bluuebunny/crossref_metadata_2025_split huggingface dataset:
The contribution of hippocampal subfields to the progression of neurodegeneration
Authors: Kwak Kichang , Niethammer Marc , Giovanello Kelly S. , Styner Martin , Dayan Eran ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: May 2020

AbstractMild cognitive impairment (MCI) is often considered the precursor of Alzheimer’s disease. However, MCI is associated with substantially variable progression rates, which are not well understood. Attempts to identify the mechanisms that underlie MCI progression have often focused on the hippocampus, but have mostly overlooked its intricate structure and subdivisions. Here, we utilized deep learning to delineate the contribution of hippocampal subfields to MCI progression using a total sample of 1157 subjects (349 in the training set, 427 in a validation set and 381 in the testing set). We propose a dense convolutional neural network architecture that differentiates stable and progressive MCI based on hippocampal morphometry. The proposed deep learning model predicted MCI progression with an accuracy of 75.85%. A novel implementation of occlusion analysis revealed marked differences in the contribution of hippocampal subfields to the performance of the model, with presubiculum, CA1, subiculum, and molecular layer showing the most central role. Moreover, the analysis reveals that 10.5% of the volume of the hippocampus was redundant in the differentiation between stable and progressive MCI. Our predictive model uncovers pronounced differences in the contribution of hippocampal subfields to the progression of MCI. The results may reflect the sparing of hippocampal structure in individuals with a slower progression of neurodegeneration.
Carbohydrate binding domains facilitate efficient oligosaccharides synthesis by enhancing mutant catalytic domain transglycosylation activity
Authors: Bandi Chandra Kanth , Goncalves Antonio , Pingali Sai Venkatesh , Chundawat Shishir P. S. 
Published: May 2020

AbstractChemoenzymatic approaches using carbohydrate-active enzymes (CAZymes) offer a promising avenue for synthesis of glycans like oligosaccharides. Here, we report a novel chemoenzymatic route for cellodextrins synthesis employed by chimeric CAZymes, akin to native glycosyltransferases, involving the unprecedented participation of a ‘non-catalytic’ lectin-like or carbohydrate-binding domains (CBMs) in the catalytic step for glycosidic bond synthesis using β-cellobiosyl donor sugars as activated substrates. CBMs are often thought to play a passive substrate targeting role in enzymatic glycosylation reactions mostly via overcoming substrate diffusion limitations for tethered catalytic domains (CDs) but are not known to participate directly in any nucleophilic substitution mechanisms that impact the actual glycosyl transfer step. Our study provides evidence for the direct participation of CBMs in the catalytic reaction step for β-glucan glycosidic bonds synthesis enhancing activity for CBM-based CAZyme chimeras by >140-fold over CDs alone. Dynamic intra-domain interactions that facilitate this poorly understood reaction mechanism were further revealed by small-angle X-ray scattering structural analysis along with detailed mutagenesis studies to shed light on our current limited understanding of similar transglycosylation-type reaction mechanisms. In summary, our study provides a novel strategy for engineering similar CBM-based CAZyme chimeras for synthesis of bespoke oligosaccharides using simple activated sugar monomers.
A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues
Authors: Glaser Adam K. , Bishop Kevin W. , Barner Lindsey A. , Susaki Etsuo A. , Kubota Shimpei I. , Gao Gan , Serafin Robert B. , Balaram Pooja , Turschak Emily , Nicovich Philip R. , Lai Hoyin , Lucas Luciano A.G. , Yi Yating , Nichols Eva K. , Huang Hongyi , Reder Nicholas P. , Wilson Jasmine J. , Sivakumar Ramya , Shamskhou Elya , Stoltzfus Caleb R. , Wei Xing , Hempton Andrew K. , Pende Marko , Murawala Prayag , Dodt Hans U. , Imaizumi Takato , Shendure Jay , Beliveau Brian J. , Gerner Michael Y. , Xin Li , Zhao Hu , True Lawrence D. , Reid R. Clay , Chandrashekar Jayaram , Ueda Hiroki R. , Svoboda Karel , Liu Jonathan T.C. 
Published: May 2020

AbstractLight-sheet microscopy has emerged as the preferred means for high-throughput volumetric imaging of cleared tissues. However, there is a need for a user-friendly system that can address imaging applications with varied requirements in terms of resolution (mesoscopic to sub-micrometer), sample geometry (size, shape, and number), and compatibility with tissue-clearing protocols and sample holders of various refractive indices. We present a ‘hybrid’ system that combines a novel non-orthogonal dual-objective and conventional (orthogonal) open-top light-sheet architecture for versatile multi-scale volumetric imaging.
Endophilin A1 promotes Actin Polymerization in response to Ca2+/calmodulin to Initiate Structural Plasticity of Dendritic Spines
Authors: Yang Yanrui , Chen Jiang , Chen Xue , Li Di , He Jianfeng , Zhao Shun , Yang Xiaoyu , Deng Shikung , Wang Dou , Guo Zhenzhen , Zhu Shaoxia , Li Dong , Ma Cong , Liang Xin , Shi Yun S. , Liu Jia-Jia 
Published: May 2020

AbstractDendritic spines of excitatory neurons undergo activity-dependent structural and functional plasticity, which are cellular correlates of learning and memory. However, mechanisms underlying the rapid morphological changes immediately after NMDAR-mediated Ca2+influx into spines remain poorly understood. Here we report that endophilin A1, a neuronal N-BAR protein, orchestrates membrane dynamics with actin polymerization to initiate spine enlargement in the induction phase of long-term potentiation (LTP). Upon LTP induction, Ca2+/calmodulin enhances its binding to both membrane and p140Cap, a cytoskeleton regulator. As a result, endophilin A1 rapidly associates with the relaxed plasma membrane and promotes actin polymerization, leading to acute expansion of spine head. Moreover, not only the p140Cap-binding, but also calmodulin- and membrane-binding capacities of endophilin A1 are required for LTP and long-term memory. Thus, endophilin A1 functions as calmodulin effector to drive spine enlargement in response to Ca2+influx in the initial phase of structural plasticity.
High-Dimensional Immunophenotyping of Murine T-cell and B-cell Subsets
Authors: Mincham Kyle T. , Young Jacob D. , Strickland Deborah H. 
Published: May 2020

Purpose and appropriate sample typesThis 19-parameter, 18-colour flow cytometry panel was designed and optimised to enable the comprehensive and simultaneous immunophenotyping of distinct T-cell and B-cell subsets within murine lymphoid tissues (Table 1). Cellular populations identified by employing this OMIP include 4 major subsets of B-cells (memory, activated, plasma cells and plasmablasts) and 7 major subsets of CD4+T-cells (naïve, central memory, effector memory, helper, regulatory, follicular helper and follicular regulatory). Staining was performed on freshly isolated splenocytes from 21-day-old neonatal BALB/c mice, however due to the omission of mouse strain-specific markers, this OMIP can be implemented across a range of murine models where in-depth immunophenotyping of the diverse repertoire of T-cell and B-cell populations localised within lymphoid tissues is required.
Transcriptional comparison of Testicular Adrenal Rest Tumors with fetal and adult tissues
Authors: Schröder Mariska A.M. , Sweep Fred C.G.J. , van Herwaarden Antonius E. , Rowan Alan E. , Korbie Darren , Mitchell Rod T. , Stikkelbroeck Nike M.M.L. , Claahsen – van der Grinten Hedi L. , Span Paul N. 
Published: May 2020

AbstractTesticular Adrenal Rest Tumors (TART) are a common complication of unknown origin in patients with Congenital Adrenal Hyperplasia. These benign tumors may derive from cells of adrenal origin or from pluripotent progenitor cells from the fetal adrenogonadal primordium. By comparing the transcriptome of TART with fetal- and adult-testis and adrenal tissues, this study aims to unravel the origin of TART. Targeted transcriptome sequencing was followed by unsupervised clustering-, differential expression-, functional enrichment- and pathway analyses. Immunohistochemistry demonstrated co-expression of adrenal-specific CYP11B1 and testis-specific HSD17B3 in TART, indicating the existence of a distinct TART cell exhibiting both adrenal- and testicular characteristics. Principal component analysis indicated that the TART transcriptome was distinct from either adrenal or testis fetal tissue, making a progenitor-like phenotype of TART unlikely. Rather, TART appears to originate from -or differentiate into-a mature cell type, with both adrenal- and testicular characteristics. The present study, the first to describe the TART transcriptome, expands knowledge about the identity and functional characteristics of TART and identifies clinically targetable pathways associated with fibrosis.
Teacher-student neural coupling during teaching and learning
Authors: Nguyen Mai , Chang Ashley , Micciche Emily , Meshulam Meir , Nastase Samuel A. , Hasson Uri 
Published: May 2020

AbstractHuman communication is remarkably versatile, enabling teachers to share highly abstracted and novel information with their students. What neural processes enable such transfer of information across brains during naturalistic teaching and learning? Here, we show that during lectures, wherein information transmission is unidirectional and flows from the teacher to the student, the student’s brain mirrors the teacher’s brain and that this neural coupling is correlated with learning outcomes. A teacher was scanned in fMRI giving an oral lecture with slides on a scientific topic followed by a review lecture. Students were then scanned watching either the intact lecture and review (N= 20) or a temporally scrambled version of the lecture (N= 20). Using intersubject correlation (ISC), we observed widespread teacher-student neural coupling spanning sensory cortex and language regions along the superior temporal sulcus as well as higher-level regions including posterior medial cortex (PMC), superior parietal lobule (SPL), and dorsolateral and dorsomedial prefrontal cortex. Teacher-student alignment in higher-level areas was not observed when learning was disrupted by temporally scrambling the lecture. Moreover, teacher-student coupling in PMC was significantly correlated with learning outcomes: the more closely the student’s brain mirrored the teacher’s brain, the more the student improved between behavioral pre-learning and post-learning assessments. Together, these results suggest that the alignment of neural responses between teacher and students may underlie effective communication of complex information across brains in classroom settings.Significance statementHow is technical, non-narrative information communicated from one brain to another during teaching and learning? In this fMRI study, we show that the DMN activity of teachers and students are coupled during naturalistic teaching. This teacher-student neural coupling emerges only during intact learning and is correlated with learning outcomes. Together, these findings suggest that teacher-student neural alignment underlies effective communication during teaching.
Soil and root nutrient chemistry structure root‐associated fungal assemblages in temperate forests
Authors: Nguyen Dung Quang , Schneider Dominik , Brinkmann Nicole , Song Bin , Janz Dennis , Schöning Ingo , Daniel Rolf , Pena Rodica , Polle Andrea 
Published: May 2020

SummaryRoot‐associated fungi (RAF) link nutrient fluxes between soil and roots and thus play important roles in ecosystem functioning. To enhance our understanding of the factors that control RAF, we fitted statistical models to explain variation in RAF community structure using data from 150 temperate forest sites covering a broad range of environmental conditions and chemical root traits. We found that variation in RAF communities was related to both root traits (e.g., cations, carbohydrates, NO3−) and soil properties (pH, cations, moisture, C/N). The identified drivers were the combined result of distinct response patterns of fungal taxa (determined at the rank of orders) to biotic and abiotic factors. Our results support that RAF community variation is related to evolutionary adaptedness of fungal lineages and consequently, drivers of RAF communities are context‐dependent.
Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non‐marine environments
Authors: Tanaka Mami , Kumakura Daiki , Mino Sayaka , Doi Hidetaka , Ogura Yoshitoshi , Hayashi Tetsuya , Yumoto Isao , Cai Man , Zhou Yu‐Guang , Gomez‐Gil Bruno , Araki Toshiyoshi , Sawabe Tomoo 
Published: May 2020

SummaryMembers of the family Vibrionaceae are generally found in marine and brackish environments, playing important roles in nutrient cycling. The Rumoiensis clade is an unconventional group in the genus Vibrio, currently comprising six species from different origins including two species isolated from non‐marine environments. In this study, we performed comparative genome analysis of all six species in the clade using their complete genome sequences. We found that two non‐marine species, Vibrio casei and Vibrio gangliei, lacked the genes responsible for algal polysaccharide degradation, while a number of glycoside hydrolase genes were enriched in these two species. Expansion of insertion sequences was observed in V. casei and Vibrio rumoiensis, which suggests ongoing genomic changes associated with niche adaptations. The genes responsible for the metabolism of glucosylglycerate, a compound known to play a role as compatible solutes under nitrogen limitation, were conserved across the clade. These characteristics, along with genes encoding species‐specific functions, may reflect the habit expansion which has led to the current distribution of Rumoiensis clade species. Genome analysis of all species in a single clade give us valuable insights into the genomic background of the Rumoiensis clade species and emphasize the genomic diversity and versatility of Vibrionaceae.
The Real Estate Frontier
Authors: Gillespie Tom 
Published: May 2020

AbstractAfrica's major cities are experiencing dramatic transformation as a result of growing real estate investment. This article explores whether existing theories can explain the dynamics of urban redevelopment in an African context, and how African cases can inform new theorizations of real estate driven urban transformation. Examining the utility of theories of gentrification and speculative urbanism for understanding urban redevelopment in Accra, Ghana, it argues that urban redevelopment in this city has been shaped by its particular (post)colonial history of state land acquisition and urban planning. Rather than simply identifying empirical variation on established theories, however, the article draws on recent research on commodity frontiers to propose an original theorization of urban redevelopment in Accra in terms of the production of a ‘real estate frontier’. This real estate frontier is characterized by the incremental and contested commodification of state land to enable the growth of the real estate sector in the city. The article concludes by calling for a comparative research agenda to better understand real estate frontiers globally.
OUT IN SPACE: Difference and Abstraction in Planetary Urbanization
Authors: Angelo Hillary , Goh Kian 
Published: May 2020

AbstractA common thread has emerged in recent critiques of planetary urbanization. Whether on empirical, epistemological or theoretical grounds, critics tend to posit ‘difference against abstraction’, arguing that planetary urbanization—as an abstract theory of large‐scale phenomena—occludes ‘everyday’ embodied, small‐scale and place‐based forms of social difference in its production and/or application. Here we engage with this critique as two queer, feminist scholars sympathetic both to critics’ arguments about the politics of knowledge production and to the planetary urbanization framework. While we agree that the theory's most visible adherents have not systematically engaged with questions of difference, especially at smaller scales of social analysis, we reject the suggestion that planetary urbanization is inherently incompatible with such concerns. Rather, we argue that the opposite is true. Using examples from our own research, we show how the planetary urbanization framework—by enforcing a multiscalar and non‐city‐centric view of apparently local phenomena—can be central to theorizing and understanding social difference at the level of everyday life in empirical research.
The impact of housing conditions on health outcomes
Authors: Palacios Juan , Eichholtz Piet , Kok Nils , Aydin Erdal 
Published: May 2020

AbstractWe investigate the relationship between housing conditions and health outcomes using a data set that tracks 25,000 German households over 25 years. We document that individuals exposed to poor housing conditions report worse mental and physical health, and experience an 11% increase in doctor visits, increasing to 20% for age groups over 64. The analysis controls for individual, dwelling, and temporal fixed effects, and is robust to changes in socioeconomic status, lifestyle choices, and neighborhood conditions. As a robustness check, we use home renovations as major a trigger of changes in housing conditions. Restricting the analysis to tenants, whose renovations are paid by landlords, we document that home renovations significantly reduce doctor visits, corroborating the findings on home conditions and health outcomes.
Ultrafiltration volume by once‐weekly hemodialysis is a predictor of technique survival of combination therapy with peritoneal dialysis and hemodialysis
Authors: Tanaka Mototsugu , Ishibashi Yoshitaka , Hamasaki Yoshifumi , Kamijo Yuka , Idei Mayumi , Nishi Takahiro , Takeda Michio , Nonaka Hiroshi , Nangaku Masaomi , Mise Naobumi 
Published: May 2020

AbstractOverhydration is a major cause of technique failure of peritoneal dialysis (PD). Hence, we investigated the impact of ultrafiltration (UF) volume by once‐weekly hemodialysis (HD), excess volume beyond their dry weight, on technique survival of PD and HD combination therapy (PD+HD). Forty‐six anuric PD+HD patients were divided into three groups according to baseline UF volume by HD: low‐UF (<mean − 1SD), middle‐UF (≥mean − 1SD and <mean + 1SD), and high‐UF (≥mean + 1SD). High‐UF group showed larger extracellular water normalized to height (P = .038) and longer HD sessions (P < .001) compared with low‐UF group, whereas low‐UF group was older than middle‐UF group (P = .001). Technique survival rate was significantly lower in high‐UF group than in low and middle‐UF groups (P < .001), and the rates at 44 months were 80%, 90%, 20% in low, middle, and high‐UF groups, respectively. Chronic overhydration was the leading cause of technique failure for all. This study suggests that fluid overload remains a major cause of technique failure of PD even after once‐weekly HD is added.
Incidental findings detected on cone beam computed tomography in an older population for pre‐implant assessment
Authors: Nguyen P‐N , Kruger E , Huang T , Koong B 
Published: May 2020

AbstractObjectivesThe aim of this retrospective study was to record incidental findings in CBCT scans taken in an older population for pre‐implant assessment, and to examine whether these findings would influence the intended dental implant placement.Methods300 consecutive CBCT scans over the age of 40 years was carried out. The incidental findings were grouped into regions as follows: dentoalveolar structures, maxilla and mandible, paranasal sinuses, temporomandibular joint (TMJ), naso/oral‐pharyngeal airway, cervical spine and neurovascular canals. The incidental findings are further categories into their significance towards the intended treatment plan.ResultIncidental findings were noted on all of the scans. 555 incidental findings (1.85 findings/scan) were identified. The highest number of incidental findings was in the sinuses (34%), followed by dentoalveolar structures (31%), nasal/oral‐pharyngeal airway (12%), maxilla and mandible (10%), TMJ (6%), cervical spine (4%) and neurovascular canals (3%). A total of 37% of findings required follow‐up. In 12% of cases detection of the incidental findings lead to amendment or abortion of the intended implant treatment plan.ConclusionIncidental findings within and beyond the region of interest are common in CBCT scans. The numbers of incidental findings per scan in an older population is higher than in a younger population.
Receptive anal sex contributes substantially to heterosexually acquired HIV infections among at‐risk women in twenty US cities: Results from a modelling analysis
Authors: Elmes Jocelyn , Silhol Romain , Hess Kristen L. , Gedge Lukyn M. , Nordsletten Ashley , Staunton Roisin , Anton Peter , Shacklett Barbara , McGowan Ian , Dang Que , Adimora Adaora A. , Dimitrov Dobromir T. , Aral Sevgi , Handanagic Senad , Paz‐Bailey Gabriela , Boily Marie‐Claude 
Published: May 2020

ProblemReceptive anal intercourse (RAI) is more efficient than receptive vaginal intercourse (RVI) at transmitting HIV, but its contribution to heterosexually acquired HIV infections among at‐risk women in the USA is unclear.Method of studyWe analysed sexual behaviour data from surveys of 9152 low‐income heterosexual women living in 20 cities with high rates of HIV conducted in 2010 and 2013 as part of US National HIV Behavioral Surveillance. We estimated RAI prevalence (past‐year RAI) and RAI fraction (fraction of all sex acts (RVI and RAI) at the last sexual episode that were RAI among those reporting past‐year RAI) overall and by key demographic characteristics. These results and HIV incidence were used to calibrate a risk equation model to estimate the population attributable fraction of new HIV infections due to RAI (PAFRAI) accounting for uncertainty in parameter assumptions.ResultsReceptive anal intercourse prevalence (overall: 32%, city range: 19%‐60%) and RAI fraction (overall: 27%, city range: 18%‐34%) were high overall and across cities, and positively associated with exchange sex. RAI accounted for an estimated 41% (uncertainty range: 18%‐55%) of new infections overall (city range: 21%‐57%). Variability in PAFRAI estimates was most influenced by uncertainty in the estimate of the per‐act increased risk of RAI relative to RVI and the number of sex acts.ConclusionReceptive anal intercourse may contribute disproportionately to new heterosexually acquired HIV infections among at‐risk low‐income women in the USA, meaning that tools to prevent HIV transmission during RAI are warranted. The number of RVI and RAI acts should also be collected to monitor heterosexually acquired HIV infections.