Miracle-dz/UniFAR-FTUs huggingface dataset:
Biomechanical parameter determination of scaffold-free cartilage constructs (SFCCs) with the hyperelastic material models Yeoh, Ogden and Demiray

Abstract The biomechanical properties are crucial indicators for the functional characterization of cartilaginous tissue. In this contribution native articular cartilage and three-dimensional scaffold-free cartilage constructs (SFCCs) are characterized by hyperelastic material models (Yeoh, Ogden and Demiray). SFCCs were developed for the therapy of damaged articular cartilage. The normalized error (NE) of fit and experiment is in the range of 0.04 and 0.13. The material model Yeoh with two parameters yields the best fit. The stress-like parameterc 20 is 0.489 MPa for native cartilage, 0.120 MPa and 0.041 MPa for SFCCs produced from mesenchymal stem cells and chondrocytes, respectively. The significance of the fits and the derived parameters are presented and evaluated.
A Randomized Crossover Trial on Acute Stress-Related Physiological Responses to Mountain Hiking

Green exercise, defined as physical activity in natural environments, might have positive effects on stress-related physiological measures. Little is known about the acute effects of green exercise bouts lasting longer than 60 min. Therefore, the aim of the present study was to analyze the acute effects of a three-hour green exercise intervention (mountain hiking) on stress-related physiological responses. Using a randomized crossover design, 42 healthy participants were exposed to three different conditions in a field-based experiment: outdoor mountain hiking, indoor treadmill walking, and sedentary control condition (three hours each). At baseline and at follow-up (five minutes after the condition), stress-related physiological responses (salivary cortisol, blood pressure, and heart rate variability) were measured. Salivary cortisol decreased in all conditions, but showed a larger decrease after both mountain hiking and treadmill walking compared to the sedentary control situation (partial η2 = 0.10). No differences were found between mountain hiking and treadmill walking in salivary cortisol. In heart rate variability and blood pressure, changes from baseline to follow-up did not significantly differ between the three conditions. The results indicate that three hours of hiking indoors or outdoors elicits positive effects on salivary cortisol concentration. Environmental effects seem to play a minor role in salivary cortisol, blood pressure, and heart rate variability.
Medical Complexity among Children with Special Health Care Needs: A Two-Dimensional View.

OBJECTIVE To identify subgroups of U.S. children with special health care needs (CSHCN) and characterize key outcomes. DATA SOURCE Secondary analysis of 2009-2010 National Survey of CSHCN. STUDY DESIGN Latent class analysis grouped individuals into substantively meaningful classes empirically derived from measures of pediatric medical complexity. Outcomes were compared among latent classes with weighted logistic or negative binomial regression. PRINCIPAL FINDINGS LCA identified four unique CSHCN subgroups: broad functional impairment (physical, cognitive, and mental health) with extensive health care (Class 1), broad functional impairment alone (Class 2), predominant physical impairment requiring family-delivered care (Class 3), and physical impairment alone (Class 4). CSHCN from Class 1 had the highest ED visit rates (IRR 3.3, p < .001) and hospitalization odds (AOR: 12.0, p < .001) and lowest odds of a medical home (AOR: 0.17, p < .001). CSHCN in Class 3, despite experiencing more shared decision making and medical home attributes, had more ED visits and missed school than CSHCN in Class 2 (p < .001); the latter, however, experienced more cost-related difficulties, care delays, and parents having to stop work (p < .001). CONCLUSIONS Recognizing distinct impacts of cognitive and mental health impairments and health care delivery needs on CSHCN outcomes may better direct future intervention efforts.
YAMATO Study (Tissue-Type Plasminogen Activator and Edaravone Combination Therapy)

Background and Purpose— We investigated whether administration of edaravone, a free radical scavenger, before or during tissue-type plasminogen activator (tPA) can enhance early recanalization in a major arterial occlusion. Methods— The YAMATO study (Tissue-Type Plasminogen Activator and Edaravone Combination Therapy) is an investigator-initiated, multicenter (17 hospitals in Japan), prospective, randomized, and open-label study. Patients with stroke secondary to occlusion of the M1 or M2 portion of the middle cerebral artery and within 4.5 hours of the onset were studied. The subjects were randomly allocated to the early group (intravenous edaravone [30 mg] was started before or during tPA) and the late group (edaravone was started after tPA and the assessment of early recanalization). Results— One-hundred sixty-five patients (96 men; median age [interquartile range], of 78 [69–85] years) were randomized 1:1 to either the early group (82 patients) or the late group (83 patients). Primary outcome, defined as an early recanalization 1.5 hour after tPA, was observed in 53% of the early group and in 53% of the late group (P=1.000). About secondary outcomes, the rate of significant recanalization of ≥50% was not different between the 2 groups (28% versus 34%; P=0.393). The symptomatic intracerebral hemorrhage has occurred in 4 patients (5%) in the early group and in 2 patients (2%) in the late group (P=0.443). The favorable outcome (modified Rankin Scale score of 0–2) at 3 months was also similar between the groups (53% versus 57%; P=0.738). Conclusions— The timing of edaravone infusion does not affect the rate of early recanalization, symptomatic intracerebral hemorrhage, or favorable outcome after tPA therapy. Clinical Trial Registration— URL: http://www.umin. ac.jp/ctr/index-j.htm. Unique identifier: UMIN000006330.
Combination of immunohistochemistry, FISH and RT-PCR shows high incidence of Xp11 translocation RCC: comparison of three different diagnostic methods

We evaluated the frequency of translocation renal cell carcinoma (RCC) by reverse transcription polymerase chain reaction (RT-PCR) and how well the TFE3 immunoreactivity is concordant with TFE3 gene translocation status proved by fluorescence in situ hybridization (FISH) assay and RT-PCR. TFE3 and Cathepsin K expression was analyzed by immunohistochemistry in 185 RCC cases, and 48 cases either of more than weak expression of TFE3 or of positivity for Cathepsin K were done for FISH analysis and RT-PCR. All the RT-PCR positive cases were confirmed by cloning and sequencing. Of the 14 cases with strong nuclear TFE3 expression, 12 showed a break-apart signal by FISH. ASPL- and PRCC-TFE3 translocations were detected in 13 and one case, respectively, by RT-PCR. Of 21 cases with weak TFE3 expression, five were translocation-positive by FISH. ASPL-, PRCC-, and PSF-TFE3 translocations were detected by RT-PCR (n=3, 3, and 1, respectively). All 13 TFE3-negative/cathepsin K-positive cases were negative by FISH and two each harbored ASPL- and PRCC-TFE3 translocations that were detected by RT-PCR. A high rate of TFE3 immunoreactivity (8.6%) was confirmed by RT-PCR (13.5%) and FISH (9.7%). Higher translocation rate of RT-PCR means RT-PCR detected translocation in TFE3 weak expression group and only cathepsin K positive group more specifically than FISH. Thus, RT-PCR would complement FISH analysis for detecting translocation RCC with fusion partners.
Effect of enhanced pCO2 levels on the production of dissolved organic carbon and transparent exopolymer particles in short-term bioassay experiments

It has been proposed that increasing levels of pCO(2) in the surface ocean will lead to more partitioning of the organic carbon fixed by marine primary production into the dissolved rather than the particulate fraction. This process may result in enhanced accumulation of dissolved organic carbon (DOC) in the surface ocean and/or concurrent accumulation of transparent exopolymer particles (TEPs), with important implications for the functioning of the marine carbon cycle. We investigated this in shipboard bioassay experiments that considered the effect of four different pCO(2) scenarios (ambient, 550, 750 and 1000 mu atm) on unamended natural phytoplankton communities from a range of locations in the northwest European shelf seas. The environmental settings, in terms of nutrient availability, phytoplankton community structure and growth conditions, varied considerably between locations. We did not observe any strong or consistent effect of pCO(2) on DOC production. There was a significant but highly variable effect of pCO(2) on the production of TEPs. In three of the five experiments, variation of TEP production between pCO(2) treatments was caused by the effect of pCO(2) on phytoplankton growth rather than a direct effect on TEP production. In one of the five experiments, there was evidence of enhanced TEP production at high pCO(2) (twice as much production over the 96 h incubation period in the 750 mu atm treatment compared with the ambient treatment) independent of indirect effects, as hypothesised by previous studies. Our results suggest that the environmental setting of experiments (community structure, nutrient availability and occurrence of phytoplankton growth) is a key factor determining the TEP response to pCO(2) perturbations.
Pseudomonas aeruginosa AmrZ Binds to Four Sites in the algD Promoter, Inducing DNA-AmrZ Complex Formation and Transcriptional Activation

ABSTRACT During late stages of cystic fibrosis pulmonary infections, Pseudomonas aeruginosa often overproduces the exopolysaccharide alginate, protecting the bacterial community from host immunity and antimicrobials. The transcription of the alginate biosynthesis operon is under tight control by a number of factors, including AmrZ, the focus of this study. Interestingly, multiple transcription factors interact with the far-upstream region of this promoter (PalgD), in which one AmrZ binding site has been identified previously. The mechanisms of AmrZ binding and subsequent activation remain unclear and require more-detailed investigation. In this study, in-depth examinations elucidated four AmrZ binding sites, and their disruption eliminated AmrZ binding and promoter activation. Furthermore, our in vitro fluorescence resonance energy transfer experiments suggest that AmrZ holds together multiple binding sites in PalgD and thereafter induces the formation of higher-order DNA-AmrZ complexes. To determine the importance of interactions between those AmrZ oligomers in the cell, a DNA phasing experiment was performed. PalgD transcription was significantly impaired when the relative phase between AmrZ binding sites was reversed (5 bp), while a full-DNA-turn insertion (10 bp) restored promoter activity. Taken together, the investigations presented here provide a deeper mechanistic understanding of AmrZ-mediated binding to PalgD. IMPORTANCE Overproduction of the exopolysaccharide alginate provides protection to Pseudomonas aeruginosa against antimicrobial treatments and is associated with chronic P. aeruginosa infections in the lungs of cystic fibrosis patients. In this study, we combined a variety of microbiological, genetic, biochemical, and biophysical approaches to investigate the activation of the alginate biosynthesis operon promoter by a key transcription factor named AmrZ. This study has provided important new information on the mechanism of activation of this extremely complex promoter.
Hyperglycemia via activation of thromboxane A2 receptor impairs the integrity and function of blood-brain barrier in microvascular endothelial cells

Diabetes is one of high risk factors for cardio- and cerebra-vascular diseases, including stroke, atherosclerosis and hypertension. This study was conducted to elucidate whether and how thromboxane receptor (TPr) activation contributes to blood-brain barrier (BBB) dysfunction in diabetes. Human brain microvascular endothelial cells (HBMECs) were cultured. The levels of phosphorylated endothelial nitric oxide synthase (eNOS) at Ser1177 (p-eNOS) and Akt at Ser473 (p-Akt) were assayed by western blot. Exposure of HBMECs to either high glucose (HG) or thromboxane A2 (TxA2) mimetic U46619, significantly reduced p-eNOS and p-Akt. These effects were abolished by pharmacological or genetic inhibitors of TPr. HG/U46619-induced suppressions of eNOS and Akt phosphorylation were accompanied by upregulation of PTEN and Ser380/Thr382/383 PTEN phosphorylation. PTEN-specific siRNA restored Akt-eNOS signaling in the face of TPr activation or HG. The small GTPase, Rho, was also activated by HG stimulation, and pretreatment of HBMECs with Y27632, a Rho-associated kinase (ROCK) inhibitor, rescued HG-impaired Akt-eNOS signaling. In STZ-injected rats, we found that hyperglycemia dramatically increased the levels of PTEN and PTEN-Ser380/Thr382/383 phosphorylation, reduced both levels of p-eNOS and p-Akt, and disrupted BBB function assayed by Evans blue staining, which were abolished by SQ29548 treatment. We conclude that hyperglycemia activates thromboxane A2 receptor to impair the integrity and function of blood-brain barrier via the ROCK-PTEN-Akt-eNOS pathway.
Social Robots for Engagement in Rehabilitative Therapies: Design Implications from a Study with Therapists

In this paper we present the results of a qualitative study with therapists to inform social robotics and human robot interaction (HRI) for engagement in rehabilitative therapies. Our results add to growing evidence that socially assistive robots (SARs) could play a role in addressing patients’ low engagement with self-directed exercise programmes. Specifically, we propose how SARs might augment or offer more pro-active assistance over existing technologies such as smartphone applications, computer software and fitness trackers also designed to tackle this issue. In addition, we present a series of design implications for such SARs based on therapists’ expert knowledge and best practices extracted from our results. This includes an initial set of SAR requirements and key considerations concerning personalised and adaptive interaction strategies.
Doubly selective channel estimation for OFDM systems

We propose a new pilot-aided algorithm for estimating doubly selective fading channels in OFDM systems. Our approach is valid for time varying channel, which occur for example, in mobile WiMAX and DVB-T. For time invariant channels, our scheme yields perfect estimates. The proposed algorithm is based on the principle of basis expansion and relies on Legendre polynomials as bases functions. We are using the block-type pilot structure in our algorithm, in which a complete OFDM symbol is dedicated to pilots before transmitting the data symbols, which my vary in number according to channel conditions. Numerical simulations illustrate the gain in the performance, bandwidth, power efficiency, and complexity gains achieved by our schemes at high Doppler frequencies. Our approach does not require any prior statistical channel information.
Optimizing Bayesian Information Revelation Strategy in Prediction Markets: the Alice Bob Alice Case

Prediction markets provide a unique and compelling way to sell and aggregate information, yet a good understanding of optimal strategies for agents participating in such markets remains elusive. To model this complex setting, prior work proposes a three stages game called the Alice Bob Alice (A-B-A) game - Alice participates in the market first, then Bob joins, and then Alice has a chance to participate again. While prior work has made progress in classifying the optimal strategy for certain interesting edge cases, it remained an open question to calculate Alice's best strategy in the A-B-A game for a general information structure. In this paper, we analyze the A-B-A game for a general information structure and (1) show a "revelation-principle" style result: it is enough for Alice to use her private signal space as her announced signal space, that is, Alice cannot gain more by revealing her information more "finely"; (2) provide a FPTAS to compute the optimal information revelation strategy with additive error when Alice's information is a signal from a constant-sized set; (3) show that sometimes it is better for Alice to reveal partial information in the first stage even if Alice's information is a single binary bit.
Understanding the Loss Surface of Neural Networks for Binary Classification

It is widely conjectured that the reason that training algorithms for neural networks are successful because all local minima lead to similar performance, for example, see (LeCun et al., 2015, Choromanska et al., 2015, Dauphin et al., 2014). Performance is typically measured in terms of two metrics: training performance and generalization performance. Here we focus on the training performance of single-layered neural networks for binary classification, and provide conditions under which the training error is zero at all local minima of a smooth hinge loss function. Our conditions are roughly in the following form: the neurons have to be strictly convex and the surrogate loss function should be a smooth version of hinge loss. We also provide counterexamples to show that when the loss function is replaced with quadratic loss or logistic loss, the result may not hold.
Genome–wide association study of carcass weight in commercial Hanwoo cattle

Objective The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. Methods Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10−6 (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. Results By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. Conclusion This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.
Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)‐based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut‐off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field‐collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU‐based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field‐based studies.
Griffin: A Tool for Symbolic Inference of Synchronous Boolean Molecular Networks

Boolean networks are important models of biochemical systems, located at the high end of the abstraction spectrum. A number of Boolean gene networks have been inferred following essentially the same method. Such a method first considers experimental data for a typically underdetermined “regulation” graph. Next, Boolean networks are inferred by using biological constraints to narrow the search space, such as a desired set of (fixed-point or cyclic) attractors. We describe Griffin, a computer tool enhancing this method. Griffin incorporates a number of well-established algorithms, such as Dubrova and Teslenko's algorithm for finding attractors in synchronous Boolean networks. In addition, a formal definition of regulation allows Griffin to employ “symbolic” techniques, able to represent both large sets of network states and Boolean constraints. We observe that when the set of attractors is required to be an exact set, prohibiting additional attractors, a naive Boolean coding of this constraint may be unfeasible. Such cases may be intractable even with symbolic methods, as the number of Boolean constraints may be astronomically large. To overcome this problem, we employ an Artificial Intelligence technique known as “clause learning” considerably increasing Griffin's scalability. Without clause learning only toy examples prohibiting additional attractors are solvable: only one out of seven queries reported here is answered. With clause learning, by contrast, all seven queries are answered. We illustrate Griffin with three case studies drawn from the Arabidopsis thaliana literature. Griffin is available at: http://turing.iimas. unam.mx/griffin.