bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dataset of new occurrence records of primates from the arc of deforestation, Brazil
Authors: Costa-Araújo Rodrigo , Canale Gustavo Rodrigues , de Melo Fabiano Rodrigues , da Silva Raimundo Rodrigues , da Silva Ivan Baptista , de Alencar Raony Macedo , da Silva Luciano Ferreira , Jerusalinsky Leandro , de Azevedo Renata Bocorny , Santos Júnior Eduardo Marques , Mourthé Italo , Hernández Ruz Emil José , de Sousa e Silva José , Roos Christian , Farias Izeni Pires , Hrbek Tomas 
Published: June 2023

AbstractThe arc of deforestation, located between the southern Amazonia and the northern Cerrado of Brazil, is a top deforestation frontier worldwide. The high deforestation rates in this region are caused by human activities and threatens a rich diversity of primates that are still poorly-known and therefore investments into taxonomy and distribution research are urgent to support science-driven conservation of primates of this region. Here we present a dataset of 192 new occurrence records for 22 species of primates of the generaAlouatta, Aotus, Ateles, Cebus, Chiropotes, Lagothrix, Leontocebus, Pithecia, Plecturocebus, Saimiri, andSapajus, collected during 10 field expeditions carried out across the arc of deforestation between 2015–2018. Based on these occurrence records we extend the ranges ofSaimiri collinsi, Sapajus apella, andAlouatta puruensis, identify a potential hybridization zone betweenA. puruensisandAlouatta discolor, and redefine the range ofPlecturocebus moloch. Moreover, this dataset is a useful source of information otherwise scarce for further researches on species distributions and habitat use patterns, on the effect of environmental variables on such patterns, for estimating population sizes, evaluating habitat suitability, for predicting effects of climate change, habitat loss and fragmentation on populations, and for assessing species extinction risks. The ranges of primates endemic to the arc of deforestation, with a few exceptions, are fragile hypotheses, which hampers the establishment of effective conservation efforts for species increasingly threatened on a global deforestation frontier.
Effects of linker length on phase separation: lessons from the Rubisco-EPYC1 system of the algal pyrenoid
Authors: GrandPre Trevor , Zhang Yaojun , Pyo Andrew G. T. , Weiner Benjamin , Li Je-Luen , Jonikas Martin C. , Wingreen Ned S. 
Published: June 2023

AbstractBiomolecular condensates are membraneless organelles formed via phase separation of macromolecules, typically consisting of bond-forming “stickers” connected by flexible “linkers”. Linkers have diverse roles, such as occupying space and facilitating interactions. To understand how linker length relative to other lengths affects condensation, we focus on the pyrenoid, which enhances photosynthesis in green algae. Specifically, we apply coarse-grained simulations and analytical theory to the pyrenoid proteins ofChlamydomonas reinhardtii: the rigid holoenzyme Rubisco and its flexible partner EPYC1. Remarkably, halving EPYC1 linker lengths decreases critical concentrations by ten-fold. We attribute this difference to the molecular “fit” between EPYC1 and Rubisco. Varying Rubisco sticker locations reveals that the native sites yield the poorest fit, thus optimizing phase separation. Surprisingly, shorter linkers mediate a transition to a gas of rods as Rubisco stickers approach the poles. These findings illustrate how intrinsically disordered proteins affect phase separation through the interplay of molecular length scales.
Knowledge and experiences of community health workers in the delivery of physical rehabilitation services in Zambia- a qualitative interview study of trained community health workers
Authors: Mapulanga Miriam , Dlungwane Thembelihle 
Published: June 2023

ABSTRACTAimTo explore the knowledge and experiences of community health workers in the delivery of physical rehabilitation services in Zambia.DesignAn exploratory qualitative studySettingLusaka district, ZambiaParticipantsTen community health workers from the Zambia Enhanced Community-Based Rehabilitation ProgramResultsNine major themes emerged from the data. Four of these themes (patient management, treatment programs, issuing of appropriate assistive devices through a multidisciplinary approach, and levels of care) were highlighted as the required knowledge base of community health care workers (CHWs), whereas five themes (patient assessment and treatment, home program and family education, assistive devices issuing, a well-functioning referral system, unrealistic caregiver expectations, and resource constraints) were revealed as the essential experiences of CHWs who delivered the required physical rehabilitation services. The CHWs under study experienced unrealistic expectations from caregivers, such as the high expectation that physical rehabilitation would heal a child. These expectations were complicated by a lack of understanding among the caregivers of the role and capabilities of CHWs. Moreover, constraints such as limited resources and a lack of permanent employment were perceived as major challenges.ConclusionTrained community health workers have adequate knowledge and experience in delivering physical rehabilitation services in areas where more specialised and qualified physical rehabilitation workers do not exist. In light of the current shortage of qualified physical rehabilitation workers in Zambia, more investments are required, particularly in the training of community health care workers, to increase physical rehabilitation service coverage.KEY MESSAGESWhat is already known regarding this topicCommunity health workers have been involved in the delivery of physical rehabilitation services. They are therefore key in improving the quality of life of the general population and that of disabled people through the various roles that are task-shifted to them by trained and qualified physical rehabilitation workers. However, their knowledge and experiences in delivering physical rehabilitation services remained relatively unknown until the current study on which this paper is based.What this study adds to the pool of knowledgeThe findings affirm that, with appropriate training in physical rehabilitation, community health workers can effectively deliver physical rehabilitation services and issue appropriate assistive devices at community level in Zambia.How this study might affect research, practice, and policyThe study proposes that appropriately trained community health care workers be utilised to effectively deliver physical rehabilitation services at community level where such services by appropriately qualified physical rehabilitation workers are lacking.
Rare but not absent: the Inverted Mitogenomes of Deep-Sea Hatchetfish
Authors: Gomes-dos-Santos André , Vilas-Arrondo Nair , Machado André M. , Román-Marcote Esther , Del Río Iglesias Jose Luís , Baldó Francisco , Pérez Montse , Fonseca Miguel M. , C. Castro L. Filipe , Froufe Elsa 
Published: June 2023

AbstractMitochondrial genomes are by definition compact and structurally stable over aeons. This generalized perception results from a vertebrate-centric vision, as very few types of mtDNA rearrangements have been described in vertebrates. By combining a panel of sequencing approaches, including short- and long-reads, we show that species from a group of illusive marine teleosts, the deep-sea hatchetfish (Stomiiforms: Sternoptychidae), display a myriad of new mtDNA structural arrangements. We show a never reported inversion of the coding direction of protein-coding genes (PGG) coupled with a strand asymmetry nucleotide composition reversal directly related to the strand location of the Control Region (which includes the heavy strand replication origin). An analysis of the 4-fold redundant sites of the PCGs, in thousands of vertebrate mtDNAs, revealed the rarity of this phenomenon, only found in 9 fish species, five of which are deep-sea hatchetfish. Curiously, in Antarctic notothenioid fishes (Trematominae), where a single PCG inversion (the only other record in fish) is coupled with the inversion of the Control Region, the standard asymmetry is disrupted for the remaining PCG but not yet reversed, suggesting a transitory state in this species mtDNA. Together, our findings hint that a relaxation of the classic vertebrate mitochondrial structuralstasis, observed in Sternoptychidae and Trematominae, promotes disruption of the natural balance of asymmetry of the mtDNA. Our findings support the long-lasting hypothesis that replication is the main molecular mechanism promoting the strand-specific compositional bias of this unique and indispensable molecule.
Decoding kinematic information from beta-band motor rhythms of speech motor cortex: A methodological/analytic approach using concurrent speech movement tracking and magnetoencephalography
Authors: Anastasopoulou Ioanna , Cheyne Douglas O. , van Lieshout Pascal , Johnson Blake W 
Published: June 2023

AbstractArticulography and functional neuroimaging are two major tools for studying the neurobiology of speech production. Until now, however, it has generally not been feasible to use both in the same experimental setup because of technical incompatibilities between the two methodologies. Here we describe results from a novel articulography system dubbed Magneto-articulography for the Assessment of Speech Kinematics (MASK; Alves et al., 2016), which is technically compatible with magnetoencephalography (MEG) brain scanning systems. In the present paper we describe our methodological and analytic approach for extracting brain motor activities related to key kinematic and coordination event parameters derived from time-registered MASK tracking measurements (Anastasopoulou et al., 2022). Data were collected from ten healthy adults with tracking coils on the tongue, lips, and jaw. Analyses targeted the gestural landmarks of reiterated utterances /ipa/ and /api/, produced at normal and faster rates (Anastasopoulou et al., 2022; Van Lieshout, 2007). The results show that (1) Speech sensorimotor cortex can be reliably located in peri-rolandic regions of the left hemisphere; (2) mu (8-12 Hz) and beta band (13-30 Hz) neuromotor oscillations are present in the speech signals and contain information structures that are independent of those present in higher-frequency bands; and (3) hypotheses concerning the information content of speech motor rhythms can be systematically evaluated with multivariate pattern analytic techniques. These results show that MASK provides the capability, for deriving subject-specific articulatory parameters, based on well-established and robust motor control parameters, in the same experimental setup as the MEG brain recordings and in temporal and spatial co-register with the brain data. The analytic approach described here provides new capabilities for testing hypotheses concerning the types of kinematic information that are encoded and processed within specific components of the speech neuromotor system.
Prenatal alcohol exposure alters expression of genes involved in cell adhesion, immune response, and toxin metabolism in adolescent rat hippocampus
Authors: Khalifa Amal , Palu Rebecca A.S. , Perkins Amy , Volz Avery 
Published: June 2023

ABSTRACTPrenatal alcohol exposure can result in mild to severe consequences for children throughout their lives, with this range of symptoms referred to as Fetal Alcohol Spectrum Disorders (FASD). These consequences are thought to be linked to changes in gene expression and transcriptional programming in the brain, but the identity of those changes, and how they persist into adolescence are unclear. In this study, we isolated RNA from the hippocampus of adolescent rats exposed to ethanol during prenatal development and compared gene expression to controls. Exposure to ethanol caused widespread downregulation of many genes as compared to control rats. Gene ontology analysis demonstrated that affected pathways included cell adhesion, toxin metabolism, and immune responses. Interestingly, these differences were not strongly affected by sex. Furthermore, these changes were consistent when comparing ethanol-exposed rats to pair-fed controls provided with a liquid diet and those fed ad libitum on a standard chow diet. We conclude from this study that changes in genetic architecture and the resulting neuronal connectivity after prenatal exposure to alcohol continue through adolescent development. Further research into the consequences of specific gene expression changes on neural and behavioral changes will be vital to our understanding of the FASD spectrum of diseases.AUTHOR SUMMARYAlcohol exposure during fetal development is associated with a wide range of behavioral and physical symptoms that can be observed from childhood throughout adolescence and beyond. It is believed that this exposure may alter gene expression patterns permanently by changing genomic architecture, but the actual changes themselves are still unclear. In this study we examined gene expression patterns in rats whose mothers were given ethanol during their pregnancies. These were compared to control rats whose mothers were fed a similar liquid diet without ethanol as well as rats fed a normal diet. We identified the top differentially expressed genes and performed gene ontology analysis to identify both genes and pathways important in the response to ethanol during fetal development. We focused on adolescent rats since prenatal alcohol exposure has been shown at this stage to influence behavior. We indeed found a number of significant changes in gene expression, suggesting that prenatal alcohol exposure has ongoing consequences throughout and likely beyond adolescence into adulthood. Pathways such as cell adhesion, immune response, and toxin response were all highlighted. Future work will focus on making connections between these gene expression changes and behavioral changes observed at this same life stage.
Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis
Authors: Fernandes Joiselle B. , Naish Matthew , Lian Qichao , Burns Robin , Tock Andrew J. , Rabanal Fernando A. , Wlodzimierz Piotr , Habring Anette , Nicholas Robert E. , Weigel Detlef , Mercier Raphael , Henderson Ian R. 
Published: June 2023

BackgroundCentromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within and between species. Despite variability in DNA sequence, centromeres are also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic and epigenetic factors responsible for suppression of centromeric crossovers remain to be completely defined.ResultsTo explore the centromere-proximal recombination landscape, we mapped 14,397 crossovers against fully assembledArabidopsis thalianagenomes.A. thalianacentromeres comprise megabase-scale satellite repeat arrays that load nucleosomes containing the CENH3 histone variant. Each chromosome possesses a structurally polymorphic 3-4 megabase region where crossovers were absent, that includes the satellite arrays, flanked by 1-2 megabase low-recombination zones. The recombination-suppressed regions are enriched for Gypsy/Ty3 retrotransposons, and additionally contain expressed genes with high genetic diversity that initiate meiotic recombination, yet do not crossover. We mapped crossovers at high-resolution in proximity toCEN3, which resolved punctate centromere-proximal hotspots that overlapped gene islands embedded in heterochromatin. Centromeres are densely DNA methylated and the recombination landscape was remodelled in DNA methylation mutants. We observed that the centromeric low-recombining zones decreased and increased crossovers in CG (met1) and non-CG (cmt3) mutants, respectively, whereas the core non recombining zones remained suppressed.ConclusionOur work relates the genetic and epigenetic organisation of theA. thalianacentromeres and flanking pericentromeric heterochromatin to the zones of crossover suppression that surround the CENH3-occupied satellite repeat arrays.
PROTAC-Design-Evaluator (PRODE) : An Advanced Method for in-silico PROTAC design
Authors: Ben Geoffrey A S , Agrawal Deepak , Kulkarni Nagaraj M , Vetrivel Rajappan , Gurram Kishan 
Published: June 2023

AbstractPROTAC (proteolysis-targeting chimeras) is a rapidly evolving technology to target undruggable targets. The mechanism by which this happens is when a bifunctional molecule binds to a target protein and also brings in proximity an E3 ubiquitin ligase to trigger ubiquitination and degradation of the target protein. Yet in-silico driven approaches to design these hetero-bifunctional molecules that have the desired functional properties to induce proximity between the target protein and E3 ligase remains to be established. In this paper we present a novel in-silico method for PROTAC design and to demonstrate the validity of our approach. We show that for a BRD4-VHL PROTAC ternary complex known in the literature, we are able to reproduce the PROTAC binding mode, the structure of ternary complex formed therein and the free energy (ΔG) thermodynamics favoring ternary complexation through theoretical computational methodologies. Further, we demonstrate the use of Thermal Titration Molecule Dynamics (TTMD) to differentiate the stability of PROTAC mediated ternary complexes. We employ the proposed methodology to design a PROTAC for a new system of FGFR1-MDM2 to degrade the FGFR1 (Fibroblast growth factor receptor 1) which is overexpressed in cancer. Our work presented here and named as PROTAC-Designer-Evaluator (PRODE) contributes to the growing literature of in-silico approaches to PROTAC design and evaluation by incorporating the latest in-silico methods and demonstrates advancement over previously published PROTAC in-silico literature.
Meniscus-enabled Projection Stereolithography (MAPS)
Authors: Kunwar Puskal , Poudel Arun , Aryal Ujjwal , Xie Rui , Geffert Zachary J , Wittmann Haven , Chiang Tsung Hsing , Maye Mathew M. , Li Zhen , Soman Pranav 
Published: June 2023

AbstractLight-based additive manufacturing methods have been widely used to print high-resolution 3D structures for applications in tissue engineering, soft robotics, photonics, and microfluidics, among others. Despite this progress, multi-material printing with these methods remains challenging due to constraints associated with hardware modifications, control systems, cross-contaminations, waste, and resin properties. Here, we report a new printing platform coined Meniscus-enabled Projection Stereolithography (MAPS), a vat-free method that relies on generating and maintaining a resin meniscus between a crosslinked structure and bottom window and to print lateral, vertical, discrete, or gradient multi-material 3D structures with little-to-no cross-contamination or waste. We also show that MAPS is compatible with a wide range of resins and can print complex multi-material 3D structures without requiring specialized hardware, software, or complex washing protocols. MAPS’s ability to print structures with microscale variations in mechanical stiffness, opacity, surface energy, cell densities, and magnetic properties provides a generic method to make advanced materials for a broad range of applications.
Labelizer: systematic selection of protein residues for covalent fluorophore labeling
Authors: Gebhardt Christian , Bawidamann Pascal , Spring Anna-Katharina , Schenk Robin , Schütze Konstantin , Moya Muñoz Gabriel G. , Wendler Nicolas D. , Griffith Douglas A. , Lipfert Jan , Cordes Thorben 
Published: June 2023

AbstractAn essential requirement for the use of fluorescent dyes in biomedicine, molecular biology, biochemistry, biophysics and optical imaging is their (covalent) attachment to biomolecules. There is, however, no systematic and automated approach for the selection of suitable labeling sites in macromolecules, which is particular problematic for proteins. Here, we present a general and quantitative strategy to identify optimal residues for protein labeling using a naïve Bayes classifier. Based on a literature search and bioinformatics analysis of >100 proteins with ~400 successfully labeled residues, we identified four parameters, which we combined into a labeling score to rank residues for their suitability as a label-site. The utility of our approach for the systematic selection of single residues and of residue pairs for FRET experiments is supported by data from the literature and by new experiments on different proteins. To make the method available to a large community of researchers, we developed a python package called “labelizer”, that performs an analysis of a pdb-structure (or structural models), label score calculation, and FRET assay scoring. We further provide a webserver (https://labelizer.bio.lmu.de/) to conveniently apply our approach and to build up a central open-access database of (non-)successfully labeled protein residues to continuously improve and refine the labelizer approach.
Typical and disrupted small-world architecture and regional communication in full-term and preterm infants
Authors: Hu Huiqing , Coppola Peter , Stamatakis Emmanuel , Naci Lorina 
Published: June 2023

AbstractOne fundamental property of conscious experiences is that they are both differentiated and integrated. Adult functional brain networks exhibit an elegant “small-world” architecture. This optimal architecture enables efficient and cost-effective localized information processing and information integration between long-distance regions across the brain. It remains unclear whether the functional small-world architecture is developed in neonates at birth and how this development may be altered by premature birth. To address this gap, we investigated the development of small-world architecture in neonates. To understand the effect of early neonate age on small-world architecture, we also assessed neonates born prematurely or before term-equivalent age (TEA). We used the Developing Human Connectome Project (dHCP), a large neonatal functional magnetic resonance imaging (MRI) dataset with high temporal and spatial resolution. Resting-state functional MRI data for full- term neonates (N = 278, age 41.2 weeks ± 12.2 days) and preterm neonates scanned at TEA (N = 72, 40.9 weeks ± 14.6 days), or before TEA (N = 70, 34.7 weeks ± 12.7 days), were obtained from the dHCP, and for a reference adult group (N = 176, 22–36 years), from the Human Connectome Project. Whole-brain functional network properties were evaluated with comprehensive spatial resolution using graph theoretical analyses. Although different from the adults’, small-world architecture was developed in full-term born neonates at birth. Premature neonates before TEA showed dramatic underdevelopment of small-world architecture and regional communication in 9/11 brain networks, with disruption in 32% of nodes primarily distributed within the somatomotor, dorsal attention, cingulo-opercular, and frontoparietal control network. By TEA, premature neonates showed large-scale recuperation of regional communication, with 1.4% of nodes, distributed in the frontoparietal, salience, and visual networks remaining significantly underdeveloped. Our results suggest that, at full- term birth or by term-equivalent age, infants possess well-developed small-world architecture, which facilitates differentiated and integrated neural processes that give rise to conscious experiences. Conversely, they suggest that this brain infrastructure is significantly underdeveloped before infants reach term-equivalent age. These findings improve understanding of the ontogeny of functional small-world architecture and efficiency of neural communication across distinct brain networks in infants at birth.