bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microglial phagocytosis dysfunction during stroke is prevented by rapamycin
Authors: Beccari S , Sierra-Torre V , Valero J , García-Zaballa M , Carretero-Guillen A , Capetillo-Zarate E , Domercq M , Huguet PR , Ramonet D , Osman A , Han W , Dominguez C , Faust TE , Touzani O , Boya P , Schafer D , Mariño G , Canet-Soulas E , Blomgren K , Plaza-Zabala A , Sierra A 
Published: November 2021

ABSTRACTMicroglial phagocytosis is rapidly emerging as a therapeutic target in neurodegenerative and neurological disorders. An efficient removal of cellular debris is necessary to prevent buildup damage of neighbor neurons and the development of an inflammatory response. As the brain professional phagocytes, microglia are equipped with an array of mechanisms that enable them to recognize and degrade several types of cargo, including neurons undergoing apoptotic cell death. While microglia are very competent phagocytes of apoptotic cells under physiological conditions, here we report their dysfunction in mouse and monkey (Macaca fascicularisandCallithrix jacchus) models of stroke by transient occlusion of the medial cerebral artery (tMCAo). The impairment of both engulfment and degradation was related to energy depletion triggered by oxygen and nutrients deprivation (OND), which led to reduced process motility, lysosomal depletion, and the induction of a protective autophagy response in microglia. Basal autophagy, which is in charge of removing and recycling intracellular elements, was critical to maintain microglial physiology, including survival and phagocytosis, as we determined both in vivo and in vitro using knock-out models of autophagy genes and the autophagy inhibitor MRT68921. Notably, the autophagy inducer rapamycin partially prevented the phagocytosis impairment induced by tMCAo in vivo but not by OND in vitro. These results suggest a more complex role of microglia in stroke than previously acknowledged, classically related to the inflammatory response. In contrast, here we demonstrate the impairment of apoptotic cell phagocytosis, a microglial function critical for brain recovery. We propose that phagocytosis is a therapeutic target yet to be explored and provide evidence that it can be modulated in vivo using rapamycin, setting the stage for future therapies for stroke patients.
CarboGrove: a resource of glycan-binding specificities through analyzed glycan-array datasets from all platforms
Authors: Klamer Zachary L. , Harris Chelsea M. , Beirne Jonathan M. , Kelly Jessica E. , Zhang Jian , Haab Brian B. 
Published: November 2021

AbstractThe volume and value of glycan-array data are increasing, but no common method and resource exists to analyze, integrate, and use the available data. To meet this need, we developed a resource of analyzed glycan-array data called CarboGrove. Building on the ability to process and interpret data from any type of glycan array, we populated the database with the results from 35 types of glycan arrays, 13 glycan families, 5 experimental methods, and 19 laboratories or companies. In meta-analyses of glycan-binding proteins, we observed glycan-binding specificities that were not uncovered from single sources. In addition, we confirmed the ability to efficiently optimize selections of glycan-binding proteins to be used in experiments for discriminating between closely related motifs. CarboGrove yields unprecedented access to the wealth of glycan-array data being produced and powerful capabilities for both experimentalists and bioinformaticians.TeaserWe introduce a resource that allows researchers to find, compare, study, and integrate analyses from all types of glycan-array data.
Neophobia and innovation in critically endangered Bali myna,Leucopsar rothschildi
Authors: Miller Rachael , Garcia-Pelegrin Elias , Danby Emily 
Published: November 2021

AbstractCognition underlies animal behaviour, which is key to successful conservation strategies, yet largely under-utilised in conservation, though there are recent calls for closer integration. Conservation-relevant cognitive abilities can impact on adaptability and survival, such as neophobia, e.g., responses to novelty, and innovation e.g., problem-solving, particularly in today’s changing world. Bali myna are a critically endangered endemic species, which are a focus of active conservation efforts, including reintroductions. Therefore, gathering cognitive data can aid in improving and developing conservation strategies, like pre-release training and individual selection for release. In 22 captive Bali myna, we tested neophobia (novel object, novel food, control conditions), innovation (bark, cup, lid conditions) and individual repeatability. We found effects of condition and social environment, including longer latencies to touch familiar food in presence than absence of novel items, and between problem-solving tasks, as well as in the presence of conspecifics, compared with being alone, or with conspecifics and competing heterospecifics. Individuals were repeatable in latency responses: 1) temporally in both experiments; 2) contextually in innovation experiment and between both experiments (and approach order), suggesting a stable behaviour trait. These findings are an important starting point for improving conservation strategies in Bali myna and other similarly threatened species.
Transcriptional regulation of neonatal neural stem cells is a determinant of social behavior
Authors: Hiramoto Takeshi , Boku Shuken , Kang Gina , Abe Seiji , Barbachan e Silva Mariel , Tanigaki Kenji , Nagashima Masako , Ye Kenny , Yamauchi Takahira , Michurina Tatyana V. , Broin Pilib Ó , Enikolopov Grigori , Hiroi Noboru 
Published: November 2021

AbstractRare gene variants confer a high level of penetrance to neurodevelopmental disorders, but their developmental origin and cellular substrates remain poorly understood. To address this limitation, we explored the role ofTBX1, a gene encoded in a rare copy number variant, in cell and mouse models. Here, we report that neonatalTbx1deficiency contributes to defective peripubertal social behavior and impairs the proliferation of neonatal neural stem/progenitor cells. Moreover, TBX1 transcriptionally regulates genes linked to post-embryonic neurogenesis and neurodevelopmental disorders associated with other rare gene variants. Our data indicate a precise time window and cell type through which the social dimension is altered by a gene encoded in a rare CNV and provide a potential common mechanistic basis for a group of neurodevelopmental disorders.One-Sentence SummaryTbx1, a gene affecting neonatal stem cell proliferation, influences peripubertal social behavior.
Multimodal interrogation of ventral pallidum projections reveals projection-specific signatures and opposite roles in cocaine withdrawal
Authors: Bernat Nimrod , Campbell Rianne , Nam Hyungwoo , Basu Mahashweta , Odesser Tal , Elyasaf Gal , Engeln Michel , Chandra Ramesh , Golden Shana , Ament Seth , Lobo Mary Kay , Kupchik Yonatan M. 
Published: November 2021

AbstractThe ventral pallidum (VP) is central to reward seeking and withdrawal from drugs of abuse. A characteristic of the VP is the diversity of its projection targets. Yet, it remains unknown whether different VP projections also differ in other aspects, such as their transcriptome, physiology and relevance to drug reward. In this study we perform a multimodal dissection of four major projections of the VP – to the lateral hypothalamus (VP→LH), ventral tegmental area (VP→VTA), lateral habenula (VP→LHb) and mediodorsal thalamus (VP→MDT) – with physiological, anatomical, genetic and behavioral tools and show significant differences between projections in all aspects. Specifically, the VP→LHand VP→VTAprojections show minimal overlap and stand out as having opposite properties – VP→LHneurons show higher excitability compared to VP→VTAneurons, different pattern of inputs and differentially expressed genes. Moreover, inhibition of VP→LHprojections diminishes, while inhibition of VP→VTAenhances cocaine preference after cocaine withdrawal. This demonstrates that VP projections are heterogenous neuron populations with different roles in cocaine withdrawal.
A Cryptic K48 Ubiquitin Chain Binding Site on UCH37 is Required for its Role in Proteasomal Degradation
Authors: Du Jiale , Babik Sandor , Li Yanfeng , Deol Kirandeep K. , Eyles Stephen J. , Fejzo Jasna , Tonelli Marco , Strieter Eric R. 
Published: November 2021

SUMMARYDegradation by the 26S proteasome is an intricately regulated process fine-tuned by the precise nature of ubiquitin modifications attached to a protein substrate. By debranching ubiquitin chains composed of K48 linkages, the proteasome-associated ubiquitin C-terminal hydrolase UCHL5/UCH37 serves as a positive regulator of protein degradation. How UCH37 achieves specificity for K48 chains is unclear. Here, we use a combination of hydrogen-deuterium mass spectrometry, chemical crosslinking, small-angle X-ray scattering, NMR, molecular docking, and targeted mutagenesis to uncover a cryptic K48 ubiquitin chain specific binding site on the opposite face of UCH37 relative to the canonical S1 ubiquitin-binding site. Biochemical assays demonstrate the K48 chain-specific binding site is required for chain debranching and proteasome-mediated degradation of proteins modified with branched chains. Using quantitative proteomics, translation shutoff experiments, and linkage-specific affinity tools, we then identify specific proteins whose degradation depends on the debranching activity of UCH37. Our findings suggest that UCH37 and potentially other DUBs could use more than one S1 site to perform different biochemical functions.
Optimization of juice production from “cempedak” (Artocarpus integer) fruit pulp liquefied with the aid of enzymes
Authors: Pui Liew Phing , Kong Ianne , Karim Roselina , Yusof Yus Aniza , Wong Chen Wai , Mohd Ghazali Hasanah 
Published: November 2021

PurposeThe purpose of this research is to produce “cempedak” juice using enzyme aided-liquefaction by examining the effects of enzyme types (Pectinex® Ultra SP-L, Celluclast® 1.5 L and Fungamyl® 800 L), enzyme concentrations (0–1.5% v/w), incubation time (0–2.5 h) and incubation temperature (35–60 °C) on juice yield and viscosity, total soluble solids and color of fruit puree.Design/methodology/approachRipe “cempedak” pulp from CH28 fruit was first pureed in a blender and then homogenized with water at 1:2 ratio. The diluted puree was then liquefied with the enzymes separately to reduce its viscosity. Analyses such as juice yield, viscosity, total soluble solids and color of the liquefied “cempedak” puree were then carried out.FindingsResults indicated that the optimized use of 1.2% (v/w) Celluclast® 1.5 L (Novozymes, Denmark), a cellulase preparation, at 45 °C and 1 h produced juice with the lowest viscosity (349.4 cP) and the highest juice yield (82.3% v/w). Liquefied “cempedak” juice was darker (with L* value of 51.17) and more yellowish (b* value of 38.88) compared to “cempedak” juice without liquefaction (control). When compared to untreated “cempedak” juice, the droplet size of “cempedak” juice obtained after liquefaction under optimized conditions was found to be lower, regardless of whether the juice was filtered (with a total reduction of 23% of droplet size) or not filtered (with a total reduction of 16% of droplet size). The results indicate the possibility of employing Celluclast® 1.5 L to produce “cempedak” juice that can be further processed such as for the production of “cempedak” fruit powder.Originality/valueThis paper provides information on the enzyme concentration, incubation time and temperature for liquefying “cempedak” pulp such that the liquefied material produced can be used as a base feed for spray-drying to produce “cempedak” fruit powder.
Proper orthogonal decomposition Pascal polynomial-based method for solving Sobolev equation
Authors: Dehghan Mehdi , Hooshyarfarzin Baharak , Abbaszadeh Mostafa 
Published: November 2021

Purpose
This study aims to use the polynomial approximation method based on the Pascal polynomial basis for obtaining the numerical solutions of partial differential equations. Moreover, this method does not require establishing grids in the computational domain.

Design/methodology/approach
In this study, the authors present a meshfree method based on Pascal polynomial expansion for the numerical solution of the Sobolev equation. In general, Sobolev-type equations have several applications in physics and mechanical engineering.

Findings
The authors use the Crank-Nicolson scheme to discrete the time variable and the Pascal polynomial-based (PPB) method for discretizing the spatial variables. But it is clear that increasing the value of the final time or number of time steps, will bear a lot of costs during numerical simulations. An important purpose of this paper is to reduce the execution time for applying the PPB method. To reach this aim, the proper orthogonal decomposition technique has been combined with the PPB method.

Originality/value
The developed procedure is tested on various examples of one-dimensional, two-dimensional and three-dimensional versions of the governed equation on the rectangular and irregular domains to check its accuracy and validity.
The relationship between intellectual capital and financial statements readability: the role of management characteristics
Authors: Moghadam Hassan Mohammadzadeh , Salehi Mahdi , Hajiha Zohreh 
Published: November 2021

Purpose
The present study aims to investigate the relationship between intellectual capital and the readability of financial statements with the mediating role of management characteristics of companies listed on the Tehran Stock Exchange. In other words, this research tries to find the answer to whether intellectual capital can positively affect the readability of financial statements.

Design/methodology/approach
A multivariate regression model was used to test the hypotheses for this purpose. The research hypotheses were tested using a sample of 1,309 observations listed on the Tehran Stock Exchange from 2012 to 2018 and a multiple regression model based on panel data and fixed-effects models.

Findings
The results indicate that intellectual capital has a positive and significant relationship with the readability of financial statements, which means that with increasing intellectual capital in companies, financial statements’ readability also increases. Based on the hypothesis test results, it has been determined that narcissism, accrual and real earnings management have a negative effect on the relationship between intellectual capital and the readability of financial statements.

Originality/value
Since the present study examines such an issue in emerging markets, it provides users, analysts and legal entities with useful information about management’s inherent and acquired characteristics that significantly impact the purchase of audit opinion. This study’s results also contribute to developing science and knowledge in this field and close the literature gap.
Reflecting on over a year of remote training, and where businesses must go from here
Authors: Kairinos Nikolas 
Published: November 2021

Purpose
The study aims to explore how businesses across the UK have adapted to over a year of remote training, and where there is room for improvement as long-term hybrid working plans are put in place. The study also uncovers what digital tools businesses have relied on to deliver learning and development initiatives during remote working, and their effects on employee engagement and experience.

Design/methodology/approach
An independent body of research was commissioned among 750 UK business leaders and 1,235 UK adults in full-time employment.

Findings
The research found that while the majority of businesses were able to leverage digital solutions during extended periods of remote work, significant numbers found it difficult to train and develop employees remotely, with many employees dissatisfied with the outcomes.

Originality/value
The research offers some valuable insights for business leaders looking to improve their training schemes as workplaces settle into new patterns of working.
Assessing Evidence of Phosphorus Concentration Trends in North American Freshwaters
Authors: Carleton James N. , Washington Benjamin J. 
Published: November 2021

AbstractThe United States Environmental Protection Agency’s National Aquatic Resource Surveys (NARS) documented evidence of widespread, unexplained total phosphorus (TP) concentration increases in lakes and streams across the United States (U.S.) during the 2000–2012 time period. To examine the robustness of evidence for this trend, we used additional monitoring datasets to calculate rates of TP change in thousands of individual waterbodies across the U.S. during the same time frame, and compared them against TP change rates calculated in the same manner for waterbodies that were resurveyed under NARS in different years. For the additional datasets, median rates of TP change were substantially lower than median rates calculated using NARS data. To further examine differences between NARS and non‐NARS results in specific waterbodies, we assembled composite datasets for 52 predominantly northern lakes that by chance had been sampled under both NARS and other sampling programs during the same time frame. Using only NARS data, the median calculated TP change rate for this set of lakes was positive and similar to that for the larger set of 401 resurveyed NARS lakes. However, when additional sample data were included, the median calculated TP change rate for these lakes was much lower. Results suggest that increasing TP concentrations in waterbodies may not have been as ubiquitous as suggested. They also illustrate a need to supplement randomized continental‐scale monitoring with detailed, site‐focused investigations.
Battling Over Bathwater: Greywater Technopolitics in Los Angeles
Authors: Randle Sayd 
Published: November 2021

AbstractIn Los Angeles, domestic wastewater recycling (“greywater”) systems are controversial, loved by local environmentalists and disdained by the city’s water agencies. Drawing on fieldwork among greywater advocates and public water agency workers, this article examines how greywater systems function as nodes that unsettle relations between residents and the public agencies that manage the city’s water grid. Elaborating the longstanding frictions over greywater reuse in LA reveals how these fixtures are mobilized by advocates to rescript the roles of both individuals and the state within the urban waterscape. Detailing public agency workers’ resistance to this form of selective disconnection from the grid helps to clarify the patterns of flows, norms of consumption, and forms of state control at stake in efforts to decentralize arrangements of urban water management.
Graduate student perspectives on transforming academia
Authors: Sykora‐Bodie Seth T. , Jones J. Leah , Hastings Zoe , Lombardi Elizabeth , Barnett Michaela , Davis Olivia N. , Ferrari Olivia M. , Garcia Polanco Vanessa , Hofner Alexandra N. , Hunter Brandon , Ippolito Tara , Krantz Will , Neyra Oscar , Perez‐Figueroa Omar , Raub Kristin B. , Sou Jennifer , Virguez Edgar , Waters Tanner , Whitten Julia 
Published: November 2021

AbstractHigher education institutions have long played a key role in solving society's most pressing problems. However, as the scale and complexity of socio‐environmental problems has grown, there has been a renewed debate about the role that academic institutions should play in developing solutions and how institutional structures should be redesigned to encourage greater interdisciplinarity. In the following pages, we present a graduate student perspective on this debate. Specifically, we identify challenges facing interdisciplinary graduate student researchers and present a series of recommendations for how institutions can better prepare them to become the next generation of leaders in interdisciplinary, action‐oriented research focused on solving socio‐environmental problems.
Importance of direct right‐to‐left shunt as high‐risk patent foramen ovale associated with cryptogenic stroke
Authors: Takaya Yoichi , Nakayama Rie , Akagi Teiji , Yokohama Fumi , Miki Takashi , Nakagawa Koji , Toh Norihisa , Ito Hiroshi 
Published: November 2021

AbstractBackgroundBecause transcatheter closure of patent foramen ovale (PFO) has become effective for preventing cryptogenic stroke (CS), it is necessary to determine high‐risk PFO associated with CS. This study aimed to clarify the importance of direct right‐to‐left (RL) shunt through the PFO for identifying high‐risk PFO.MethodsWe analyzed 137 patients with and without CS who were confirmed to have PFO. The timing of RL shunt through the PFO was evaluated by cardiac cycles after right atrium (RA) opacification on saline contrast transesophageal echocardiography. Direct RL shunt was defined as microbubbles crossing the PFO before and at the same time of RA opacification.ResultsCardiac cycles of microbubbles crossing the PFO were shorter in patients with CS than in those without CS (2.0 ± 2.2 vs .5 ± 1.1, p < 0.01). Direct RL shunt was more frequently observed in patients with CS than in those without CS (77% vs 29%, p < 0.01), with a sensitivity of 79% and a specificity of 71% for the association with CS. Multivariate analysis revealed that direct RL shunt was related to atrial septal aneurysm and low‐angle PFO. Regarding functional features of PFO, the detection rate of CS was 50% for large RL shunt alone, and was increased to 83% when direct RL shunt was added.ConclusionDirect RL shunt was associated with CS and had the incremental value in detecting PFO associated with CS for large RL shunt. The timing of RL shunt can be valuable for identifying high‐risk PFO.
Fibrinogen β chain and FXIII polymorphisms affect fibrin clot properties in acute pulmonary embolism
Authors: Klajmon Adrianna , Chmiel Jakub , Ząbczyk Michał , Pociask Elżbieta , Wypasek Ewa , Malinowski Krzysztof P. , Undas Anetta , Natorska Joanna 
Published: November 2021

AbstractBackgroundProthrombotic fibrin clot properties, including increased clot density, are in part genetically determined. We investigated whether fibrinogen alpha‐chain gene (FGA) c.991A>G (rs6050), fibrinogen beta chain gene (FGB) −455G>A (rs1800790) and factor XIII gene (F13) c.103G>T (rs5985) polymorphisms affect plasma fibrin clot properties in patients with acute pulmonary embolism (PE).MethodsAs many as 126 normotensive patients with PE, free of cancer, were genotyped by TaqMan assay. Fibrin clot permeability (Ks), clot lysis time (CLT) and endogenous thrombin potential (ETP) were assessed on admission.ResultsThe minor allele frequencies were as follows: FGA rs6050 (n = 62, 0.31), FGB rs1800790 (n = 40, 0.17) and F13 rs5985 (n = 49, 0.23). There were no differences related to any of the polymorphisms with regard to demographic, clinical and laboratory data, except for fibrinogen concentration, which was higher in carriers of F13 rs5985 polymorphism (p = .024), and PE combined with deep‐vein thrombosis, which was less prevalent in FGB rs1800790 polymorphism carriers (p = .004). Carriers of FGB rs1800790 A allele and F13 rs5985 T allele had lower Ks, prolonged CLT and higher ETP compared with major homozygotes (all p < .05). After adjustment for fibrinogen, all differences remained significant (all p < .01). There were no associations between the FGA rs6050 polymorphism and Ks, CLT or ETP.ConclusionOur study showed that FGB rs1800790 and F13 rs5985 polymorphisms contribute to the prothrombotic fibrin clot phenotype and these effects are strong enough to be observed in the acute phase of PE.