bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monobloc Differential Distraction Osteogenesis
Authors: Polley John W. , Figueroa Alvaro A. , Girotto John A. , Dietze-Fiedler Megan L. 
Published: September 2021

Abstract
Midface advancement at the monobloc level can be the seminal life event for patients with craniofacial dysostosis. Monobloc reconstruction, when planned appropriately, can simultaneously and definitively address multiple functional and aesthetic deficiencies in these patients. The application of distraction has reduced the morbidity experienced with traditional monobloc surgery. The purpose of this study is to report on the outcomes, stability, and growth in younger patients after monobloc advancement in syndromic craniosynostosis patients. The authors report a consecutive series of thirty patients with craniofacial dysostosis treated through monobloc differential distraction osteogenesis. Detailed history, photographic, and long-term radiographic data are reviewed, including a subset of patients who were skeletally immature at the time of their treatment. Differential distraction allows control of midface pitch, roll, and yaw, optimizing functional and aesthetic outcomes. There were no infectious complications requiring reoperation. The average surgical age for all patients was 12.5 years. For the 7 patients age <7 years, average age was 6 years. For all patients, the mean horizontal movement was 12 mm at nasion and 10 mm at A-point. At mean follow-up (4.8 years entire group and 6.2 years age <7 years group) a positive horizontal advancement of 1.1 mm at nasion and 0.8 mm at A-point was observed. More pronounced positive horizontal changes were seen in the age <7 years group. Monobloc differential distraction osteogenesis affords safe and precise repositioning of the midface. The advancement is skeletally stable and young patients show moderate continued growth.
Epidemiological Characteristics of Children With Non-Cleft Lip/Palate Craniofacial Anomalies
Authors: Sawasdipanich Nantaga , Chaithat Bussara , Rojvachiranonda Nond , Dangsomboon Artiteeya 
Published: September 2021

Abstract
Non-cleft craniofacial anomalies are not as common as cleft lip and palate but resultant disability can be very severe. Although there are epidemiological studies of the clefts in the medical literature, the non-cleft group is still not well known. This study was to examine the epidemiological characteristics of the non-cleft craniofacial anomalies. Patients younger than 18 years old were included during a 1-year period. Patient information was retrieved from medical records and a questionnaire filled by primary caregivers.
There were 139 patients included in the study with an average age of 6 years and 7 months (4–194 months). Fifty-eight percent were male, 56% were first-born children, whereas 61.9% had siblings. Family history was positive in 6.5%. Almost all patients were in age-appropriate educational levels. Using Whitaker classification, Synostoses was the most common at 48.9%, followed by Unclassified, Clefts, Neoplasia-Hyperplasia, and Atrophy-Hypoplasia. Their anomalies were mostly detected at the regional hospitals. Outpatient visits throughout the course ranged from 1 to 100. Eighty-two percent of patients had at least 1 hospitalization, whereas 78% experienced at least 1 surgical treatment.
Generally, non-cleft craniofacial anomalies were nonfamilial. We found a wide variety of anomalies. Patients were from all regions of the country. Their geographical location did not prevent access to receiving proper care and education. Having a child with an anomaly did not discourage the family from having more descendants. Among the available classifications, the Whitaker system is easier for clinical use.
Predictions of primate–parasite coextinction
Authors: Herrera James P. , Moody James , Nunn Charles L. 
Published: September 2021

Future biodiversity loss threatens the integrity of complex ecological associations, including among hosts and parasites. Almost half of primate species are threatened with extinction, and the loss of threatened hosts could negatively impact parasite associations and ecosystem functions. If endangered hosts are highly connected in host–parasite networks, then future host extinctions will also drive parasite extinctions, destabilizing ecological networks. If threatened hosts are not highly connected, however, then network structure should not be greatly affected by the loss of threatened hosts. Networks with high connectance, modularity, nestedness and robustness are more resilient to perturbations such as the loss of interactions than sparse, nonmodular and non-nested networks. We analysed the interaction network involving 213 primates and 763 parasites and removed threatened primates (114 species) to simulate the effects of extinction. Our analyses revealed that connections to 23% of primate parasites (176 species) may be lost if threatened primates go extinct. In addition, measures of network structure were affected, but in varying ways because threatened hosts have fewer parasite interactions than non-threatened hosts. These results reveal that host extinctions will perturb the host–parasite network and potentially lead to secondary extinctions of parasites. The ecological consequences of these extinctions remain unclear.
This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
The future of zoonotic risk prediction
Authors: Carlson Colin J. , Farrell Maxwell J. , Grange Zoe , Han Barbara A. , Mollentze Nardus , Phelan Alexandra L. , Rasmussen Angela L. , Albery Gregory F. , Bett Bernard , Brett-Major David M. , Cohen Lily E. , Dallas Tad , Eskew Evan A. , Fagre Anna C. , Forbes Kristian M. , Gibb Rory , Halabi Sam , Hammer Charlotte C. , Katz Rebecca , Kindrachuk Jason , Muylaert Renata L. , Nutter Felicia B. , Ogola Joseph , Olival Kevin J. , Rourke Michelle , Ryan Sadie J. , Ross Noam , Seifert Stephanie N. , Sironen Tarja , Standley Claire J. , Taylor Kishana , Venter Marietjie , Webala Paul W. 
Published: September 2021

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges?
This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
Land-use change and rodent-borne diseases: hazards on the shared socioeconomic pathways
Authors: García-Peña Gabriel E. , Rubio André V. , Mendoza Hugo , Fernández Miguel , Milholland Matthew T. , Aguirre A. Alonso , Suzán Gerardo , Zambrana-Torrelio Carlos 
Published: September 2021

Land-use change has a direct impact on species survival and reproduction, altering their spatio-temporal distributions. It acts as a selective force that favours the abundance and diversity of reservoir hosts and affects host–pathogen dynamics and prevalence. This has led to land-use change being a significant driver of infectious diseases emergence. Here, we predict the presence of rodent taxa and map the zoonotic hazard (potential sources of harm) from rodent-borne diseases in the short and long term (2025 and 2050). The study considers three different land-use scenarios based on the shared socioeconomic pathways narratives (SSPs): sustainable (SSP1-Representative Concentration Pathway (RCP) 2.6), fossil-fuelled development (SSP5-RCP 8.5) and deepening inequality (SSP4-RCP 6.0). We found that cropland expansion into forest and pasture may increase zoonotic hazards in areas with high rodent-species diversity. Nevertheless, a future sustainable scenario may not always reduce hazards. All scenarios presented high heterogeneity in zoonotic hazard, with high-income countries having the lowest hazard range. The SSPs narratives suggest that opening borders and reducing cropland expansion are critical to mitigate current and future zoonotic hazards globally, particularly in middle- and low-income economies. Our study advances previous efforts to anticipate the emergence of zoonotic diseases by integrating past, present and future information to guide surveillance and mitigation of zoonotic hazards at the regional and local scale.
This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification
Authors: De Baets Kenneth , Huntley John Warren , Scarponi Daniele , Klompmaker Adiël A. , Skawina Aleksandra 
Published: September 2021

Growing evidence suggests that biodiversity mediates parasite prevalence. We have compiled the first global database on occurrences and prevalence of marine parasitism throughout the Phanerozoic and assess the relationship with biodiversity to test if there is support for amplification or dilution of parasitism at the macroevolutionary scale. Median prevalence values by era are 5% for the Paleozoic, 4% for the Mesozoic, and a significant increase to 10% for the Cenozoic. We calculated period-level shareholder quorum sub-sampled (SQS) estimates of mean sampled diversity, three-timer (3T) origination rates, and 3T extinction rates for the most abundant host clades in the Paleobiology Database to compare to both occurrences of parasitism and the more informative parasite prevalence values. Generalized linear models (GLMs) of parasite occurrences and SQS diversity measures support both the amplification (all taxa pooled, crinoids and blastoids, and molluscs) and dilution hypotheses (arthropods, cnidarians, and bivalves). GLMs of prevalence and SQS diversity measures support the amplification hypothesis (all taxa pooled and molluscs). Though likely scale-dependent, parasitism has increased through the Phanerozoic and clear patterns primarily support the amplification of parasitism with biodiversity in the history of life.This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula
Authors: Chhetri Geeta , Kim Inhyup , Kang Minchung , Kim Jiyoun , So Yoonseop , Seo Taegun 
Published: September 2021

An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10T was affiliated to the genus

Nocardioides

and the closest species were

Nocardioides glacieisoli

HLT3-15T (98.8 %),

Nocardioides zhouii

HLT2-9T (98.8 %),

Nocardioides ganghwensis

JC2055T (98.7 %),

Nocardioides cavernae

YIM A1136T (98.6 %),

Nocardioides flavus

Y4T (98.5 %),

Nocardioides oleivorans

DSM 16090T (98.3 %),

Nocardioides alpinus

Cr7-14T (98.2 %),

Nocardioides exalbidus

DSM 22017T (98.1 %) and

Nocardioides hwasunensis

KCTC 19197T (98.1 %). Strain G10T formed a monophyletic cluster with

N. glacieisoli

HLT3-15T,

N. zhouii

HLT2-9T and

N. hwasunensis

KCTC 19197T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C16 : 0 and C17 : 1
ω8c. MK-8(H4) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA–DNA hybridization values were 78.6–88.7 % and 21.5–36.2 %, respectively, with the type strains of related species of the genus

Nocardioides

, suggesting that strain G10T represents a novel species. The genome of strain G10T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10T represent a novel species within the genus

Nocardioides

, for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10T (=KCTC 49626T=NBRC 114801T).
The aging lung mucosa: A proteomics study
Authors: Garcia-Vilanova Andreu , Olmo-Fontánez Angélica M. , Moliva Juan I. , Allué-Guardia Anna , Singh Harjinder , Merrit Robert E. , Caceres Diego M. , Peters Jay , Wang Yufeng , Schlesinger Larry S. , Turner Joanne , Weintraub Susan T. , Torrelles Jordi B. 
Published: September 2021

AbstractThe elderly population is at increased risk of acute and chronic respiratory infections and other pulmonary diseases, and it is estimated that this population will double in the next 30 years. Biochemical changes in the lung alveolar mucosa and lung cells alter local immune response as we age, creating opportunities for invading pathogens to establish successful infections. Indeed, the lungs of the elderly are a pro-inflammatory, pro-oxidative, dysregulated environment but this environment has remained understudied. We performed a comprehensive, quantitative proteomic profile of the lung mucosa in the elderly, developing insight into the molecular fingerprints, pathways, and regulatory networks that characterize the lung in old age. We identified neutrophils in the lungs of elderly individuals as possible contributors to dysregulated lung tissue environment. This study establishes a baseline for future investigations to develop strategies to mitigate susceptibility to respiratory infections in the elderly.
Biomechanical interactions of Schistosoma mansoni eggs with vascular endothelial cells facilitate egg extravasation
Authors: Yeh Yi-Ting , Skinner Danielle E. , Criado-Hidalgo Ernesto , Chen Natalie Shee , Garcia-De Herreros Antoni , El-Sakary Nelly , Liu Lawrence , Zhang Shun , Chien Shu , Lasheras Juan C. , del Álamo Juan C. , Caffrey Conor R. 
Published: September 2021

AbstractThe eggs of the parasitic blood fluke, Schistosoma, are the main drivers of the chronic pathologies associated with schistosomiasis, a disease of poverty afflicting approximately 220 million people worldwide. Eggs laid by Schistosoma mansoni in the bloodstream of the host are encapsulated by vascular endothelial cells (VECs), the first step in the migration of the egg from the blood stream into the lumen of the gut and eventual exit from the body. The biomechanics associated with encapsulation and extravasation of the egg are poorly understood. We demonstrate that S. mansoni eggs induce VECs to form two types of membrane extensions during encapsulation; filopodia that probe eggshell surfaces and intercellular nanotubes that presumably facilitate VEC communication. Encapsulation efficiency, the number of filopodia and intercellular nanotubes, and the length of these structures depend on the egg’s vitality and, to a lesser degree, its maturation state. During encapsulation, live eggs induce VEC contractility and membranous structures formation, in a Rho/ROCK pathway-dependent manner. Using elastic hydrogels embedded with fluorescent microbeads as substrates to culture VECs, live eggs induce VECs to exert significantly greater contractile forces during encapsulation than dead eggs, which leads to 3D deformations on both the VEC monolayer and the flexible substrate underneath. These significant mechanical deformations cause the VEC monolayer tension to fluctuate with eventual rupture of VEC junctions, thus facilitating egg transit out of the blood vessel. Overall, our data on the mechanical interplay between host VECs and the schistosome egg improve our understanding of how this parasite manipulates its immediate environment to maintain disease transmission.
SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural source
Authors: Borges Rafael J. , Salvador Guilherme H. M. , Pimenta Daniel C. , dos Santos Lucilene D. , Fontes Marcos R. M. , Usón Isabel 
Published: September 2021

ABSTRACTProteins isolated from natural source can be composed of a mixture of isoforms with similar physicochemical properties that coexists in final steps of purification, toxins being prominent examples. Sequence composition is enforced throughout structural studies even when unsubstantiated. Herein, we propose a novel perspective to address the usually neglected heterogeneity of natural products by integrating biophysical, genetic and structural data in our program SEQUENCE SLIDER.The aim is to assess the evidence supporting chemical composition in structure determination. Locally, we interrogate the experimental map to establish which side chains are supported by the structural data and the genetic information relating sequence conservation is integrated in this statistic. Hence, we build a constrained peptide database, containing most probable sequences to interpret mass spectrometry data (MS). In parallel, we perform MSde novosequencing with genomic-based algorithms that foresee point mutations.We calibrated SLIDER withGallus galluslysozyme, for which sequence is unequivocally established and numerous natural isoforms are reported. We used SLIDER to characterise a metalloproteinase and a phospholipase A2-like protein from the venom ofBothrops moojeniand a crotoxin fromCrotalus durissus collilineatus. This integrated approach offers a more realistic structural descriptor to characterize macromolecules isolated from natural source.Key pointsThe method SEQUENCE SLIDER integrates biophysical, genetic and structural data to assign sequence.It joins crystallography, mass spectrometry and phylogenetic data to characterize isoforms.Sequence heterogeneity of four proteins purified directly from snake venom was established.
Synchronous spiking of cerebellar Purkinje cells during control of movements
Authors: Sedaghat-Nejad Ehsan , Pi Jay S. , Hage Paul , Fakharian Mohammad Amin , Shadmehr Reza 
Published: September 2021

AbstractThe information that the brain transmits from one region to another is often viewed through the lens of firing rates. However, if the output neurons could vary the timing of their spikes with respect to each other, then through synchronization they could highlight information that may be critical for control of behavior. In the cerebellum, the computations that are performed by the cerebellar cortex are conveyed to the nuclei via inhibition. Yet, synchronous activity entrains nucleus neurons, making them fire. Does the cerebellar cortex rely on spike synchrony within populations of Purkinje cells (P-cells) to convey information to the nucleus? We recorded from multiple P-cells while marmosets performed saccadic eye movements and organized them into populations that shared a complex spike response to error. Before movement onset, P-cells transmitted information via a rate code: the simple spike firing rates predicted the direction and velocity of the impending saccade. However, during the saccade, the spikes became temporally aligned within the population, signaling when to stop the movement. Thus, the cerebellar cortex relies on spike synchronization within a population of P-cells, not individual firing rates, to convey to the nucleus when to stop a movement.
Cognitive processing of a common stimulus synchronizes brains, hearts, and eyes
Authors: Madsen Jens , Parra Lucas C. 
Published: September 2021

AbstractNeural, physiological and behavioral signals synchronize between human subjects in a variety of settings. Multiple hypotheses have been proposed to explain this interpersonal synchrony, but there is no clarity under which conditions it arises, for which signals, or whether there is a common underlying mechanism. We hypothesized that similar cognitive processing of a shared stimulus is the source of synchrony between subjects, measured here as inter-subject correlation. To test this we presented informative videos to participants in an attentive and distracted condition and subsequently measured information recall. Inter-subject correlation was observed for electro-encephalography, gaze position, pupil size and heart rate, but not respiration and head movements. The strength of correlation was co-modulated in the different signals, changed with attentional state, and predicted subsequent recall of information presented in the videos. There was robust within-subject coupling between brain, heart and eyes, but not respiration or head movements. The results suggest that inter-subject correlation is the result of similar cognitive processing and thus emerges only for those signals that exhibit a robust brain-body connection. While physiological and behavioral fluctuations may be driven by multiple features of the stimulus, correlation with other individuals is co-modulated by the level of attentional engagement with the stimulus.
SMAP: A pipeline for sample matching in proteogenomics
Authors: Li Ling , Niu Mingming , Erickson Alyssa , Luo Jie , Rowbotham Kincaid , Huang He , Li Yuxin , Jiang Yi , Liu Chunyu , Peng Junmin , Wang Xusheng 
Published: September 2021

AbstractIntegration of genomics and proteomics (proteogenomics) offers unprecedented promise for in-depth understanding of human diseases. However, sample mix-up is a pervasive, recurring problem, due to complex sample processing in proteogenomics. Here we present a pipeline for Sample Matching in Proteogenomics (SMAP) for verifying sample identity to ensure data integrity. SMAP infers sample-dependent protein-coding variants from quantitative mass spectrometry (MS), and aligns the MS-based proteomic samples with genomic samples by two discriminant scores. Theoretical analysis with simulation data indicates that SMAP is capable of uniquely match proteomic and genomic samples, when ≥20% genotypes of individual samples are available. When SMAP was applied to a large-scale proteomics dataset from 288 biological samples generated by the PsychENCODE BrainGVEX project, we identified and corrected 18.8% (54/288) mismatched samples. The correction was further confirmed by ribosome profiling and assay for transposase-accessible chromatin sequencing data from the same set of samples. Thus our results demonstrate that SMAP is an effective tool for sample verification in a large-scale MS-based proteogenomics study. The source code, manual, and sample data of the SMAP are publicly available at https://github.com/UND-Wanglab/SMAP, and a web-based SMAP can be accessed at https://smap.shinyapps.io/smap/.