bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arch Asymmetry in Patients With Cleft Lip and Palate After Rehabilitation Treatment Using Stereophotogrammetry
Authors: Pucciarelli Maria Giulia Rezende , Toyoshima Guilherme Hideki , Cardoso Jefferson Freire , de Oliveira Thaís Marchini , Neppelenbroek Karin Hermana , Soares Simone 
Published: January 2021

Abstract
Arch asymmetry in cleft patients is a current problem that interdisciplinary treatment aims to solve. This research proposed to analyze the final rehabilitation, according to the arch symmetry of these patients. Thirty-five patients aged between 18 and 30 years, rehabilitated with a fixed partial denture or implants in the cleft area. The analysis was performed using digitalized dental casts with a laser model scanner (R700TM; 3Shape A/S, Holmens Kanal 7, 1060, Copenhagen/Denmark), analyzed with a Vectra Analysis Module software program (VECTRA H1; Canfield Scientific, 4 Wood Hollow Road, Parsippany, NJ 07054). Three linear measurements were evaluated, incisal-canine, canine-molar, and incisal-molar distance. The Student t test was applied to test the significance (P = 0.05) of an observed sample by correlation coefficient test (r-value). Female patients showed a significant correlation in arch symmetry. According to the rehabilitation treatment, patients who received implants showed a high correlation and significant symmetry at all maxillary distances. Finally, according to the cleft side in the maxillary dimensions, even though the majority of patients had clefts on the left side, only patients with a cleft on the right side showed symmetry in this area. Patients rehabilitated with implants in the cleft area showed a more symmetrical maxillary arch than those restored with fixed partial dentures.
Jinshanibacter, a new genus of Budviciaceae: identification of Jinshanibacter zhutongyuii sp. nov. and Jinshanibacter xujianqingii sp. nov. isolated from cloacal content of snow finch (Montifringilla taczanowskii)
Authors: Ge Yajun , Wang Bin , Yang Jing , Lai Xin-He , Zhang Gui , Lu Shan , Jin Dong , Huang Ying , Cheng Yanpeng , Zhang Xiaoyan , Xu Jianguo 
Published: January 2021

Four novel strains isolated from the cloacal contents of snow finches (Montifringilla taczanowskii) were characterized as aerobic, Gram-stain-negative, slightly motile, and rod-shaped. Analysis of the 16S rRNA gene sequence revealed that strain CF-458T had the highest similarities of 96.9 and 96.4 % with

Limnobaculum parvum

HYN0051T and

Pragia fontium

DSM 5563T, while strain CF-1111T shared the highest similarities of 96.4 and 96.1 % with

Pantoea rodasii

LMG 26273T and

Pectobacterium punjabense

SS95T. Phylogenomic analysis showed the four isolates were separated into group Ⅰ (CF-458T and CF-917) and group Ⅱ (CF-1111T and CF-509), and clustered independently in the vicinity of the genera

Limnobaculum

and

Pragia

. Summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c, 23.9 and 17.2 %, respectively), C16 : 0 (21.8 and 22.1 %, respectively) and C14 : 0 (10.6 and 17.7 %, respectively) were the common major fatty acids, and summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c, 12.3 %) was also a major fatty acid for strain CF-458T while cyclo-C17 : 0 (13.1%) was for strain CF-1111T. Both had Q-8 as the sole quinone and contained phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids. The DNA G+C content of strains CF-458T and CF-1111T was 45.7 and 45.4 mol%, respectively. Based on taxonomic position in the phylogenomic tree and phenotypic properties, two novel species of a new genus within the family

Budviciaceae

are thus proposed, with the name Jinshanibacter gen. nov., zhutongyuii sp. nov. (type strain CF-458T=CGMCC 1.16483T=GDMCC 1.1586T=JCM 33489T) and Jinshanibacter xujianqingii sp. nov. (type strain CF-1111T=CGMCC 1.16786T=GDMCC 1.1587T=JCM 33490T), respectively.
Mutants libraries reveal negative design shielding proteins from mis-assembly and re-localization in cells
Authors: Seisdedos Hector Garcia , Levin Tal , Shapira Gal , Freud Saskia , Levy Emmanuel 
Published: January 2021

ABSTRACTUnderstanding the molecular consequences of mutations in proteins is essential to map genotypes to phenotypes and interpret the increasing wealth of genomic data. While mutations are known to disrupt protein structure and function, their potential to create new structures and localization phenotypes has not yet been mapped to a sequence space. To map this relationship, we employed two homo-oligomeric protein complexes where the internal symmetry exacerbates the impact of mutations. We mutagenized three surface residues of each complex and monitored the mutations’ effect on localization and assembly phenotypes in yeast cells. While surface mutations are classically viewed as benign, our analysis of several hundred mutants revealed they often trigger three main phenotypes in these proteins: nuclear localization, the formation of puncta, and fibers. Strikingly, more than 50% of random mutants induced one of these phenotypes in both complexes. Analyzing the mutant’s sequences showed that surface stickiness and net charge are two key physicochemical properties associated with these changes. In one complex, more than 60% of mutants self-assembled into fibers. Such a high frequency is explained by negative design: charged residues shield the complex from misassembly, and the sole removal of the charges induces its assembly. A subsequent analysis of several other complexes targeted with alanine mutations suggested that negative design against mis-assembly and mislocalization is common. These results highlight that minimal perturbations in protein surfaces’ physicochemical properties can frequently drive assembly and localization changes in a cellular context.
Population dynamics of the primary malaria vectorNyssorhynchus darlingiin a high transmission setting dominated by fish farming in western Amazonian Brazil
Authors: Rufalco-Moutinho Paulo , Kadri Samir Moura , Alonso Diego Perez , Moreno Marta , Carrasco-Escobar Gabriel , Prussing Catharine , Gamboa Dionicia , Vinetz Joseph M. , Mureb Sallum Maria Anice , Conn Jan E. , Martins Ribolla Paulo Eduardo 
Published: January 2021

AbstractVale do Rio Juruáin western Acre, Brazil, has reported highest malaria numbers since 2005, and is considered persistent transmission hotspot. Fish farming development was encouraged to improve standard of living, resulting in productive breeding sites for Amazonian malaria vector species, includingNyssorhynchus darlingithat, combined with the high human density and mobility, adds to the local malaria burden. This study reports entomological profile of immature and adultNy. darlingiat three sites in Mâncio Lima, Acre, during the rainy and dry season (February to September, 2017). From 63 fishponds, 10,859 larvae were collected, including 5,512 first-instar Anophelinae larvae and 4,927 second, third and fourth-instars, of which 8.5% (n = 420) wereNy. darlingi. This species was most abundant in not-abandoned fishponds and in the presence of emerging aquatic vegetation. Seasonal analysis of immatures in urban landscapes found no significant difference in the numbers ofNy. darlingi, corresponding to equivalent population density during the rainy to dry transition period. However, in the rural landscape, significantly higher numbers ofNy. darlingilarvae were collected in August (IRR = 5.80,p= 0.037) and September (IRR = 6.62,p= 0.023) (dry season), compared to February (rainy season), suggesting important role of fishponds for vector population maintenance during the seasonal transition in this landscape type. Adult sampling detected mainlyNy. darlingi(~93%), with similar outdoor feeding behavior, but different abundance according to landscape profile: urban site 1 showed higher peaks of human biting rate in May (46 bites/person/hour), than February (4) and September (15), while rural site 3 shows similar HBR during the same sampling period (22, 24 and 21, respectively). This study contributes to a better understanding of the larvae biology of the main malaria vector in theVale do Rio Juruáregion and, ultimately will support vector control efforts.
Conserved epigenetic programming and enhanced heme metabolism drive memory B cell reactivation
Authors: Price Madeline J. , Scharer Christopher D. , Kania Anna K. , Randall Troy D. , Boss Jeremy M. 
Published: January 2021

ABSTRACTMemory B cells (MBCs) have enhanced capabilities to differentiate to plasma cells and generate a rapid burst of antibodies upon secondary stimulation. To determine if MBCs harbor an epigenetic landscape that contributes to increased differentiation potential, we derived the chromatin accessibility and transcriptomes of influenza-specific IgM and IgG MBCs compared to naïve cells. MBCs possessed an accessible chromatin architecture surrounding plasma cell specific genes, as well as altered expression of transcription factors and genes encoding cell cycle, chemotaxis, and signal transduction processes. Intriguingly, this MBC signature was conserved between humans and mice. MBCs of both species possessed a heightened heme signature compared to naïve cells. Differentiation in the presence of hemin enhanced oxidative phosphorylation metabolism and MBC differentiation into antibody secreting plasma cells. Thus, these data define conserved MBC transcriptional and epigenetic signatures that include a central role for heme and multiple other pathways in augmenting MBC reactivation potential.Key PointsInfluenza-specific memory B cells have accessible chromatin structure.Human and mouse memory B cells upregulate heme metabolic pathways.Heme enhances PC differentiation and augments mitochondrial metabolism in ex vivo.
The elephant retina examined across a range of ages
Authors: Freed James , Joyce Saskia , Whalley Rachel , Purse Edward , Ingram Thomas L , Yon Lisa , Chakrabarti Lisa 
Published: January 2021

AbstractThe effect of aging in the human retina has been well documented, as have the signs of age-related retinal disease. Comparative studies in animals allow us to further investigate how the retina ages in different species. The African bush elephant (Loxodonta africana) has a retina comparable to other mammalian species, but with some reported distinctive differences in retinal ganglion cell (RGC) distribution and type. This is a first survey of the retina ofLoxodonta africanafrom individuals aged 2 months to 32 years old. Gross examination, H&E staining and cell counts were used to compare calves (0-5 years), juveniles (6-10 years), sub-adults (11-20 years) and adults (>20 years). Dorsal-ventral eye diameter was shown to be significantly greater with age, whilst no significant changes in photoreceptor number were found. Changes in retinal thickness differed from past findings in elephants and humans, with thickness decreasing, then increasing in adults. Various morphological differences were evident in the samples including the presence of nuclei in the outer plexiform layer (OPL), degeneration of the inner plexiform layer (IPL), interruptions in nuclei columns of the outer nuclear layer (ONL), and larger unidentified cells within the inner nuclear layer (INL). These are initial observations provide some baseline information for a species where this range of samples has not been described previously.
Indirect restoration of ecological interactions: reintroduction of a dung-beetle associated primate increases the recruitment of large seeds
Authors: Landim Anna R. , Fernandez Fernando A. S. , Pires Alexandra S. 
Published: January 2021

AbstractThe biased loss of large and medium frugivores alters seed dispersal and plant regeneration. Species reintroductions have been proposed as a strategy to reverse the consequences of species loss. However, the effects of reintroductions on ecological processes are seldom accessed, which hinders the comprehension of reintroductions’ potential to reestablish functioning ecosystems. In this study, we investigate the effect of howler monkey (Alouatta guariba) reintroduction on the plant regeneration of Tijuca National Park (TNP), a defaunated Atlantic Forest fragment. Howlers are folivore-frugivore primates, whose large clumped defecations attract dung beetles, which provide secondary dispersal by burying seeds present in the howlers’ feces. Thus, we expect that the fate of seeds dispersed by howlers will differ from those dispersed by other frugivores present in the Park. We followed the fate of seeds between 3 and 14mm in diameter in three steps of the seed dispersal loop, each one consisting of a different experiment. First, we estimated secondary seed dispersal and burial depth probabilities according to the frugivores’ defecation pattern; then, predation probability in different burial depths and defecation patterns; and, finally, recruitment probability in different burial depths. Considering the final result of the three experiments, the howlers’ reintroduction affected positively the regeneration of large seeds. The fate of 3mm seeds was little affected because they were seldom preyed upon at shallower depths anyway and could not recruit when deeply buried. On the other hand, seeds larger than 3mm reached the seedling stage more frequently when dispersed by howlers than when dispersed by other animals present in the Park. Thus, howler monkey reintroduction in defaunated areas, in addition to smaller frugivores, whose defecation patterns are less attractive for dung beetles, improves the regeneration of large seeds. We hope that this study will stimulate new howler reintroductions in defaunated areas.
Data-poor stock assessment of fish stocks co-exploited by commercial and recreational fisheries: applications to pike (Esox lucius) in the western Baltic Sea
Authors: van Gemert Rob , Koemle Dieter , Winkler Helmut , Arlinghaus Robert 
Published: January 2021

AbstractInformation on catch and effort of recreational angling in mixed-use fisheries (co-exploited by commercial and recreational fishers) is often scarce, preventing the application of data-rich stock assessments typically performed for industrialized commercial fisheries. Here, we show how data-poor stock assessment methods developed for marine fisheries, particularly a class of models labelled as “catch-only” models (COMs), offer a possible solution. As a case study, we use COMs to assess a northern pike stock around the German Baltic island of Rügen. We fit multiple COMs to a time-series of total pike removals, and use their outputs as explanatory variables in superensemble models. We conclude that the stock is fully exploited and currently declining. Our study highlights the potential for using COMs to determine status of previously-unassessed coastal and freshwater stocks facing recreational fishing pressure, and demonstrates how incorporating recreational removals is crucial for achieving reliable insights into the status of mixed-use stocks.
Anterior expansion and posterior addition to the notochord mechanically coordinate embryo axis elongation
Authors: McLaren Susannah B.P. , Steventon Benjamin J. 
Published: January 2021

AbstractDuring development the embryo body progressively elongates from head-to-tail along the anterior-posterior (AP) axis. Multiple tissues contribute to this elongation through a combination of convergence and extension and/or volumetric growth. How force generated by the morphogenesis of one tissue impacts the morphogenesis of other axial tissues to achieve an elongated axis is not well understood. The notochord, a rod-shaped tissue possessed by all vertebrates, runs across the entire length of the somitic compartment and is flanked on either side by the developing somites in the segmented region of the axis and presomitic mesoderm in the posterior. Cells in the notochord undergo an expansion that is constrained by a stiff sheath of extracellular matrix, that increases the internal pressure in the notochord allowing it to straighten and elongate. Therefore, it is appropriately positioned to play a role in mechanically elongating the somitic compartment. Here, we use multi-photon mediated cell ablation to remove specific regions of the developing notochord and quantify the impact on axis elongation. We show that anterior notochord cell expansion generates a force that displaces notochord cells posteriorly relative to adjacent axial tissues and contributes to the elongation of segmented tissue during post-tailbud stages of development. Crucially, unexpanded cells derived from progenitors at the posterior end of the notochord provide resistance to anterior notochord cell expansion, allowing for force generation across the AP axis. Therefore, notochord cell expansion beginning in the anterior, and addition of cells to the posterior notochord, act as temporally coordinated morphogenetic events that shape the zebrafish embryo AP axis.
The human olfactory bulb process odor valence representation and initiate motor avoidance behavior
Authors: Iravani Behzad , Schaefer Martin , Wilson Donald A. , Arshamian Artin , Lundström Johan N. 
Published: January 2021

ABSTRACTDetermining the valence of an odor to provide information to guide rapid approach-avoidance behavior is thought to be one of the core tasks of the olfactory system, yet little is known of its initial neural mechanisms or subsequent behavioral manifestation in humans. In two experiments, we measured the functional processing of odor valence perception in the human olfactory bulb (OB)—the first processing stage of the olfactory system—using a non-invasive method as well as assessed subsequent motor avoidance response. We demonstrate that odor valence perception is associated with both gamma and beta activity in the human OB. Moreover, we show that negative, but not positive, odors initiate an early beta response in the OB, a response that is linked to a preparatory neural motor response in motor cortex. Finally, in a separate experiment we show that negative odors trigger a full-body motor avoidance response, manifested as a rapid leaning away from the odor, in the time period predicted by the OB results. Taken together, these results demonstrate that the human OB processes odor valence in a sequential manner in both the gamma and beta frequency bands and suggest that early processing of unpleasant odors in the OB might underlie rapid approach-avoidance decisions.
Characterising the spatio-temporal threats, conservation hotspots, and conservation gaps for the most extinction-prone bird family (Aves: Rallidae)
Authors: Lévêque Lucile , Buettel Jessie C. , Carver Scott , Brook Barry W. 
Published: January 2021

ABSTRACTWith thousands of vertebrate species now threatened with extinction, there is an urgent need to understand and mitigate the causes of wildlife collapse. As distinct evolutionary clades can follow different routes to endangerment, there is value in taxon-specific analyses when assessing species’ vulnerability to threats and identifying gaps in conservation actions. Rails (Aves: Rallidae), being the most extinction-prone bird Family globally, and with one third of extant rail species now threatened or near-threatened, are an emphatic case in point. Yet even for this well-studied group, there is uncertainty in our understanding of what factors might be causing this vulnerability, whether the current threats are consistent with those that led to recent extinctions, and ultimately, what conservation actions might be necessary to mitigate further losses. Here, we undertook a global synthesis of the temporal and spatial threat patterns for Rallidae and determined conservation priorities and gaps. We found two key pathways in the threat pattern for rails. One follows the same trajectory as extinct rails, where island endemic and flightless rails are most threatened, mainly due to invasive predators. The second, created by the recent diversification of anthropogenic activities, involves continental rails (generally in the Neotropics), threatened most commonly by agriculture, natural-system modifications and residential and commercial development. Conservation efforts around most-at-risk species should be adapted according to the most relevant geographic scale (bioregions or countries), and principal locality type of the population (continental or island endemic). Indonesia, the U.S.A., the United Kingdom, New Zealand, and Cuba were the priority countries identified by our classification system incorporating species’ unique evolutionary features and level of endangerment, but also among the countries that lack conservation actions the most. Future efforts should predominantly target improvements in ecosystem protection and management, as well as ongoing research and monitoring. Forecasting the impacts of climate change on island endemic rails and disentangling the specific roles of extrinsic and intrinsic traits (like flightlessness), will be particularly valuable avenues of research for improving our forecasts of rail vulnerability.
Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS
Authors: Wang Kun , Patkar Sushant , Lee Joo Sang , Gertz E. Michael , Robinson Welles , Schischlik Fiorella , Crawford David R. , Schäffer Alejandro A. , Ruppin Eytan 
Published: January 2021

AbstractThe tumor microenvironment (TME) is a complex mixture of cell types whose interactions affect tumor growth and clinical outcome. To discover such interactions, we developed CODEFACS (COnfident DEconvolution For All Cell Subsets), a tool deconvolving cell-type-specific gene expression in each sample from bulk expression, and LIRICS (LIgand Receptor Interactions between Cell Subsets), a statistical framework prioritizing clinically relevant ligand-receptor interactions between cell types from the deconvolved data. We first demonstrate the superiority of CODEFACS versus the state-of-the-art deconvolution method, CIBERSORTx. Second, analyzing the TCGA, we uncover cell-type-specific interactions of mismatch-repair-deficient tumors that are associated with their higher anti-PD1 response rates, including specific T-cell co-stimulating interactions that enhance immunotherapy response independently of the tumors mutation burden levels. Finally, we identify a subset of ligand-receptor interactions in the melanoma TME that predict patient response to anti-PD1 therapy better than recently published transcriptomics-based methods.
Striatal fiber photometry reflects primarily non-somatic activity
Authors: Legaria Alex A. , Yang Ben , Ahanonu Biafra , Licholai Julia A. , Parker Jones G. , Kravitz Alexxai V. 
Published: January 2021

AbstractCalcium recording via fiber photometry is commonly used as a proxy for recording population neuronal activityin vivo, yet the biological source of the photometry signal remains unclear. Here, using simultaneousin vivoextracellular electrophysiology and fiber photometry in the striatum, along with endoscopic 1-photon and 2-photon calcium imaging, we determined that the striatal fiber photometry signal reflects primarily non-somatic, and not somatic, changes in calcium.