Miracle-dz/UniFAR-FTUs huggingface dataset:
Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA (slincR) Using the Zebrafish Model

Background: A structurally diverse group of chemicals, including dioxins [e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)] and polycyclic aromatic hydrocarbons (PAHs), can xenobiotically activate the aryl hydrocarbon receptor (AHR) and contribute to adverse health effects in humans and wildlife. In the zebrafish model, repression of sox9b has a causal role in several AHR-mediated toxic responses, including craniofacial cartilage malformations; however, the mechanism of sox9b repression remains unknown. We previously identified a long noncoding RNA, sox9b long intergenic noncoding RNA (slincR), which is increased (in an AHR-dependent manner) by multiple AHR ligands and is required for the AHR-activated repression of sox9b. Objective: Using the zebrafish model, we aimed to enhance our understanding of the signaling events downstream of AHR activation that contribute to toxic responses by identifying: a) whether slincR is enriched on the sox9b locus, b) slincR’s functional contributions to TCDD-induced toxicity, c) PAHs that increase slincR expression, and d) mammalian orthologs of slincR. Methods: We used capture hybridization analysis of RNA targets (CHART), qRT-PCR, RNA sequencing, morphometric analysis of cartilage structures, and hemorrhaging screens. Results: The slincR transcript was enriched at the 5′ untranslated region (UTR) of the sox9b locus. Transcriptome profiling and human ortholog analyses identified processes related to skeletal and cartilage development unique to TCDD-exposed controls, and angiogenesis and vasculature development unique to TCDD-exposed zebrafish that were injected with a splice-blocking morpholino targeting slincR. In comparison to TCDD exposed control morphants, slincR morphants exposed to TCDD resulted in abnormal cartilage structures and a smaller percentage of animals displaying the hemorrhaging phenotype. In addition, slincR expression was significantly increased in six out of the sixteen PAHs we screened. Conclusion: Our study establishes that in zebrafish, slincR is recruited to the sox9b 5′ UTR to repress transcription, can regulate cartilage development, has a causal role in the TCDD-induced hemorrhaging phenotype, and is up-regulated by multiple environmentally relevant PAHs. These findings have important implications for understanding the ligand-specific mechanisms of AHR-mediated toxicity. https://doi.org/10.1289/EHP3281
Multi-Functional Soft Strain Sensors for Wearable Physiological Monitoring

Wearable devices which monitor physiological measurements are of significant research interest for a wide number of applications including medicine, entertainment, and wellness monitoring. However, many wearable sensing systems are highly rigid and thus restrict the movement of the wearer, and are not modular or customizable for a specific application. Typically, one sensor is designed to model one physiological indicator which is not a scalable approach. This work aims to address these limitations, by developing soft sensors and including conductive particles into a silicone matrix which allows sheets of soft strain sensors to be developed rapidly using a rapid manufacturing process. By varying the morphology of the sensor sheets and electrode placement the response can be varied. To demonstrate the versatility and range of sensitivity of this base sensing material, two wearable sensors have been developed which show the detection of different physiological parameters. These include a pressure-sensitive insole sensor which can detect ground reaction forces and a strain sensor which can be worn over clothes to allow the measurements of heart rate, breathing rate, and gait.
Visualization of the Topic Space of Argument Search Results in args.me

In times of fake news and alternative facts, pro and con arguments on controversial topics are of increasing importance. Recently, we presented args.me as the first search engine for arguments on the web. In its initial version, args.me ranked arguments solely by their relevance to a topic queried for, making it hard to learn about the diverse topical aspects covered by the search results. To tackle this shortcoming, we integrated a visualization interface for result exploration in args.me that provides an instant overview of the main aspects in a barycentric coordinate system. This topic space is generated ad-hoc from controversial issues on Wikipedia and argument-specific LDA models. In two case studies, we demonstrate how individual arguments can be found easily through interactions with the visualization, such as highlighting and filtering.
A simple geometric model for elastic deformations

We advocate a simple geometric model for elasticity: distance between the differential of a deformation and the rotation group. It comes with rigorous differential geometric underpinnings, both smooth and discrete, and is computationally almost as simple and efficient as linear elasticity. Owing to its geometric non-linearity, though, it does not suffer from the usual linearization artifacts. A material model with standard elastic moduli (Lamé parameters) falls out naturally, and a minimizer for static problems is easily augmented to construct a fully variational 2nd order time integrator. It has excellent conservation properties even for very coarse simulations, making it very robust. Our analysis was motivated by a number of heuristic, physics-like algorithms from geometry processing (editing, morphing, parameterization, and simulation). Starting with a continuous energy formulation and taking the underlying geometry into account, we simplify and accelerate these algorithms while avoiding common pitfalls. Through the connection with the Biot strain of mechanics, the intuition of previous work that these ideas are "like" elasticity is shown to be spot on.
Recruiting Primary Care Practices for Research: Reflections and Reminders

Background: Recruiting primary care practices for research projects has always required carefully tended relationships, a compelling message, and good timing. Recruiting practices to participate in practice transformation research trials may take more and different efforts. We reflect on practice recruitment for a recently-concluded trial of a diabetes self-management support system in 2 states and 36 practices. Methods: Iterative qualitative analysis of field notes, semistructured clinician and staff interviews, and meeting notes from a 2-state, cluster-randomized trial that aimed to improve self-management support for patients with type 2 diabetes mellitus. Results: Although all 36 enrolled practices finished the study, fully recruiting practices early on took considerable effort, yielding 2 primary lessons: 1) practice-based research networks (PBRNs) must recruit more stakeholders at more levels, at the clinic, in the system, and across roles; and 2) practice recruitment is a process and may take longer than expected with unplanned turnover of key contacts. Adjusting our recruitment strategies required: helping with communication efforts in practices; aligning our study message according to stakeholders' interests; allowing for minor adaptations at the practice-level to align with critical practice workflows, staffing, and resources; re-engaging with clinical leadership over time; and identifying a “backup” champion due to turnover. Conclusions: When undertaking a pragmatic clinical trial requiring substantial practice change in a PBRN setting across a large number of practices, it is important that PBRN leaders develop a comprehensive strategy to identify and engage a broad group of stakeholders within each practice, understand their needs and priorities around research, and design and implement a structured communications strategy to maintain engagement throughout every phase of the project.
Latent Iron Deficiency as a Marker of Negative Symptoms in Patients with First-Episode Schizophrenia Spectrum Disorder

Iron deficiency may alter dopaminergic transmission in the brain. This study investigated whether iron metabolism is associated with negative symptoms in patients with first-episode psychosis. The study enrolled 121 patients with first-episode schizophrenia spectrum disorder, whose duration of treatment was 2 months or less. Negative symptoms were measured using the Positive and Negative Syndrome Scale (PANSS) and Clinician-Rated Dimensions of Psychosis Symptom Severity (Dimensional) scale of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5). Prominent negative symptoms were defined as moderate or severe negative symptoms on the Dimensional scale of the DSM-5. Iron deficiency was defined as a serum ferritin ≤ 20 ng/mL. Patients with iron deficiency were significantly more likely to have prominent negative symptoms (45.2 vs. 22.2%; p = 0.014) and a higher PANSS negative symptoms score (p = 0.046) than those with normal ferritin levels. Patients with prominent negative symptoms had significantly lower ferritin levels (p = 0.025). The significance of these results remained after controlling for the duration of illness and other confounding variables. Our finding of an independent association between iron deficiency and negative symptoms in patients at the very early stage of illness implies that iron dysregulation has an effect on negative symptoms in patients with schizophrenia. The possibility of therapeutic intervention with iron should be further investigated.
Peste des petits ruminants virus infection of Black Bengal goats showed altered haematological and serum biochemical profiles

In Bangladesh, veterinarians often claim to reduce the mortality of natural peste des petits ruminants (PPR) outbreaks with the help of supportive fluid and electrolyte therapy. Information on haematological and biochemical parameters of PPR-infected goats, which is often altered because of associated tissue damages, is necessary to formulate the appropriate supportive therapy. This study determined the haematological and serum biochemical parameters of Black Bengal goats naturally infected with PPR virus. Blood and serum samples from 13 PPR-affected Black Bengal goats from 13 field outbreaks and 5 healthy goats were collected and analysed by routine haematological and biochemical examination. Haematological analysis of PRR-affected goats showed severe anaemia characterised by significant decrease in the values of haemoglobin, total erythrocyte counts (TECs) and packed cell volume (PCV). On the contrary, PPR-affected goats showed marked leucocytosis with absolute increase in lymphocytes and neutrophils counts compared to the healthy goats. Biochemical analysis revealed significant decrease in total protein and albumin level and increased creatine kinase, aspartate transaminase and alanine transaminase that mirrored the gross and histopathological changes in the PPR-affected goats. Significant increase in the values of sodium and chloride ions was found in the sera of PPR-infected goats. Peste des petits ruminants virus altered the haematological and serum biochemical parameters of the infected goats. Antidiarrheal agents with aqua solution together with other drugs to support liver and kidney function could help improve therapy of PPR-infected goats.
"As Long as You Ask": A Qualitative Study of Biobanking Consent-Oncology Patients' and Health Care Professionals' Attitudes, Motivations, and Experiences-the B-PPAE Study.

INTRODUCTION Consent to biobanking remains controversial, with little empirical data to guide policy and practice. This study aimed to explore the attitudes, motivations, and concerns of both oncology patients and health care professionals (HCPs) regarding biobanking. MATERIALS AND METHODS Qualitative interviews were conducted with oncology patients and HCPs purposively selected from five Australian hospitals. Patients were invited to give biobanking consent as part of a clinical trial and/or for future research were eligible. HCPs were eligible if involved in consenting patients to biobanking or to donate specimens to clinical trials. RESULTS Twenty-two patients participated, with head and neck (36%) and prostate (18%) the most common cancer diagnoses; all had consented to biobanking. Twenty-two HCPs participated, from across eight cancer streams and five disciplines. Themes identified were (a) biobanking is a "no brainer"; (b) altruism or scientific enquiry; (c) trust in clinicians, science, and institutions; (d) no consent-just do it; (e) respecting patient choice ("opt-out"); (f) respectful timing of the request; (g) need for emotional/family support; (h) context of the biobanking request matters; and (i) factors for biobanking success. DISCUSSION These findings reinforced previous findings regarding high public trust in, and support for, biobanking. An initial opt-in consent approach with the option of later opt-out was favored by patients to respect and recognize donor generosity, whereas HCPs preferred an upfront opt-out model. Factors impacting biobanking success included the context of the request for use in a trial or specific research question, pre-existing patient and HCP rapport, a local institution champion, and infrastructure. IMPLICATIONS FOR PRACTICE Patients and health care professionals (HCPs) who experienced cancer biobanking consent were overwhelmingly supportive of biobanking. The motivations and approaches to seeking consent were largely mirrored between the groups. The findings of this study support the opt-in model of biobanking favored by patients; however, HCPs preferred an opt-out model. Both groups recognize the importance of making the request for biobanking at an appropriate time, preferably with emotional or family support, and respecting the timing of the request and privacy of the patient. Biobanking success can be promoted by hospital departments with a research focus by identifying an institutional biobanking champion and ensuring local infrastructure is available.
Down‐regulation of the long non‐coding RNA XIST ameliorates podocyte apoptosis in membranous nephropathy via the miR‐217–TLR4 pathway

What is the central question of this study? What is the role of the long non‐coding RNA X‐inactive specific transcript (XIST), which is up‐regulated in injured podocytes and membranous nephropathy, in the pathogenesis of membranous nephropathy? What is the main finding and its importance? XIST was up‐regulated in kidney tissue with membranous nephropathy and in injured podocytes. Down‐regulation of XIST inhibited podocyte apoptosis. XIST negatively regulated miR‐217, and miR‐217 modulated Toll‐like receptor 4. Inhibition of XIST suppressed podocyte apoptosis induced by angiotensin II via miR‐217.
Molecular dynamics simulations of the thermal conductivity of graphene for application in wearable devices

Graphene has been highlighted as a great potential material in wearable devices, owing to its extraordinary properties such as mechanical softness, high electrical conductivity and ultra-thin thickness. However, there are remaining challenges in thermal dissipation of graphene under such complicated conditions, which significantly affect the performance of portable electronics. Using molecular dynamics simulations, we have performed systematic analysis of thermal performance for the application in wearable devices in terms of graphene with defects, under uniaxial tensile strain, and vertical stress. Three kinds morphology of defects (horizontal line defect, circular defect, and vertical line defect) are constructed by deleting atoms on the pristine graphene plane. The thermal conductivity is related to the projected defected area perpendicular to the direction of the heat current. The relative thermal conductivity displays a cubic decreasing trend with the increase of uniaxial tensile strain. Besides, the thermal conductivity of graphene is not only related to the deformation quantity, but also related to the type of compression region. Our results show that the thermal conductivity decreases a lot under local stress with larger vertical deformation, while no obvious decline is observed under the global stress. This study aims to provide guidelines and ballpark estimates for experimentalists fabricating flexible devices from graphene.
High-Frequency Ultrasound Imaging for Examination of Early Dental Caries

The extent of dental tissue destruction during the treatment of white spot lesions (WSLs) increases with the severity of the lesion. If the depth and shape of WSLs can be predicted with a noninvasive diagnostic method before dental caries treatment, more conservative interventions can be planned. Given the superiority of high-frequency ultrasound (HFUS) imaging in observing the internal structures of the body, the present study aimed to verify the possibility of HFUS imaging to examine the depth and shape of WSLs. We prepared tooth samples and developed a biomicroscopic system with a HFUS transducer to obtain images of normal and WSL regions. HFUS images were compared with conventional ultrasound images and micro–computed tomography images. HFUS distinctly differentiated demineralization within WSL and normal regions. WSL depth calculated in the micro–computed tomography image was similar to that in HFUS. This study revealed that HFUS imaging has the potential to detect early dental caries and offer information on the invasion depth of early dental caries quantitatively.
Utility of an Alzheimer's Disease Risk-Weighted Polygenic Risk Score for Predicting Rates of Cognitive Decline in Preclinical Alzheimer's Disease: A Prospective Longitudinal Study.

BACKGROUND With the exception of APOE, genetic variants associated with increased Alzheimer's disease (AD) risk are characterized by small effect sizes. Polygenic risk scores (PRS) have shown utility in predicting AD risk; however, their utility for predicting decline in cognition at preclinical stages of AD is poorly understood. OBJECTIVE To validate associations of a 22-variant AD-risk-weighted PRS with AD risk and related biomarkers and to assess its utility to predict cognitive decline. METHODS The PRS was evaluated with respect to brain amyloid-β (Aβ) burden, cerebrospinal fluid (CSF) Aβ42, total-tau, and phospho-tau, and decline in cognition in 643 (570 cognitively normal (CN), 73 AD) PET-imaged participants from the longitudinal Australian Imaging, Biomarkers and Lifestyle (AIBL) Study of Ageing. Cognition was assessed using three composite measures; global cognition, verbal episodic memory, and a Pre-Alzheimer's Cognitive Composite (PACC). RESULTS PRS, both with and without APOE, were positively correlated with brain Aβ burden, CSF total-tau, and phospho-tau in CN older adults. Further, in CN biomarker positive (Aβhigh) participants, significant associations were observed with baseline and longitudinal cognition. However, this association was not observed after the removal of APOE. Partitioning the PRS into quartiles revealed that the PRS associations with cognitive decline in Aβhigh CN older adults is due to a saturating effect of APOE genotype. CONCLUSIONS An AD-risk-weighted PRS is associated with cognitive decline in CN older adults. However, this association is absent when APOE genotype is excluded from the PRS, suggesting that associations with cognitive decline in this model of polygenic risk are driven by APOE genotype alone. Further research is needed to define appropriate PRSs with greater utility for predicting preclinical AD cognitive decline.
GENERALIZATION BOUNDS FOR DOMAIN ADAPTATION VIA DOMAIN TRANSFORMATIONS

Many domain adaptation methods are based on learning a projection or a transformation of the source and target domains to a common domain and training a classifier there, while the performance of such algorithms has not been theoretically studied yet. Previous studies proposing generalization bounds for domain adaptation relate the target loss to the discrepancy between the source and target distributions, however, do not take into account the possible effects of learning a transformation between the two domains. In this work, we present generalization bounds that study the target performance of domain adaptation methods learning a transformation of the source and target domains along with a hypothesis. We show that, under some conditions on the loss regularity, if the domain transformations reduce the distribution distance at a sufficiently high rate, then the expected target loss can be bounded with probability improving at an exponential rate with the number of labeled samples.
Self-assembled gold micro/nanostructure arrays based on superionic conductor RbAg4I5 films

Herein, we propose a new strategy to fabricate gold (Au) micro/nanostructure arrays by photocatalytic solid-state electrochemical reaction between superionic conductor RbAg4I5 and Au films. The Au and RbAg4I5 films were successively deposited on a clean quartz substrate by vacuum thermal deposition method. A copper microgrid possessing periodic holes 100 μm in diameter was put above the RbAg4I5 film as a mask plate, whereupon irradiation from a 405 nm wavelength laser was used to diffuse gold ions (Au+ ions) into vacant silver sites of RbAg4I5 and transfer Au+ through ion passageways in the RbAg4I5 film. When the laser was turned off, the Au+ ions were easily reduced due to low activity compared to the silver (Ag+) ions. After multiple on/off cycles of the 405 nm laser, the irradiated area of uniform Au film exhibited a periodic structural unit array whose period was the same as that of the mask plate hole array. Atomic force microscope and scanning electron microscope images revealed that a self-assembled needle-like nanostructure array grew perpendicular to the substrate surface inside each circle’s structural unit. The height of the grown nanostructure array increased with laser power density. Raman enhancement of the gold nanostructure array as substrate was detected using Rhodamine 6G (R6G) ethanol solutions as probe molecules. The enhancement effect increased with the height of the grown nanostructure array, and could increase by two orders of magnitude greater than that of unirradiated Au film. This strategy offers a new method for the micro/nanostructure processing of gold and provides microscale-array-mediated surface-enhancement Raman-scattering (SERS) substrates comprising Au nanostructures for application in high-sensitivity spectrum analysis.
Form-finding with polyhedral meshes made simple

We solve the form-finding problem for polyhedral meshes in a way which combines form, function and fabrication; taking care of user-specified constraints like boundary interpolation, planarity of faces, statics, panel size and shape, enclosed volume, and last, but not least, cost. Our main application is the interactive modeling of meshes for architectural and industrial design. Our approach can be described as guided exploration of the constraint space whose algebraic structure is simplified by introducing auxiliary variables and ensuring that constraints are at most quadratic. Computationally, we perform a projection onto the constraint space which is biased towards low values of an energy which expresses desirable "soft" properties like fairness. We have created a tool which elegantly handles difficult tasks, such as taking boundary-alignment of polyhedral meshes into account, planarization, fairing under planarity side conditions, handling hybrid meshes, and extending the treatment of static equilibrium to shapes which possess overhanging parts.