Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characterization of avian reovirus causing tenosynovitis outbreaks in broiler flocks, Iran

ABSTRACT Avian reoviruses (ARVs) cause arthritis, tenosynovitis, retarded growth, and malabsorption syndrome. After a long time of effective prevention and low rates of viral arthritis/ tenosynovitis in Iran, outbreaks of tenosynovitis in broiler flocks have increased in recent years. Lameness, splay legs, high rate of cull birds, poor performance, uneven birds at harvest, and condemnation at processing cause huge economic losses. In this study, ARVs from the tendons of birds from 23 broiler flocks with marked tenosynovitis were characterized, and their genetic relationship was examined. Analysis of the amino acid sequence of Sigma C protein revealed that all ARVs detected in affected broiler flocks shared genetic homogeneity and this suggests that a single genotype is involved in recent outbreaks. This genotype, so-called “Ardehal strain”, is grouped in cluster I with vaccine strains. The amino acid sequence similarity between Ardehal and vaccine strains, including S1133, 1733, and 2408 was less than 80%. As the outbreaks have occurred in progenies of vaccinated flocks, it is proposed here that the difference between vaccine and field strains might contribute to the failure of currently available vaccines to induce protective immunity against Ardehal strain and this led to widespread viral tenosynovitis in Iran.
A requirement of Polo-like kinase 1 in murine embryonic myogenesis and adult muscle regeneration

Muscle development and regeneration require delicate cell cycle regulation of embryonic myoblasts and adult muscle satellite cells (MuSCs). Through analysis of the Polo-like kinase (Plk) family cell-cycle regulators in mice, we show that Plk1’s expression closely mirrors myoblast dynamics during embryonic and postnatal myogenesis. Cell-specific deletion of Plk1 in embryonic myoblasts leads to depletion of myoblasts, developmental failure and prenatal lethality. Postnatal deletion of Plk1 in MuSCs does not perturb their quiescence but depletes activated MuSCs as they enter the cell cycle, leading to regenerative failure. The Plk1-null MuSCs are arrested at the M-phase, accumulate DNA damage, and apoptose. Mechanistically, Plk1 deletion upregulates p53, and inhibition of p53 promotes survival of the Plk1-null myoblasts. Pharmacological inhibition of Plk1 similarly inhibits proliferation but promotes differentiation of myoblasts in vitro, and blocks muscle regeneration in vivo. These results reveal for the first time an indispensable role of Plk1 in developmental and regenerative myogenesis.
The Fluctuating Cell-Specific Light Environment and Its Effects on Cyanobacterial Physiology1[OPEN]

Dynamic and rapid changes in light during growth in a photobioreactor do not induce nonphotochemical quenching; however, alternative electron transport is a major sink for reductant. Individual cells of cyanobacteria or algae are supplied with light in a highly irregular fashion when grown in industrial-scale photobioreactors (PBRs). These conditions coincide with significant reductions in growth rate compared to the static light environments commonly used in laboratory experiments. We grew a dense culture of the model cyanobacterium Synechocystis sp. PCC 6803 under a sinusoidal light regime in a bench-top PBR (the Phenometrics environmental PBR [ePBR]). We developed a computational fluid dynamics model of the ePBR, which predicted that individual cells experienced rapid fluctuations (∼6 s) between 2,000 and <1 µmol photons m−2 s−1, caused by vertical mixing and self-shading. The daily average light exposure of a single cell was 180 µmol photons m−2 s−1. Physiological measurements across the day showed no in situ occurrence of nonphotochemical quenching, and there was no significant photoinhibition. An ex situ experiment showed that up to 50% of electrons derived from PSII were diverted to alternative electron transport in a rapidly changing light environment modeled after the ePBR. Collectively, our results suggest that modification of nonphotochemical quenching may not increase cyanobacterial productivity in PBRs with rapidly changing light. Instead, tuning the rate of alternative electron transport and increasing the processing rates of electrons downstream of PSI are potential avenues to enhance productivity. The approach presented here could be used as a template to investigate the photophysiology of any aquatic photoautotroph in a natural or industrially relevant mixing regime.
Implementation of support vector machine for classification of speech marked hijaiyah letters based on Mel frequency cepstrum coefficient feature extraction

Support Vector Machine or commonly called SVM is one method that can be used to process the classification of a data. SVM classifies data from 2 different classes with hyperplane. In this study, the system was built using SVM to develop Arabic Speech Recognition. In the development of the system, there are 2 kinds of speakers that have been tested that is dependent speakers and independent speakers. The results from this system is an accuracy of 85.32% for speaker dependent and 61.16% for independent speakers.
Early Fibrinogen Depletion and Symptomatic Intracranial Hemorrhage After Reperfusion Therapy.

Background and Purpose- We aimed to thoroughly investigate the relationship between early fibrinogen depletion and symptomatic intracranial hemorrhage (sICH) in patients receiving reperfusion therapy including intravenous thrombolysis (IVT) with or without endovascular thrombectomy (EVT). Methods- This study included 1135 stroke patients with baseline and follow-up fibrinogen levels at 2 hours after the beginning of alteplase infusion for those with IVT only or immediately after the end of EVT for those with combined IVT and EVT. Patients received alteplase up to 9 hours after the onset or on awakening based on automated perfusion imaging. sICH was ascertained using ECASS II (The Second European-Australasian Acute Stroke Study) criteria. Δfibrinogen was calculated as follow-up fibrinogen minus baseline fibrinogen. Results- In patients with IVT only, baseline fibrinogen level was 3.36±0.94 g/L and decreased to 2.47±0.80 g/L at 2 hours after the beginning of alteplase infusion. In patients with IVT followed by EVT, baseline fibrinogen level was 3.35±0.82 g/L and decreased to 2.52±0.83 g/L immediately after the end of EVT. sICH was observed in 44 (3.9%) patients. The extent of Δfibrinogen was associated with sICH in patients with IVT only (odds ratio, 1.929; 95% CI, 1.402-2.654; P<0.001) and in those with IVT followed by EVT (odds ratio, 1.765; 95% CI, 1.135-2.743; P=0.012). Conclusions- An early decrease in fibrinogen levels was related to sICH after reperfusion therapy with alteplase. More fibrin-specific thrombolytic agents are warranted to be tested in acute ischemic stroke patients. Clinical Trial Registration- URL: https://www.clinicaltrials. gov. Unique identifier: NCT03367286.
Low‐Cost Fetal Magnetocardiography: A Comparison of Superconducting Quantum Interference Device and Optically Pumped Magnetometers

Background Fetal magnetocardiography (fMCG) is a highly effective technique for evaluation of fetuses with life‐threatening arrhythmia, but its dissemination has been constrained by the high cost and complexity of Superconducting Quantum Interference Device (SQUID) instrumentation. Optically pumped magnetometers (OPMs) are a promising new technology that can replace SQUIDs for many applications. This study compares the performance of an fMCG system, utilizing OPMs operating in a person‐sized magnetic shield, to that of a conventional fMCG system, utilizing SQUID magnetometers operating in a magnetically shielded room. Methods and Results fMCG recordings were made in 24 subjects using the SQUID system with the mother lying supine in a magnetically shielded room and the OPM system with the mother lying prone in a person‐sized, cylindrical shield. Signal‐to‐noise ratios of the OPM and SQUID recordings were not statistically different and were adequate for diagnostic purposes with both technologies. Although the environmental noise was higher using the small open‐ended shield, this was offset by the higher signal amplitude achieved with prone positioning, which reduced the distance between the fetus and sensors and improved patient comfort. In several subjects, fMCG provided a differential diagnosis that was more precise and/or definitive than was possible with echocardiography alone. Conclusions The OPM‐based system was portable, improved patient comfort, and performed as well as the SQUID‐based system at a small fraction of the cost. Electrophysiological assessment of fetal rhythm is now practical and will have a major impact on management of fetuses with long QT syndrome and other life‐threatening arrhythmias.
Semaphorin-3A, semaphorin-7A gene single nucleotide polymorphisms, and systemic lupus erythematosus susceptibility

Abstract Background: Semaphorin-3A (Sema3A) and Semaphorin-7A (Sema7A) play crucial roles in immune system by inhibiting T cell proliferation and leading to the secretion of pro-inflammatory cytokines. Increasing evidence suggest that Sema3A and Sema7A may link to the development and pathogenesis of systemic lupus erythematosus (SLE). Objective: This study aims to evaluate the association of Sema3A, Sema7A gene single-nucleotide polymorphisms (SNPs) with susceptibility to SLE. Methods: There were 495 SLE patients and 493 healthy controls in the study. Sema3A gene and Sema7A gene were genotyped by improved multiple ligase detection reaction (iMLDR), their plasma expression levels were detected by enzyme-linked immunosorbent assay (ELISA). Results: No differences in genotype and allele frequencies of these SNPs were observed between SLE patients and healthy controls. However, analysing Sema3A and Sema7A SNPs with clinical manifestations of SLE indicated that, in Sema3A, the A allele frequencies of rs7804122 polymorphism was higher in patients with oral ulcers. In Sema7A, there were differences in allele frequencies of the rs2075589 and rs28362930 polymorphisms between SLE patients with haematological disorder and those without. The GG genotype and G allele frequencies of rs28362930 and the CC genotype, and C allele frequencies of rs741761 were both related to discoid rash in SLE patients. The allele frequency of G (rs28362930) was higher in SLE patients with renal disorder. There were differences in the genotype frequencies and allele frequencies of rs741761 between SLE patients with and without arthritis. No differences in plasma Sema3A and Sema7A levels were detected in SLE patients of different genotypes. Conclusions: Sema3A and Sema7A gene polymorphisms are not related to SLE genetic susceptibility, but may link to several clinical features of SLE.
Advanced Photocatalysts Based on Reduced Nanographene Oxide–TiO2 Photonic Crystal Films

Surface functionalization of TiO2 inverse opals by graphene oxide nanocolloids (nanoGO) presents a promising modification for the development of advanced photocatalysts that combine slow photon-assisted light harvesting, surface area, and mass transport of macroporous photonic structures with the enhanced adsorption capability, surface reactivity, and charge separation of GO nanosheets. In this work, post-thermal reduction of nanoGO–TiO2 inverse opals was investigated in order to explore the role of interfacial electron transfer vs. pollutant adsorption and improve their photocatalytic activity. Photonic band gap-engineered TiO2 inverse opals were fabricated by the coassembly technique and were functionalized by GO nanosheets and reduced under He at 200 and 500 °C. Comparative performance evaluation of the nanoGO–TiO2 films on methylene blue photodegradation under UV-VIS and visible light showed that thermal reduction at 200 °C, in synergy with slow photon effects, improved the photocatalytic reaction rate despite the loss of nanoGO and oxygen functional groups, pointing to enhanced charge separation. This was further supported by photoluminescence spectroscopy and salicylic acid UV-VIS photodegradation, where, in the absence of photonic effects, the photocatalytic activity increased, confirming that fine-tuning of interfacial coupling between TiO2 and reduced nanoGO is a key factor for the development of highly efficient photocatalytic films.
Highly Sensitive Temperature and Humidity Sensor Based on Carbon Nanotube-Assisted Mismatched Single-Mode Fiber Structure

Here we report on a miniaturized optical interferometer in one fiber based on two mismatched nodes. The all-fiber structure shows stable performance of temperature and humidity sensing. For temperature sensing in large ranges, from 40 to 100 °C, the sensor has a sensitivity of 0.24 dB/°C, and the adjusted R-squared value of fitting result reaches 0.99461 which shows a reliable sensing result. With carbon nanotubes coating the surface of the fiber, the temperature sensitivity is enhanced from 0.24561 to 1.65282 dB/°C in a small region, and the performance of humidity sensing becomes more linear and applicable. The adjusted R-squared value of the linear fitting line for humidity sensing shows a dramatic increase from 0.71731 to 0.92278 after carbon nanotube coating, and the humidity sensitivity presents 0.02571 nm/%RH.
Episodic Memory in Minicolumn Associative Knowledge Graphs

A generalization of active neural associative knowledge graphs (ANAKGs) to their minicolumn form is presented in this paper. Each minicolumn represents a single symbol, and the activation of an individual neuron in a minicolumn depends on the context of the activation of the presynaptic neuron. The implemented memory model combines the ANAKG associative spiking neuron idea with the idea of the hierarchical temporal memory. This new associative memory organization preserves all properties of ANAKG memories, such as storage of knowledge based on the association of spatiotemporal input sequences, self-organization, quick learning, and recall of the sequential memories, while increasing the recall quality and the memory capacity. The recall quality advantage of the new approach over ANAKG increases with the length of the recalled episodes and the number of neurons used in each minicolumn. We introduced a new distance measure to compare the recalled sequences and defined a recall quality to determine the memory capacity. Performed tests confirmed our claims. Additional tests were performed to illustrate the computational complexity and the efficiency of the developed approach.
12-Month stability of neurological soft signs in stabilized patients with schizophrenia

Abstract Objective: Neurological soft signs (NSS) are a group of minor non-localizable neurological abnormalities found more often in patients with schizophrenia. The aim of the current study was to investigate their temporal stability and relationship to the overall outcome over a 12-month period. Material and methods: The study sample included 133 stabilized patients suffering from schizophrenia (77 males and 56 females; aged 33.55 ± 11.22 years old). The assessment included the application at baseline and after 12 months of the Neurological Evaluation Scale (NES), and a number of scales assessing the clinical symptoms and adverse effects. The statistical analysis included ANOVA, exploratory t-test and Pearson correlation coefficients with Bonferroni correction. Results: In stabilized patients, NSS are stable over a 12-month period with only the subscale of NES-sensory integration manifesting a significant worsening, while, in contrast, most of the clinical variables improved significantly. There was no relationship of NES scores with the magnitude of improvement. The only significant negative correlation was between NES-motor coordination and Positive and Negative Syndrome Scale-GP change at 1 year. Discussion: The results of the current study suggest that after stabilization of patients with schizophrenia, there are probably two separate components, a ‘trait’ which is stable over a 12-month period, and a ‘degenerative’ component with a tendency to worsen probably in parallel with the progression of the illness and in correlation with the worsening of negative symptoms. However, the statistical support of the ‘degenerative’ component is weak. Significant outcomes Neurological softs signs are stable over a 12-month period, with the exception of ‘sensory integration’ which manifests significant improvement irrespective of treatment response. They do not respond to treatment with antipsychotics. They do not constitute a prognostic factor to predict improvement over a period of 1 year. Neurological soft signs constitute a trait symptom of schizophrenia which is stable though time. Limitations All the subjects have been previously hospitalized which may represent a more severe form of schizophrenia. Also, all patients were under antipsychotic and some also under benzodiazepine medications. Patients with comorbid somatic disorders were excluded which may decrease generalizability of results.
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations

Molecular recognition underpins all specific protein-ligand interactions and is essential for biomolecular functions. Prediction of canonical binding poses and distinguishing binders from non-binders are much sought after goals. Here, we apply the generalized replica exchange with solute tempering method, gREST, combined with a flat-bottom potential to evaluate binder and non-binder interaction with T4 lysozyme L99A mutant. The buried hydrophobic cavity and possibility of coupled conformational changes in this protein make binding predictions difficult. The present gREST simulations, enabling enhanced flexibilities of the ligand and protein residues near the binding site, sample bindings in multiple poses and correctly portray X-ray structures. The free-energy profiles of binders (benzene, ethylbenzene, and n-hexylbenzene) are distinct from those of non-binders (phenol and benzaldehyde). Bindings of the two larger molecules seem to be associated with a structural change toward an excited conformation of the protein, which agrees with experimental findings. The protocol is generally applicable to various proteins having buried cavities with limited access for ligands with different shapes, sizes and chemical properties.
Generalized Dynamic Analytical Model of Piezoelectric Materials for Characterization Using Electrical Impedance Spectroscopy

Piezoelectric materials have the intrinsic reversible ability to convert a mechanical strain into an electric field and their applications touch our daily lives. However, the complex physical mechanisms linking mechanical and electrical properties make these materials hard to understand. Computationally onerous models have historically been unable to adequately describe dynamic phenomena inside real piezoelectric materials, and are often limited to over-simplified first-order analytical, quasi-static, or unsatisfying phenomenological numerical approaches. We present a generalized dynamic analytical model based on first-principles that is efficiently computable and better describes these exciting materials, including higher-order coupling effects. We illustrate the significance of this model by applying it to the important 3m crystal symmetry class of piezoelectric materials that includes lithium niobate, and show that the model accurately predicts the experimentally observed impedance spectrum. This dynamic behavior is a function of almost all intrinsic properties of the piezoelectric material, so that material properties, including mechanical, electrical, and dielectric coefficients, can be readily and simultaneously extracted for any size crystal, including at the nanoscale; the only prior knowledge required is the crystal class of the material system. In addition, the model’s analytical approach is general in nature, and can increase our understanding of traditional and novel ferroelectric and piezoelectric materials, regardless of crystal size or orientation.
The Pebble Game

References: [1] Hopcroft, J.; Paul, W. ; Valiant, L. , On time versus space, J. ACM, 24, 332-337, (1977) · Zbl 0358.68082 [2] Lengauer, T. ; Tarjan, R.E. , Upper and lower bounds on time-space tradeoffs, Proc. 11th annual ACM symposium on theory of computing, 262-277, (1979) [3] Paterson, M.S.; Fischer, M.J.; Meyer, A.R. , An improved overlap argument for on-line multiplication, (), 97-111 [4] Paul, W.J.; Tarjan, R.E. ; Celoni, J.R. , Space bounds for a game on graphs, Math. systems theory, 10, 239-251, (1977) · Zbl 0366.90150 [5] Pippenger, N. , A time-space trade-off, J. ACM, 25, 509-515, (1978) · Zbl 0379.68009 This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.
Biological Response to Macroporous Chitosan-Agarose Bone Scaffolds Comprising Mg- and Zn-Doped Nano-Hydroxyapatite

Modification of implantable scaffolds with magnesium and zinc for improvement of bone regeneration is a growing trend in the engineering of biomaterials. The aim of this study was to synthesize nano-hydroxyapatite substituted with magnesium (Mg2+) (HA-Mg) and zinc (Zn2+) (HA-Zn) ions in order to fabricate chitosan-agarose-hydroxyapatite (HA) scaffolds (chit/aga/HA) with improved biocompatibility. Fabricated biomaterials containing Mg2+ or Zn2+ were tested using osteoblasts and mesenchymal stem cells to determine the effect of incorporated metal ions on cell adhesion, spreading, proliferation, and osteogenic differentiation. The study was conducted in direct contact with the scaffolds (cells were seeded onto the biomaterials) and using fluid extracts of the materials. It demonstrated that incorporation of Mg2+ ions into chit/aga/HA structure increased spreading of the osteoblasts, promoted cell proliferation on the scaffold surface, and enhanced osteocalcin production by mesenchymal stem cells. Although biomaterial containing Zn2+ did not improve cell proliferation, it did enhance type I collagen production by mesenchymal stem cells and extracellular matrix mineralization as compared to cells cultured in a polystyrene well. Nevertheless, scaffolds made of pure HA gave better results than material with Zn2+. Results of the experiments clearly showed that modification of the chit/aga/HA scaffold with Zn2+ did not have any positive impact on cell behavior, whereas, incorporation of Mg2+ ions into its structure may significantly improve biocompatibility of the resultant material, increasing its potential in biomedical applications.