bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes of Humoral Immunity Response in SARS-CoV-2 Convalescent Patients over 8 months
Authors: Peng Pai , Hu Jie , Deng Hai-jun , Liu Bei-zhong , Wang Kai , Tang Ni , Huang Ai-long 
Published: November 2020

AbstractMany countries around the world have all seen a sharp rise in COVID-19 cases as the second wave since the beginning of October 2020. Decline of antibodies response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) that was reported exclusively in the early month increases the risk of reinfection for convalescent individuals. There is a current need to follow the maintenance of special antibodies against SARS-CoV-2. Here, we reported changes of antibodies against SARS-CoV-2 in convalescent patients over 8 months. Antibodies of all 20 participants targeting SARS-CoV-2 spike receptor binding-domain (RBD) had decreased from a mean OD450value 1.78 to 0.38 over 8 months. The neutralizing antibody (NAb) titers decreased from the mean ID50value 836 to 170. The NAb titers were significantly correlated with IgG level during 8 months (P<0.001). Furthermore, while RBD-specific IgG existence of 25% (5/20) convalescent plasma was undetectable, the NAb titers of 15% (3/20) convalescent plasma decreased below the threshold. In addition, compared to wild-type SARS-CoV-2 (S-D614), lower titers of neutralizing antibodies against its G614 variant were shown at 8 months after symptom onset. This study has important implications when considering antibody protection against SARS-CoV-2 reinfection.
The role of directionality in determining spatiotemporal tau pathology differs between AD-Like and Non-AD-Like mouse models
Authors: Mezias Christopher , Raj Ashish 
Published: November 2020

ABSTRACTIntroductionCurrent research indicates divergent spatiotemporal tauopathy progression between conditions and implicates transsynaptic connectome-based spread as a main mechanism. We examine tauopathy and connectome interactions to investigate why different spatiotemporal patterns of pathology arise.MethodsWe test whether divergent spatiotemporal tau pathology patterns from 15 mouse-model datasets can be explained by a directional bias in tau transmission along fiber tracts via a mathematical model called Directed Network Transmission (DNT).ResultsAmyloid-comorbid tauopathic mouse models meant to mimic AD demonstrate spatiotemporal tauopathy patterns consistent with retrograde direction spread biases. Non-amyloid-comorbid mice demonstrate no consistent spread biases. Further, canonically ‘early’ tau pathology regions in AD are implicated as having earliest pathology in a simulation with random tauopathy seeding locations with retrograde biased spread.DiscussionThese results implicate directional biases in tau pathology spread along fiber tracts as a strong candidate explanation for divergent spatiotemporal tau progression between conditions.
Whitebait conservation and protected areas at non-tidal rivermouths: integrating biogeography and environmental controls on īnanga (Galaxias maculatus) spawning grounds
Authors: Orchard Shane , Schiel David R. 
Published: November 2020

AbstractGalaxias maculatusis a declining amphidromous fish that supports culturally-important whitebait fisheries in New Zealand and elsewhere in the Pacific. As a largely annual species, the seasonal productivity of spawning grounds has a strong influence on the availability of recruits. Spawning ground protection is urgently required to reverse historical degradation and improve prospects for the maintenance of sustainable fisheries. Although spawning habitat has been well characterised in tidal rivers where it is structured by water level changes on spring high tides, there has been no previous study of spawning in non-tidal rivermouths. We assessed seven non-tidal rivers over four months using a census survey approach to quantify spawning activity, identify environmental cues, and characterise fundamental aspects of the biogeography of spawning grounds. We report conclusive results that include a) identification of compact spawning reaches near the rivermouths, b) triggering of spawning events by periods of elevated water levels that were often of very short duration, suggesting that potential lunar cues were less important and that rapid fish movements had likely occurred within the catchment prior to spawning events, and c) consistent vertical structuring of spawning grounds above typical low-flow levels with associated horizontal translation away from the river channel, leading to increased exposure to anthropogenic stressors and associated management implications for protecting the areas concerned. These consistent patterns provide a sound basis for advancing the management of non-tidal rivermouths. Attention to flood management, vegetation control, and bankside recreational activities is required and may be assisted by quantifying spawning ground biogeography. The identification of rapid responses to environmental cues deserves further research to assess implications for floodplain connectivity management to support fish movements in emphemeral flowpaths, and as a potential source of bias in commonly-used fish survey methodologies.
Library-free BoxCarDIA solves the missing value problem in label-free quantitative proteomics
Authors: Mehta Devang , Scandola Sabine , Uhrig R. Glen 
Published: November 2020

AbstractThe last decade has seen significant advances in the application of quantitative mass spectrometry-based proteomics technologies to tackle important questions in plant biology. The current standard for quantitative proteomics in plants is the use of data-dependent acquisition (DDA) analysis with or without the use of chemical labels. However, the DDA approach preferentially measures higher abundant proteins, and often requires data imputation due to quantification inconsistency between samples. In this study we systematically benchmarked a recently developed library-free data-independent acquisition (directDIA) method against a state-of-the-art DDA label-free quantitative proteomics workflow for plants. We next developed a novel acquisition approach combining MS1-level BoxCar acquisition with MS2-level directDIA analysis that we call BoxCarDIA. DirectDIA achieves a 33% increase in protein quantification over traditional DDA, and BoxCarDIA a further 8%, without any changes in instrumentation, offline fractionation, or increases in mass-spectrometer acquisition time. BoxCarDIA, especially, offers wholly reproducible quantification of proteins between replicate injections, thereby addressing the long-standing missing-value problem in label-free quantitative proteomics. Further, we find that the gains in dynamic range sampling by directDIA and BoxCarDIA translate to deeper quantification of key, low abundant, functional protein classes (e.g., protein kinases and transcription factors) that are underrepresented in data acquired using DDA. We applied these methods to perform a quantitative proteomic comparison of dark and light grown Arabidopsis cell cultures, providing a critical resource for future plant interactome studies. Our results establish BoxCarDIA as the new method of choice in quantitative proteomics using Orbitrap-type mass-spectrometers, particularly for proteomes with large dynamic range such as that of plants.
The evolution of a placenta is not linked to increased brain size in poeciliid fishes
Authors: Rowiński P. K. , Näslund J. , Sowersby W. , Eckerström-Liedholm S. , Rogell B. 
Published: November 2020

ABSTRACTMaternal investment is considered to have a direct influence on the size of energetically costly organs, including the brain. In placental organisms, offspring are supplied with nutrients during pre-natal development, potentially modulating brain size. However, the coevolution of the placenta and brain size remains largely unknown in non-mammalian taxa. Here, using eight poeciliid fish species, we test if species with placental structures invest more resources into offspring brain development than species without placental structures. We predict that matrotrophy may entail higher nutrient provisioning rates to the developing embryo than lecithotrophy, resulting in larger brain sizes in offspring of matrotrophic species, and that a relatively larger part of the total brain growth would occur at younger ages (leading to a shallower ontogenetic brain size allometry). We took non-invasive brain size measurements during the first four weeks of life, and compared these to somatic growth measurements. Contrary to our expectations, we did not find any differences in brain size between the two maternal strategies. Furthermore, we did not find any differences in how relative brain size changed over ontogenetic development, between placental and non-placental species. In contrast to the marsupial/placental transition, the species investigated here only exhibit pre-natal provisioning, which may reduce the potential for maternal investment into brain size. Consequently, our results suggest that coevolution between placental structures and juvenile brain size is not a general pattern.
Enriching neural stem cell and pro-healing glial phenotypes with electrical stimulation after traumatic brain injury in male rats
Authors: Park Eunyoung , Lyon Johnathan G. , Alvarado-Velez Melissa , Betancur Martha I. , Mokarram Nassir , Shin Jennifer H. , Bellamkonda Ravi V. 
Published: November 2020

AbstractTraumatic Brain Injury (TBI) by an external physical impact results in compromised brain function via undesired neuronal death. Following the injury, resident and peripheral immune cells, astrocytes, and neural stem cells (NSCs) cooperatively contribute to the recovery of the neuronal function after TBI. However, excessive pro-inflammatory responses of immune cells, and the disappearance of endogenous NSCs at the injury site during the acute phase of TBI, can exacerbate TBI progression leading to incomplete healing. Therefore, positive outcomes may depend on early interventions to control the injury-associated cellular milieu in the early phase of injury. Here, we explore electrical stimulation (ES) of the injury site in a rodent model (male Sprague-Dawley rats) to investigate its overall effect on the constituent brain cell phenotype and composition during the acute phase of TBI. Our data showed that a brief ES for 1h on day 2 of TBI promoted pro-healing phenotypes of microglia as assessed by CD206 expression and increased the population of NSCs and Nestin+astrocytes at 7 days post-TBI. Also, ES effectively increased the number of viable neurons when compared to the unstimulated control group. Given the salience of microglia and neural stem cells for healing after TBI, our results strongly support the potential benefit of the therapeutic use of ES during the acute phase of TBI to regulate neuroinflammation and to enhance neuroregeneration.Significance StatementTraumatic brain injury (TBI) occurs when a head injury leads to a disruption of normal function in the brain and is a major cause of death and disability, worldwide. The authors used electrical stimulation during the acute phase of TBI, which promoted pro-healing phenotypes of microglia and increased the number of neural stem cells and Nestin+astrocytes, thereby enhancing neuronal viability. These findings support further study of electrical stimulation to regulate neuroinflammation and to enhance neuroregeneration after TBI.Graphical AbstractFIGURE 1.
Mapping the planet’s critical natural assets
Authors: Chaplin-Kramer Rebecca , Neugarten Rachel A , Sharp Richard P , Collins Pamela M , Polasky Stephen , Hole David , Schuster Richard , Strimas-Mackey Matthew , Mulligan Mark , Brandon Carter , Diaz Sandra , Fluet-Chouinard Etienne , Gorenflo LJ , Johnson Justin A , Kennedy Christina M , Keys Patrick W , Longley-Wood Kate , McIntyre Peter B , Noon Monica , Pascual Unai , Liermann Catherine Reidy , Roehrdanz Patrick R , Schmidt-Traub Guido , Shaw M Rebecca , Spalding Mark , Turner Will R , van Soesbergen Arnout , Watson Reg A 
Published: November 2020

ABSTRACTSustaining the organisms, ecosystems, and processes that underpin human well-being is necessary to achieve sustainable development. Here we identify critical natural assets, natural and semi-natural ecosystems that provide 90% of the total current magnitude of 14 types of nature’s contributions to people (NCP). Critical natural assets for maintaining local-scale NCP (12 of the 14 NCP mapped) comprise 30% of total global land area and 24% of national territorial waters, while 44% of land area is required for maintaining all NCP (including those that accrue at the global scale, carbon storage and moisture recycling). At least 87% of the world’s population lives in the areas benefiting from critical natural assets for local-scale NCP, while only 16% lives on the lands containing these assets. Critical natural assets also overlap substantially with areas important for biodiversity (covering area requirements for 73% of birds and 66% of mammals) and cultural diversity (representing 96% of global Indigenous and non-migrant languages). Many of the NCP mapped here are left out of international agreements focused on conserving species or mitigating climate change, yet this analysis shows that explicitly prioritizing critical natural assets for NCP could simultaneously advance development, climate, and conservation goals. Crafting policy and investment strategies that protect critical natural assets is essential for sustaining human well-being and securing Earth’s life support systems.
Tau-mediated synaptic dysfunction is coupled with HCN channelopathy
Authors: Goniotaki Despoina , Tamagnini Francesco , Biasetti Luca , Rumpf Svenja-Lotta , Troakes Claire , Pollack Saskia J. , Ukwesa Shalom , Sun Haoyue , Serpell Louise C. , Noble Wendy , Staras Kevin , Hanger Diane P. 
Published: November 2020

AbstractProgressive neurodegeneration in tauopathies is mediated through an elusive mechanism. Here, we show that hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are functionally linked to disease-associated abnormalities in tau. Selective rises in the proportion of HCN-positive neurons are detected both in post-mortem human brain from Alzheimer’s disease and in the Tau35 mouse model of tauopathy. Tau35 mice develop progressive abnormalities including increased phosphorylated tau, enhanced HCN channel expression and decreased dendritic branching, as well as reduced synapse density that is accompanied by vesicle clustering defects. Notably, altered spine density and increased HCN channel expression in Tau35 neurons correlates with functional abnormalities in network properties, including enhanced hyperpolarization-induced membrane voltage ‘sag’ and changes in the frequency and kinetics of spontaneous excitatory postsynaptic currents. Our findings are consistent with pathological changes in tauopathies impacting on HCN channels to drive network-wide structural and functional synaptic deficits, providing new targets for therapeutic intervention.
Improving the efficiency of de Bruijn graph construction using compact universal hitting sets
Authors: Ben-Ari Yael , Flomin Dan , Pu Lianrong , Orenstein Yaron , Shamir Ron 
Published: November 2020

AbstractHigh-throughput sequencing techniques generate large volumes of DNA sequencing data at ultra-fast speed and extremely low cost. As a consequence, sequencing techniques have become ubiquitous in biomedical research and are used in hundreds of genomic applications. Efficient data structures and algorithms have been developed to handle the large datasets produced by these techniques. The prevailing method to index DNA sequences in those data structures and algorithms is by usingk-mers (k-long substrings) known as minimizers. Minimizers are the smallestk-mers selected in every consecutive window of a fixed length in a sequence, where the smallest is determined according to a predefined order, e.g., lexicographic. Recently, a newk-mer order based on a universal hitting set (UHS) was suggested. While several studies have shown that orders based on a small UHS have improved properties, the utility of using them in high-throughput sequencing analysis tasks has not been demonstrated to date.Here, we demonstrate the practical benefit of UHSs for the first time, in the genome assembly task. Reconstructing a genome from billions of short reads is a fundamental task in high-throughput sequencing analyses. De Bruijn graph construction is a key step in genome assembly, which often requires very large amounts of memory and long computation time. A critical bottleneck lies in the partitioning of DNA sequences into bins. The sequences in each bin are assembled separately, and the final de Bruijn graph is constructed by merging the bin-specific subgraphs. We incorporated a UHS-based order in the bin partition step of the Minimum Substring Partitioning algorithm of Liet al. (2013). Using a UHS-based order instead of lexicographic- or random-ordered minimizers produced lower density minimizers with more balanced bin partitioning, which led to a reduction in both runtime and memory usage.
Micromechanical homogenisation of a hydrogel-filled electrospun scaffold for tissue-engineered epicardial patching of the infarcted heart
Authors: Abdalrahman Tamer , Mandel Nicolas , Sack Kevin L. , Pugno Nicola M. , Bezuidenhout Deon , Limbert Georges , Moscato Francesco , Davies Neil H. , Franz Thomas 
Published: November 2020

AbstractThis study aimed at developing a formulation to link microscopic structure and macroscopic mechanics of a fibrous scaffold filled with a hydrogel for use as a tissue-engineered patch for local epicardial support of the infarcted heart. Mori-Tanaka mean field homogenisation, closed-cell foam mechanics and finite element (FE) methods were used to represent the macroscopic elastic modulus of the filled fibrous scaffold. The homogenised constitutive description of the scaffold was implemented for an epicardial patch in a FE model of a human cardiac left ventricle (LV) to assess effects of patching on myocardial mechanics and ventricular function in presences of an infarct. The macroscopic elastic modulus of the scaffold was predicted to be 0.287 MPa with the FE method and 0.290 MPa with the closed-cell model for the realistic fibre structure of the scaffold, and 0.108 and 0.540 MPa with mean field homogenization for randomly oriented and completely aligned fibres. Epicardial patching was predicted to reduce maximum myocardial stress in the infarcted LV from 19 kPa (no patch) to 9.5 kPa (patch), and to increase the ventricular ejection fraction from 40% (no patch) to 43% (patch). The predictions of the macroscopic elastic modulus of the realistic scaffold with the FE and the closed-cell model agreed well, and were bound by the mean field homogenisation prediction for random and fully aligned fibre orientation of the scaffold. This study demonstrates the feasibility of homogenization techniques to represent complex multiscale structural features in an simplified but meaningful manner.
Enacting anti-racist visualities through photo-dialogues on race in Paris
Authors: Sobande Francesca , Schoonejans Alice , Johnson Guillaume D. , Thomas Kevin D. , Harrison Anthony Kwame 
Published: November 2020

PurposeGrounded in experience of co-organizing a two-day photography-based workshop in Paris, this paper explores how photo-dialogues can facilitate anti-racist pedagogy and generative discussions about how race and racism function in marketplace contexts.Design/methodology/approachThis paper draws on the authors' involvement in a cross-national and cross-disciplinary team of scholars who worked with local community stakeholders—including activists, artists and practitioners—to discuss, theorize and photo-document issues regarding race and racism in the Parisian marketplace.FindingsThis paper contributes to the literature on visual culture studies and critical race studies as it demonstrates the potentials of photography combined with dialogue to challenge the White supremacy over archiving and visuality in the context of urban spaces. This new methodology is an opportunity to reflect on archetypes of visuality that depart from the traditional Parisian flâneur to be consistent with and reinforce anti-racist stances.Originality/valuePhotography and visual methods often play peripheral roles in anti-racist education across various disciplines and research areas, including critical marketplace studies. This paper expands understanding of the potentials of using photographic methods as part of critical and anti-racist work related to racial and racist dynamics, including issues regarding power, White supremacy and public space. It outlines the use of photographic dialogues in a context (Paris, France) where discussion of race is regularly societally discouraged. Thus, this work shifts the focus away from decontextualized research that regards race as an object, to specifically foreground understandings of racialized experiences and how the photographic gaze produces and is produced by racialized viewers.
Evaluation of passive design strategies to achieve NZEB in the corporate facilities: the context of Bangladeshi subtropical monsoon climate
Authors: Rana Md. Jewel , Hasan Md. Rakibul , Sobuz Md. Habibur Rahman , Sutan Norsuzailina Mohamed 
Published: November 2020

PurposeThis study investigates the impact and economic viability of energy-efficient building envelope and orientation for contributing net zero energy building (NZEB) and suggests optimum thermal insulation thickness, optimum wall thickness, appropriate orientation and glazing types of window in the contexts of unique Bangladeshi subtropical monsoon climate.Design/methodology/approachThe whole study was conducted through energy simulation perspective of an existing office building using building information modeling (BIM) and building energy modeling (BEM) tools which are Autodesk Revit 2017, Autodesk Green Building Studio (GBS) and eQUEST. Numerous simulation patterns were created for energy simulation considering building envelope parameters and orientations. A comprehensive data analysis of simulation results was conducted to sort out efficient passive design strategies.FindingsThe optimum thermal mass and thermal insulation thickness are 6.5 and 0.5 inches, respectively, considering energy performance and economic viability. This study highly recommends that a building should be designed with a small window-to-wall ratio in the south and west face. The window should be constructed with double glazing Low-E materials to reduce solar heat gain. The studied building saves 9.14% annual energy consumption by incorporating the suggested passive design strategies of this study.Originality/valueThe output of this work can add some new energy-efficient design strategies to Bangladesh National Building Code (BNBC) because BNBC has not suggested any codes or regulations regarding energy-efficient passive design strategies. It will also be useful to designers of Bangladesh and other countries with similar subtropical climatic contexts which are located in Southeast Asia and Northern Hemisphere of Earth.