bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deforestation projections imply range-wide population decline for critically endangered Bornean orangutan
Authors: Voigt Maria , Kühl Hjalmar S. , Ancrenaz Marc , Gaveau David , Meijaard Erik , Santika Truly , Sherman Julie , Wich Serge A. , Wolf Florian , Struebig Matthew J. , Pereira Henrique M. , Rosa Isabel M.D. 
Published: July 2021

AbstractAssessing where wildlife populations are at risk from future habitat loss is particularly important for land-use planning and avoiding biodiversity declines. Combining projections of future deforestation with species density information provides an improved way to anticipate such declines. Using the endemic and critically endangered Bornean orangutan (Pongo pygmaeus) as a case study we applied a spatio-temporally explicit deforestation model to forest loss data from 2001-2017 and projected future impacts on orangutans to the 2030s. Our projections point to continued deforestation across the island, amounting to a loss of forest habitat for 26,200 (CI: 19,500–34,000) orangutans. Populations currently persisting in forests gazetted for industrial timber and oil palm concessions, or unprotected forests outside of concessions, were projected to experience the worst losses within the next 15 years, amounting to 15,400 (CI: 12,000–20,500) individuals. Lowland forests with high orangutan densities in West and Central Kalimantan were also projected to be at high risk from deforestation, irrespective of land-use. In contrast, most protected areas and logging concessions currently harboring orangutans will continue to face low levels of deforestation. Our business-as-usual projections indicate the importance of protected areas, efforts to prevent the conversion of logged forests for the survival of highly vulnerable wildlife, and protecting orangutan habitat in plantation landscapes. The modeling framework could be expanded to other species with available density or occurrence data. Our findings highlight that species conservation should not only attempt to act on the current situation, but also be adapt to changes in drivers to be effective.
Left-handedness and its genetic influences are associated with structural asymmetries mapped across the cerebral cortex in 31,864 individuals
Authors: Sha Zhiqiang , Pepe Antonietta , Schijven Dick , Carrion Castillo Amaia , Roe James M. , Westerhausen René , Joliot Marc , Fisher Simon E. , Crivello Fabrice , Francks Clyde 
Published: July 2021

AbstractRoughly 10% of the human population is left-handed, and this rate is increased in some brain-related disorders. The neuroanatomical correlates of hand preference have remained equivocal. We re-sampled structural brain image data from 28,802 right-handers and 3,062 left-handers (UK Biobank population dataset) to a symmetrical surface template, and mapped asymmetries for each of 8,681 vertices across the cerebral cortex in each individual. Left-handers and right-handers showed average differences of surface area asymmetry within fusiform, anterior insular, anterior-middle-cingulate and precentral cortex. Meta-analyzed functional imaging data implicated these regions in executive functions and language. Polygenic disposition to left-handedness was associated with two of these regional asymmetries, and 18 loci previously linked with left-handedness by genome-wide screening showed associations with one or more of these asymmetries. Implicated genes included six encoding microtubule-related proteins: TUBB, TUBA1B, TUBB3, TUBB4A, MAP2 and NME7 – the latter is mutated in left-right reversal of the visceral organs. There were also two cortical regions where average thickness asymmetry was altered in left-handedness: on the postcentral gyrus and inferior occipital cortex, functionally annotated with hand sensorimotor and visual roles. These cortical thickness asymmetries were not heritable. Heritable surface area asymmetries of language-related regions may link the etiologies of hand preference and language, whereas non-heritable asymmetries of sensorimotor cortex may manifest as consequences of hand preference.
Airborne environmental DNA for terrestrial vertebrate community monitoring
Authors: Lynggaard Christina , Bertelsen Mads Frost , Jensen Casper V. , Johnson Matthew S. , Guldberg Frøslev Tobias , Olsen Morten Tange , Bohmann Kristine 
Published: July 2021

SummaryAssessing and studying the distribution, ecology, diversity and movements of species is key in understanding environmental and anthropogenic effects on natural ecosystems. Although environmental DNA is rapidly becoming the tool of choice to assess biodiversity 1–3 there are few eDNA sample types that effectively capture terrestrial vertebrate diversity and those that do can be laborious to collect, require special permits and contain PCR inhibitory substances, which can lead to detection failure. Thus there is an urgent need for novel environmental DNA approaches for efficient and cost-effective large-scale routine monitoring of terrestrial vertebrate diversity. Here we show that DNA metabarcoding of airborne environmental DNA filtered from air can be used to detect a wide range of local vertebrate taxa. We filtered air at three localities in Copenhagen Zoo, detecting mammal, bird, amphibian and reptile species present in the zoo or its immediate surroundings. Our study demonstrates that airDNA has the capacity to complement and extend existing terrestrial vertebrate monitoring methods and could form the cornerstone of programs to assess and monitor terrestrial communities, for example in future global next generation biomonitoring frameworks 4,5.
Beneficial Lactiplantibacillus plantarum promote Drosophila growth by down-regulating the expression of PGRP-SC1
Authors: Gallo Marialaura , Vento Justin M. , Joncour Pauline , Quagliariello Andrea , Maritan Elisa , Beisel Chase L. , Martino Maria Elena 
Published: July 2021

ABSTRACTAnimals and their commensal bacteria are known to reciprocally influence many traits of their physiology. Specifically, microbes contribute to the maintenance of the immune system homeostasis, improve host digestive processes, and sustain host growth and development. Several studies have reported that such effects result from an intricate network of nutritional, metabolic and immune inputs and partly rely on the capacity of microbes to regulate the host’s transcriptional response. However, these evidences mainly come from comparing the transcriptional response caused by commensal bacteria with that of axenic animals, making it difficult to identify the specific animal genes that are regulated by beneficial microbes. Here, we employ a well-established model of nutritional symbiosis, Drosophila melanogaster associated with Lactiplantibacillus plantarum, to understand the host genetic pathways regulated by beneficial bacteria and leading to improved host growth and development. Using isogenic L. plantarum strains bearing different growth-promoting effects, we show that the microbial benefit to the host relies on the down-regulation of peptidoglycan- recognition proteins. In particular, we report that the lower expression of PGRP-SC1 exerted by growth-promoting bacteria is responsible for their higher proliferation and the consequent increased production of beneficial metabolites, which ultimately leads to improved host growth and development. Our study helps elucidate the mechanisms underlying the beneficial effect exerted by commensal bacteria, defining the role of PGRP-SC1 in the relationship between Drosophila and its gut microbes.IMPORTANCECommensal bacteria are in constant association with their animal hosts, significantly affecting animal physiology through an intricate network of nutritional, metabolic and immune inputs. Yet, how beneficial bacteria specifically improve animal health is not fully understood. Here, we used a well-established model of nutritional symbiosis to understand how beneficial gut microbes improve host growth via regulation of its transcriptional response. Our study advances the current knowledge in host-microbe interactions by demonstrating that commensal bacteria improve fly growth by actively regulating the expression of immune effectors, which lead to higher immune tolerance. This leads to higher bacterial proliferation and the increased production of beneficial microbial metabolites, which are then consumed by the host. Our results shed light on the complex mechanisms underlying the relationships between a host and its gut microbes.
Exploring the human cerebral cortex using confocal microscopy
Authors: Pesce Luca , Laurino Annunziatina , Scardigli Marina , Yang Jiarui , Boas David A. , Hof Patrick R. , Destrieux Christophe , Costantini Irene , Pavone Francesco Saverio 
Published: July 2021

AbstractCover-all mapping of the distribution of neurons in the human brain would have a significant impact on the deep understanding of brain function. Therefore, complete knowledge of the structural organization of different human brain regions at the cellular level would allow understanding their role in the functions of specific neural networks. Recent advances in tissue clearing techniques have allowed important advances towards this goal. These methods use specific chemicals capable of dissolving lipids, making the tissue completely transparent by homogenizing the refractive index. However, labeling and clearing human brain samples is still challenging. Here, we present an approach to perform the cellular mapping of the human cerebral cortex coupling immunostaining with SWITCH/TDE clearing and confocal microscopy. A specific evaluation of the contributions of the autofluorescence signals generated from the tissue fixation is provided as well as an assessment of lipofuscin pigments interference. Our evaluation demonstrates the possibility of obtaining an efficient clearing and labeling process of parts of adult human brain slices, making it an excellent method for morphological classification and antibody validation of neuronal and non-neuronal markers.
Structural and functional analysis of lorlatinib analogs reveals roadmap for targeting diverse compound resistance mutations in ALK-positive lung cancer
Authors: Shiba-Ishii Aya , Johnson Ted W , Dagogo-Jack Ibiayi , Mino-Kenudson Mari , Johnson Theodore R , Wei Ping , Weinrich Scott L , McTigue Michele A , Walcott Makeba A , Nguyen-Phuong Linh , Dionne Kristin , Acker Adam , Kiedrowski Lesli , Do Andrew , Peterson Jennifer L , Barth Jaimie L , Yeap Beow Y , Gainor Justin F , Lin Jessica J , Yoda Satoshi , Hata Aaron N 
Published: July 2021

ABSTRACTThe treatment approach to advanced, ALK-positive non-small cell lung cancer (NSCLC) utilizing sequential ALK tyrosine kinase inhibitors (TKIs) represents a paradigm of precision oncology. Lorlatinib is currently the most advanced, potent and selective ALK tyrosine kinase inhibitor (TKI) in the clinic. However, tumors invariably acquire resistance to lorlatinib, and after sequential ALK TKIs culminating with lorlatinib, diverse refractory compound ALK mutations can emerge. Here, we determine the spectrum of lorlatinib-resistant compound ALK mutations identified in patients after treatment with lorlatinib, the majority of which involve ALK G1202R or I1171N/S/T. By assessing a panel of lorlatinib analogs against compound ALK mutant in vitro and in vivo models, we identify structurally diverse lorlatinib analogs that harbor differential selective profiles against G1202R- versus I1171N/S/T-based compound ALK mutations. Structural analysis revealed that increased potency against compound mutations was achieved primarily through two different mechanisms of improved targeting of either G1202R- or I1171N/S/T-mutant kinases. Based on these results, we propose a classification of heterogenous ALK compound mutations designed to focus the development of distinct therapeutic strategies for precision targeting of compound resistance mutations following sequential TKIs.
Very Long-Chain Unsaturated Sphingolipids Mediate Oleate-Induced Rat β-Cell Proliferation
Authors: Castell Anne-Laure , Vivoli Alexis , Tippetts Trevor S. , Frayne Isabelle Robillard , Moullé Valentine S. , Ruiz Matthieu , Ghislain Julien , Des Rosiers Christine , Holland William L. , Summers Scott A. , Poitout Vincent 
Published: July 2021

ABSTRACTFatty-acid (FA) signaling contributes to β-cell mass expansion in the face of nutrient excess, but the underlying mechanisms are poorly understood. Here we tested the hypothesis that sphingolipids, generated by the intracellular metabolism of FA, are implicated in the β-cell proliferative response to FA. Isolated rat islets were exposed to individual FA in the presence of 16.7 mM glucose for 48 h and the contribution of the de novo sphingolipid synthesis pathway was tested using the serine palmitoyltransferase inhibitor myriocin, the sphingosine kinase (SphK) inhibitor SKI II, or adenovirus-mediated knockdown of SphK, fatty-acid-elongase-1 (ELOVL1) and acyl-CoA-binding protein (ACBP). Wistar rat were infused with glucose and the lipid emulsion ClinOleic and received SKI II by gavage. B-cell proliferation was assessed by immunochemistry or flow cytometry. Sphingolipidomic analyses were performed by LC-MS/MS. Amongst the various FA tested, only oleate increased β-cell proliferation. Myriocin, SKI II, and SphK knockdown all decreased oleate-induced β-cell proliferation. Oleate exposure did not increase the total amount of sphingolipids but led to a specific rise in 24:1 species. Knockdown of ACBP or ELOVL1 inhibited oleate-induced β-cell proliferation. We conclude that unsaturated very long-chain sphingolipids produced from the available pool of C24:1 acyl-CoA mediate oleate-induced β-cell proliferation in rats.
LGR6 is necessary for attaining peak bone mass and regulates osteogenesis through differential ligand use
Authors: Khedgikar Vikram , Charles Julia F. , Lehoczky Jessica A. 
Published: July 2021

ABSTRACTLeucine-rich repeat containing G-protein-coupled receptor 6 (LGR6) is a marker of osteoprogenitor cells and is dynamically expressed during in vitro osteodifferentation of mouse and human mesenchymal stem cells (MSCs). While the Lgr6 genomic locus has been associated with osteoporosis in human cohorts, the precise molecular function of LGR6 in osteogenesis and maintenance of bone mass are not yet known. In this study, we performed in vitro Lgr6 knockdown and overexpression experiments in murine osteoblastic cells and find decreased Lgr6 levels results in reduced osteoblast proliferation, differentiation, and mineralization. Consistent with these data, overexpression of Lgr6 in these cells leads to significantly increased proliferation and osteodifferentiation. To determine whether these findings are recapitulated in vivo, we performed microCT and ex vivo osteodifferentiation analyses using our newly generated CRISPR-Cas9 mediated Lgr6 mouse knockout allele (Lgr6-KO). We find that ex vivo osteodifferentiation of Lgr6-KO primary MSCs is significantly reduced, and 8 week-old Lgr6-KO mice have less trabecular bone mass as compared to Lgr6 wildtype controls, indicating that Lgr6 is necessary for normal osteogenesis and to attain peak bone mass. Toward mechanism, we analyzed in vitro signaling in the context of two LGR6 ligands, RSPO2 and MaR1. We find that RSPO2 stimulates LGR6-mediated WNT/β-catenin signaling whereas MaR1 stimulates LGR6-mediated cAMP activity, suggesting two ligand-dependent functions for LGR6 receptor signaling during osteogenesis. Collectively, this study reveals that Lgr6 is necessary for wildtype levels of proliferation and differentiation of osteoblasts, and achieving peak bone mass.
Genomic insights into the differentiated population admixture structure and demographic history of North East Asians
Authors: He Guanglin , Wang Mengge , Zou Xing , Tang Renkuan , Yeh Hui-Yuan , Wang Zheng , Yang Xiaomin , Xia Ziyang , Li Yingxiang , Guo Jianxin , Wang Rui , Liu Jing , Zhu Kongyang , Chen Jing , Yang Meiqing , Shen Qu , Chen Jinwen , Zhao Jing , Ma Hao , Wei Lan-Hai , Chen Ling , Liu Changhui , Liu Chao , Chen Gang , Hou Yiping , Wang Chuan-Chao 
Published: July 2021

ABSTRACTNorth China and South Siberia, mainly populated by Altaic-speaking populations, possess extensive ethnolinguistic diversity and serve as the crossroad for the initial peopling of America and western-eastern trans-continental communication. Yet, the complex scenarios of genetic origin, population structure, and admixture history of North-East Asia remain to be fully characterized, especially for Mongolic people in China with a genome-wide perspective. Thus, we genotyped genome-wide SNPs for 510 individuals from 38 Chinese Mongolic, Tungusic, and Sinitic populations to explore the sharing alleles and haplotypes within the studied groups and following merged it with 3508 modern and ancient Eurasian individuals to reconstruct the deep evolutionary and natural selection history of northern East Asians. We identified significant substructures within Altaic-speaking populations with the primary common ancestry linked to the Neolithic northern East Asians: Western Turkic people harbored more western Eurasian ancestry; Northern Mongolic people in Siberia and eastern Tungusic people in Amur River Basin (ARB) possessed dominant Neolithic Mongolian Plateau (MP) or ARB ancestry; Southern Mongolic people in China owned obvious genetic impact from Neolithic Yellow River Basin (YRB) farmers. Additionally, we found the differentiated admixture history between western and eastern Mongolians and geographically close Northeast Hans: the former received a genetic impact from western Eurasians and the latter retained the dominant YRB and ARB Neolithic ancestry. Moreover, we demonstrated that Kalmyk people from the northern Caucasus Mountain possessed a strong genetic affinity with Neolithic MP people, supporting the hypothesis of their eastern Eurasian origin and long-distance migration history. We also illuminated that historic pastoral empires in the MP contributed considerably to the gene pool of northern Mongolic people but rarely to southern ones. We finally found natural signatures in Mongolians associated with alcohol metabolism. Generally, our results not only illuminated that complex population migration and admixture of Neolithic ancestral sources from the MP or ARB played an important role in the spread of Altaic-speaking populations and Proto-Altaic language, which partly supported the Northeast Asia-origin hypothesis, but also demonstrated that the observed multi-sources of genetic diversity contributed significantly to the modern existing extensive ethnolinguistic diversity in North-East Asia.
How would you like your Turkish coffee? Tourist experiences of Turkish coffee houses in Istanbul
Authors: Yiğit Serkan , Şahin Perçin Nilüfer 
Published: July 2021

Purpose
The purpose of this study is to examine and understand the experiences of tourists in the Turkish coffee houses in Istanbul, Turkey.

Design/methodology/approach
In this study, a qualitative case study method was used to analyze tourists’ comments with user-generated content technique by analyzing tourists’ comments. The data used in the study was collected through TripAdvisor, which is considered one of the most famous websites with tourist reviews and comments, between 20 May and 10 June 2020 from tourists’ reviews (n:219).

Findings
The findings show that Turkish coffee house experiences are heterogeneous based on the dimensions of coffee characteristics, place, satisfaction, recommendation and revisit intention, value/price and value-added experience. Moreover, value-added experience includes some sub-themes such as a memorable experience, authentic experience and culture learning experience.

Originality/value
There are some studies on Turkish coffee and Turkish coffee culture in the literature, but there have been no empirical studies investigating the Turkish coffee house experiences of tourists. For this reason, this study aims to examine and understand the experiences of tourists in Turkish coffee houses. Therefore, it is believed that this study will fill the current gap in the literature on tourists’ experiences of Turkish coffee houses.
GeoForge: investigating integrated virtual reality and personalized websites for collaboration in middle school science
Authors: Brenner Corinne , DesPortes Kayla , Ochoa Hendrix Jessica , Holford Mandë 
Published: July 2021

Purpose
This paper aims to describe the design and user testing of GeoForge, a multiple-player digital learning experience for middle school that leverages virtual reality (VR) and individualized websites for learning concepts in planetary science. This paper investigates how specific instructional design choices and features of the technology fostered collaborative behaviors.

Design/methodology/approach
GeoForge was implemented in 3 middle school classrooms with a total of 220 students. Learners used GeoForge in class in groups of 3–4 to learn about planetary science. A mixed-methods approach examined collaboration using classroom observations, teacher interviews, student surveys and student artifacts. Using Jeong and Hmelo-Silver’s (2016) seven affordances of technology for collaborative learning, this paper identifies ways in which features of GeoForge supported collaborative behaviors.

Findings
Instructional design which combined VR and the digital science journal (DSJ) helped foster collaboration. Some collaborative behaviors were especially notable in classrooms that did not regularly practice these skills. Segmenting tasks in the DSJ, clarifying instructions to articulate ideas, showing other group members’ responses onscreen and enabling multiuser VR environments contributed to collaborative behaviors and a satisfying learning experience as observed and documented through multiple methods.

Originality/value
GeoForge successfully integrated VR and personalized websites in a classroom planetary science lesson, an approach which balanced instructional design and logistical challenges while creating opportunities for collaboration.
System dynamics for humanitarian operations revisited
Authors: Besiou Maria , Van Wassenhove Luk N. 
Published: July 2021

PurposeThe purpose of this study is to show that the current complexity of humanitarian operations has only increased the usefulness of system dynamics (SD) in helping decision-makers better understand the challenges they face.Design/methodology/approachA critical analysis to evaluate how SD methodology has been applied to humanitarian operations.FindingsToday's humanitarian operations are characterized by huge complexity given the increased number of stakeholders, feedback loops, uncertainty, scarce resources and multiple objectives. The authors argue that SD's tools (causal-loop diagram, data layer, simulation model) have the capacity to appropriately capture this complexity, thereby enhancing intuition and understanding.Originality/valueResearchers and practitioners hesitate to use system dynamics when data is missing. The authors suggest alternatives to deal with this common situation.