Miracle-dz/UniFAR-FTUs huggingface dataset:
Numerical Simulation Study on Flow Field Microenvironment of Chondrocytes in Articular Cartilage Defect Repair Area

Multi-scale numerical simulation was used to study the change of flow field microenvironment of chondrocytes after repair of cartilage defects. A solid-liquid coupling biphasic finite element model for articular cartilage and finite element micro-model for chondrocyte were established, using coupling variables to establish consistent boundary conditions between macroscopic models for cartilage and microscopic models for chondrocytes. After defect repair, the flow field of chondron and extracellular matrix in the middle layer changed significantly under cyclic compression loading, and it was also influenced by the properties of tissue-engineered cartilage. The flow velocity of chondron and extracellular matrix in middle layer increased, and the flow velocity of chondron and extracellular matrix in deep layer increased changed little. When the elastic modulus of TEC was 0.3 MPa, the flow field microenvironment was closer to the intact cartilage. The finite element method make up for the lack of the current technical means to measure the microscopic mechanical environment of chondrocytes in vivo. It has some guiding significance for the study of the mechanism of the effect of biomechanical factors on chondrocytes and the prevention and treatment of cartilage diseases.
Heck Transformations of Biological Compounds Catalyzed by Phosphine-Free Palladium

The development and optimization of synthetic methods leading to functionalized biologically active compounds is described. Two alternative pathways based on Heck-type reactions, employing iodobenzene or phenylboronic acid, were elaborated for the arylation of eugenol and estragole. Cinnamyl alcohol was efficiently transformed to saturated arylated aldehydes in reaction with iodobenzene using the tandem arylation/isomerization sequential process. The arylation of cinnamyl alcohol with phenylboronic acid mainly gave unsaturated alcohol, while the yield of saturated aldehyde was much lower. Catalytic reactions were carried out using simple, phosphine-free palladium precursors and water as a cosolvent, following green chemistry rules as much as possible.
Measuring Thiols in Single Cultivar South African Red Wines Using 4,4-Dithiodipyridine (DTDP) Derivatization and Ultraperformance Convergence Chromatography-Tandem Mass Spectrometry

Wine varietal thiols are important contributors to wine aroma. The chemical nature of thiols makes them difficult to measure due to low concentrations, high sensitivity to oxidation, and low ionization. Methods for the measurement of thiols usually consist of multiple steps of sample preparation followed by instrumental measurement. Studies have collected large datasets of thiols in white wine but not in red wine, due to the lack of availability of suitable methods. In this study, for the first time, convergence chromatography was used to measure thiols in red wine at ultratrace levels with improved sensitivity compared to previous methods. Performance parameters (selectivity, linearity, limits of detection, precision, accuracy) were tested to demonstrate the suitability of the method for the proposed application. Red wine thiols were measured in South African Pinotage, Shiraz, and Cabernet Sauvignon wines (n = 16 each). Cultivar differentiation using the thiol profile was demonstrated.
Using concurrent gait and cognitive assessments to identify impairments after concussion: a narrative review

Understanding how a concussion affects an individual is oftentimes difficult for clinicians due to the varying symptom profiles reported by the patient and the multifaceted and heterogeneous nature of the injury. Accordingly, the interpretation of postconcussion performance can be challenging, because many different testing paradigms have been reported as potentially useful in the literature. Among the types of tests clinicians use to understand how concussion affects an individual, both gait and neurocognitive evaluations have demonstrated utility. Our purpose is to describe how combined gait and cognitive (i.e., dual task), as well as single-task gait and computerized neurocognitive examinations can assist clinical decision-making.
Nature of Long-Range Evolutionary Constraint in Enzymes: Insights from Comparison to Pseudoenzymes with Similar Structures

Enzymes are known to fine-tune their sequences to optimize catalytic function, yet quantitative evolutionary design principles of enzymes remain elusive on the proteomic scale. Recently, it was found that the catalytic site in enzymes induces long-range evolutionary constraint, where even sites distant to the catalytic site are more conserved than expected. Given that protein-fold usage is generally different between enzymes and nonenzymes, it remains an open question to what extent this long-range evolutionary constraint in enzymes is dictated, either directly or indirectly, by the special three-dimensional structure of the enzyme. To investigate this question, we have compared evolutionary properties of enzymes with those of counterpart pseudoenzymes that share the same protein fold but are catalytically inactive. We found that the long-range evolutionary constraint observed in enzymes is significantly reduced in pseudoenzyme counterparts, despite very high structural similarity (∼1.5 Å RMSD on average). Furthermore, this significant reduction in long-range evolutionary constraint is observed even in pseudoenzyme counterparts which retain the ligand-binding ability of enzymes. Finally, the distance between the site that induces the highest gradient of sequence conservation and the pseudocatalytic site in pseudoenzymes is significantly larger than the corresponding distance in enzymes. Taken together, our results suggest that the long-range evolutionary constraint in enzymes is induced mainly by the presence of the catalytic site rather than by the special three-dimensional structure of the enzyme, and that such long-range evolutionary constraint in enzymes depends mainly on the catalytic function of the active site rather than on the ligand-binding ability of the enzyme.
Association of Asthma and Allergic Rhinitis With Sleep-Disordered Breathing in Childhood

Objective: Asthma and allergic rhinitis (AR) are the most common chronic conditions in childhood and have previously been linked to sleep-related breathing disorder (SRBD). Aim of the study was to examine the association between SRBD risk and asthma control in children with asthma and with or without AR. Methods: The assessment of FeNO and pulmonary function tests were performed in 140 children (65 with asthma, 57 with both asthma, and AR, 18 with only AR). Children with asthma completed the childhood Asthma Control Test (c-ACT), and the Sleep-Related Breathing Disorder scale, extracted from the Pediatric Sleep Questionnaire (PSQ). C-ACT scores ≤ 19 are indicative of poor asthma control whereas SRBD from PSQ scores ≥ 0.33 are suggestive of high risk for SRBD. Results: Mean age ± SD was 7.8 ± 3.1 years. Mean PSQ ± SD and c-ACT ± SD scores were 0.17 ± 0.14 and 24.9 ± 3.2, respectively. High risk for SRBD was identified in 26 children. Children at high risk for SRBD had significantly decreased c-ACT score (P = 0.048), verified by a negative association between c-ACT and PSQ-SRBD scores (r = −0.356, P < 0.001). Additionally a difference in diagnosis distribution between children at high or low risk for SRBD was observed. More specifically, among children at high risk, 88.5% were diagnosed with both atopic conditions, while this percentage among children at low risk was 29.8%. Asthma was mainly diagnosed in the latter group (P < 0.001). Conclusions: Poor asthma control is associated with SRBD. The presence of AR in children with asthma seems to increase the prevalence of SRBD in that particular population, requiring further investigation toward this direction.
Chorioamnionitis Is a Risk Factor for Intraventricular Hemorrhage in Preterm Infants: A Systematic Review and Meta-Analysis

Although chorioamnionitis (CA) is a well-known risk factor for white matter disease of prematurity, the association with intraventricular hemorrhage (IVH) is controversial and has not been yet systematically reviewed. We performed a systematic review and meta-analysis of studies exploring the association between CA and IVH. A comprehensive literature search was conducted using PubMed/MEDLINE and EMBASE, from their inception to 1 July 2017. Studies were included if they examined preterm infants and reported primary data that could be used to measure the association between exposure to CA and the presence of IVH. A random-effects model was used to calculate odds ratios (OR) and 95% confidence intervals (CI). We found 1284 potentially relevant studies, of which 85 met the inclusion criteria (46,244 infants, 13,432 CA cases). Meta-analysis showed that CA exposure was significantly associated with all grades IVH (OR 1.88, 95% CI 1.61-2.19), with grades 1-2 IVH (OR 1.69, 95% CI 1.22-2.34), and with grades 3-4 IVH (OR 1.62, 95% CI 1.42-1.85). Both clinical and histological CA were associated with an increased risk for developing IVH in very preterm infants. In contrast, the presence of funisitis did not increase IVH risk when compared to CA in the absence of funisitis (OR 1.22, 95% CI 0.89-1.67). Further meta-analyses confirmed earlier findings that CA-exposed infants have significantly lower gestation age (GA; mean difference [MD] −1.20 weeks) and lower birth weight (BW; MD −55g) than the infants not exposed to CA. However, meta-regression and subgroup analysis could not demonstrate an association between the lower GA and BW and the risk of IVH in the CA-exposed infants. In conclusion, our data show that CA is a risk factor for IVH, but also a risk factor for greater prematurity and more clinical instability. In contrast to other complications of prematurity, such as patent ductus arteriosus, retinopathy of prematurity, or bronchopulmonary dysplasia, the effect of CA on IVH appears to be independent of CA as causative factor for very preterm birth.
VPR 5.0: FPGA cad and architecture exploration tools with single-driver routing, heterogeneity and process scaling

The VPR toolset [6, 7] has been widely used to perform FPGA architecture and CAD research, but has not evolved over the past decade to include many architectural features now present in modern FPGAs. This paper describes a new version of the toolset that includes four significant features: first, it now supports a broad range of single-driver routing architectures [29, 4, 16]. Single-driver routing has significantly different architectural and electrical properties from the multi-driver approach previously modelled, and is now employed in the majority of FPGAs sold. Second, the new release can now model a heterogeneous selection of hard logic blocks, which could include the hard memory and multipliers that are now ubiquitous in FPGAs. Third, we provide optimized electrical models of a wide range of architectures in different process technologies, including a range of area-delay tradeoffs for each single architecture. Prior releases of VPR did not publish even one architecture file with accurate resistance and capacitance parameters. Finally, to maintain robustness and to support future development the release includes a set of regression tests to check functionality and quality of result of the output of the tools. To illustrate the use of the new features, we present a new look at the FPGA area vs. logic block LUT size question that shows that small LUT sizes, with the use of carefully optimized electrical design and single-driver architectures, have better area (relative to 4-LUTs) than previously thought. Another experiment shows that several of the previous architectural results are invariant in moving from multi-driver to single-driver routing architecture and across a range of process technologies.
Synthetic Polymer Contamination in Bottled Water

Eleven globally sourced brands of bottled water, purchased in 19 locations in nine different countries, were tested for microplastic contamination using Nile Red tagging. Of the 259 total bottles processed, 93% showed some sign of microplastic contamination. After accounting for possible background (lab) contamination, an average of 10.4 microplastic particles >100 um in size per liter of bottled water processed were found. Fragments were the most common morphology (66%) followed by fibers. Half of these particles were confirmed to be polymeric in nature using FTIR spectroscopy with polypropylene being the most common polymer type (54%), which matches a common plastic used for the manufacture of bottle caps. A small fraction of particles (4%) showed the presence of industrial lubricants. While spectroscopic analysis of particles smaller than 100 um was not possible, the adsorption of the Nile Red dye indicates that these particles are most probably plastic. Including these smaller particles (6.5–100 um), an average of 325 microplastic particles per liter of bottled water was found. Microplastic contamination range of 0 to over 10,000 microplastic particles per liter with 95% of particles being between 6.5 and 100 um in size. Data suggests the contamination is at least partially coming from the packaging and/or the bottling process itself. Given the prevalence of the consumption of bottled water across the globe, the results of this study support the need for further studies on the impacts of micro- and nano- plastics on human health.
Research on the Crushing Process of PELE Casing Material Based on the Crack-Softening Algorithm and Stochastic Failure Algorithm

In order to more realistically reflect the penetrating and crushing process of a PELE (Penetration with Enhanced Lateral Efficiency) projectile, the stochastic failure algorithm and crack-softening algorithm were added to the corresponding material in this paper. According to the theoretical analysis of the two algorithms, the material failure parameters (stochastic constant γ, fracture energy Gf, and tensile strength σT) were determined. Then, four sets of simulation conditions ((a) no crack softening, (b) no stochastic failure, (c) no crack softening and no stochastic failure, and (d) crack softening and stochastic failure) were designed to qualitatively describe the influences of the failure algorithms, which were simulated by the finite element analysis software AUTODYN. The qualitative comparison results indicate that the simulation results after adding the two algorithms were closer to the actual situation. Finally, ten groups of simulation conditions were designed to quantitatively analyze the coincidence degree between the simulation results and the experimental results by means of two parameters: the residual velocity of the projectile and the maximum radial velocity of fragments. The results show that the simulation results coincide well with the experimental results and the errors were small. Therefore, the ideas proposed in this paper are scientific, and the conclusions obtained can provide guidance for engineering research.
Supportive Care Needs in Glioma Patients and Their Caregivers in Clinical Practice: Results of a Multicenter Cross-Sectional Study

Objective: Supportive care needs in glioma patients often remain unrecognized, and optimization in assessment is required. First, we aimed at assessing the support needed using a simple structured questionnaire. Second, we investigated the psychosocial burden and support requested from caregivers. Methods: Patients were assessed at three centers during their outpatient visits. They completed the Distress Thermometer (DT; score ≥ 6 indicated significant burden in brain tumor patients), the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ)-C30+BN20, and the Patients' Perspective Questionnaire (PPQ) that assessed psychosocial distress as well as support requested and received by patients for specific domains (e.g., family, doctor, and mobile care). In each subgroup, patients' caregivers were assessed simultaneously by a questionnaire developed for the study. Multivariate backward logistic regressions were performed for investigating predictors of patients' request for support. Results: Assessments were conducted for 232 patients. Most patients (82%) had a high-grade glioma and a mean age of 52 years (range 20–87). The male to female ratio was 1.25:1. According to the PPQ results, 38% (87) of the patients felt depressed; 44% (103), anxious; and 39% (91), tense/nervous. Desired support was highest from doctors (59%) and psychologists (19%). A general request for support was associated with lower global health status (p = 0.03, odds ratio (OR) = 0.96, 95% CI: 0.92–0.99) according to EORTC QLQ-C30. Most of the assessed caregivers (n = 96) were life partners (64%; n = 61) who experienced higher distress than the corresponding patients (caregivers: 6.5 ± 2.5 vs. patients: 5.3 ± 2.4). When patients were on chemotherapy, caregivers indicated DT ≥ 6 significantly more frequently than patients themselves (p = 0.02). Conclusion: Our data showed that glioma patients and their caregivers were both highly burdened. The PPQ allowed us to evaluate the psychosocial support requested and perceived by patients, detect supportive care needs, and provide information at a glance. Patients in poorer clinical condition are at risk of having unmet needs. The caregivers' burden and unmet needs are not congruent with the patients' need for support. In particular, caregivers of patients on chemotherapy were more highly burdened than patients themselves.
Landscape Structures Affect Risk of Canine Distemper in Urban Wildlife

Urbanization rapidly changes landscape structure worldwide, thereby enlarging the human-wildlife interface. The emerging urban structures should have a key influence on the spread and distribution of wildlife diseases such as canine distemper, by shaping density, distribution and movements of wildlife. However, little is known about the role of urban structures as proxies for disease prevalence. To guide management, especially in densely populated cities, assessing the role of landscape structures in hampering or promoting disease prevalence is thus of paramount importance. Between 2008 and 2013, two epidemic waves of canine distemper hit the urban red fox (Vulpes vulpes) population of Berlin, Germany. The directly transmitted canine distemper virus (CDV) causes a virulent disease infecting a range of mammals with high host mortality, particularly in juveniles. We extracted information about CDV serological state (seropositive or seronegative), sex and age for 778 urban fox carcasses collected by the state laboratory Berlin Brandenburg. To assess the impact of urban landscape structure heterogeneity (e.g. richness) and shares of green and grey infrastructures at different spatial resolutions (areal of 28 ha, 78 ha, 314 ha) on seroprevalence we used Generalized Linear Mixed-Effects Models with binomial distributions. Our results indicated that predictors derived at a 28 ha resolution were most informative for describing landscape structures effects (AUC = 0.92). The probability to be seropositive decreased by 66% (0.6 to 0.2) with an increasing share of grey infrastructure (40 % to 80 %), suggesting that urbanization might hamper CDV spread in urban areas, owing to a decrease in host density (e.g. less foxes or raccoons) or an absence of wildlife movement corridors in strongly urbanized areas. However, less strongly transformed patches such as close-to-nature areas in direct proximity to water bodies were identified as high risk areas for CDV transmission. Therefore, surveillance and disease control actions targeting urban wildlife or human-wildlife interactions should focus on such areas. The possible underlying mechanisms may be increased isolation, the absence of alternative hosts or an abiotic environment, all impairing the ability of CDV to persist without a host.
An insight into gingival depigmentation techniques: The pros and cons

Pigmentation of gingiva not just has an impact on esthetics but also creates psychological negativity. Although a wide array of depigmentation techniques are available to manage this condition, there is a scarcity of literature that guides clinicians to choose the most appropriate technique. Hence, the aim of this review is to evaluate the available depigmentation therapeutic modalities with an emphasis on their merits and demerits. The databases of MEDLINE and Cochrane databases of systematic reviews were searched to collect relevant scientific literature. Cryosurgery followed by lasers has been reported to be the superior techniques with better esthetic results and low rate of recurrence. However, further randomized controlled longitudinal studies are warranted to elaborate the efficiency and effectiveness of available techniques.
Klebsiella grimontii, a New Species Acquired Carbapenem Resistance

Klebsiella grimontii is a newly identified species closely related to Klebsiella oxytoca, but carbapenem resistance was not identified in the species before. We found a carbapenem-resistant K. oxytoca-like clinical strain, WCHKG020121. The strain was subjected to whole genome sequencing using Illumina HiSeq X10. The precise species identification was established based on average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) between strain WCHKG020121 and type strains of Klebsiella species. Antimicrobial resistance genes were identified from the genome sequence. The sequence of the blaKPC-2-carrying plasmid was completed using PCR and Sanger sequencing. Conjugation experiments were performed to obtain the plasmid carrying blaKPC-2. All K. grimontii genomes were retrieved from GenBank and were analyzed for antimicrobial resistance genes. Strain WCHKG020121 was resistant to imipenem and meropenem (MIC for both, 32 μg/ml) but was susceptible to colistin (1 μg/ml). Strain WCHKG020121 was initially identified as K. oxytoca using Vitek II but it actually belongs to K. grimontii as it had a 98.81% ANI and 83.4% isDDH value with K. grimontii type strain. Strain WCHKG020121 had blaKPC-2; by contrast, none of other K. grimontii genomes carry any known carbapenemase genes. blaKPC-2 was carried by a 95,734-bp plasmid, designated pKPC2_020121, which contained two different FII(Y) replicons. pKPC2_020121 was closest (93% coverage, 99% identity) to blaKPC-2-carrying plasmids from Enterobacter hormaechei recovered in 2014 at the same hospital. pKPC2_020121 was not self-transmissible, which could be explained by the absence of a conjugation essential gene, traY. In conclusion, we reported the first K. grimontii strain that produced the KPC carbapenemase. Carbapenem resistant K. grimontii may represent a new threat.