bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cortical depth-dependent human fMRI of resting-state networks using EPIK
Authors: Pais-Roldán Patricia , Yun Seong Dae , Palomero-Gallagher Nicola , Shah N. Jon 
Published: December 2020

AbstractRecent laminar-fMRI studies have substantially improved understanding of theevokedcortical responses in multiple sub-systems; in contrast, the laminar component ofresting-state networksspread over the whole brain has been less studied due to technical limitations. Animal research strongly suggests that the supragranular layers of the cortex play a critical role in maintaining communication within the default mode network (DMN); however, whether this is true in this and other human cortical networks remains unclear. Here, we used EPIK, which offers unprecedented coverage at sub-millimeter resolution, to investigate cortical broad resting-state dynamics with depth specificity in healthy volunteers. Our results suggest that human DMN connectivity is primarily supported by intermediate and superficial layers of the cortex, and furthermore, the preferred cortical depth used for communication can vary from one network to another. This has major implications for the characterization of network-related diseases and should occupy future high-resolution studies. In addition, the laminar connectivity profile of some networks showed a tendency to change upon engagement in a motor task. In line with these connectivity changes, we observed that the amplitude of the low-frequency-fluctuations (ALFF), as well as the regional homogeneity (ReHo), exhibited a different laminar slope when subjects were either performing a task or were in a resting state (less variation among laminae, i.e., lower slope, during task performance compared to rest). The varied laminar profiles concerning network connectivity, ALFF, and ReHo, observed across two brain states (task vs. rest) suggest the potential diagnostic value of laminar fMRI in psychiatric diseases, e.g., to differentiate the cortical dynamics associated with disease stages linked, or not linked, to behavioral changes. The evaluation of laminar-fMRI across the brain encompasses computational challenges; nonetheless, it enables the investigation of a new dimension of the human neocortex, which may be key to understanding neurological disorders from a novel perspective.
Single cell transcriptomics of primate sensory neurons identifies cell types associated with human chronic pain
Authors: Kupari Jussi , Usoskin Dmitry , Lou Daohua , Parisien Marc , Hu Yizhou , Fatt Michael , Lönnerberg Peter , Spångberg Mats , Eriksson Bengt , Barkas Nikolaos , Kharchenko Peter V , Loré Karin , Khoury Samar , Diatchenko Luda , Ernfors Patrik 
Published: December 2020

AbstractDistinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of human chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.
Genomic Evidence for the Chinese Mountain Cat as a Wildcat Conspecific (Felis silvestris bieti) and Its Introgression to Domestic Cats
Authors: Yu He , Xing Yue-Ting , Meng Hao , He Bing , Li Wen-Jing , Qi Xin-Zhang , Zhao Jian-You , Zhuang Yan , Xu Xiao , O’Brien Stephen J. , Luo Shu-Jin 
Published: December 2020

AbstractThe enigmatic Chinese mountain cat, endemic to the Qinghai-Tibet Plateau, has a controversial taxonomic status, whether a true species or conspecific with the wildcat(Felis silvestris) and whether it may have contributed to the domestication of cats(F. s. catus) in Asia. Here, we sampled 270 domestic and wild cats across China, sequenced 51 nuclear genomes, 55 mitogenomes, and multi-locus regions from modern and museum specimens. Genome-wide phylogenies supported taxonomic classification of the Chinese mountain cat as wildcat subspecies,F. s. bieti. No involvement ofF. s. bietiin cat domestication in East Asia was detected, confirming that domestic cats shared a single origin from the African wildcat(F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat(F. s. ornata) toF. s. bieti, and contemporary gene flow betweenF. s. bietiand sympatric domestic cats in the Tibetan region, raises the prospect of disrupting the genetic integrity ofF. s. bieti, an issue with profound conservation implications.
A framework for predicting potential host ranges of pathogenic viruses based on receptor ortholog analysis
Authors: Du Guifang , Ding Yang , Li Hao , Wang Xuejun , Wang Junting , Sun Yu , Tao Huan , Huang Xin , Xu Kang , Hong Hao , Jiang Shuai , Wang Shengqi , Chen Hebing , Bo Xiaochen 
Published: December 2020

AbstractViral zoonoses are a serious threat to public health and global security, as reflected by the current scenario of the growing number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases. However, as pathogenic viruses are highly diverse, identification of their host ranges remains a major challenge. Here, we present a combined computational and experimental framework, called REceptor ortholog-based POtential virus hoST prediction (REPOST), for the prediction of potential virus hosts. REPOST first selects orthologs from a diverse species by identity and phylogenetic analyses. Secondly, these orthologs is classified preliminarily as permissive or non-permissive type by infection experiments. Then, key residues are identified by comparing permissive and non-permissive orthologs. Finally, potential virus hosts are predicted by a key residue–specific weighted module. We performed REPOST on SARS-CoV-2 by studying angiotensin-converting enzyme 2 orthologs from 287 vertebrate animals. REPOST efficiently narrowed the range of potential virus host species (with 95.74% accuracy).
The diversification of termites: inferences from a complete species-level phylogeny
Authors: Pie Marcio R. , Carrijo Tiago F. , Caron Fernanda S. 
Published: December 2020

AbstractTermites play a major role in a variety of ecological processes in tropical and subtropical biomes worldwide, such as decomposition, soil formation and aeration, and nutrient cycling. These important ecosystem services were achieved through their highly complex societies and remarkable adaptations, including the evolution of sterile worker castes, the acquisition of endosymbionts, and the capacity for extensive environmental engineering, yet the causes and consequences of their ecological success are still poorly understood. The goals of our study were (1) to provide the first complete, species-level phylogeny of all currently recognized termite species by integrating the available genetic and taxonomic data, as well as methods of phylogenetic imputation and divergence time estimation; and (2) to explore variation in speciation rates among termite lineages. We provide the inferred relationships as a set of 1,000 pseudo-posterior trees, which can be used in future comparative analyses. We demonstrate that speciation rates have been relatively constant throughout the history of termites, with two positive shifts in speciation rates: one at their origin of Euisoptera and the other concordant with evolution of Termitidae. On the other hand, there was no obvious trend towards deceleration in speciation rates for termites as a whole, nor within the most species-rich families. The provided trees might represent a valuable resource for termite comparative studies by summarizing the available phylogenetic information, while accounting for uncertainty in the inferred topologies.
Testing for the resistance of newly generated hybrid cacao germplasm in the gene pool of Cocoa Research Institute of Nigeria (CRIN) againstPhytophthora megakaryapathogen causing black pod disease of cocoa
Authors: Tijani A. A. , Otuonye A. H. , Otusanya M. O. , Olaiya A. O. , Adenuga O. O. , Afolabi C. G. 
Published: December 2020

ABSTRACTBlack pod disease caused byP. PalmivoraandP. megakaryais an important disease affectingcacaoin West Africa which produces 70% of the world output. Resistance to the pathogen is therefore, an important factor to be considered when breeding for high yielding and earliness in fruiting. Resistance to the pathogen using Leaf Disc Test (LDT) was conducted at the Plant Pathology Laboratory, Ibadan, on detached 15mm diameter discs of two-month-old leaves obtained from nineteen newly generatedcacaohybrids in the gene pool of the Institute. Attached Whole Leaf Test (AWLT) was also conducted on few selected hybrids in the screen house at the same institute. Ten μl zoospores suspension ofP. megakaryapathogen adjusted to inoculum strength of 3×105zoospores/ml using haemocytometer was used for the inoculation of thecacaoLD. Using 0-5 disease rating scale, data was taken on the 5thand 7thday after inoculation for LDT and on the 6thday after inoculation for AWLT. Data obtained were subjected to Analysis of Variance and significant means were separated using Student Newman Kuels Test at p<0.05. The LDT classified the hybrids into five groups namely: Resistant (hybrid 001, 003 and 005); Moderately Resistant (hybrid 006, 007, 008,013,015,018 and 019) Moderately Susceptible (hybrid 004, 014 and 017); Susceptible (hybrid 002, 010, 011 and 016) and Highly Susceptible (hybrid 009 and 012). Scores from LDT significantly correlated (r= 0.92**) with that of AWLT. It was observed from the study thatcacaohybrid 001, 003 and 005 showed traits of resistant and therefore, could be incorporated into the national breeding programs for the development of high-yielding and resistantcacaocultivars. The moderately resistant hybrids could be conserved for future germplasm enhancement program.
Oxidative stress conditions result in trapping of PHF-core tau (297-391) intermediates
Authors: Maina Mahmoud B. , Al-Hilaly Youssra K. , Burra Gunashekar , Rickard Janet , Harrington Charlie , Wischik Claude , Serpell Louise C. 
Published: December 2020

AbstractThe self-assembly of tau into paired helical filaments (PHF) in neurofibrillary tangles (NFTs) is a significant event in Alzheimer’s disease (AD) pathogenesis. Oxidative stress, which accompanies AD, induces multiple post-translational modifications in proteins including the formation of dityrosine (DiY) cross-links, previously observed for Aβ. Here, metal catalysed- and ultra-violet oxidation were used to study the influence of DiY cross-linking on the self-assembly of the PHF-core tau fragment. We report that DiY cross-linking facilitates tau assembly into tau oligomers and prevents their elongation into filaments. The DiY cross-linked tau oligomers were not toxic to cells. Our findings suggest that DiY cross-linking of pre-assembled tau, promotes the formation of soluble tau oligomers that show no acute toxicity.
DOT1L Complex Regulates Transcriptional Initiation in Human Cells
Authors: Wu Aiwei , Zhi Junhong , Tian Tian , Chen Lixue , Liu Ziling , Fu Lei , Roeder Robert G. , Yu Ming 
Published: December 2020

SUMMARYDOT1L, the only H3K79 methyltransferase in human cells and a homolog of the yeast Dot1, normally forms a complex with AF10, AF17 and ENL/AF9, is dysregulated in most of the cases of mixed lineage leukemia (MLL) and is believed to regulate transcriptional elongation without much evidence. Here we show that the depletion of DOT1L reduced the global occupancy without affecting the traveling ratio or the elongation rate of Pol II, suggesting it not a major elongation factor. An examination of general transcription factors (GTFs) binding revealed globally reduced TBP and TFIIA occupancies near promoters after DOT1L loss, pointing to a role in transcriptional initiation. Proteomic studies uncovered that DOT1L regulates transcriptional initiation likely by facilitating the recruitment of TFIID. Moreover, ENL, a DOT1L complex subunit with a known role in DOT1L recruitment, also regulates transcriptional initiation. Furthermore, DOT1L stimulates H2B monoubiquitination by limiting the recruitment of human SAGA complex, and the connection between Dot1/DOT1L and SAGA complex is conserved between yeast and human. These results advanced current understanding of roles of DOT1L complex in transcriptional regulation and MLL.
The Relative Roles of Voice and Gesture in Early Communication Development
Authors: Burkhardt-Reed Megan M. , Long Helen L. , Bowman Dale D. , Bene Edina R. , Oller D. Kimbrough 
Published: December 2020

AbstractBoth vocalization and gesture are universal modes of communication and fundamental features of language development. Many believe that language evolved out of early gestural use; however, evidence reported here suggests vocalization precedes gesture in human communication and forms the predominant foundation for language. To our knowledge no prior research has investigated the rates of emergence of both gesture and vocalization in human infants to evaluate this question. We evaluated the rates of gesture and speech-like vocalizations (protophones) of 10 infants at 4, 7, and 11 months of age using parent-infant laboratory recordings. We found that infant protophones outnumbered gestures substantially at all three ages, ranging from >30 times more protophones than gestures at 3 months, to more than twice as many protophones as gestures at 11 months. The results suggest that vocalization is the predominant mode of communication in human infants from the beginning of life.
Application of mid-infrared free-electron laser for structural analysis of biological materials
Authors: Kawasaki Takayasu , Zen Heishun , Ozaki Kento , Yamada Hironari , Wakamatsu Kazumasa , Ito Shosuke 
Published: December 2020

A mid-infrared free-electron laser (MIR-FEL) is a synchrotron-radiation-based femto- to pico-second pulse laser. It has unique characteristics such as variable wavelengths in the infrared region and an intense pulse energy. So far, MIR-FELs have been utilized to perform multi-photon absorption reactions against various gas molecules and protein aggregates in physical chemistry and biomedical fields. However, the applicability of MIR-FELs for the structural analysis of solid materials is not well recognized in the analytical field. In the current study, an MIR-FEL is applied for the first time to analyse the internal structure of biological materials by using fossilized inks from cephalopods as the model sample. Two kinds of fossilized inks that were collected from different strata were irradiated at the dry state by tuning the oscillation wavelengths of the MIR-FEL to the phosphoryl stretching mode of hydroxyapatite (9.6 µm) and to the carbonyl stretching mode of melanin (5.8 µm), and the subsequent structural changes in those materials were observed by using infrared microscopy and far-infrared spectroscopy. The structural variation of these biological fossils is discussed based on the infrared-absorption spectral changes that were enhanced by the MIR-FEL irradiation, and the potential use of MIR-FELs for the structural evaluation of biomaterials is suggested.
Integrated mode of transport: a predictive model for route guidance
Authors: Ravish Roopa , Rangaswamy Shanta 
Published: December 2020

PurposeThe purpose of this study is to provide real-time route guidance within city to help commuters.Design/methodology/approachIn urban areas to avoid road congestion and to reach the destination on time, intelligent transport system (ITS) utilizes recent advanced technology. To support this, existing route guidance system (RGS) suggests alternative route to commuters. However, ITS requires a system which suggests the alternative route along with the mode of transport such as public, private, taxi services etc. Integrated mode of transport (IMT) implemented in this paper guides the commuters of urban area with the best mode of transport. Inputs to our IMT predictive model are the commuter's choice of (1) minimum travel time (2) minimum cost (3) flexible route and (4) less traffic intensity along with source and destination locations. Based on these user inputs, IMT predictive model suggests optimal mode of transport. In this paper to implement the IMT model, we have considered the transport facility available in Bangalore, a city in India. The city has metro train, bus and taxi services available to the commuters. Implementation is divided into two parts. In the first part, the model checks for the end-to-end connectivity/availability of metro train facility. If metro train connectivity exists, the model concludes this as the best mode of travel. In the second part, for the routes which are not connected by metro train, the optimal mode of transport through road network will be suggested. In the first part, to check the existence of metro train along the routes between source and destination, location-IQ API is used. In the later part, to suggest transport along the road network, Q-learning algorithm of reinforcement learning technique is used.FindingsThe findings are the predictive model algorithm to find the best mode of transfer and reinforcement model used in real time route guidance system.Originality/valueThis is a new Idea, not proposed in any research work.
Factors influencing customer switching behavior in Islamic banks: evidence from Kuwait
Authors: Ghamry Sherif , Shamma Hamed M. 
Published: December 2020

Purpose
With increasing competition, Islamic banks in Kuwait are currently facing difficulties in retaining their customers as customers now have the option to switch from one bank to another. As the banking industry offers almost identical products and services, customers are more likely to change their bank when they get a better offer from another bank, especially if the customer is dissatisfied with the current bank. Thus, this study aims at identifying the most significant factors that make Islamic bank customers switch their bank.

Design/methodology/approach
The data for this study was collected through a survey with a response rate of 25.5%. Logistic regression was used to analyze the collected data and examine the effect of each factor on the customer switching behavior.

Findings
The results of empirical analysis reveal that the service convenience, service reliability, level of technology and Sharia compliance are the most significant factors influencing the customer switching behavior in Kuwaiti Islamic banks. Thus, Islamic bank managers should focus on these factors when building their strategies to increase their customer’s satisfaction and loyalty. Loyal customers are more profitable than new customers as they are more likely to use more services, spread a positive word of mouth and, more importantly, they are more likely to resist competitors’ offers.

Practical implications
Identifying and understanding these factors will enable Islamic bank managers to direct their efforts and resources to the most cost-effective ways that help them to retain their customers, and accordingly, increase bank profits.

Originality/value
To the best of the authors’ knowledge, this is the first study to examine the customer switching behavior in Kuwait, and one of the few to present a model that explains the stages through which customers pass until they reach the switching decision.
The challenge of online privacy preservation in Muslim-majority countries during the COVID-19 pandemic
Authors: El-Bassiouny Dina , El-Bassiouny Noha 
Published: December 2020

Purpose
E-learning has become a predominant platform for education as a result of the COVID-19 pandemic. Yet, privacy issues have emerged from online learning that posed challenges on the users of e-learning systems. Privacy preservation in Muslim-majority countries with conservative cultures was a concern based on socio-cultural norms. This paper aims to analyze this situation through the lens of social identity theory.

Design/methodology/approach
This practice paper represents a conceptual viewpoint.

Findings
In this paper, the authors offer recommended solutions as best practices for Muslim-majority countries and similar contexts. Such proposed solutions consider social and cultural influences in e-learning systems to have an effective education process.

Originality/value
This practice paper is unique in its approach, as it documents the privacy concerns in Muslim-majority countries during the COVID-19 pandemic.
Impact of socio‐economic deprivation on endometrial cancer survival in the North West of England: a prospective database analysis
Authors: Njoku K , Barr CE , Hotchkies L , Quille N , Wan YL , Crosbie EJ 
Published: December 2020

ObjectiveTo assess the impact of socio‐economic deprivation on endometrial cancer survival.DesignSingle‐centre prospective database study.SettingNorth West England.PopulationWomen with endometrial cancer treated between 2010 and 2015.MethodsAreal‐level socio‐economic status, using the English indices of multiple deprivation from residential postcodes, was analysed in relation to survival using Kaplan–Meier estimation and multivariable Cox regression.Main outcome measuresOverall survival, cancer‐specific survival and patterns and rates of recurrence.ResultsA total of 539 women, with a median age of 66 years (interquartile range, IQR 56–73 years) and a body mass index (BMI) of 32 kg/m2 (IQR 26–39 kg/m2), were included in the analysis. Women in the most deprived social group were younger (median 64 years, IQR 55–72 years) and more obese (median 34 kg/m2, IQR 28–42 kg/m2) than women in the least deprived group (median age 68 years, IQR 60–74 years; BMI 29 kg/m2, IQR 25–36 kg/m2; P = 0.002 and <0.001, respectively). There were no differences in endometrial cancer type, stage or grade between social groups. There was no difference in recurrence rates, however, women in the middle and most deprived social groups were more likely to present with distant/metastatic recurrence (80.6 and 79.2%, respectively) than women in the least deprived group (43.5%, P < 0.001). Women in the middle and most deprived groups had a two‐fold (adjusted hazard ratio, HR = 2.00, 95% CI 1.07–3.73, P = 0.030) and 53% (adjusted HR = 1.53, 95% CI 0.77–3.04, P = 0.221) increase in cancer‐specific mortality compared with women in the least deprived group. There were no differences in overall survival.ConclusionsWe found that socio‐economically deprived women with endometrial cancer were more likely to develop fatal recurrence. Larger studies are needed to confirm these findings and to identify modifiable contributing factors.Tweetable abstractSocio‐economic deprivation is linked to an increased risk of death from endometrial cancer in the North West of England.