bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma FIB milling for the determination of structures in situ
Authors: Berger Casper , Dumoux Maud , Glen Thomas , Yee Neville B.-y. , Mitchels John M. , Patáková Zuzana , Darrow Michele C. , Naismith James H. , Grange Michael 
Published: February 2023

AbstractStructural biology studies inside cells and tissues require methods to thin vitrified specimens to electron transparency. Until now, focused ion beams based on gallium have been used. However, ion implantation, changes to surface chemistry and an inability to access high currents limit gallium application. Here, we show that plasma-coupled ion sources can produce cryogenic lamellae of vitrified human cells in a robust and automated manner, with quality sufficient for pseudo-atomic structure determination. Lamellae were produced in a prototype microscope equipped for long cryogenic run times (> 1 week) and with multi-specimen support fully compatible with modern-day transmission electron microscopes. We demonstrate that plasma ion sources can be used for structural biology within cells, determining a structure in situ to 4.9 Å, and characterise the resolution dependence on particle distance from the lamella edge. We describe a workflow upon which different plasmas can be examined to further streamline lamella fabrication.
Datasets for learning of unknown characteristics of dynamical systems
Authors: Szczęsna Agnieszka , Augustyn Dariusz , Harężlak Katarzyna , Josiński Henryk , Świtoński Adam , Kasprowski Paweł 
Published: February 2023

AbstractThe ability to uncover characteristics based on empirical measurement is an important step in understanding the underlying system that gives rise to an observed time series. This is especially important for biological signals whose characteristic contributes to the underlying dynamics of the physiological processes. Therefore, by studying such signals, the physiological systems that generate them can be better understood. The datasets presented consist of 33,000 time series of 15 dynamical systems (five chaotic and ten non-chaotic) of the first, second, or third order. Here, the order of a dynamical system means its dimension. The non-chaotic systems were divided into the following classes: periodic, quasi-periodic, and non-periodic. The aim is to propose datasets for machine learning methods, in particular deep learning techniques, to analyze unknown dynamical system characteristics based on obtained time series. In technical validation, three classifications experiments were conducted using two types of neural networks with long short-term memory modules and convolutional layers.
The unique fibrilar to platy nano- and microstructure of twinned rotaliid foraminiferal shell calcite
Authors: Lastam J. , Griesshaber E. , Yin X. , Rupp U. , Sánchez-Almazo I. , Heß M. , Walther P. , Checa A. , Schmahl W. W. 
Published: February 2023

AbstractDiversification of biocrystal arrangements, incorporation of biopolymers at many scale levels and hierarchical architectures are keys for biomaterial optimization. The planktonic rotaliid foraminiferPulleniatina obliquiloculatadisplays in its shell a new kind of mesocrystal architecture. Shell formation starts with crystallization of a rhizopodial network, the primary organic sheet (POS). On one side of the POS, crystals consist of blocky domains of 1 μm. On the other side of the POS crystals have dendritic-fractal morphologies, interdigitate and reach sizes of tens of micrometers. The dendritic-fractal crystals are twinned. At the site of nucleation, twinned crystals consist of minute fibrils. With distance away from the nucleation-site, fibrils evolve to bundles of crystallographically well co-oriented nanofibrils and to, twinned, platy-blade-shaped crystals that seam outer shell surfaces. The morphological nanofibril axis is the crystallographic c-axis, both are perpendicular to shell vault. The nanofibrillar calcite is polysynthetically twinned according to the 60°/[100] (= m/{001}) twin law. We demonstrate for the twinned, fractal-dendritic, crystals formation at high supersaturation and growth through crystal competition. We show also that c-axis-alignment is already induced by biopolymers of the POS and is not simply a consequence of growth competition. We discuss determinants that lead to rotaliid calcite formation.
Risk factors and prognosis of postoperative delirium in nonagenarians with hip fracture
Authors: Zhao Shengjie , Sun Tiansheng , Zhang Jianzheng , Chen Xiaobin , Wang Xiaowei 
Published: February 2023

AbstractHip fractures in nonagenarians is one of the great challenges for patients of this age, the family and the larger society. The purpose of this study was to investigate the risk factors and prognosis of postoperative delirium in nonagenarians with hip fracture. 199 Eligible patients were enrolled. Confusion Assessment Method (CAM) were used to identify the delirium. Logistic regressions were used to investigate the effect of 18 pre-existing conditions on postoperative delirium. Prognosis of postoperative delirium in nonagenarians with hip fracture were also be evaluated. The results indicated the following: (1) the prevalence of postoperative delirium among nonagenarians with hip fracture was 28.1% (56 of 199); (2) coexisting disease ≥ 4 (OR = 5.355, 95% CI = 1.394–9.074, P = 0.007), longer admission to operating time (OR = 1.514, 95% CI = 1.247–1.837, P = 0.000), and general anesthesia (OR = 2.086, 95% CI = 1.804–7.968, P = 0.032) were independent risk factors for postoperative delirium in nonagenarians with hip fracture; (3) nonagenarians with postoperative delirium had a predominantly high burden of perioperative complications, long length of stay, and postoperative mortality at 30 days follow-up and 1 year follow-up than the patients without postoperative delirium. The results could enable clinicians to improve outcome after operation in nonagenarians with hip fracture.
Prevalence, predictors, and outcomes of major congenital anomalies: A population-based register study
Authors: Al-Dewik Nader , Samara Muthanna , Younes Salma , Al-jurf Rana , Nasrallah Gheyath , Al-Obaidly Sawsan , Salama Husam , Olukade Tawa , Hammuda Sara , Marlow Neil , Ismail Mohamed , Abu Nada Taghreed , Qoronfleh M. Walid , Thomas Binny , Abdoh Ghassan , Abdulrouf Palli Valapila , Farrell Thomas , Al Qubaisi Mai , Al Rifai Hilal 
Published: February 2023

AbstractCongenital anomalies (CAs) are a leading cause of morbidity and mortality in early life. We aimed to assess the incidence, risk factors, and outcomes of major CAs in the State of Qatar. A population-based retrospective data analysis of registry data retrieved from the Perinatal Neonatal Outcomes Research Study in the Arabian Gulf (PEARL-Peristat Study) between April 2017 and March 2018. The sample included 25,204 newborn records, which were audited between April 2017 and March 2018, of which 25,073 live births were identified and included in the study. Maternal risk factors and neonatal outcomes were assessed for association with specific CAs, including chromosomal/genetic, central nervous system (CNS), cardiovascular system (CVS), facial, renal, multiple congenital anomalies (MCAs) using univariate and multivariate analyses. The incidence of any CA among live births was 1.3% (n = 332). The most common CAs were CVS (n = 117; 35%), MCAs (n = 69, 21%), chromosomal/genetic (51; 15%), renal (n = 39; 12%), CNS (n = 20; 6%), facial (14, 4%), and other (GIT, Resp, Urogenital, Skeletal) (n = 22, 7%) anomalies. Multivariable regression analysis showed that multiple pregnancies, parity ≥ 1, maternal BMI, and demographic factors (mother’s age and ethnicity, and infant’s gender) were associated with various specific CAs. In-hospital mortality rate due to CAs was estimated to be 15.4%. CAs were significantly associated with high rates of caesarean deliveries (aOR 1.51; 95% CI 1.04–2.19), Apgar < 7 at 1 min (aOR 5.44; 95% CI 3.10–9.55), Apgar < 7 at 5 min (aOR 17.26; 95% CI 6.31–47.18), in-hospital mortality (aOR 76.16; 37.96–152.8), admission to neonatal intensive care unit (NICU) or perinatal death of neonate in labor room (LR)/operation theatre (OT) (aOR 34.03; 95% CI 20.51–56.46), prematurity (aOR 4.17; 95% CI 2.75–6.32), and low birth weight (aOR 5.88; 95% CI 3.92–8.82) before and after adjustment for the significant risk factors. This is the first study to assess the incidence, maternal risk factors, and neonatal outcomes associated with CAs in the state of Qatar. Therefore, a specialized congenital anomaly data registry is needed to identify risk factors and outcomes. In addition, counselling of mothers and their families may help to identify specific needs for pregnant women and their babies.
Epidemiological and genomic analysis of dengue cases in Guangzhou, China, from 2010 to 2019
Authors: Jiang Liyun , Liu Yuan , Su Wenzhe , Liu Wenhui , Dong Zhiqiang , Long Yuxiang , Luo Lei , Jing Qinlong , Cao Yimin , Wu Xinwei , Di Biao 
Published: February 2023

AbstractWith a long epidemic history and a large number of dengue cases, Guangzhou is a key city for controlling dengue in China. The demographic information regarding dengue cases, and the genomic characteristics of the envelope gene of dengue viruses, as well as the associations between these factors were investigated from 2010 to 2019, to improve the understanding of the epidemiology of dengue in Guangzhou. Demographic data on 44,385 dengue cases reported to the Notifiable Infectious Disease Report System were analyzed using IBM SPSS Statistics v. 20. Dengue virus isolates from patient sera were sequenced, and phylogenetic trees were constructed using PhyML 3.1. There was no statistical difference in the risk of dengue infection between males and females. Unlike other areas in which dengue is endemic, the infection risk in Guangzhou increased with age. Surveillance identified four serotypes responsible for dengue infections in Guangzhou. Serotype 1 remained prevalent for most of the study period, whereas serotypes 3 and 4 were prevalent in 2012 and 2010, respectively. Different serotypes underwent genotype and sublineage shifts. The epidemiological characteristics and phylogeny of dengue in Guangzhou suggested that although it has circulated in Guangzhou for decades, it has not been endemic in Guangzhou. Meanwhile, shifts in genotypes, rather than in serotypes, might have caused dengue epidemics in Guangzhou.
Upwelling, climate change, and the shifting geography of coral reef development
Authors: Rodriguez-Ruano Victor , Toth Lauren T. , Enochs Ian C. , Randall Carly J. , Aronson Richard B. 
Published: February 2023

AbstractThe eastern tropical Pacific is oceanographically unfavorable for coral-reef development. Nevertheless, reefs have persisted there for the last 7000 years. Rates of vertical accretion during the Holocene have been similar in the strong-upwelling Gulf of Panamá (GoP) and the adjacent, weak-upwelling Gulf of Chiriquí (GoC); however, seasonal upwelling in the GoP exacerbated a climate-driven hiatus in reef development in the late Holocene. The situation is now reversed and seasonal upwelling in the GoP currently buffers thermal stress, creating a refuge for coral growth. We developed carbonate budget models to project the capacity of reefs in both gulfs to keep up with future sea-level rise. On average, the GoP had significantly higher net carbonate production rates than the GoC. With an estimated contemporary reef-accretion potential (RAP) of 5.5 mm year−1, reefs in the GoP are projected to be able to keep up with sea-level rise if CO2 emissions are reduced, but not under current emissions trajectories. With an estimated RAP of just 0.3 mm year−1, reefs in the GoC are likely already unable to keep up with contemporary sea-level rise in Panamá (1.4 mm year−1). Whereas the GoP has the potential to support functional reefs in the near-term, our study indicates that their long-term persistence will depend on reduction of greenhouse gases.
Optimal spatial evaluation of a pro rata vaccine distribution rule for COVID-19
Authors: Castonguay François M. , Blackwood Julie C. , Howerton Emily , Shea Katriona , Sims Charles , Sanchirico James N. 
Published: February 2023

AbstractThe COVID-19 Vaccines Global Access (COVAX) is a World Health Organization (WHO) initiative that aims for an equitable access of COVID-19 vaccines. Despite potential heterogeneous infection levels across a country, countries receiving allotments of vaccines may follow WHO’s allocation guidelines and distribute vaccines based on a jurisdictions’ relative population size. Utilizing economic—epidemiological modeling, we benchmark the performance of this pro rata allocation rule by comparing it to an optimal one that minimizes the economic damages and expenditures over time, including a penalty representing the social costs of deviating from the pro rata strategy. The pro rata rule performs better when the duration of naturally- and vaccine-acquired immunity is short, when there is population mixing, when the supply of vaccine is high, and when there is minimal heterogeneity in demographics. Despite behavioral and epidemiological uncertainty diminishing the performance of the optimal allocation, it generally outperforms the pro rata vaccine distribution rule.
Integrative taxonomy reveals new, widely distributed tardigrade species of the genus Paramacrobiotus (Eutardigrada: Macrobiotidae)
Authors: Kayastha Pushpalata , Stec Daniel , Sługocki Łukasz , Gawlak Magdalena , Mioduchowska Monika , Kaczmarek Łukasz 
Published: February 2023

AbstractIn a moss sample collected in Ribeiro Frio, Madeira, Paramacrobiotus gadabouti sp. nov. was found and described using the integrative taxonomy approach. The new species is described based on morphological and morphometric data from both phase-contrast light microscopy (PCM), as well as scanning electron microscopy (SEM). Moreover, four DNA markers, three nuclear (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial (COI) markers, were used to elucidate the phylogenetic position of the new species within the family Macrobiotidae. The new species has a microplacoid that placed it within Parmacrobiotus richtersi group and exhibit richtersi-type eggs having processes terminated with cap-like structures. Paramacrobiotus gadabouti sp. nov. is most similar to Pam. alekseevi, Pam. filipi and Pam. garynahi, but differs from them mainly in details of egg morphology and morphometrics. Unlike other species from this group, which were confirmed as bisexual and showed limited distribution, Paramacrobiotus gadabouti sp. nov. is yet another parthenogenetic species with a wide distribution, demonstrating that at least some tardigrades confirm to the hypothesis of 'everything is everywhere'.
Dealing with disruptions in railway track inspection using risk-based machine learning
Authors: Kaewunruen Sakdirat , Osman Mohd Haniff 
Published: February 2023

AbstractUnplanned track inspections can be a direct consequence of any disruption to the operation of on-board track geometry monitoring activities. A novel response strategy to enhance the value of the information for supplementary track measurements is thus established to construct a data generation model. In this model, artificial (synthetic) data is assigned on each measurement point along the affected track segment over a short period of time. To effectively generate artificial track measurement data, this study proposes a NARX (nonlinear autoregressive with exogenous variables) model, which incorporates short-range memory dependencies in the dependent variable and integrates interdependent effects from external factors. Nonlinearities in the proposed model have been determined using an artificial neural network that allowed fast computation of a mapping function in line with the needs of effective disruption management. The risk of over fitting the data generation model, which reflected its generalisation ability, has been effectively managed through risk aversion concept. For the model evaluation, the deviation of track longitudinal level has been taken as a case study, predicted using its degradation rate and track alignment and gauge as exogenous variables. Simulation results on two datasets that are statistically different showed that the data generation model for disrupted track measurements is reliable, accurate, and easy-to-use. This novel model is an essential breakthrough in railway track integrity prediction and resilient operation management.
A single point mutation expands the applicability of ostreolysin A6 in biomedicine
Authors: Panevska Anastasija , Čegovnik Nastja , Fortuna Klavdija , Vukovič Alen , Grundner Maja , Modic Špela , Bajc Gregor , Skočaj Matej , Mravinec Bohte Martina , Popošek Lara Larisa , Žigon Primož , Razinger Jaka , Veranič Peter , Resnik Nataša , Sepčić Kristina 
Published: February 2023

AbstractAn aegerolysin protein ostreolysin A6 (OlyA6) binds to cholesterol-complexed sphingomyelin and can be used for specific labelling of lipid rafts. In addition, OlyA6 interacts with even higher affinity with ceramide phosphoethanolamine (CPE), a sphingolipid that dominates in invertebrate cell membranes. In the presence of pleurotolysin B, a protein bearing the membrane-attack complex/perforin domain, OlyA6 forms pores in insect midgut cell membranes and acts as a potent bioinsecticide. It has been shown that a point mutation of glutamate 69 to alanine (E69A) allows OlyA6 to bind to cholesterol-free sphingomyelin. Using artificial lipid membranes and mammalian MDCK cells, we show that this mutation significantly enhances the interaction of OlyA6 with sphingomyelin and CPE, and allows recognition of these sphingolipids even in the absence of cholesterol. Our results suggest that OlyA6 mutant E69A could serve as complementary tool to detect and study cholesterol-associated and free sphingomyelin or CPE in membranes. However, the mutation does not improve the membrane-permeabilizing activity after addition of pleurotolysin B, which was confirmed in toxicity tests on insect and mammalian cell lines, and on Colorado potato beetle larvae.
Part orientation optimization for Wire and Arc Additive Manufacturing process for convex and non-convex shapes
Authors: Alomari Yazan , Birosz Márton Tamás , Andó Mátyás 
Published: February 2023

AbstractBuilding orientation optimization for Additive Manufacturing (AM) process is a crucial step because it has a vital effect on the accuracy and performance of the created part. Wire and Arc Additive Manufacturing’s (WAAM) working space is less limited, and the production time is significantly shorter than the other metal 3D printers. However, one of the adverse effects of WAAM is the defect at the start and endpoints of the welding beads. In this paper, an algorithm has been invented to define the optimal printing position, reducing the number of these defects by rotating the 3D object in a loop around the X and Y axes by a small constant degree and then selecting the degree of rotation that has the fewest uninterrupted surfaces and the largest area of the first layer. The welding process will be interrupted as little as possible by the torch if there are the fewest possible uninterrupted surfaces. As a result, there will be fewer defects in the production and finishing of the welding beads. In order to have a sufficient connection surface with the build tray, which will aid in holding the workpiece in place, the largest first layer should also be sought. Therefore, it has been found that a properly defined orientation relative to the build tray can reduce the number of uninterrupted surfaces within the layers, which will improve the expected dimensional accuracy of the parts. The efficiency of the process is highly affected by the shape of the part, but in most cases, the print errors can be drastically minimized.
Flavescence dorée phytoplasma enters insect cells by a clathrin-mediated endocytosis allowing infection of its insect vector
Authors: Arricau-Bouvery Nathalie , Dubrana Marie-Pierre , Canuto Francesca , Duret Sybille , Brocard Lysiane , Claverol Stéphane , Malembic-Maher Sylvie , Foissac Xavier 
Published: February 2023

AbstractTo perform its propagative and circulative cycle into its insect vector, the flavescence dorée phytoplasma invades different cell types. Clathrin-mediated endocytosis is used by a wide range of bacteria to infect eukaryote cells. Among the insect proteins interacting with the phytoplasma adhesin VmpA, we identified the adaptor protein complex AP-1 and AP-2 suggesting that phytoplasmas could enter the insect cells via clathrin-mediated endocytosis. By infection assays of insect cells in culture, we showed that phytoplasmas entry into Drosophila S2 cells was more efficient than infection of the Euva cell line developed from the insect vector Euscelidius variegatus. Chlorpromazine, cytochalasin D and knockdown of clathrin heavy chain (chc) gene expression using RNA interference inhibited entry of phytoplasmas into S2 cells. During invasion of S2 cells, phytoplasmas were observed very closed to recombinant GFP-labelled clathrin light chain. To verify the role of clathrin in the insect colonization by phytoplasmas, RNAi was performed via artificial feeding of chc dsRNA by the vector E. variegatus. This decreased the expression of chc gene in the midgut and heads of E. variegatus. The chc lower expression correlated to a decreased of midgut and salivary gland cells colonization after the insects had ingested phytoplasmas from infected plants. In conclusion, results indicate that clathrin is important for the FD phytoplasma to enter insect cells and colonize its insect vector.
Prediction of hydrophilic and hydrophobic hydration structure of protein by neural network optimized using experimental data
Authors: Sato Kochi , Oide Mao , Nakasako Masayoshi 
Published: February 2023

AbstractThe hydration structures of proteins, which are necessary for their folding, stability, and functions, were visualized using X-ray and neutron crystallography and transmission electron microscopy. However, complete visualization of hydration structures over the entire protein surface remains difficult. To compensate for this incompleteness, we developed a three-dimensional convolutional neural network to predict the probability distribution of hydration water molecules on the hydrophilic and hydrophobic surfaces, and in the cavities of proteins. The neural network was optimized using the distribution patterns of protein atoms around the hydration water molecules identified in the high-resolution X-ray crystal structures. We examined the feasibility of the neural network using water sites in the protein crystal structures that were not included in the datasets. The predicted distribution covered most of the experimentally identified hydration sites, with local maxima appearing in their vicinity. This computational approach will help to highlight the relevance of hydration structures to the biological functions and dynamics of proteins.
Dual visible and near-infrared luminescence in mononuclear macrocyclic erbium(iii) complexes via ligand and metal centred excitation
Authors: Gil Yolimar , de Santana Ricardo Costa , de Camargo Andréa Simone Stucchi , Merízio Leonnam Gotardo , Carreño Patricia Farías , Fuentealba Pablo , Manzur Jorge , Spodine Evgenia 
Published: February 2023

The optical studies of three macrocyclic ErIII complexes showed visible upconversion and NIR-downshifted emission upon metal centred excitation. Besides, macrocyclic ligands with aliphatic spacers act as antennas to sensitize the ErIII luminescence.
Copper-free click bioconjugation of technetium-99m complexes using strained cyclononyne derivatives
Authors: Schlesinger Marlene , Jentschel Christian , Pietzsch Hans-Jürgen , Kopka Klaus , Mamat Constantin 
Published: February 2023

A new, powerful and Cu-free click-labelling method based on the diazacyclononyne (DACN) structure was elaborated using the 99mTc-tricarbonyl core.