bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted biomass degradation by the higher termite gut system - integrative omics applied to host and its gut microbiome
Authors: Calusinska Magdalena , Marynowska Martyna , Bertucci Marie , Untereiner Boris , Klimek Dominika , Goux Xavier , Sillam-Dussès David , Gawron Piotr , Halder Rashi , Wilmes Paul , Ferrer Pau , Gerin Patrick , Roisin Yves , Delfosse Philippe 
Published: February 2020

AbstractMiscanthussp. is regarded as suitable biomass for different biorefinery value chains. However, due to high recalcitrance, its wide use is yet untapped. Termite is the most efficient lignocellulose degrading insect, and its success results from synergistic cooperation with its gut microbiome. Here, we investigated at holobiont level the dynamic adaptation of a higher termiteCortaritermessp. to imposedMiscanthusdiet, with a long-term objective of overcoming lignocellulose recalcitrance. We used an integrative omics approach, comprising amplicon sequencing, metagenomics and metatranscriptomics that we combined with enzymatic characterisation of carbohydrate active enzymes from termite gut Fibrobacteres and Spirochaetae. Adaptation to the new diet was evidenced by reduced gut bacterial diversity and modified gene expression profiles, further suggesting a shift towards utilisation of cellulose and arabinoxylan, two main components ofMiscanthuslignocellulose. Low identity of reconstructed microbial genomes to microbes from closely related termite species, supported the hypothesis of a strong phylogenetic relationship between host and its gut microbiome. Application-wise, this makes each termite gut system an endless source of enzymes that are potentially industrially relevant.This study provides a framework for better understanding the complex lignocellulose degradation by the higher termite gut system and paves a road towards its future bioprospecting.
The tapejarid pterosaurTupandactylus imperatorfrom Crato Formation and the preservation of cranial integuments
Authors: Campos Hebert Bruno Nascimento , Kischlat Edio-Ernst 
Published: February 2020

AbstractThe group Tapejaridae forms a clade of toothless pterosaurs easily recognized by their premaxillary sagittal crests and particularly large nasoantorbital fenestrae. The tapejarids represent the most representative group of pterosaurs from the Lower Cretaceous Crato Formation of the Araripe Basin (Northeastern Brazil). The holotype of the large tapejaridTupandactylus imperatorCampos and Kellner, 1997 is known by two main slabs from the New Olinda Member of the Crato Formation, however, only one of the slabs containing the sagittally bipartite skull is referred to the holotype ofTupandactylus imperator, remain the counter-slab be properly described. The cotype is fragmented in several broken pieces and presents a significative number of cranial elements. A medial internasal septum completely preserved inside the nasoantorbital fenestra is reported for the first time for pterosaurs. The exceptional preservation of a collagenous septum and other integumentary structures visible in the cotype specimen is extremely rare and supports the concept of the unusual pattern of soft tissue observed in the fossils from the Crato Konservat-Lagerstätte, specially pterosaurs. Herein is presented the description of the cotype ofTupandactylus imperator, in complementation to the previously designated slab of the holotype of this tapejarid species. The occurrence of casques in pterosaurs is supported by comparative anatomy with the bird galliformPauxi(Cracidae). Besides that, it is discussed on the skull with extravagant cranial crests ofTupandactylus imperatorand the significance of the associated soft tissues and other cranial integuments, which indicates an expressive morphological and taxonomic diversity among the tapejarid pterosaurs.
Method for inferring migration routes from phylogenetic trees
Authors: Bermúdez Juanjo 
Published: February 2020

AbstractInferring migration routes from a phylogenetic tree is something that has been done since we have phylogenetic trees. The usual method is just human inference, also known as intuition. Here I present a method for automating this task. Applied to phylogenetic trees with thousands of branches it makes possible to see for the first time inferred routes that were previously too complex to estimate.
Distinct error rates for reference and non-reference genotypes estimated by pedigree analysis
Authors: Wang Richard J. , Radivojac Predrag , Hahn Matthew W. 
Published: February 2020

AbstractErrors in genotype calling can have perverse effects on genetic analyses, confounding association studies and obscuring rare variants. Analyses now routinely incorporate error rates to control for spurious findings. However, reliable estimates of the error rate can be difficult to obtain because of their variance between studies. Most studies also report only a single estimate of the error rate even though genotypes can be miscalled in more than one way. Here, we report a method for estimating the rates at which different types of genotyping errors occur at biallelic loci using pedigree information. Our method identifies potential genotyping errors by exploiting instances where the haplotypic phase has not been faithfully transmitted. The expected frequency of inconsistent phase depends on the combination of genotypes in a pedigree and the probability of miscalling each genotype. We develop a model that uses the differences in these frequencies to estimate rates for different types of genotype error. Simulations show that our method accurately estimates these error rates in a variety of scenarios. We apply this method to a dataset from the whole-genome sequencing of owl monkeys (Aotus nancymaae) in three-generation pedigrees. We find significant differences between estimates for different types of genotyping error, with the most common being homozygous reference sites miscalled as heterozygous and vice versa. The approach we describe is applicable to any set of genotypes where haplotypic phase can reliably be called, and should prove useful in helping to control for false discoveries.
A convNet based multi label microRNA sub cellular location predictor, by incorporating k-mer positional encoding
Authors: Asim Muhammad Nabeel , Dengel Andreas , Ahmed Sheraz 
Published: February 2020

ABSTRACTMicroRNAs are special RNA sequences containing 22 nucleotides and are capable of regulating almost 60% of highly complex mammalian transcriptome. Presently, there exists very limited approaches capable of visualizing miRNA locations inside cell to reveal the hidden pathways, and mechanisms behind miRNA functionality, transport, and biogenesis. State-of-the-art miRNA sub-cellular location prediction MIRLocatar approach makes use of sequence to sequence model along with pre-train k-mer embeddings. Existing pre-train k-mer embedding generation methodologies focus on the extraction of semantics of k-mers. In RNA sequences, rather than semantics, positional information of nucleotides is more important because distinct positions of four basic nucleotides actually define the functionality of RNA molecules. Considering the dynamicity and importance of nucleotides positions, instead of learning representation on the basis of k-mers semantics, we propose a novel kmerRP2vec feature representation approach that fuses positional information of k-mers to randomly initialized neural k-mer embeddings. Effectiveness of proposed feature representation approach is evaluated with two deep learning based convolutional neural network CNN and recurrent neural network RNN methodologies using 8 evaluation measures. Experimental results on a public benchmark miRNAsubloc dataset prove that proposed kmerRP2vec approach along with a simple CNN model outperforms state-of-the-art MirLocator approach with a significant margin of 18% and 19% in terms of precision and recall.
Formal model of Parkinson’s disease neurons unveils possible causality links in the pathophysiology of the disease
Authors: Nadal Morgane , Schierle Gabriele S. Kaminski , Dikicioglu Duygu 
Published: February 2020

SummaryParkinson’s Disease is the second most common neurodegenerative disease after Alzheimer’s disease. Despite extensive research, the initial cause of the disease is still unknown, although substantial advances were made in understanding of its genetics and the cognate neurophysiological mechanisms. Determining the causality relationships and the chronological steps pertaining to Parkinson’s Disease is essential for the discovery of novel drug targets. We developed a systematicin silicomodel based on available data, which puts the possible sequence of events occurring in a neuron during disease onset into light. This is the first ever attempt, to our knowledge, to model comprehensively the primary modifications in the molecular pathways that manifest in compromised neurons from the commencement of the disease to the consequences of its progression. We showed that our proposed disease pathway was relevant for unveiling yet incomplete knowledge on calcium homeostasis in mitochondria, ROS production and α-synuclein misfolding.Graphical abstractHighlightsVarying calcium concentration in aging dopaminergic neurons triggers disease onset.ROS production in the mitochondria potentially causes iron accumulation.Iron homeostasis dysregulation is linked to α-synuclein aggregation.
The TIM22 complex regulates mitochondrial one-carbon metabolism by mediating the import of Sideroflexins
Authors: Jackson Thomas D. , Hock Daniella , Palmer Catherine S. , Kang Yilin , Fujihara Kenji M. , Clemons Nicholas J. , Thorburn David R. , Stroud David A. , Stojanovski Diana 
Published: February 2020

AbstractThe Acylglycerol Kinase (AGK) is a mitochondrial lipid kinase that contributes to protein biogenesis as a subunit of the TIM22 complex at the inner mitochondrial membrane. Mutations inAGKcause Sengers syndrome, an autosomal recessive condition characterized by congenital cataracts, hypertrophic cardiomyopathy, skeletal myopathy and lactic acidosis. We undertook proteomic profiling of Sengers patient fibroblasts and an AGKKOcell line to map the proteomic changes that ensue upon AGK dysfunction. This uncovered extensive remodelling of mitochondrial one-carbon metabolism enzymes and showed that inner membrane serine transporters, Sideroflexins (SFXNs), are novel substrates of the TIM22 complex. Deletion ofSFXN1recapitulates the remodelling of one-carbon metabolism observed in Sengers patient cells. Proliferation of cells lacking AGK is perturbed in the absence of exogenous serine and rescuable through addition of formate, highlighting the dysregulation of one carbon metabolism as a key molecular feature in the biology of Sengers syndrome.
Wiskott Aldrich syndrome protein regulates non-selective autophagy and mitochondrial homeostasis in human myeloid cells
Authors: Rivers E , Rai R , Lötscher J , Hollinshead M , Markelj G , Thaventhiran J , Worth A , Cavazza A , Hess C , Bajaj-Elliott M , Thrasher AJ 
Published: February 2020

AbstractThe actin cytoskeletal regulator Wiskott Aldrich syndrome protein (WASp) has been implicated in maintenance of the autophagy-inflammasome axis in innate murine immune cells. Here, we show that WASp deficiency is associated with impaired rapamycin-induced autophagosome formation and trafficking to lysosomes in primary human monocyte-derived macrophages (MDMs). WASp reconstitutionin vitroand in WAS patients following clinical gene therapy restores autophagic flux and is dependent on the actin-related protein complex ARP2/3. Induction of mitochondrial damage with CCCP, as a model of selective autophagy, also reveals a novel ARP2/3-dependent role for WASp in formation of sequestrating actin cages and maintenance of mitochondrial network integrity. Furthermore, mitochondrial respiration is suppressed in WAS patient MDMs and unable to achieve normal maximal activity when stressed, indicating profound intrinsic metabolic dysfunction. Taken together, we provide evidence of new and important roles of human WASp in autophagic processes and immunometabolic regulation, which may mechanistically contribute to the complex WAS immunophenotype.
Sex-specific crossover rates did not change with parental age inArabidopsis
Authors: Saini Ramswaroop , Singh Amit Kumar , Hyde Geoffrey J. , Baskar Ramamurthy 
Published: February 2020

AbstractCrossing over, the exchange of DNA between the chromosomes during meiosis, contributes significantly to genetic variation. The rate of crossovers (CO) varies depending upon the taxon, population, age, external conditions, and also, sometimes, between the sexes, a phenomenon called heterochiasmy. In the model plantArabidopsis thaliana, the male rate of crossovers (mCO) is typically nearly double the female rate (fCO). With increasing parental age, it has been reported that the disparity decreases, because fCO rises while mCO remains stable. That finding, however, is based on chromosome-based averaging, and it is unclear whether all parts of the genome respond similarly. We addressed this point by examining how the level of heterochiasmy responded to parental age in eight genomic intervals distributed across the five chromosomes ofArabidopsis. Unlike the previous work, in each of the eight intervals, the level of heterochiasmy did not change with age, that is, the ratio mCO:fCO remained stable. As expected, though, amongst the intervals, the levels of heterochiasmy at any of the four ages examined, did vary. We propose that while the levels of heterochiasmy inArabidopismight decrease with age on a chromosomal basis, as reported earlier, this is not true for all locations within each chromosome. This has practical implications for plant breeding research, a major aim of which is identifying ways to induce local increases in CO rates.
Strategic development of flexible manufacturing facilities
Authors: Madson Katherine M. , Franz Bryan , Molenaar Keith R. , Okudan Kremer Gül 
Published: February 2020

PurposeThis article addresses the lack of formal design guidance that supports flexibility within the architectural and engineered systems of manufacturing facilities through the development of a taxonomy and associated terminology.Design/methodology/approachThis research performed a comparative analysis of 15 manufacturing facilities located both within the United States (73 percent of cases) and internationally (27 percent of cases). These case studies provided details on how and where flexibility was incorporated into the design of a manufacturing facility. Specific consideration was given to the primary design features that enabled a decoupling of the facility from the manufacturing process. These design features were then clustered to identify main design strategies that enable flexibility.FindingsBy grouping the design features together and creating a common vocabulary, three coherent design approaches for flexible facilities were identified, each having a different potential for responding to short-term and long-term changes. These include general purpose, scalable, and dedicated facilities.Research limitations/implicationsBy delineating three high-level strategies for early flexible facility design, this research synthesizes a conceptual understanding of flexibility with practical and implementable designs. This synthesis provides an incremental advance to a complex challenge for researchers. It also provides decision support to design teams by aiding in project definition, when flexibility is desirable. This research is primarily limited by the number of cases reviewed. With more cases, additional facility design strategies may be identified.Practical implicationsThe findings in this research allow for a basic understanding of how a flexible facility can be designed with only limited or vague information about the product and manufacturing processes contained within. The development of terminology associated with each facility design strategy provides standardization for the discussion and implementation of flexibility early in the design process. In doing so, flexible designs become easier to create and more efficient to implement.Originality/valueThis research provides the first synthesized approach for considering flexible facility design strategies within the manufacturing sector.
Housing attributes affecting buyers in India
Authors: Ghumare Pavan Namdeo , Chauhan Krupesh A. , Yadav Sanjay Kumar M. 
Published: February 2020

Purpose
The purpose of this paper is to provide affordable housing to low- and middle-income groups. The gravity of India’s housing affordability problem has led us to study and analyse the attributes hindering affordable housing for economically weaker section (EWS) and low-income group (LIG). The attributes such as viable parameters, economic parameters, location and communication, regulatory, source of finance, construction, services and infrastructure parameters affect the supply and demand of affordable housing in Indian urban areas for EWS and LIG with an annual household income below 2 lakhs.

Design/methodology/approach
The judgement sampling is used amongst housing and planning professionals working in five different sectors, including local authorities, housing developers, housing sectors, town planning and property/affordable housing consultant. The Analytical hierarchy process method of multi-criteria decision-making was used to analyse the data collected.

Findings
A detailed analysis of the data collected reveals that a viable parameter is the most governing attribute in the supply and demand process of developing affordable housing. Major reforms can be implemented at various levels of housing development in the urban area that can help in reducing the affordability gap for EWS/LIG. The suggested approach will be helpful for developers, urban planners and decision makers while designing an affordable housing project.

Originality/value
The model being proposed in this paper seeks for a proficient allotment of policies and assets, to some extent, by remedying the current market distortions and different inconsistencies that negatively influence the incentive structure of the affordable housing section in India. This paper offers a plan for a housing procedure that is applicable to all measurements of housing poverty and the groups that sustain it. In this way, the current study is, to a greater extent, a facilitator, and not an immediate solution of affordable housing.
Critical success factors for campus interaction spaces and services – a systematic literature review
Authors: Jansz Sascha Naomi , van Dijk Terry , Mobach Mark P. 
Published: February 2020

Purpose
The purpose of this paper is to create an overview of current literature and identify gaps in what is known about stimulating interaction through spaces and services provided on university campuses.

Design/methodology/approach
The authors used the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement methodology for systematic literature review. In total, 3,616 articles were screened, 31 articles were included. Facility Directors from 13 Dutch Universities were asked to define the search terms related to services.

Findings
Spaces and services were mostly studied separately. The majority of papers (18/31) were based on perceptions (surveys or interviews). The following critical success factors were identified in the literature: geographic proximity, cognitive proximity, scale, transitional spaces, comfort and experience, shared facilities and events, local buzz and networks. These factors are interrelated. The authors present a new relational model, from spaces and services, through interaction to innovation, visualising how the identified papers are related.

Research limitations/implications
The scope of possible findings may have been narrowed because prior relevant studies were rather limited and as a consequence of the search strategy designed to limit the number of unrelated hits. Some knowledge gaps may not have been identified, as only a few mainstream concepts related to the critical success factors were used for comparison. Nevertheless, the literature review provides a reliable overview of current academic knowledge regarding critical success factors for spaces and services that stimulate interaction on campuses.

Originality/value
This paper offers a novel perspective by emphasising the relational chain from interaction to innovation, visualising the large diversity in research fields and summarising the critical success factors in the literature.
Socio-economics and management of Muslim cemeterywaqfusing istibdal and GIS method in Penang state
Authors: Asni Fathullah , Mahamud Mohd Amirul , Sulong Jasni 
Published: February 2020

PurposeThe purpose of this paper is to implement the istibdalwaqfconcept using a geographical information system (GIS) for the benefit of socio-economics and Muslim cemeterywaqfmanagement. GIS is a technique that provides clearer, precise and faster access to a location based on actual space data. It attempts to analyze the area that one wishes to develop to establish whether it fulfills the criteria set for istibdal.Design/methodology/approachThis research was conducted qualitatively. The study begins with the development of the concept of istibdalwaqfand the concept of GIS. The concept was developed by conducting a literature review of books, articles, newspapers, fatwa and circulars related to istibdalwaqfand GIS. After the concept was formed, field studies were conducted on two mosques, namely, Jamek Jelutong Mosque and Masjid Jamek Sungai Nibong because both mosques have gravesites located within their compound. To obtain information on the problems faced by the mosques Jemaah community, researchers have interviewed the Mosque Committee Members and Jemaah Community in both mosques using the unstructured interviewing method. This process is essential in managing both material and spiritual for sustaining socio-economics of the society.FindingsThe results showed that by applying GIS technique could identify new land locations according to the criteria set by istibdal. Additionally, new location environments found through the GIS application can be viewed more clearly and accurately than using the manual method. The findings also revealed that some of the mosque managers and the heirs of thewaqfgrave land were not open-minded in accepting the istibdal concept of the grave that had been allowed by the Syarak until the process of expanding the mosque was affected. The study also found that the maslahah consideration was considered between doing istibdalwaqfand not doing istibdalwaqf, the maslahah of doing istibdalwaqfis greater because general (umum) maslahah should be prioritized compared to the special (khusus) maslahah. In addition, this effort can appreciate the morality and ethics ofwaqfdonors to donate their wealth or properties for benefit of society.Research limitations/implicationsThis study only focuses on Muslim cemeterywaqfin Penang Island.Practical implicationsThis study is expected to benefit both material and spiritual where Muslim cemetery site can be developed for expanding mosque site and consequently able to accommodate the increasing of Muslim using the mosque.Originality/valueThis study proposes the transformation of the concept of istibdalwaqffrom the traditional methods to modern and advanced methods using the GIS application. The study also demonstrates how the software for solving the real problem can be used, i.e. the problem of a limited mosque space for sharing space with a cemetery in Penang.