bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epistatic genetic interactions govern morphogenesis during sexual reproduction and infection in a global human fungal pathogen
Authors: Sun Sheng , Roth Cullen , Averette Anna Floyd , Magwene Paul , Heitman Joseph 
Published: December 2021

AbstractCellular development is orchestrated by evolutionarily conserved signaling pathways, which are often pleiotropic and involve intra- and inter-pathway epistatic interactions that form intricate, complex regulatory networks.Cryptococcusspecies are a group of closely-related human fungal pathogens that grow as yeasts yet transition to hyphae during sexual reproduction. Additionally, during infection they can form large, polyploid titan cells that evade immunity and develop drug resistance. Multiple known signaling pathways regulate cellular development, yet how these are coordinated and interact with genetic variation is less well understood. Here, we conducted quantitative trait locus (QTL) analyses of a mapping population generated by sexual reproduction of two parents, only one of which is unisexually fertile. We observed transgressive segregation of the unisexual phenotype among progeny, as well as a novel large-cell phenotype under mating-inducing conditions. These large-cell progeny were found to produce titan cells bothin vitroand in infected animals. Two major QTLs and corresponding quantitative trait genes (QTGs) were identified:RIC8(encoding a guanine-exchange factor) andCNC06490(encoding a putative Rho-GTPase activator), both involved in G-protein signaling. The two QTGs interact epistatically with each other and with the mating-type locus in phenotypic determination. These findings provide insights into the complex genetics of morphogenesis during unisexual reproduction and pathogenic titan cell formation and illustrate how QTL analysis can be applied to identify epistasis between genes. This study shows that phenotypic outcomes are influenced by the genetic background upon which mutations arise, implicating dynamic, complex genotype-to-phenotype landscapes in fungal pathogens and beyond.Significance statementCellular development is regulated by a complex web of signaling pathways that respond to both intracellular and extracellular cues. Morphological transitions in pathogenic fungi, such as those observed during sexual reproduction or in response to the host environment, offer tractable models for understanding the principles that govern eukaryotic cell development and morphogenesis. Using the human fungal pathogenCryptococcus deneoformansas a model and applying QTL analysis, we defined novel genes and gene-gene interactions involved in the yeast-hyphal transition and titanization, two morphological developments that are important for adaptation, pathogenesis, and evolution of this fungal pathogen. Our study provides new insights into the conservation and complexity of key signaling pathways in regulating cell development in fungi, as well as other eukaryotes.
Estimating real snakebite incidence in Colombia by using mathematical modelling and statistical inference
Authors: Bravo-Vega Carlos , Renjifo-Ibañez Camila , Santos-Vega Mauricio , Leon Nuñez Leonardo Jose , Angarita-Sierra Teddy , Cordovez Juan Manuel 
Published: December 2021

ABSTRACTSnakebite envenoming is a Neglected Tropical Disease affecting mainly deprived populations. Its burden is normally underestimated because patients prefer to seek for traditional medicine. Thus, applying strategies to optimize disease’ management and treatment delivery is difficult. We propose a framework to estimate snakebite incidence at a fine political scale based on available data, testing it in Colombia. First, we produced snakebite fine-scale risk maps based on the most medically important venomous snake species (Bothrops asper and B. atrox). We validated them with reported data in the country. Then, we proposed a generalized mixed effect model that estimates total incidence based on produced risk maps, poverty indexes, and an accessibility score that reflects the struggle to reach a medical center. Finally, we calibrated our model with national snakebite reported data from 2010 to 2019 using a Markov chain Monte Carlo (MCMC) algorithm and estimated underreporting based on the total incidence estimation. Our results suggest that 10.3% of total snakebite cases are not reported in Colombia and do not seek medical attention. The Orinoco and Amazonian regions (east of Colombia) share a high snakebite risk with a high underreporting. Our work highlights the importance of multidisciplinary approaches to face snakebite.
Time-dependent memory and individual variation in Arctic brown bears (Ursus arctos)
Authors: Thompson Peter R. , Lewis Mark A. , Edwards Mark A. , Derocher Andrew E. 
Published: December 2021

1AbstractAnimal movement modelling provides unique insight about how animals perceive their landscape and how this perception may influence space use. When coupled with data describing an animal’s environment, ecologists can fit statistical models to location data to describe how spatial memory informs movement. We performed such an analysis on a population of brown bears (Ursus arctos) in the Canadian Arctic using a model incorporating time-dependent spatial memory patterns. Brown bear populations in the Arctic lie on the periphery of the species’ range, and as a result endure harsh environmental conditions. In this kind of environment, effective use of memory to inform movement strategies could spell the difference between survival and mortality. The model we fit tests four alternate hypotheses (some incorporating memory; some not) against each other, and we found a high degree of individual variation in how brown bears used memory. We found that 52% (11 of 21) of the bears used complex, time-dependent spatial memory to inform their movement decisions. These results, coupled with existing knowledge on individual variation in the population, highlight the diversity of foraging strategies for Arctic brown bears while also displaying the inference that can be drawn from this innovative movement model.
Manipulating the microbiome alters regenerative outcomes inXenopus laevistadpoles via lipopolysaccharide signalling
Authors: Chapman Phoebe A. , Gilbert Campbell B. , Devine Thomas J. , Hudson Daniel T. , Ward Joanna , Morgan Xochitl C. , Beck Caroline W. 
Published: December 2021

ABSTRACTXenopus laevistadpoles can regenerate functional tails, containing spinal cord, notochord, muscle, fin, blood vessels and nerves, except for a brief refractory period at around one week of age. At this stage, amputation of the tadpole’s tail may either result in scarless wound healing, or the activation of a regeneration programme, which replaces the lost tissues. We recently demonstrated a link between bacterial lipopolysaccharides and successful tail regeneration in refractory stage tadpoles, and proposed that this could result from lipopolysaccharides binding to Toll-like receptor 4 (TLR4). Here, we have used 16S rRNA sequencing to show that the tadpole skin microbiome is highly variable between sibships and that the community can be altered by raising embryos in the antibiotic gentamicin. Six gram-negative genera, includingDelftia and Chryseobacterium, were over-represented in tadpoles that underwent tail regeneration. Lipopolysaccharides purified from a commensalChryseobacterium spp. XDS4, an exogenousDelftia spp. orEscherichia colicould significantly increase the number of antibiotic-raised tadpoles that attempted regeneration. Conversely, the quality of regeneration was impaired in native-raised tadpoles exposed to the antagonistic lipopolysaccharide ofRhodobacter sphaeroides. Editing TLR4 using CRISPR/Cas9 also reduced regeneration quality, but not quantity, at the level of the cohort. However, we found that the editing level of individual tadpoles was a poor predictor of regenerative outcome. In conclusion, our results suggest that variable regeneration in refractory stage tadpoles depends at least in part on the skin microbiome and lipopolysaccharide signalling, but that signalling via TLR4 cannot account for all of this effect.
A single-cell genomic strategy for alternative transcript start sites identification
Authors: Peng Yanling , Huang Qitong , Kamada Rui , Ozato Keiko , Zhang Yubo , Zhu Jun 
Published: December 2021

AbstractAlternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-β stimulated mouse embryonic fibroblasts (MEFs). We quantify the performance of our method and find it as accurate as other single cell methods for the detection of TSSs. Our data are also clearly discriminate two IFN-β stimulated MEFs. Moreover, our results indicate 82% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on CAGE (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future.
Speech Sound Discrimination by Mongolian Gerbils
Authors: Jüchter Carolin , Beutelmann Rainer , Klump Georg Martin 
Published: December 2021

AbstractThe present study establishes the Mongolian gerbil (Meriones unguiculatus) as a model for investigating the perception of human speech sounds. We report data on the discrimination of logatomes (CVCs1- consonant-vowel-consonant combinations with outer consonants /b/, /d/, /s/ and /t/ and central vowels /a/, /a:/, /ε/, /e:/, /I/, /i:/, /ɔ/, /o:/, /℧/ and /u:/, VCVs2- vowel-consonant-vowel combinations with outer vowels /a/, /I/ and /℧/ and central consonants /b/, /d/, /f/, /g/, /k/, /l/, /m/, /n/, /p/, /s/, /t/ and /v/) by young gerbils. Four young gerbils were trained to perform an oddball target detection paradigm in which they were required to discriminate a deviant CVC or VCV in a sequence of CVC or VCV standards, respectively. The experiments were performed with an ICRA-1 noise masker with speech-like spectral properties, and logatomes of multiple speakers were presented at various signal-to-noise ratios. Response latencies were measured to generate perceptual maps employing multidimensional scaling, which visualize the gerbils’ internal representations of the sounds. The dimensions of the perceptual maps were correlated to multiple phonetic features of the speech sounds for evaluating which features of vowels and consonants are most important for the discrimination. The perceptual representation of vowels and consonants in gerbils was similar to that of humans, although gerbils needed higher signal-to-noise ratios for the discrimination of speech sounds than humans. The gerbils’ discrimination of vowels depended on differences in the frequencies of the first and second formant determined by tongue height and position. Consonants were discriminated based on differences in combinations of their articulatory features. The similarities in the perception of logatomes by gerbils and humans renders the gerbil a suitable model for human speech sound discrimination.HighlightsPerceptual maps of vowels and consonants in Mongolian gerbils are derivedGerbils perceive vowels and consonants in the same way as humansGerbils discriminate vowels based on frequency differences of the formantsGerbils discriminate consonants based on differences in articulatory features
Colorimetric and fluorescent TRAP assays for visualising and quantifying fish osteoclast activity
Authors: Ethiraj Lalith Prabha , Lei Samuel Fong En , Liu Ranran , Winkler Christoph , Carney Tom James 
Published: December 2021

AbstractHistochemical detection of tartrate-resistant acid phosphatase (TRAP) activity is a fundamental technique for visualizing osteoclastic bone resorption and assessing osteoclast activity status in tissues. This approach has mostly employed colorimetric detection, which has limited quantification of activity in situ and co-labelling with other skeletal markers. Here we report simple colorimetric and fluorescent TRAP assays in zebrafish and medaka, two important model organisms for investigating the pathogenesis of bone disorders. We show fluorescent TRAP staining, utilising the ELF97 substrate, is a rapid, robust and stable system to visualise and quantify osteoclast activity in zebrafish, and is compatible with other fluorescence stains, transgenic lines and antibody approaches. Using this approach, we show that TRAP activity is predominantly found around the base of the zebrafish pharyngeal teeth, where osteoclast activity state appears to be heterogeneous.
North and East African mitochondrial genetic variation needs further characterization towards precision medicine
Authors: Fähnrich Anke , Stephan Isabel , Hirose Misa , Haarich Franziska , Awadelkareem Mosab Ali , Ibrahim Saleh , Busch Hauke , Wohlers Inken 
Published: December 2021

AbstractIntroductionMitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied.ObjectivesTo address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial dataset to date and use it for characterizing mitochondrial genetic variation in this region.MethodsWe compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n=2,504) and the Human Genome Diversity Project (n=828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples.ResultsUsing a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1.ConclusionOur findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.
Syntheses, structures and magnetic properties of two CoII/NiII isostructural coordination polymers based on an asymmetric semirigid tricarboxylate ligand
Authors: Li Shao-Dong , Su Feng , Zhou Cheng-Yong , Hu Qi-Long , Li Ya-Qi , Wang Zhi-Jun 
Published: December 2021

Two new isostructural complexes, namely, poly[aqua[μ3-2-(4-carboxyphenoxy)terephthalato-κ3
O
1:O
4:O
4′](1,10-phenanthroline-κ2
N,N′)cobalt(II)], [Co(C15H8O7)(C12H8N2)(H2O)]
n
or [Co(μ3-Hcpota)(phen)(H2O)]
n
, I, and poly[aqua[μ3-2-(4-carboxyphenoxy)terephthalato-κ3
O
1:O
4:O
4′](1,10-phenanthroline-κ2
N,N′)nickel(II)], [Ni(C15H8O7)(C12H8N2)(H2O)]
n
or [Ni(μ3-Hcpota)(phen)(H2O)]
n
, II, have been synthesized by solvothermal reactions. Complexes I and II were fully characterized by IR spectroscopy, elemental analyses, thermogravimetric analyses, and powder and single-crystal X-ray diffraction. They both present two-dimensional structures based on [M
2(μ-COO)2]2+ (M = CoII or NiII) dinuclear metal units with a fes topology and a vertex symbol (4·82). Interestingly, the positions of the two dimeric metal motifs and the two partially deprotonated Hcpota2− ligands reproduce regular flying butterfly arrangements flipped upside down and sharing wings in the ab plane. Magnetic studies indicate antiferromagnetic interactions (J = −5.21 cm−1 for I and −11.53 cm−1 for II) in the dimeric units, with Co...Co and Ni...Ni distances of 4.397 (1) and 4.358 (1) Å, respectively, that are related to double syn–anti carboxylate bridges.
Fear vs humor appeals: a comparative study of children's responses to anti-smoking advertisements
Authors: Nicolini Valentina , Cassia Fabio 
Published: December 2021

PurposeThis study aims to examine the different effects that the fear and humor appeals in anti-smoking advertisements for children have on their affective reactions to the advertisements, on their beliefs about smoking and on their behavioral intentions to smoke.Design/methodology/approachThis paper presents the findings of a qualitative research study conducted in Italy with children aged from 8 to 11 years.FindingsThe results indicated that the humor appeal is a useful method for conveying a social theme in a pleasant way and creating a likable character that becomes an example for children to imitate; however, it is necessary to employ the fear appeal to make children reflect carefully about the negative consequences of smoking.Research limitations/implicationsThis study examined only children's behavioral intentions derived from anti-smoking advertisements, but future research should also examine their real behaviors after a period following repeated viewing of public service announcements about smoking prevention or other social issues.Practical implicationsUnderstanding how different types of appeals can influence children represents an important result for the prevention of youth smoking and the promotion of healthy lifestyle habits during childhood.Social implicationsUnderstanding how different types of appeals can influence children represents an important result for the prevention of youth smoking and the promotion of healthy lifestyle habits during childhood.Originality/valueFew studies have examined the impact of social advertisements on children, and particularly little is known about the effectiveness of fear appeals on this group.
Journal selection behavior among early-career academicians in Iran: how they choose the most appropriate journal for their publications
Authors: Shamsi Amrollah , Lund Brady D_ , SeyyedHosseini Shohreh , BasirianJahromi Reza 
Published: December 2021

Purpose
Journals are the essential tools of researchers, especially academicians, to present their scientific findings. So, choosing the right journal helps not only science development but also their academic promotion. The purpose of this study is to examine the factors that Iranian medical researchers consider when selecting scholarly journals in which to submit their work.

Design/methodology/approach
A self-administered online questionnaire was emailed in May 2021, with 101 responses received. The sample included all the faculty members with the role of “lecturer” in Iranian medical universities and who have 1–5 articles in the Scopus database as early-career Iranian medical researchers. The questionnaire consisted of 36 items, divided into five sections: basic information, attitudes and beliefs, ways to choose a journal, problems and familiarity with the components of scientometrics/validity metrics related to journals.

Findings
The findings indicate that these researchers value the expertise of experienced researchers and professionals, like librarians, when selecting publication venues. They often use journal indexes to guide journal selection. They also consider factors like the length of typical peer review and the complexity of submission guidelines when making decisions.

Research limitations/implications
The study of one country, though detecting requirements of journal selection behavior, cannot be generalized to the entire region.

Practical implications
The current study has academic implications as far as decisions on journal selection are concerned. University policymakers in Iran may consider re-examining their emphasis on academicians’ promotion policies at Iranian universities of medical sciences.

Originality/value
These findings may support the work of early-career researchers and those individuals (e.g., librarians) that serve them, as well as publishers and editors of scholarly journals.
Causal interactions among essential factors of Industry 4.0 innovation using DEMATEL technique in manufacturing industries
Authors: Nimawat Dheeraj , Gidwani B.D. 
Published: December 2021

Purpose
Industry 4.0 implementation appears to have a far-reaching effect on consumer demand. Research findings on market prospects and implementation status are also rare. The purpose of this study is to address the essential factors regarding the implementation status of the Indian manufacturing industries that would entail a complete implementation of the Industry 4.0 innovations in developing nations and execute them entirely to achieve related benefits.

Design/methodology/approach
The primary factors impacting the Industry 4.0 implementation status recognized a focus on comprehensive literature analysis and its validation by recommendations from 12 specialists with substantial expertise in Industry 4.0. The DEMATEL technique has been implemented in this analysis to examine the structure of causal interactions among the recognized essential factors.

Findings
From a literature analysis and recommendations from specialists, 16 essential factors are recognized. Using DEMATEL techniques, ranking of the essential factors has been obtained according to their importance. Moreover, the findings show the cause and effect interactions among essential factors in the perspective of Industry 4.0 innovations in Indian manufacturing industries.

Research limitations/implications
The current research is restricted to Indian manufacturing industries (developing nations).

Practical implications
It will help industries move towards an Industry 4.0 implementation by knowing their status. A research model is being developed, including specific vital features of Industry 4.0 as indicators for its implementation. Nevertheless, few are renowned for how industries, especially in developing nations, perceive the possible effects of Industry 4.0 technological innovations and industrial efficiency.

Originality/value
To the best of the authors’ knowledge, the present research contributes first to be carried out regarding the model of information about the nature of causal interactions among the recognized essential factors of Industry 4.0 in the surrounding of Indian manufacturing industries to address the implementation status of Industry 4.0 innovations using DEMATEL technique.