bluuebunny/crossref_metadata_2025_split huggingface dataset:
RELATIONSHIP BETWEEN PARENTAL AGE AND SEVERITY OF OROFACIAL CLEFTS
Authors: Adamson Olawale , Oladugba Abimibola V. , Alade Azeez , Awotoye Waheed O. , Busch Tamara , Li Mary , Olotu Joy , Sule Veronica C. , Fashina Azeez , Olutayo James , Ogunlewe Mobolanle O. , Adeyemo Wasiu L. , Butali Azeez 
Published: February 2021

ABSTRACTOBJECTIVESThis study aims to investigate the relationship between paternal age, maternal age, and both on the severity of orofacial clefts.DESIGNThis was a retrospective study of cases which were subjects clinically diagnosed with non-syndromic cleft lip and/or palate (CL/P). Data was obtained from the AFRICRAN project database on Nigerian non-syndromic orofacial cleft cases.SETTINGThe samples for cases in this study were obtained at the Cleft clinic of Oral and Maxillofacial surgery at the Lagos University Teaching Hospital, Lagos.OUTCOMEPrimary outcome measure is severity of orofacial clefts and secondary outcome measure is to evaluate the effect of parental age in determining the incidence of left or right sided orofacial clefts.RESULTSThere is no statistical significant association between type of CL ± P and parental age in young fathers (p=0.93). When old fathers are considered, percentage of complete (more severe) CL ± P cases increases especially in old mothers and this was statistically significant (p=0.036). In old fathers, the risk of CL ± P is increased (OR: 2.66, CI: 1.04-6.80) and also there is increased risk of developing right sided CL ± P (OR: 1.61, CI: 1.0-2.59). There is reduced risk of isolated cleft palate in young fathers (OR: 0.36, CI: 0.07-1.71) but the risk increases when considering complete types (more severe) of isolated cleft palates (OR: 1.63, CI: 0.71-3.7)CONCLUSIONThe study shows a higher risk of CL ± P is associated with increase father’s age.
Acidogenic Fermentation of Sugarcane Vinasse and Glucose Using Two Different Anaerobic Digestion Inocula
Authors: Martins Juliana , de Araújo Hugo Valença , Mockaitis Gustavo , da Silva Ariovaldo José 
Published: February 2021

ABSTRACTVinasse is an agroindustrial wastewater obtained at large amounts in countries such as Brazil, which is one of the world greatest sugar and ethanol producers from sugarcane. Despite its most common use is as nutrient for fertirrigation in sugarcane crops nowadays, alternative processing has been intensely sought in last decades for vinasse aiming primarily the production of energy carriers and high-added value chemicals. One of these alternatives is the anaerobic digestion promoted by bacteria, which results in several products of economic importance. In view of these information, this work presents an investigation of acidogenic fermentation byC. acetobutylicumATCC 824 andC. beijerinckiiATCC 25752 was conducted in batch reactors by using synthetic vinasse and aqueous glucose solution as substrates. Evaluation of effects of microorganism and carbon source was focused mainly on the production of short chain organic acids (SCOAs), although other metabolites, such as ethanol, were also detected. Carbohydrates were effectively consumed by bacteria, so remaining concentrations of sucrose and glucose (Suc and Glu) in both substrates were considerably low at the end of tests. Lactic acid (HLa) was the prevailing metabolite in all experiments, determining the trends observed for total SCOAs content as a function of incubation time, while other acids were generated in much lesser amounts. Moreover, ethanol (EtOH) attained notably higher concentrations in batch reactors containing glucose as substrate, which showed more relevant production of this chemical. Maximum of 14.1 g HLa L−1was quantified for lactic acid at incubation time 96 h in reactor using synthetic vinasse andC. beijerinckii(VB), linked to a productivityP= 146.46 mg HLa L−1h−1and a yieldY= 1108.03 mg HLa (g Sue)−1. For ethanol, maximum was 1.6 g EtOH L−1, occurring in reactor containing glucose andC. acetobutylicum(GA) also at incubation time 90 h, resulting inP= 13.60 mg EtOH L−1h−1andY= 73.04 mg EtOH (g Glu)−1. Finally, kinetic models were adjusted to experimental data of carbohydrate content, lactate concentration and optical density (indicative of microorganism growth), showing good prediction capability as suggested by values of fit quality parameters such as Residual Sum of Squares (RSS) andR2.
A combined EM and proteomic analysis places HIV-1 Vpu at the crossroads of retromer and ESCRT complexes: PTPN23 is a Vpu-cofactor
Authors: Stoneham Charlotte A. , Langer Simon , De Jesus Paul D. , Wozniak Jacob M. , Lapek John , Deerinck Thomas , Thor Andrea , Pache Lars , Chanda Sumit K. , Gonzalez David J. , Ellisman Mark , Guatelli John 
Published: February 2021

AbstractThe HIV-1 accessory protein Vpu modulates membrane protein trafficking and degradation to provide evasion of immune surveillance. Targets of Vpu include CD4, HLAs, and BST-2. Several cellular pathways co-opted by Vpu have been identified, but the picture of Vpu’s itinerary and activities within membrane systems remains incomplete. Here, we used fusion proteins of Vpu and the enzyme ascorbate peroxidase (APEX2) to compare the ultrastructural locations and the proximal proteomes of wild type Vpu and Vpu-mutants. The proximity-omes of the proteins correlated with their ultrastructural locations and placed wild type Vpu near both retromer and ESCRT-0 complexes. Hierarchical clustering of protein abundances across the mutants was essential to interpreting the data and identified Vpu degradation-targets including CD4, HLA-C, and SEC12 as well as Vpu-cofactors including HGS, STAM, clathrin, and PTPN23, an ALIX-like protein. The Vpu-directed degradation of BST-2 required PTPN23 but not the retromer subunits. These data suggest that Vpu directs targets from sorting endosomes to degradation at multi-vesicular bodies via ESCRT-0 and PTPN23.Author SummaryVpu triggers the degradation or mis-localization of proteins important to the host’s immune response. Vpu acts as an adaptor, linking cellular protein targets to the ubiquitination and membrane trafficking machinery. Vpu has been localized to various cellular membrane systems. By fusing wild type Vpu and Vpu-mutants to the enzyme ascorbate peroxidase, we defined the cellular proteome in proximity to Vpu and correlated this with the protein’s location. We found that wild type Vpu is proximal to ESCRT proteins, retromer complexes, and sorting and late endosomal proteins. Functionally, we found that the Vpu-mediated degradation of the innate defense protein BST-2 required PTPN23, an ALIX-like protein, consistent with our observation of Vpu’s presence at the limiting membranes of multi-vesicular bodies.
The multidimensional nutritional niche of fungus-cultivar provisioning in free-ranging colonies of a neotropical leafcutter ant
Authors: Crumière Antonin J.J. , James Aidan , Lannes Pol , Mallett Sophie , Michelsen Anders , Rinnan Riikka , Shik Jonathan Z. 
Published: February 2021

AbstractThe foraging trails ofAttaleafcutter colonies are among the most iconic scenes in Neotropical ecosystems, with thousands of ants carrying freshly cut plant fragments back to their nests where they are used to provision a fungal food crop. We tested a hypothesis that the fungal cultivar’s multidimensional requirements for macronutrients (protein and carbohydrates) and minerals (Al, Ca, Cu, Fe, K, Mg, Mn, Na, P and Zn) govern the foraging breadth ofAtta colombicaleafcutter ants in a Panamanian rainforest. Analyses of freshly cut plant fragments carried by leafcutter foragers showed that the combination of fruits, flowers, and leaves provide for a broad realized nutritional niche that can maximize cultivar’s performance. And, while the leaves that comprised the most harvested resource also delivered an intake target containing protein in excess of the amounts that can maximize cultivar growth,in vitroexperiments showed that the minerals P, Al, and Fe can enhance the cultivar’s tolerance to protein-biased substrates, and potentially expand the ants’ foraging niche. Yet, the cultivar also exhibits narrow margins between mineral limitation and toxicity that may render plant fragments with seemingly optimal blends of macronutrients unsuitable for provisioning. Our approach highlights that optimal foraging is inherently multidimensional and links the foraging behavior of a generalist insect herbivore to the fundamental nutritional niche of its microbial symbiont.Significance StatementColonies ofAtta colombicaleafcutter ants can contain millions of specialized workers exhibiting large-scale generalist herbivory. Yet, this generalist foraging niche also depends on the poorly understood physiological needs of the ants’ domesticated fungal cultivar. We show the cultivar’s fundamental nutritional niche is broad for carbohydrates but narrower for protein and a suite of minerals, but that the cultivar’s sensitivity to excess protein is also mediated by Al, Fe, and P. More generally, this study decouples the multidimensional foraging strategies that enable a generalist herbivore to navigate a complex nutritional landscape and mix many imbalanced foods to achieve balanced cultivar provisioning.
Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy
Authors: Wang Chao , Fan Li , Zhan Lihong , Kodama Lay , Liu Bangyan , Chin Marcus , Li Yaqiao , Le David , Zhou Yungui , Condello Carlo , Grinberg Lea , Seeley William W. , Miller Bruce , Mok Sue-Ann , Gestwicki Jason , Gan Li 
Published: February 2021

AbstractActivation of microglia, the brain’s innate immune cells, is a prominent pathological feature in tauopathies, including Alzheimer’s disease. How microglia activation contributes to tau toxicity remains largely unknown. Here we show that nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, activated by tau, drives microglial-mediated tau propagation and toxicity. Constitutive activation of microglial NF-κB exacerbated, while inactivation diminished, tau seeding and spreading in PS19 mice, consistent with the observation that NF-κB activation accelerates processing of internalized tau fibrils in primary microglia. Remarkably, inhibition of microglial NF-κB specifically also rescued tau-mediated learning and memory deficits, and restored overall transcriptomic changes while increasing tau inclusions. On a single cell level, we discovered that tau-associated disease states in microglia were diminished by NF-κB inactivation and further transformed by constitutive NF-κB activation. Our study establishes a central role for microglial NF-κB signaling in mediating tau toxicity in tauopathy.
Planum Temporale grey matter volume asymmetries in new-born monkeys (Papio anubis)
Authors: Becker Yannick , Phelipon Romane , Sein Julien , Velly Lionel , Renaud Luc , Meguerditchian Adrien 
Published: February 2021

AbstractThe Planum Temporale (PT)is one of the key hubs of the language network in the human brain. The gross asymmetry of this perisylvian region toward the left brain was considered as the most emblematic marker of hemispheric specialization of language processes in the brain. Interestingly, this neuroanatomical signature was documented also in newborn infants and preterms, suggesting the early brain’s readiness for language acquisition. Nevertheless, this latter interpretation was questioned by a recent report in nonhuman primates of a potential similar signature in newborn baboonsPapio anubisbased onPTsurface measures. Whether this “tip of the iceberg”PTasymmetry is actually reflecting asymmetry of its underlying grey matter volume remain unclear but critical to investigate potential continuities of cortical specialization with human infants. Here we report a population-level leftward asymmetry of the Planum Temporale grey matter volume inin vivo34 newborn baboonsPapio anubis, which showed intra-individual positive correlation withPTsurface’s asymmetry measures but also a more pronounced degree of leftward asymmetry at the population-level. This finding demonstrates thatPTleftward structural asymmetry in this Old World monkey species is a robust phenomenon in early primate development, which clearly speaks for a continuity with early human brain specialization. Results also strengthen the hypothesis that early PT asymmetry might be not a human-specific marker for the pre-wired language-ready brain in infants.
Catabolism of lysosome-related organelles in color-changing spiders supports intracellular turnover of pigments
Authors: Figon Florent , Hurbain Ilse , Heiligenstein Xavier , Trépout Sylvain , Medjoubi Kadda , Somogyi Andrea , Delevoye Cédric , Raposo Graça , Casas Jérôme 
Published: February 2021

AbstractPigment organelles of vertebrates belong to the lysosome-related organelle (LRO) family, of which melanin-producing melanosomes are the prototypes. While their anabolism has been extensively unraveled through the study of melanosomes in skin melanocytes, their catabolism remains poorly known. Here, we tap into the unique ability of crab spiders to reversibly change body coloration to examine the catabolism of their pigment organelles. By combining ultrastructural and metal analyses on high-pressure frozen integuments, we first assess whether pigment organelles of crab spiders belong to the LRO family and, second, how their catabolism is intracellularly processed. Using scanning-transmission electron microscopy, electron tomography and nanoscale Synchrotron-based scanning X-ray fluorescence, we show that pigment organelles possess ultrastructural and chemical hallmarks of LROs, including intraluminal vesicles and metal deposits, similar to melanosomes. Monitoring ultrastructural changes during bleaching suggests that the catabolism of pigment organelles involves the degradation and removal of their intraluminal content, possibly through lysosomal mechanisms. In contrast to skin melanosomes, anabolism and catabolism of pigments proceed within the same cell without requiring either cell death or secretion/phagocytosis. Our work hence provides support for the hypothesis that the endolysosomal system is fully functionalized for within-cell turnover of pigments, leading to functional maintenance under adverse conditions and phenotypic plasticity. First formulated for eye melanosomes in the context of human vision, the hypothesis of intracellular turnover of pigments gets unprecedented strong support from pigment organelles of spiders.
Chemotherapy coupled to macrophage inhibition leads to enhanced T and B cell infiltration and durable triple negative breast cancer regression
Authors: Singh Swarnima , Lee Nigel , Pedroza Diego A. , Bado Igor , Zhang Licheng , Aguirre Sergio , Hamor Clark , Shen Yichao , Xu Yitian , Hu Jingyuan , Gao Yang , Zhao Na , Chen Shu-Hsia , Wan Ying-Wooi , Liu Zhandong , Chang Jeffrey T. , Hollern Daniel , Perou Charles M. , Zhang Xiang H.F. , Rosen Jeffrey M. 
Published: February 2021

AbstractImmunosuppressive elements within the tumor microenvironment such as Tumor Associated Macrophages (TAMs) can present a barrier to successful anti-tumor responses by cytolytic T cells. We employed preclinical syngeneic p53 null mouse models of triple negative breast cancer (TNBC) to develop a treatment regimen that harnessed the immunostimulatory effects of low-dose cyclophosphamide coupled with the pharmacologic inhibition of TAMs using either a small molecule CSF1R inhibitor or an anti-CSF1R antibody. This therapeutic combination was used to successfully treat several highly aggressive TNBC murine mammary tumors and lung metastasis. Using this regimen and single cell RNA sequencing we characterized tumor infiltrating lymphocytes (TILs) including helper T cells and antigen-presenting B cells that were highly enriched in good responders to combination therapy. Using high dimensional imaging techniques, we identified the close spatial localization of B220+ CD86+ activated B cells and CD4+ T cells in tertiary lymphoid structures that were present up to 6 weeks post-treatment in one model that also exhibited long-term tumor regression post-treatment. We also characterized the transcriptional and metabolic heterogeneity of TAMS in these two closely related claudin-low/mesenchymal subtype tumor models with differential treatment responses. A murine TAM signature derived from the T12 model is highly expressed and conserved in human claudin-low breast cancers, and high expression of the T12 signature correlated with reduced overall survival. This T12 tumor TAM signature may help identify human claudin-low breast cancer patients that will benefit from the combination of cyclophosphamide and anti-CSF1R therapy. These studies illustrate the complexity of the tumor immune microenvironment and highlight different immune responses that result from rationale combinations of immunotherapy.SignificanceA treatment regimen that harnessed the immunostimulatory effects of cyclophosphamide coupled with the inhibition of CSF1R was used to successfully treat several highly aggressive claudin-low TNBC murine mammary tumors and lung metastasis.
Rewritable Two-Dimensional DNA-Based Data Storage with Machine Learning Reconstruction
Authors: Pan Chao , Tabatabaei S. Kasra , Tabatabaei Yazdi SM Hossein , Hernandez Alvaro G. , Schroeder Charles M. , Milenkovic Olgica 
Published: February 2021

AbstractDNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores high-density images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy.
Dynamic large-scale connectivity of intrinsic cortical oscillations supports adaptive listening in challenging conditions
Authors: Alavash Mohsen , Tune Sarah , Obleser Jonas 
Published: February 2021

AbstractIn multi-talker situations individuals adapt behaviorally to the listening challenge mostly with ease, but how do brain neural networks shape this adaptation? We here establish a long-sought link between large-scale neural communications in electrophysiology and behavioral success in the control of attention in difficult listening situations. In an age-varying sample of N = 154 individuals, we find that connectivity between intrinsic neural oscillations extracted from source-reconstructed electroencephalography is regulated according to the listener’s goal during a challenging dual­ talker task. These dynamics occur as spatially organized modulations in power-envelope correlations of alpha and low-beta neural oscillations during ~2 seconds intervals most critical for listening behavior relative to resting-state baseline. First, left frontoparietal low-beta connectivity (16-24 Hz) increased during anticipation and processing of spatial-attention cue before speech presentation. Second, posterior alpha connectivity (7-11 Hz) decreased during comprehension of competing speech, particularly around target-word presentation. Connectivity dynamics of these networks were predictive of individual differences in the speed and accuracy of target-word identification, respectively, but proved unconfounded by changes in neural oscillatory activity strength. Successful adaptation to a listening challenge thus latches onto two distinct yet complementary neural systems: a beta-tuned frontoparietal network enabling the flexible adaptation to attentive listening state and an alpha-tuned posterior network supporting attention to speech.Significance StatementAttending to relevant information during listening is key to human communication. How does this adaptive behavior rely upon neural communications? We here follow up on the long-standing conjecture that, large-scale brain network dynamics constrain our successful adaptation to cognitive challenges. We provide evidence in support of two intrinsic, frequency-specific neural networks that underlie distinct behavioral aspects of successful listening: a beta-tuned frontoparietal network enabling the flexible adaptation to attentive listening state, and an alpha-tuned posterior cortical network supporting attention to speech. These findings shed light on how large-scale neural communication dynamics underlie attentive listening and open new opportunities for brain network-based intervention in hearing loss and its neurocognitive consequences.
Solving the Sample Size Problem for Resource Selection Analysis
Authors: Street Garrett M. , Potts Jonathan R. , Börger Luca , Beasley James C. , Demarais Stephen , Fryxell John M. , McLoughlin Philip D. , Monteith Kevin L. , Prokopenko Christina M. , Ribeiro Miltinho C. , Rodgers Arthur R. , Strickland Bronson K. , van Beest Floris M. , Bernasconi David A. , Beumer Larissa T. , Dharmarajan Guha , Dwinnell Samantha P. , Keiter David A. , Keuroghlian Alexine , Newediuk Levi J. , Oshima Júlia Emi F. , Rhodes Olin , Schlichting Peter E. , Schmidt Niels M. , Wal Eric Vander 
Published: February 2021

AbstractSample size sufficiency is a critical consideration for conducting Resource-Selection Analyses (RSAs) from GPS-based animal telemetry. Cited thresholds for sufficiency include a number of captured animalsM≥ 30 and as many relocations per animalNas possible. These thresholds render many RSA-based studies misleading if large sample sizes were truly insufficient, or unpublishable if small sample sizes were sufficient but failed to meet reviewer expectations.We provide the first comprehensive solution for RSA sample size by deriving closed-form mathematical expressions for the number of animalsMand the number of relocations per animalNrequired for model outputs to a given degree of precision. The sample sizes needed depend on just 2 biologically meaningful quantities: habitat selection strength and a novel measure of landscape complexity, which we define rigorously. The mathematical expressions are calculable for any environmental dataset at any spatial scale and are applicable to any study involving resource selection (including sessile organisms). We validate our analytical solutions using globally relevant empirical data including 5,678,623 GPS locations from 511 animals from 10 species (omnivores, carnivores, and herbivores living in boreal, temperate, and tropical forests, montane woodlands, swamps, and arctic tundra).Our analytic expressions show that the requiredMandNmust decline with increasing selection strength and increasing landscape complexity, and this decline is insensitive to the definition of availability used in the analysis. Our results contradict conventional wisdom by demonstrating that the most biologically relevant effects on the utilization distribution (i.e. those landscape conditions with the greatest absolute magnitude of resource selection) can often be estimated with far fewer data than is commonly assumed.We identify several critical steps in implementing these equations, including (i) a priori selection of expected model coefficients, and (ii) sampling intensity for background (absence/pseudo-absence) data within a given definition of availability. We show that random sampling of background data violates the underlying mathematics of RSA, leading to incorrect values for necessaryMandNand potentially incorrect RSA model outputs. We argue that these equations should be a mandatory component for all future RSA studies.