Miracle-dz/UniFAR-FTUs huggingface dataset:
Finite-Time Synchronization of Neural Networks With Infinite Discrete Time-Varying Delays and Discontinuous Activations

This article investigates finite-time synchronization of neural networks (NNs) with infinite discrete time-varying delays and discontinuous activations (DDNNs). By virtue of theory of differential inclusions, comparison strategies, and inequality techniques, finite-time synchronization of the underlying DDNNs can be developed via a discontinuous state feedback control law, and the synchronous settling time can be estimated. The delayed state feedback controller and finite-time stability theorem are not employed during the analysis. As a special case, finite-time synchronization of NNs with bounded delays and discontinuous activations is given. Finally, two examples are provided to illustrate the validity of the theories.
Thrombolysis by PLAT/tPA increases serum free IGF1 leading to a decrease of deleterious autophagy following brain ischemia

ABSTRACT Cerebral ischemia is a pathology involving a cascade of cellular mechanisms, leading to the deregulation of proteostasis, including macroautophagy/autophagy, and finally to neuronal death. If it is now accepted that cerebral ischemia induces autophagy, the effect of thrombolysis/energy recovery on proteostasis remains unknown. Here, we investigated the effect of thrombolysis by PLAT/tPA (plasminogen activator, tissue) on autophagy and neuronal death. In two in vitro models of hypoxia reperfusion and an in vivo model of thromboembolic stroke with thrombolysis by PLAT/tPA, we found that ischemia enhances neuronal deleterious autophagy. Interestingly, PLAT/tPA decreases autophagy to mediate neuroprotection by modulating the PI3K-AKT-MTOR pathways both in vitro and in vivo. We identified IGF1R (insulin-like growth factor I receptor; a tyrosine kinase receptor) as the effective receptor and showed in vitro, in vivo and in human stroke patients and that PLAT/tPA is able to degrade IGFBP3 (insulin-like growth factor binding protein 3) to increase IGF1 (insulin-like growth factor 1) bioavailability and thus IGF1R activation. Abbreviations: AKT/protein kinase B: thymoma viral proto-oncogene 1; EGFR: epidermal growth factor receptor; Hx: hypoxia; IGF1: insulin-like growth factor 1; IGF1R: insulin-like growth factor I receptor; IGFBP3: insulin-like growth factor binding protein 3; Ka: Kainate; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/ERK: mitogen-activated protein kinase; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; OGD: oxygen and glucose deprivation; OGDreox: oxygen and glucose deprivation + reoxygentation; PepA: pepstatin A1; PI3K: phosphoinositide 3-kinase; PLAT/tPA: plasminogen activator, tissue; PPP: picropodophyllin; SCH77: SCH772984; ULK1: unc-51 like kinase 1; Wort: wortmannin
Neural mechanisms of pain processing differ between endurance athletes and nonathletes: A functional connectivity magnetic resonance imaging study

Pain perception and the ability to modulate arising pain vary tremendously between individuals. It has been shown that endurance athletes possess higher pain tolerance thresholds and a greater effect of conditioned pain modulation than nonathletes, both indicating a more efficient system of endogenous pain inhibition. The aim of the present study was to focus on the neural mechanisms of pain processing in endurance athletes that have not been investigated yet. Therefore, we analyzed the pain processing of 18 male athletes and 19 healthy male nonathletes using functional magnetic resonance imaging. We found lower pain ratings in endurance athletes compared to nonathletes to physically identical painful stimulation. Furthermore, brain activations of athletes versus nonathletes during painful heat stimulation revealed reduced activation in several brain regions that are typically activated by nociceptive stimulation. This included the thalamus, primary and secondary somatosensory cortex, insula, anterior cingulate cortex, midcingulate cortex, dorsolateral prefrontal cortex, and brain stem (BS). Functional connectivity analyses revealed stronger network during painful heat stimulation in athletes between the analyzed brain regions except for connections with the BS that showed reduced functional connectivity in athletes. Post hoc correlation analyses revealed associations of the subject's fitness level and the brain activation strengths, subject's fitness level and functional connectivity, and brain activation strengths and functional connectivity. Together, our results demonstrate for the first time that endurance athletes do not only differ in behavioral variables compared to nonathletes, but also in the neural processing of pain elicited by noxious heat.
A multiple-method comparative study using GC-MS, AMDIS and in-house-built software for the detection and identification of "unknown" volatile organic compounds in breath.

The human respiratory system is a highly complex matrix that exhales many volatile organic compounds (VOCs). Breath-exhaled VOCs are often "unknowns" and possess low concentrations, which make their analysis, peak digging and data processing challenging. We report a new methodology, applied in a proof-of-concept experiment, for the detection of VOCs in breath. For this purpose, we developed and compared four complementary analysis methods based on solid-phase microextraction and thermal desorption (TD) tubes with two GC-mass spectrometer (MS) methods. Using eight model compounds, we obtained an LOD range of 0.02-20 ng/ml. We found that in breath analysis, sampling the exhausted air from Tedlar bags is better when TD tubes are used, not only because of the preconcentration but also due to the stability of analytes in the TD tubes. Data processing (peak picking) was based on two data retrieval approaches with an in-house script written for comparison and differentiation between two populations: sick and healthy. We found it best to use "raw" AMDIS deconvolution data (.ELU) rather than its NIST (.FIN) identification data for comparison between samples. A successful demonstration of this method was conducted in a pilot study (n = 21) that took place in a closed hospital ward (Covid-19 ward) with the discovery of four potential markers. These preliminary findings, at the molecular level, demonstrate the capabilities of our method and can be applied in larger and more comprehensive experiments in the omics world.
Urticarial vasculitis: A potential signpost for multisystem inflammatory syndrome in children

Multisystem inflammatory syndrome in children (MIS‐C) is a rare and serious complication of Sars‐Cov‐2 infection. Dermatologic manifestations are present in the majority of patients. Skin lesions found in children with MIS‐C are classified into four categories: morbilliform, reticulated, scarlatiniform, and urticarial lesions. Clinicopathologic characterization within these categories is limited. Thus, we present a clear example of an urticarial lesion in the context of MIS‐C with well‐documented clinicopathologic phenomena. A previously healthy 16‐year‐old female presented with 3 weeks of an itchy, burning rash initially presenting on her right forearm (and lasting greater than 24 hours without migration) before spreading diffusely. She also reported fever, cough, myalgias, nausea, and vomiting of 4 weeks' duration. Physical examination revealed an edematous, maculopapular, nonblanching, erythematous rash covering the patient's upper extremities, abdomen, back, anterior thighs, and face. The patient tested positive for COVID‐19. A low‐grade leukocytoclastic vasculitis was noted along with intraluminal fibrin and rare microthrombi in vessels of the mid to deep dermis. The patient was diagnosed with MIS‐C and urticarial vasculitis. She was treated with steroids and naproxen for subsequent MIS‐C flares. Dapsone treatment was started for the urticarial vasculitis.
Clinically Relevant Influenza Virus Evolution Reconstituted in a Human Lung Airway-on-a-Chip

The rapid evolution of viruses, such as influenza viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is challenging the use and development of antivirals and vaccines. Studies of within-host viral evolution can contribute to our understanding of the evolutionary and epidemiological factors that shape viral global evolution as well as development of better antivirals and vaccines. ABSTRACT Human-to-human transmission of viruses, such as influenza viruses and coronaviruses, can promote virus evolution and the emergence of new strains with increased potential for creating pandemics. Clinical studies analyzing how a particular type of virus progressively evolves new traits, such as resistance to antiviral therapies, as a result of passing between different human hosts are difficult to carry out because of the complexity, scale, and cost of the challenge. Here, we demonstrate that spontaneous evolution of influenza A virus through both mutation and gene reassortment can be reconstituted in vitro by sequentially passaging infected mucus droplets between multiple human lung airway-on-a-chip microfluidic culture devices (airway chips). Modeling human-to-human transmission of influenza virus infection on chips in the continued presence of the antiviral drugs amantadine or oseltamivir led to the spontaneous emergence of clinically prevalent resistance mutations, and strains that were resistant to both drugs were identified when they were administered in combination. In contrast, we found that nafamostat, an inhibitor targeting host serine proteases, did not induce viral resistance. This human preclinical model may be useful for studying viral evolution in vitro and identifying potential influenza virus variants before they appear in human populations, thereby enabling preemptive design of new and more effective vaccines and therapeutics. IMPORTANCE The rapid evolution of viruses, such as influenza viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is challenging the use and development of antivirals and vaccines. Studies of within-host viral evolution can contribute to our understanding of the evolutionary and epidemiological factors that shape viral global evolution as well as development of better antivirals and vaccines. However, little is known about how viral evolution of resistance to antivirals occurs clinically due to the lack of preclinical models that can faithfully model influenza infection in humans. Our study shows that influenza viral evolution through mutation or gene reassortment can be recapitulated in a human lung airway-on-a-chip (airway chip) microfluidic culture device that can faithfully recapitulate the influenza infection in vitro. This approach is useful for studying within-host viral evolution, evaluating viral drug resistance, and identifying potential influenza virus variants before they appear in human populations, thereby enabling the preemptive design of new and more effective vaccines and therapeutics.
Attitude Matters! How Attitude towards Bariatric Surgery Influences the Effects of Behavioural Weight Loss Treatment

Introduction: Multidisciplinary obesity services at university hospitals usually treat patients with more complex and severe obesity. In addition, patients with Class 3 obesity, in particular, have different attitudes regarding the choices of therapy. Methods: This explorative study investigated the effect of patient attitudes towards bariatric surgery on body weight change (primary outcome) and psychological improvement (secondary outcomes: quality of life, depression, anxiety, and eating behaviour) in a 6-month moderate behavioural weight loss (BWL) programme in a university outpatient setting. Results: 297 patients with mostly Class 3 obesity participated in the programme. The patients did not yet have any indications for bariatric surgery. Of the participants, 37% had a positive attitude towards bariatric surgery (POS), whereas 38% had a negative attitude (NEG). The drop-out rate was 8%. NEG participants lost significantly more body weight than the POS participants (intention-to-treat population: 4.5 [SD: 6.3] kg versus 0.4 [SD: 5.8] kg; p < 0.001). In both subgroups, anxiety, depression, the mental score for quality of life, and eating behaviour improved. Conclusion: A BWL treatment in a clinical setting identified 2 distinct groups with different attitudes towards bariatric surgery that were associated with different body weight change outcomes. These groups may require differently targeted programmes to achieve the best body weight loss results.
Assessment of Long-Term in vitro Multiplied Human Wharton’s Jelly-Derived Mesenchymal Stem Cells prior to Their Use in Clinical Administration

The quantity of mesenchymal stem/stromal cells (MSCs) required for a particular therapy demands their subsequent expansion through ex vivo culture. During in vitro multiplication, they undergo replicative senescence which may alter their genetic stability. Therefore, this study was aimed to analyze cellular, molecular, and chromosomal alterations in Wharton’s jelly-derived MSCs (WJ-MSCs) during their in vitro sequential passages, where WJ-MSCs were sequentially passaged up to P14 and cells were evaluated at an interval of P2, P6, P10, and P14. They were examined for their morphology, tumorigenicity, surface markers, stemness markers, DNA damage, chromosomal aberration, and telomere length. We have processed five full-term delivered human umbilical cord samples to obtain WJ-MSCs. Morphological appearance observed at initial stages was small fine spindle-shaped WJ-MSCs which were transformed to flat, long, and broader cells in later passages. The cell proliferation rate was gradually decreased after the 10th passage. WJ-MSCs have expressed stemness markers OCT-4 and NANOG, while they showed high expression of positive surface markers CD90 and CD105 and lower expression of CD34 and CD45. They were non-tumorigenic with slow cellular aging during subsequent passages. There was no chromosomal abnormality up to the 14th passage, while increase in comet score and decrease in telomere length were observed in later passages. Hence, our study suggests that early and middle passaged (less than P10) WJ-MSCs are good candidates for clinical administration for treatment.
RelA binding of mRNAs modulates translation or sRNA‐mRNA basepairing depending on the position of the GGAG site

Previously, we reported that RelA protein facilitates Hfq‐mediated mRNA‐sRNA regulation by binding sRNAs carrying a Shine‐Dalgarno‐like GGAG sequence. In turn, sRNA‐Hfq monomers are stabilized, enabling the attachment of more Hfq subunits to form a functional hexamer. Here, using CLIP‐seq, we present a global analysis of RelA‐bound RNAs showing that RelA interacts with sRNAs as well as with mRNAs carrying a GGAG motif. RelA binding of mRNAs carrying GGAG at position −7 relative to the initiation codon (AUG) inhibits translation by interfering with the binding of 30S ribosomes. The extent of inhibition depends on the distance of GGAG relative to the AUG, as shortening the spacing between GGAG and AUG abrogates RelA‐mediated inhibition. Interestingly, RelA binding of target mRNAs carrying GGAG in the coding sequence or close to AUG facilitates target gene regulation by sRNA partners that lack GGAG. However, translation inhibition caused by RelA binding of mRNAs carrying GGAG at position −7 relative to the AUG renders sRNA‐mRNA basepairing regulation ineffective. Our study indicates that by binding RNAs carrying GGAG the ribosome‐associated RelA protein inhibits translation of specific newly synthesized incoming mRNAs or enables basepairing regulation by their respective sRNA partners, thereby introducing a new regulatory concept for the bacterial response.
Improved accuracy and reduced uncertainty in greenhouse gas inventories by refining the IPCC emission factor for direct N2O emissions from nitrogen inputs to managed soils

Most national GHG inventories estimating direct N2O emissions from managed soils rely on a default Tier 1 emission factor (EF1) amounting to 1% of nitrogen inputs. Recent research has, however, demonstrated the potential for refining the EF1 considering variables that are readily available at national scales. Building on existing reviews, we produced a large dataset (n = 848) enriched in dry and low latitude tropical climate observations as compared to former global efforts and disaggregated the EF1 according to most meaningful controlling factors. Using spatially explicit N fertilizer and manure inputs, we also investigated the implications of using the EF1 developed as part of this research and adopted by the 2019 IPCC refinement report. Our results demonstrated that climate is a major driver of emission, with an EF1 three times higher in wet climates (0.014, 95% CI 0.011–0.017) than in dry climates (0.005, 95% CI 0.000–0.011). Likewise, the form of the fertilizer markedly modulated the EF1 in wet climates, where the EF1 for synthetic and mixed forms (0.016, 95% CI 0.013–0.019) was also almost three times larger than the EF1 for organic forms (0.006; 95% CI 0.001–0.011). Other factors such as land cover and soil texture, C content, and pH were also important regulators of the EF1. The uncertainty associated with the disaggregated EF1 was considerably reduced as compared to the range in the 2006 IPCC guidelines. Compared to estimates from the 2006 IPCC EF1, emissions based on the 2019 IPCC EF1 range from 15% to 46% lower in countries dominated by dry climates to 7%–37% higher in countries with wet climates and high synthetic N fertilizer consumption. The adoption of the 2019 IPCC EF1 will allow parties to improve the accuracy of emissions’ inventories and to better target areas for implementing mitigation strategies.
GPU_PBTE: an efficient solver for three and four phonon scattering rates on graphics processing units

Lattice thermal conductivity (LTC) is a key parameter for many technological applications. Based on the Peierls–Boltzmann transport equation (PBTE), many unique phonon transport properties of various materials were revealed. Accurate calculation of LTC with PBTE, however, is a time-consuming task, especially for compounds with a complex crystal structure or taking high-order phonon scattering into consideration. Graphical processing units (GPUs) have been extensively used to accelerate scientific simulations, making it possible to use a single desktop workstation for calculations that used to require supercomputers. Due to its fundamental differences from traditional processors, GPUs are especially suited for executing a large group of similar tasks with minimal communication, but require completely different algorithm design. In this paper, we provide a new algorithm optimized for GPUs, where a two-kernel method is used to avoid divergent branching. A new open-source code, GPU_PBTE, is developed based on the proposed algorithm. As demonstrations, we investigate the thermal transport properties of silicon and silicon carbide, and find that accurate and reliable LTC can be obtained by our software. GPU_PBTE performed on NVIDIA Tesla V100 can extensively improve double precision performance, making it two to three orders of magnitude faster than our CPU version performed on Intel Xeon CPU Gold 6248 @2.5 GHz. Our work also provides an idea of accelerating calculations with other novel hardware that may come out in the future.
Influence of water quality on the macroinvertebrate community in a tropical estuary (Buenaventura Bay)

The anthropogenic discharges of inorganic nutrients impact water quality, affecting the macroinvertebrate assemblage and food safety. The main objective of this study was to examine the seawater quality and macroinvertebrate dynamics in muddy habitats of Buenaventura Bay, Colombian Pacific. Macroinvertebrates were captured using artisanal trawl nets during different seasons and along four sampling sites. Multivariate analyses (canonical correspondence analysis and generalized additive model) were used to assess the effects of variations in nitrite, nitrates, phosphate concentrations, and physicochemical variables (salinity, pH, dissolved oxygen [DO], temperature, and total dissolved solids [TDS]) of water on the macroinvertebrate assemblage. Richness was the highest at sites with high salinity and temperature and low concentrations of nitrites and TDS. The densities of the commercial shrimp species Xiphopenaeus riveti and Rimapenaeus byrdi were the highest at sites with higher DO and alkalinity, and lower nitrate concentrations. The swimming crab Callinectes arcuatus was dominant at sites with low water quality. In summary, in the transitional season and at the inner sites of Buenaventura Bay, it was observed the lowest water quality due to high nitrate concentration. High nitrate concentration was highlighted as the main anthropogenic factor that could decrease the capture of target macroinvertebrate species for food and livelihoods of artisanal fishermen and their families. Thus, macroinvertebrate communities may be vulnerable to increased inorganic nutrient inputs, which could affect estuarine water quality and ecosystems services. Integr Environ Assess Manag 2022;18:796–812. © 2021 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
Biodegradation of cyanide to ammonia and carbon dioxide by an industrially valuable enzyme from the newly isolated Enterobacter zs

Abstract The biodetoxification of cyanide-rich wastewater has been suggested as an appropriate technique due to its environmental friendliness and cost effectiveness. In this research, Enterobacter zs that was newly isolated from cyanide-polluted wastewater was selected to catalyze cyanide via an enzymatic mechanism. Enzyme was purified and its activity was also determined by ammonia assay. Subsequently, the operational procedure was optimized to enhance cyanide biodegradation at variable pH values, temperatures and cyanide concentrations using response surface methodology (RSM). The results revealed that the interactions between pH and temperature, as well as those between pH and cyanide concentration, were significant, and the concentration of cyanide in a 650 mg.L−1 solution was decreased by 73%. According to this study, it can be proposed that due to its higher activity level compared with those of similar enzymes, this enzyme can prove useful in enzymatic biodegradation of cyanide which is a promising approach in the treatment of industrial effluent.