bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore sequencing with T2T‐CHM13 for accurate detection and preventing the transmission of structural rearrangements in highly repetitive heterochromatin regions in human embryos
Authors: Xia Qiuping , Ding Taoli , Chang Tianli , Ruan Jiangxing , Yang Ji , Ma Menglin , Liu Jiaqi , Liu Zhen , Jiao Shujing , Wu Jian , Ren Jun , Lu Sijia , Li Yanping , Yao Zhongyuan 
Published: March 2024

AbstractBackgroundStructural rearrangements in highly repetitive heterochromatin regions can result in miscarriage or foetal malformations; however, detecting and preventing the transmission of these rearrangements has been challenging. Recently, the completion of sequencing of the complete human genome (T2T‐CHM13) has made it possible to accurately characterise structural rearrangements in these regions. We developed a method based on T2T‐CHM13 and nanopore sequencing to detect and block structural rearrangements in highly repetitive heterochromatin sequences.MethodsT2T‐CHM13‐based “Mapping Allele with Resolved Carrier Status” was performed for couples who carry structural rearrangements in heterochromatin regions. Using nanopore sequencing and the T2T‐CHM13 reference genome, the precise breakpoints of inversions and translocations close to the centromere were detected and haplotypes were constructed using flanking single‐nucleotide polymorphisms (SNPs). Haplotype linkage analysis was then performed by comparing consistent parental SNPs with embryonic SNPs to determine whether the embryos carried hereditary inversions or balanced translocations. Based on copy number variation and haplotype linkage analysis, we transplanted normal embryos, which were further verified by an amniotic fluid test.ResultsTo validate this approach, we used nanopore sequencing of families with inversions and reciprocal translocations close to the centromere. Using the T2T‐CHM13 reference genome, we accurately detected inversions and translocations in centromeres, constructed haplotypes and prevented the transmission of structural rearrangements in the offspring.ConclusionsThis study represents the first successful application of T2T‐CHM13 in human reproduction and provides a feasible protocol for detecting and preventing the transmission of structural rearrangements of heterochromatin in embryos.
Design, synthesis, in silico, and in vitro evaluation of novel benzyloxybenzene substituted (S)‐α‐amino amide derivatives as cholinesterases and monoaminoxidases inhibitor
Authors: Akıncıoğlu Akın 
Published: March 2024

AbstractIn this study, a series of novel benzyloxybenzene substituted (S)‐α‐amino acid methyl esters and their amide derivatives were synthesized and evaluated for their inhibitory actions against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), monoamine oxidase A (MAO‐A), and monoamine oxidase B (MAO‐B). The synthetic strategy was based on starting from benzyl bromide (5) and 4‐hydroxybenzaldehyde (6). The reaction of 5 and 6 in the presence of K2CO3 gave benzyloxybenzaldehyde 7. Benzyloxybenzene substituted (S)‐α‐amino acid methyl esters 11, 12, 13, (±)‐19, and (±)‐20 were obtained from the reaction of
L‐amino acid methyl esters with benzyloxybenzaldehyde (7) followed by in situ reduction with NaBH4. The reaction of (S)‐11, (S)‐12, 13, (±)‐19, and (±)‐20 with excess ammonia gave amides (S)‐14, (S)‐15, 16, (±)‐21, and (±)‐22. The in vitro inhibitory activities of compounds against MAO‐A, MAO‐B, AChE, and BChE were investigated. Within the α‐amino acid methyl ester series, 13 (21.32 ± 0.338 µM) showed selectivity by inhibiting the MAO‐B better than MAO‐A. 13 emerged as the most active member of this series, exhibiting a 12‐fold selectivity for MAO‐B. 14 (4.501 ± 0.295 µM) demonstrated a pronounced selectivity for MAO‐A over MAO‐B, with a selectivity ratio of 110‐fold. In addition, it was determined that compound 15 (95.65 ± 3.09 µM) had high selectivity for BChE inhibition. 21 was demonstrated the most potent inhibition (18.36 ± 1.36 µM) against AChE.
The role of biogeographical barriers on the historical dynamics of passerine birds with a circum‐Amazonian distribution
Authors: Bolívar‐Leguizamón Sergio D. , Bocalini Fernanda , Silveira Luís F. , Bravo Gustavo A. 
Published: March 2024

AbstractCommon distributional patterns have provided the foundations of our knowledge of Neotropical biogeography. A distinctive pattern is the “circum‐Amazonian distribution”, which surrounds Amazonia across the forested lowlands south and east of the basin, the Andean foothills, the Venezuelan Coastal Range, and the Tepuis. The underlying evolutionary and biogeographical mechanisms responsible for this widespread pattern of avian distribution have yet to be elucidated. Here, we test the effects of biogeographical barriers in four species in the passerine family Thamnophilidae by performing comparative demographic analyses of genome‐scale data. Specifically, we used flanking regions of ultraconserved regions to estimate population historical parameters and genealogical trees and tested demographic models reflecting contrasting biogeographical scenarios explaining the circum‐Amazonian distribution. We found that taxa with circum‐Amazonian distribution have at least two main phylogeographical clusters: (1) Andes, often extending into Central America and the Tepuis; and (2) the remaining of their distribution. These clusters are connected through corridors along the Chaco–Cerrado and southeastern Amazonia, allowing gene flow between Andean and eastern South American populations. Demographic histories are consistent with Pleistocene climatic fluctuations having a strong influence on the diversification history of circum‐Amazonian taxa, Refugia played a crucial role, enabling both phenotypic and genetic differentiation, yet maintaining substantial interconnectedness to keep considerable levels of gene flow during different dry/cool and warm/humid periods. Additionally, steep environmental gradients appear to play a critical role in maintaining both genetic and phenotypic structure.
Invasion genomics of lionfish in the Mediterranean Sea
Authors: Bernardi Giacomo , Azzurro Ernesto , Bariche Michel , Jimenez Carlos , Kalogirou Stefanos , Kleitou Periklis 
Published: March 2024

AbstractThe rate of biological invasions is steadily increasing, with major ecological and economic impacts accounting for billions of dollars in damage as a result. One spectacular example is the western Atlantic invasion by lionfishes. In the Mediterranean Sea, invasions from the Red Sea via the Suez Canal (termed Lessepsian invasions) comprise more than 100 fish species, including a recent invasion by lionfish. In light of the devastating effects of lionfish in the Caribbean Sea, understanding the dynamics of Mediterranean lionfish invasion is crucial. The Lessepsian lionfish invasion started in 2012, and rapidly spread to the central Mediterranean. Here, we used thousands of RAD seq genomic markers to study the population dynamics of this invasion. While we did not find a reduction in genetic diversity between source (Red Sea) and invasive (Mediterranean) populations (i.e., bottleneck effects), we found evidence of population structure within the invasive range in the Mediterranean Sea. We found that loci that are potentially under selection may play an important role in invasion success (in particular, genes involved in osmoregulation and fin spine sizes). Genomic approaches proved powerful in examining the ecological and evolutionary patterns of successful invaders and may be used as tools to understand and potentially mitigate future invasions.
Gypsum lichens: A global data set of lichen species from gypsum ecosystems
Authors: Muriel Sergio , Aragón Gregorio , Martínez Isabel , Prieto María 
Published: March 2024

AbstractLichens are significant components of the biological soil crust communities in gypsum ecosystems and are involved in several processes related to ecosystem functioning, such as water and nutrient cycles or protection against soil erosion. Although numerous studies centered on lichen taxonomy and ecology have been performed in these habitats, global information about lichen species from gypsum substrates or their distributional ranges at a global scale is lacking. Thus, we compiled a global data set of recorded lichen species growing on gypsum. This review is based on systematic searches in two bibliographic databases (Web of Science and the more specialized database Mattick's Literature Index) using various keywords related to the substrate or ecology (i.e., gypsum, gypsiferous, semiarid, saxicolous, terricolous). In addition, we revised lichen literature from countries with gypsum soils using Mattick's, Hamburg University's Worldwide checklist, and different national lichen checklists. Ultimately the review includes a total of 321 studies. This data set included 6114 specimen records belonging to 336 recorded lichen species from 26 countries throughout the world. The results showed large differences in the number of species recorded among countries, reflecting differences in the sampling effort. We provide a table with the number of studies and species in relation to gypsum surface in order to account for the bias produced by sampling effort. The number of studies carried out per country was not related to the gypsum surface but probably to other factors, such as accessibility to field sampling, economic or political factors, or the presence of a wider community of lichenologists. Thus, Spain and Germany hosted the highest number of recorded species (160 and 114 species, respectively). Outside the European continent, only a few countries had a large number of species: Morocco (46), United States (42), and Iran (37). Remarkably, countries from the southern hemisphere (i.e., Australia, Chile, Namibia, and South Africa) showed a low number of studies from gypsum lands, supporting the stated biases observed in sampling efforts among countries. Considering the most studied countries, the results show that Teloschistaceae was the most represented family in gypsum ecosystems followed by Verrucariaceae and Cladoniaceae. Regarding particular species, Psora decipiens and Squamarina lentigera were some of the most widespread and abundant species in these habitats. This data set constitutes a basic and first step toward a much more comprehensive database, to be periodically updated in future releases, which also serves to identify countries or territories where future studies should be accomplished. There are no copyright restrictions on the data; please cite this data paper if the data are used in publications and teaching events.
Rapid exometabolome footprinting combined with multivariate statistics: A powerful tool for bioprocess optimization
Authors: Reiter Alexander , Wesseling Lars , Wiechert Wolfgang , Oldiges Marco 
Published: March 2024

AbstractCorynebacterium glutamicum is used as an industrial platform organism for amino acid production. Previously, the organism was utilized to produce l‐histidine with research focusing on metabolic engineering approaches to increase titer and yield. Only a few studies have been published that provide information on bioprocess development, with media optimization and fed‐batch cultivation procedure being particularly promising areas. In this work, we show how experimental setups such as miniature cultivation technology, dynamic and time‐optimized LC‐MS/MS metabolic footprinting tools, and automated workflows for the detection of local and global metabolic patterns can significantly accelerate bioprocess development. Potential media bottlenecks in form of phosphate and magnesium availability were identified by sensitivity analysis in parallelized microscale cultivation assisted by lab automation. A rapid dilute‐and‐shoot flow‐injection‐analysis tandem mass spectrometry approach was used to cope with the resulting cultivation throughput and allowed to quantify amino acids with 1 min per sample. We were able to increase the l‐histidine titer of a C. glutamicum random mutagenesis mutant by a factor of 5.8 through process optimization while also identifying both known and previously unknown targets for additional strain improvements. The presented methodology can be seen as a supplement to traditional approaches in the field of bioprocess development.
Surveying neurologist perspectives and knowledge of epilepsy surgery to identify barriers to surgery referral
Authors: Seneviratne Namal U. , Ho Sophey Y. , Correa Daniel J. 
Published: March 2024

AbstractObjectiveEpilepsy surgery is an effective means of treating medically refractory epilepsy (MRE), but it remains underused. We aimed to analyze the perspectives and knowledge of referring neurologists in the New York metropolitan area, who serve a large epilepsy population.MethodsWe adapted a previous Canadian survey by Roberts et al. (2015), adding questions regarding demographic descriptors, insurance coverage, training and practice details, and perceived social barriers for patients. We surveyed neurologists directly affiliated with Montefiore Medical Center and those referring to Montefiore's Comprehensive Epilepsy Center. Participants had 10 weeks to fill out an online Qualtrics survey with weekly reminders.ResultsOf 117 neurologists contacted, 51 eligible neurologists completed the survey (63.8% Montefiore, 35.0% referring group). A high proportion of the results were from epilepsy‐trained individuals (41.2%) and neurologists who graduated residency ≤19 years ago (80.4%). 80.4% of respondents felt that epilepsy surgery is safe, but only 56.9% would refer a patient for surgical workup after two failed trials of anti‐seizure medications. Epileptologists and providers with a larger volume of epilepsy patients and electroencephalogram readings had better knowledge of the epilepsy surgery workup guidelines. When asked to rank social barriers to patients receiving surgery, participants were most concerned about lack of social support, financial insecurity, and a patient's dual role as a caregiver.SignificanceOur study suggests continued reluctance of neurologists regarding epilepsy surgery, and deficiencies in the knowledge and adherence to the recommended guidelines. In the context of prior studies, these results showed improved understanding of the definition of MRE (80.4%) and an increased likelihood to refer eligible patients as early as possible (78.4%) in line with current consensus recommendations. The finding that epilepsy‐trained and more epilepsy/electroencephalogram‐facing neurologists showed better understanding of the guidelines suggests that increased education efforts should be targeted at non‐epileptologists.Plain Language SummaryOur study asked New York City doctors about their approach to epilepsy surgery. Many do not consider it as early as they could in treatment plans. The doctors with extra epilepsy training were better at knowing when to consider surgery.
Research on the deformation mechanism and ACC control technology of gob‐side roadway in an extra‐thick coal seam with varying thickness
Authors: Shan Renliang , Liu Shuai , Wang Hailong , Li Zhaolong , Huang Pengcheng , Dou Haoyu 
Published: March 2024

AbstractTo improve the extraction of coal resources, gob‐side entry driving is gradually being promoted and applied. However, as the thickness of the coal seam increases, the deformation control of the roadway becomes more difficult. Aiming at this problem, a combination of theoretical calculation, numerical simulation, and field test was used to analyze the aspects of the stress environment, surrounding rock properties, and support forms. The phenomenon and mechanization of intensified deformation and failure of roadway with increasing coal seam thickness were revealed. The specific results include: (1) The ratio of principal stress at the excavation position controls the maximum failure depth of roadway, and the direction of principal stress determines the location of the maximum failure depth; (2) As the thickness of the coal seam increases, the properties of the surrounding rock at the excavation position decrease, the principal stress ratio increases, and the deflection angle of the principal stress increases, which lead to an intensification of the deformation and failure of the roadway. Based on the deformation and failure characteristics of the roadway and the shortcomings of the original support form, a control strategy and support scheme based on a new support structure called “Anchor Cable with C‐shaped Tube” is proposed, which has achieved better deformation control effect in on‐site application.
Anodes for Li‐ion batteries based on titanium fluorides
Authors: Astrova Ekaterina V. , Parfeneva Alesya V. , Li Galina V. , Ulin Vladimir P. , Yagovkina Maria A. , Nashchekin Alexey V. , Beregulin Eugene V. , Rumyantsev Aleksander M. 
Published: March 2024

AbstractThe work is devoted to a comparative study of the electrochemical behavior and molecular level transformations in TiF3 and TiOF2 electrodes of Li‐ion batteries at charge‐discharge processes. Based on analysis of the electrode voltage profiles, we propose possible redox reactions which occur with the change of Ti oxidizing state. According to these models, titanium trifluoride has a reversible capacity of 600 mAh/g, TiOF2 of 395 mAh/g. It has been shown that titanium oxyfluoride is characterized by a long cycle life while specific capacity of the titanium trifluoride rapidly degrades. The degradation of TiF3 is associated with a temporal molecular ordering and decrease in the chemical activity of titanium and lithium fluoride formed during the reversible introduction of lithium. The related effect lies under the superreversibility phenomenon in TiOF2 electrodes (Coulomb efficiency more than 100%). The dependences of the equilibrium voltage and chemical diffusion coefficient of Li on the concentration of Li were determined from GITT analysis.
Building forests for the future
Authors: MacKenzie A. Robert , Ullah Sami , Foyer Christine H. 
Published: March 2024

AbstractMany governments have set ambitious targets for tree planting and increased woodland cover as a key part of actions to reach net‐zero carbon emissions by 2050. However, many uncertainties remain concerning how and where to expand tree cover, what species to plant, and how best to manage new plantations. Much contemporary forestry has been based on even‐aged monocultures, largely because of perceived advantages for timber production. However, in order to play a key role in climate change mitigation future forests will have to achieve timber production (and wider ecosystem service provision) alongside resilience to biotic and abiotic challenge. It is therefore crucial that appropriate informed decisions are made with regard to the structure, composition, and planning of future forests, in order to provide sustainable solutions that provide environmental, economic, and health benefits to society. Genetically diverse, mixed, and irregular forests, with their higher biodiversity and niche complementarity, are promising new forest configurations for regulating the water cycle, storing carbon, and delivering other goods and services. In the following discussion, we have used UK information to illustrate the benefits of mixed woodland versus monocultures and highlighted current issues related to government initiatives and policies for current and future forests. However, similar issues and problems are encountered globally.
Data‐driven MEG analysis to extract fMRI resting‐state networks
Authors: Pelzer Esther A. , Sharma Abhinav , Florin Esther 
Published: March 2024

AbstractThe electrophysiological basis of resting‐state networks (RSN) is still under debate. In particular, no principled mechanism has been determined that is capable of explaining all RSN equally well. While magnetoencephalography (MEG) and electroencephalography are the methods of choice to determine the electrophysiological basis of RSN, no standard analysis pipeline of RSN yet exists. In this article, we compare the two main existing data‐driven analysis strategies for extracting RSNs from MEG data and introduce a third approach. The first approach uses phase–amplitude coupling to determine the RSN. The second approach extracts RSN through an independent component analysis of the Hilbert envelope in different frequency bands, while the third new approach uses a singular value decomposition instead. To evaluate these approaches, we compare the MEG‐RSN to the functional magnetic resonance imaging (fMRI)‐RSN from the same subjects. Overall, it was possible to extract RSN with MEG using all three techniques, which matched the group‐specific fMRI‐RSN. Interestingly the new approach based on SVD yielded significantly higher correspondence to five out of seven fMRI‐RSN than the two existing approaches. Importantly, with this approach, all networks—except for the visual network—had the highest correspondence to the fMRI networks within one frequency band. Thereby we provide further insights into the electrophysiological underpinnings of the fMRI‐RSNs. This knowledge will be important for the analysis of the electrophysiological connectome.
Dynamic threat–reward neural processing under semi‐naturalistic ecologically relevant scenarios
Authors: Levitas Daniel J. , James Thomas W. 
Published: March 2024

AbstractStudies of affective neuroscience have typically employed highly controlled, static experimental paradigms to investigate the neural underpinnings of threat and reward processing in the brain. Yet our knowledge of affective processing in more naturalistic settings remains limited. Specifically, affective studies generally examine threat and reward features separately and under brief time periods, despite the fact that in nature organisms are often exposed to the simultaneous presence of threat and reward features for extended periods. To study the neural mechanisms of threat and reward processing under distinct temporal profiles, we created a modified version of the PACMAN game that included these environmental features. We also conducted two automated meta‐analyses to compare the findings from our semi‐naturalistic paradigm to those from more constrained experiments. Overall, our results revealed a distributed system of regions sensitive to threat imminence and a less distributed system related to reward imminence, both of which exhibited overlap yet neither of which involved the amygdala. Additionally, these systems broadly overlapped with corresponding meta‐analyses, with the notable absence of the amygdala in our findings. Together, these findings suggest a shared system for salience processing that reveals a heightened sensitivity toward environmental threats compared to rewards when both are simultaneously present in an environment. The broad correspondence of our findings to meta‐analyses, consisting of more tightly controlled paradigms, illustrates how semi‐naturalistic studies can corroborate previous findings in the literature while also potentially uncovering novel mechanisms resulting from the nuances and contexts that manifest in such dynamic environments.