bronchoalveolar lavage fluid and lung tissue were obtained on day 7. Human pulmonary alveolar epithelial cells (A549 cells) and mouse pulmonary alveolar epithelial cells (LA-4 cells) were stimulated with bleomycin to induce apoptosis. Administration of BIP-V5 improved the survival rate and degree of bleomycin-induced lung injury by suppressing Bax activation in mice. BIP-V5 treatment decreased bleomycin-induced apoptosis of alveolar epithelial cell lines (A549 cells and LA-4 cells) by suppressing Bax activation. These results indicate that administration of BIP-V5 may constitute a novel therapeutic strategy against lung injury. Summary: The inhibiting peptide for Bax, a pro-apoptotic member of the Bcl-2 family of proteins, ameliorates bleomycin-induced lung injury in mice via apoptosis suppression in epithelial cells.
Systematic evaluation of skeletal fractures caused by induction of electroconvulsive seizures in rat state a need for attention and refinement of the procedure

Objective Electroconvulsive therapy (ECT) is one of the most efficient treatments for major depression. Electroconvulsive seizures (ECS), the animal model of ECT, is widely used to study both mechanisms of action and adverse effects of ECT. As the treatment itself serves as an instant anaesthetic and anaesthetic agents may affect memory functions and behaviour, ECS is traditionally administered without muscle relaxation and anaesthesia. A major problem of unmodified ECS, which has only been addressed peripherally in the literature, is that some animals sustain spinal fractures and subsequent hind leg paralysis (paraplegia). This phenomenon leads to a higher degree of suffering and these animals need to be excluded from the studies. To reach sufficient statistical power, the group sizes are therefore often increased and this may lead to a pre-selected study group in risk of skewing the results. Moreover, the study design of the experiments do not comply with the 3R principles, which advocate for both refinement and reduction of animal experiments. The objective of this study is to systematically evaluate injuries caused by ECS. Methods We summarise the incidence of spinal fractures from 24 studies conducted during 2009–2015 in six different rat strains and report preliminary findings on scapular fractures following auricular ECS. Results In total, 12.8% of all tested animals suffered from spinal fractures and we find an increase in spinal fracture incidence over time. Furthermore, X-ray analyses revealed that some animals displayed scapular fractures. Conclusion We discuss consequences of and possible explanations for ECS-induced fractures. Modifications of the method are highly warranted and we furthermore suggest that all animals are thoroughly examined for discrete fractures.
Speaker-Aware Neural Network Based Beamformer for Speaker Extraction in Speech Mixtures

In this work, we address the problem of extracting one target speaker from a multichannel mixture of speech. We use a neural network to estimate masks to extract the target speaker and derive beamformer filters using these masks, in a similar way as the recently proposed approach for extraction of speech in presence of noise. To overcome the permutation ambiguity of neural network mask estimation, which arises in presence of multiple speakers, we propose to inform the neural network about the target speaker so that it learns to follow the speaker characteristics through the utterance. We investigate and compare different methods of passing the speaker information to the network such as making one layer of the network dependent on speaker characteristics. Experiments on mixture of two speakers demonstrate that the proposed scheme can track and extract a target speaker for both closed and open speaker set cases.
The effect of discrete vs. continuous-valued ratings on reputation and ranking systems

When users rate objects, a sophisticated algorithm that takes into account ability or reputation may produce a fairer or more accurate aggregation of ratings than the straightforward arithmetic average. Recently a number of authors have proposed different co-determination algorithms where estimates of user and object reputation are refined iteratively together, permitting accurate measures of both to be derived directly from the rating data. However, simulations demonstrating these methods' efficacy assumed a continuum of rating values, consistent with typical physical modelling practice, whereas in most actual rating systems only a limited range of discrete values (such as a 5-star system) is employed. We perform a comparative test of several co-determination algorithms with different scales of discrete ratings and show that this seemingly minor modification in fact has a significant impact on algorithms' performance. Paradoxically, where rating resolution is low, increased noise in users' ratings may even improve the overall performance of the system.
Smooth path planning for autonomous parking system

In this paper, we present a path planning algorithm for autonomous parking system. We focus on the kinematics of the car-like vehicle and improve the conventional geometric parking algorithm by proposing a new curve element named linearly steering spiral. A path planning algorithm based on smooth path searching and optimizing are presented. This method can generate smooth paths incrementally, and the reference control signals can be deduced directly once the path is determined. A simple closed-loop controller is designed in order to deal with the uncertainty from various aspects. Simulations are implemented in different scenarios including obstacle-free and cluttered environments, moreover, a real-world online experiment is executed. The results indicate that the proposed method achieves good performance on both accuracy and computational cost.
An exploration into patient preference for injectable therapy over surgery in the treatment of female urinary incontinence.

OBJECTIVE To explore patient preference for injectable therapy over open surgery in the treatment of urinary incontinence. MATERIAL AND METHODS Fifty-eight female patients presented for treatment of urinary incontinence. During the initial interview process, they were asked to quantify their preference for injectable therapy over surgery by specifying the lowest success rate they would accept and still try injectable therapy. The results were summarized and assessed in relation to patient age and history of previous urogynecologic surgery. RESULTS The mean lowest acceptable success rate for all 58 surveyed patients was 34%, with 23 (40%) accepting a success rate of only 10%. Although not statistically significant, the data suggested that older patients may tend to accept lower success rates than younger patients (mean of 39% for patients aged less than 60 years compared to 22% for those aged 80 years or older). There was no difference in response based on history of previous urogynecologic surgery. CONCLUSION Patients appear willing to accept a relatively low success rate for injectable therapy compared to open surgery.
InterActor: Speech-driven embodied interactive actor

A speech-driven embodied interactive actor called InterActor with both functions of speaker and listener is developed for activating human interaction and communication by generating expressive actions and motions coherently related to speech input. InterActor is the electronic media version of physical interaction robot called InterRobot for robot-mediated communication support, which sets free from the hardware restriction. By using InterActor, the concept of speech driven embodied interaction system is proposed for human interaction sharing by the entrainment between human speech and InterActor's motions in remote communication. The prototype of the system is developed, and the sensory evaluation and behavioral analysis in human communication through InterActor demonstrate the effectiveness of the system. Actual applications of InterActor to human interface are also demonstrated.