bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sampling rare conformational transitions with a quantum computer
Authors: Ghamari Danial , Hauke Philipp , Covino Roberto , Faccioli Pietro 
Published: September 2022

AbstractStructural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, Molecular Dynamics (MD) simulations enable us to investigate these thermally activated processes with an atomic level of resolution. In practice, an exponentially large fraction of computational resources must be invested to simulate thermal fluctuations in metastable states. Path sampling methods focus the computational power on sampling the rare transitions between states. One of their outstanding limitations is to efficiently generate paths that visit significantly different regions of the conformational space. To overcome this issue, we introduce a new algorithm for MD simulations that integrates machine learning and quantum computing. First, using functional integral methods, we derive a rigorous low-resolution spatially coarse-grained representation of the system’s dynamics, based on a small set of molecular configurations explored with machine learning. Then, we use a quantum annealer to sample the transition paths of this low-resolution theory. We provide a proof-of-concept application by simulating a benchmark conformational transition with all-atom resolution on the D-Wave quantum computer. By exploiting the unique features of quantum annealing, we generate uncorrelated trajectories at every iteration, thus addressing one of the challenges of path sampling. Once larger quantum machines will be available, the interplay between quantum and classical resources may emerge as a new paradigm of high-performance scientific computing. In this work, we provide a platform to implement this integrated scheme in the field of molecular simulations.
Measuring sensitivity to social distancing behavior during the COVID-19 pandemic
Authors: Kontokosta Constantine E. , Hong Boyeong , Bonczak Bartosz J. 
Published: September 2022

AbstractSocial distancing remains an effective nonpharmaceutical behavioral interventions to limit the spread of COVID-19 and other airborne diseases, but monitoring and enforcement create nontrivial challenges. Several jurisdictions have turned to “311” resident complaint platforms to engage the public in reporting social distancing non-compliance, but differences in sensitivity to social distancing behaviors can lead to a mis-allocation of resources and increased health risks for vulnerable communities. Using hourly visit data to designated establishments and more than 71,000 social distancing complaints in New York City during the first wave of the pandemic, we develop a method, derived from the Weber-Fechner law, to quantify neighborhood sensitivity and assess how tolerance to social distancing infractions and complaint reporting behaviors vary with neighborhood characteristics. We find that sensitivity to non-compliance is lower in minority and low-income neighborhoods, as well as in lower density areas, resulting in fewer reported complaints than expected given measured levels of overcrowding.
Visualizing interface-specific chemical bonds in adhesive bonding of carbon fiber structural composites using soft X-ray microscopy
Authors: Yamane Hiroyuki , Oura Masaki , Yamazaki Noriko , Ishihara Tomoko , Hasegawa Koichi , Ishikawa Tetsuya , Takagi Kiyoka , Hatsui Takaki 
Published: September 2022

AbstractAdhesion is a technology for assembling carbon fiber (CF) reinforced polymer (CFRP), enabling them to maintain their lightweight and high-stiffness properties. Despite the importance of adhesion, the lack of a molecular-level understanding of the adhesion mechanisms has limited the reliability of adhesion for use in next-generation aircraft and automobiles. Here, we focused on the chemical-state distribution at a practical adhesive interface composed of an epoxy-based adhesive film bonded to an epoxy-based CF matrix. By fluorinating the OH group, we succeeded in visualizing the chemical state at the CF-matrix/adhesive interface using soft X-ray microscopy. The soft X-ray images exhibited a decrease in OH-related signals at the interface due to the local chemical interaction at the epoxy-epoxy adhesive interface. We also found that the N and O Kα signals were observable at the CF's surface, indicating the presence of nitrogen- and oxygen-containing functional groups. Based on these observations, we discuss the molecular-level adhesion mechanism at the CF-matrix/adhesive interface.
Time series reconstructing using calibrated reservoir computing
Authors: Chen Yeyuge , Qian Yu , Cui Xiaohua 
Published: September 2022

AbstractReservoir computing, a new method of machine learning, has recently been used to predict the state evolution of various chaotic dynamic systems. It has significant advantages in terms of training cost and adjusted parameters; however, the prediction length is limited. For classic reservoir computing, the prediction length can only reach five to six Lyapunov times. Here, we modified the method of reservoir computing by adding feedback, continuous or discrete, to “calibrate” the input of the reservoir and then reconstruct the entire dynamic systems. The reconstruction length appreciably increased and the training length obviously decreased. The reconstructing of dynamical systems is studied in detail under this method. The reconstruction can be significantly improved both in length and accuracy. Additionally, we summarized the effect of different kinds of input feedback. The more it interacts with others in dynamical equations, the better the reconstructions. Nonlinear terms can reveal more information than linear terms once the interaction terms are equal. This method has proven effective via several classical chaotic systems. It can be superior to traditional reservoir computing in reconstruction, provides new hints in computing promotion, and may be used in some real applications.
Changes in nanomechanical properties of single neuroblastoma cells as a model for oxygen and glucose deprivation (OGD)
Authors: Zieliński Tomasz , Pabijan Joanna , Zapotoczny Bartłomiej , Zemła Joanna , Wesołowska Julita , Pera Joanna , Lekka Małgorzata 
Published: September 2022

AbstractAlthough complex, the biological processes underlying ischemic stroke are better known than those related to biomechanical alterations of single cells. Mechanisms of biomechanical changes and their relations to the molecular processes are crucial for understanding the function and dysfunction of the brain. In our study, we applied atomic force microscopy (AFM) to quantify the alterations in biomechanical properties in neuroblastoma SH-SY5Y cells subjected to oxygen and glucose deprivation (OGD) and reoxygenation (RO). Obtained results reveal several characteristics. Cell viability remained at the same level, regardless of the OGD and RO conditions, but, in parallel, the metabolic activity of cells decreased with OGD duration. 24 h RO did not recover the metabolic activity fully. Cells subjected to OGD appeared softer than control cells. Cell softening was strongly present in cells after 1 h of OGD and with longer OGD duration, and in RO conditions, cells recovered their mechanical properties. Changes in the nanomechanical properties of cells were attributed to the remodelling of actin filaments, which was related to cofilin-based regulation and impaired metabolic activity of cells. The presented study shows the importance of nanomechanics in research on ischemic-related pathological processes such as stroke.
DNA methylation landscapes from pig’s limbic structures underline regulatory mechanisms relevant for brain plasticity
Authors: Perdomo-Sabogal Alvaro , Trakooljul Nares , Hadlich Frieder , Murani Eduard , Wimmers Klaus , Ponsuksili Siriluck 
Published: September 2022

AbstractEpigenetic dynamics are essential for reconciling stress-induced responses in neuro-endocrine routes between the limbic brain and adrenal gland. CpG methylation associates with the initiation and end of regulatory mechanisms underlying responses critical for survival, and learning. Using Reduced Representation Bisulfite Sequencing, we identified methylation changes of functional relevance for mediating tissue-specific responses in the hippocampus, amygdala, hypothalamus, and adrenal gland in pigs. We identified 4186 differentially methylated CpGs across all tissues, remarkably, enriched for promoters of transcription factors (TFs) of the homeo domain and zinc finger classes. We also detected 5190 differentially methylated regions (DMRs, 748 Mb), with about half unique to a single pairwise. Two structures, the hypothalamus and the hippocampus, displayed 860 unique brain-DMRs, with many linked to regulation of chromatin, nervous development, neurogenesis, and cell-to-cell communication. TF binding motifs for TFAP2A and TFAP2C are enriched amount DMRs on promoters of other TFs, suggesting their role as master regulators, especially for pathways essential in long-term brain plasticity, memory, and stress responses. Our results reveal sets of TF that, together with CpG methylation, may serve as regulatory switches to modulate limbic brain plasticity and brain-specific molecular genetics in pigs.
Dichloroacetate as a metabolic modulator of heart mitochondrial proteome under conditions of reduced oxygen utilization
Authors: Andelova Natalia , Waczulikova Iveta , Kunstek Lukas , Talian Ivan , Ravingerova Tanya , Jasova Magdalena , Suty Simon , Ferko Miroslav 
Published: September 2022

AbstractMyocardial compensatory mechanisms stimulated by reduced oxygen utilization caused by streptozotocin-induced diabetes mellitus (DM) and treated with dichloroacetate (DCA) are presumably associated with the regulation of mitochondria. We aimed to promote the understanding of key signaling pathways and identify effectors involved in signal transduction. Proteomic analysis and fluorescence spectroscopy measurements revealed significantly decreased membrane potential and upregulated protein amine oxidase [flavin-containing] A (AOFA) in DM mitochondria, indicative of oxidative damage. DCA in diabetic animals (DM + DCA) downregulated AOFA, increased membrane potential, and stimulated thioredoxin-dependent peroxide reductase, a protein with antioxidant function. Furthermore, the DM condition was associated with mitochondrial resistance to calcium overload through mitochondrial permeability transition pores (mPTPs) regulation, despite an increased protein level of voltage-dependent anion-selective protein (VDAC1). In contrast, DM + DCA influenced ROS levels and downregulated VDAC1 and VDAC3 when compared to DM alone. The diabetic myocardium showed an identical pattern of mPTP protein interactions as in the control group, but the interactions were attenuated. Characterization of the combined effect of DM + DCA is a novel finding showing that DCA acted as an effector of VDAC protein interactions, calcium uptake regulation, and ROS production. Overall, DM and DCA did not exhibit an additive effect, but an individual cardioprotective pathway.
Establishing farm dust as a useful viral metagenomic surveillance matrix
Authors: Kwok Kirsty T. T. , de Rooij Myrna M. T. , Messink Aniek B. , Wouters Inge M. , Smit Lidwien A. M. , Cotten Matthew , Heederik Dick J. J. , Koopmans Marion P. G. , Phan My V. T. 
Published: September 2022

AbstractFarm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85–100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.
Seroepidemiological study of factors affecting anti-spike IgG antibody titers after a two-dose mRNA COVID-19 vaccination in 3744 healthy Japanese volunteers
Authors: Sugiyama Aya , Kurisu Akemi , Nagashima Shintaro , Hando Kiyomi , Saipova Khilola , Akhmedova Sayyora , Abe Kanon , Imada Hirohito , Hussain Md Razeen Ashraf , Ouoba Serge , E Bunthen , Ko Ko , Akita Tomoyuki , Yamazaki Shinichi , Yokozaki Michiya , Tanaka Junko 
Published: September 2022

AbstractSeveral factors related to anti-spike(S) IgG antibody titers after mRNA COVID-19 vaccination have been elucidated, but the magnitude of the effects of each factor has not been fully understood. This cross-sectional study assessed anti-S and anti-nucleocapsid (N) antibody titers on 3744 healthy volunteers (median age, 36 years; IQR, 24–49 years; females, 59.0%) who received two doses of mRNA-1273 or BNT162b2 vaccine and completed a survey questionnaire. Multiple regression was conducted to identify factors associated with antibody titers. All but one participant tested positive for anti-S antibodies (99.97%). The following factors were independently and significantly associated with high antibody titer: < 3 months from vaccination (ratio of means 4.41); mRNA-1273 vaccine (1.90, vs BNT162b2); anti-N antibody positivity (1.62); age (10’s: 1.50, 20’s: 1.37, 30’s: 1.26, 40’s: 1.16, 50’s: 1.15, vs ≧60’s); female (1.07); immunosuppressive therapy (0.54); current smoking (0.85); and current drinking (0.96). The largest impact on anti-S IgG antibody titers was found in elapsed time after vaccination, followed by vaccine brand, immunosuppressants, previous SARS-CoV-2 infection (anti-N antibody positive), and age. Although the influence of adverse reactions after the vaccine, gender, smoking, and drinking was relatively small, they were independently related factors.
Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater
Authors: Nishikawa Yohei , Kogawa Masato , Hosokawa Masahito , Wagatsuma Ryota , Mineta Katsuhiko , Takahashi Kai , Ide Keigo , Yura Kei , Behzad Hayedeh , Gojobori Takashi , Takeyama Haruko 
Published: September 2022

Abstract
Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1–25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.
Early MRI for Pediatric Wrist Injuries—Prospective Case Series of 150 Cases
Authors: Courcey Cynthia de , Jester Andrea , Kaur Sarbjit , Lindau Tommy R. , Oestreich Kerstin 
Published: September 2022

Abstract
Background Pediatric carpal injuries are a clinical challenge due to their non-specific clinical features and occult nature on plain radiography. We hypothesized that early magnetic resonance imaging (MRI) will allow prompt diagnosis and treatment stratification, and that distal pole fracture of the scaphoid requires a shorter duration of immobilization. This study aims to assess the injury pattern and clinical outcomes of under-16-year-olds treated with acute post-traumatic wrist injuries in accordance with the unit's protocol.
Methods All patients under the age of 16 years treated for suspected pediatric wrist injuries in our tertiary pediatric hand and upper limb service were included. Prospectively collected data included patient demographics, radiological findings, treatment and adherence to the unit's protocol.
Results There were 151 patients with a mean age of 12 years. The majority (72%) had occult bony injury with radiological evidence of fracture on MRI. The sensitivity and specificity of plain film radiography were 42.7% and 71.4%, respectively. Almost one in four patients benefitted from early MRI demonstrating no injuries, permitting early mobilization and discharge. The scaphoid was the most commonly injured carpal bone. Non-displaced fractures of the distal pole of the scaphoid in patients over 10 years old were treated with 4 weeks' immobilization with no adverse outcome.
Conclusion Standardized care in our unit has yielded good results with low complication rate and fewer hospital appointments. Our results support the routine early use of MRI and a shorter duration of immobilization in fracture of the distal pole of the scaphoid at 4 weeks.
Level of Evidence This is a level IV, case series study.
Is Vitamin D Deficiency Prothrombotic? A Systematic Review
Authors: Rüdiger Isabella Hangaard , Andersen Matilde Kanstrup , Vestergaard Anna Louise , Bor Pinar , Larsen Agnete , Bor Mustafa Vakur 
Published: September 2022

AbstractObservational studies indicate a relationship between vitamin D deficiency and an increased risk of venous and arterial thrombotic events, but the underlying mechanisms behind this association are uncertain. This systematic review explores if there is an association between decreased vitamin D levels and a prothrombotic profile. The systematic literature search initially identified 3,214 studies (published until December 21, 2021) investigating the relationship between vitamin D and numerous hemostatic parameters. After the screening process, 18 observational and intervention studies fulfilled the inclusion criteria and were included in this systematic review. Parameters of primary hemostasis, secondary hemostasis, and fibrinolysis were investigated in six, thirteen, and fifteen of these studies, respectively. Most of the eligible studies did not identify significant associations between decreased vitamin D levels and hemostatic parameters. Some conflicting results were found between decreased vitamin D levels and thrombin generation parameters and the tissue factor pathway inhibitor. Conflicting results were also found between decreased vitamin D levels and fibrinolytic parameters, although the evidence may point toward weak associations with some regulators of fibrinolysis, mostly decreased tissue type plasminogen activator. Overall, our systematic review did not identify any definitive link between vitamin D deficiency and a prothrombotic profile, which might otherwise help explain the observed association between vitamin D deficiency and increased risk of thrombotic events. Moreover, there is no clinical evidence to confirm or refute a possible antithrombotic effect of vitamin D. Larger high-quality randomized controlled trials are needed to better elucidate the link between vitamin D deficiency and a prothrombotic risk profile.
The Pathophysiological Role of Platelet-Derived Extracellular Vesicles
Authors: Mabrouk Meryem , Guessous Fadila , Naya Abdallah , Merhi Yahye , Zaid Younes 
Published: September 2022

AbstractPlatelets are very abundant in the blood, where they play a role in hemostasis, inflammation, and immunity. When activated, platelets undergo a conformational change that allows the release of numerous effector molecules as well as the production of extracellular vesicles, which are circulating submicron vesicles (10 to 1,000 nm in diameter) released into the extracellular space. Extracellular vesicles are formed by the budding of platelet and they carry some of its contents, including nucleic acids, surface proteins, and organelles. While platelets cannot cross tissue barriers, platelet-derived extracellular vesicles can enter the lymph, bone marrow, and synovial fluid. This allows the transfer of diverse contents carried by these platelet-derived vesicles to cell recipients and organs inaccessible to platelets where they can perform many functions. This review highlights the importance of these platelet-derived extracellular vesicles under different physiological and pathophysiological conditions.
An Infant with Persistent Respiratory Failure Associated with Refractory Pulmonary Hypertension: Pulmonary Interstitial Glycogenosis
Authors: Tomarelli Gianfranco , Donoso Alejandro , Andrades Francisca , Montes Soledad 
Published: September 2022

AbstractPulmonary interstitial glycogenosis (PIG) is a disease of unknown etiology. It is part of the interstitial lung diseases, corresponding to the compartment of the fetal pulmonary interstitium. It typically presents within the first week of life as refractory respiratory distress with tachypnea and persistent hypoxemia, and it is not associated with glycogen deposition in other organs. Usually, there is a clinical improvement and good prognosis after steroid therapy unless there are associated conditions such as congenital heart disease, pulmonary hypertension, or genetic disorders. We report a case diagnosed by lung biopsy at 4 months of age in a male preterm born, small for gestational age infant, who developed refractory hypoxemia and pulmonary hypertension with fatal outcome. There was no response to steroids and hydroxychloroquine. He was not candidate for extracorporeal membrane oxygenation. PIG should be considered in the differential diagnosis of persistent respiratory distress and hypoxemia despite standard treatment, even after the first month of life.