bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maxillomandibular Advancement for the Treatment of Obstructive Sleep Apnea in Patients With Normal or Class I Malocclusion
Authors: Buller Mitchell , Jodeh Diana S. , Rottgers S. Alex 
Published: February 2020

Background:
Maxillomandibular advancement is an effective surgical option for obstructive sleep apnea (OSA) that achieves enlargement of the upper airway by physically expanding the facial skeleton. The authors sought to determine whether an advancement of 10 mm predicts surgical success and if any correlation existed between the magnitude of mandibular/maxillary advancement and improvement in polysomnography metrics using aggregated individual patient data from multiple studies.

Methods:
A search of the PubMed database was performed to identify relevant articles that included preoperative and postoperative polysomnography data and measurements of the advancement of both the maxillary and mandibular portions of the face in patients with normal or class I malocclusion. Each patient was stratified into “Success” or “Failure” groups based on criteria defining a “Success” as a 50% preoperative to post-operative decrease in AHI or RDI and a post-operative AHI or RDI <20.

Results:
A review of the PubMed database yielded 162 articles. Review of these resulted in 9 manuscripts and a total of 109 patients who met the inclusion criteria. There was no statistically significant difference in the amount of anterior advancement of either the mandible (P = 0.96) or the maxilla (P = 0.23) between the “Success” or “Failure” groups.

Conclusions:
While there is a paucity of individual data available, the current data does not support an ideal amount of maxillary or mandibular advancement that is required to obtain a surgical success in the treatment of OSA. Until a multicenter, prospective, randomized trial is performed, surgical planning should be tailored to patient-specific anatomy to achieve the desired result.
Sleep-Disordered Breathing and Airway Assessment Using Polysomnography in Pediatric Patients With Craniofacial Disorders
Authors: Bekisz Jonathan M. , Wang Maxime M. , Rickert Scott M. , Rodriguez Alcibiades J. , Flores Roberto L. 
Published: February 2020

Abstract
Children with cleft and craniofacial conditions commonly present with concurrent airway anomalies, which often manifest as sleep disordered breathing. Craniofacial surgeons and members of the multidisciplinary team involved in the care of these patients should appreciate and understand the scope of airway pathology as well as the proper means of airway assessment. This review article details the prevalence and assessment of sleep disordered breathing in patients with craniofacial anomalies, with emphasis on indications, limitations, and interpretation of polysomnography.
HDAC Inhibitor Attenuated NETs Formation Induced by Activated Platelets In Vitro, Partially Through Downregulating Platelet Secretion
Authors: Chen Zhenxing , Liu Chang , Jiang Yu , Liu Hanchi , Shao Lina , Zhang Kaiyuan , Cheng Daye , Zhou Ying , Chong Wei 
Published: February 2020

ABSTRACT

Background:
Accumulating studies in recent years have revealed that platelet activation is an important factor inducing neutrophil extracellular traps (NETs) formation in vivo, while the mechanism of this process is not fully elaborated, restricting its clinical use. Our previous study found that a histone deacetylase inhibitor (HDACi) could attenuate serum H3 elevation in septic mice, which was related to NETs formation, and others found HDAC6 to be involved in platelet activation, indicating that HDACis may attenuate platelet activation and result in reduced NETs formation.

Methods:
Freshly isolated human platelets were activated by TRAP-6 with or without a HDACi, and secretion of α-granules was evaluated by testing PF4 in the supernatant using ELISA. NETs were induced by coincubating neutrophils with preactivated platelets, quantified by fluorescent intensity of Sytox green, monitored by live-cell imaging, and qualitatively analyzed by immunofluorescence.

Main Results:
An in vitro bioreactive system to induce and monitor NETs formation using platelets and neutrophils was established. The PF4 elevation stimulated by TRAP-6 in the supernatant of platelets was attenuated by the HDACi, and NETs formation that was induced by coincubating neutrophils with the preactivated platelets was decreased in the presence of the HDACi.

Conclusion:
The HDACi attenuates NETs formation induced by activated platelets partially by modulating the secretion of platelets.
A Predictive Model for Intracardiac Pressures in Patients Free From Rejection or Allograft Vasculopathy After Pediatric Heart Transplantation
Authors: Mills Marcos F. , Long Jin , Quin Feifei , Collins R. Thomas , Rosenthal David N. , Almond Christopher S. , Hollander Seth A. 
Published: February 2020

Background.
Despite the routine use of hemodynamic assessment in pediatric heart transplant (HT) patients, expected intracardiac pressure measurements in patients free of significant complications are incompletely described. A better understanding of the range of intracardiac pressures in these HT patients is important for the clinical interpretation of these indices and consequent management of patients.

Methods.
We conducted a retrospective chart review of pediatric HT recipients who had undergone HT between January 2010 and December 2015 at Lucile Packard Children’s Hospital. We analyzed intracardiac pressures measured in the first 12 mo after HT. We excluded those with rejection, graft coronary artery disease, mechanical support, or hemodialysis. We used a longitudinal general additive model with bootstrapping technique to generate age and donor–recipient size-specific curves to characterize filling pressures through 1-y post-HT.

Results.
Pressure measurements from the right atrium, pulmonary artery, and pulmonary capillary wedge pressure were obtained in 85 patients during a total of 829 catheterizations. All pressure measurements were elevated in the immediate post-HT period and decreased to a stable level by post-HT day 90. Pressure measurements were not affected by age group, donor–recipient size differences, or ischemic time.

Conclusions.
Intracardiac pressures are elevated in the early post-HT period and decrease to levels typical of the native heart by 90 d. Age, donor-to-recipient size differences, and ischemic time do not contribute to differences in expected intracardiac pressures in the first year post-HT.
Reduced model for the surface dynamics of a generally anisotropic elastic half-space
Authors: Fu Yibin , Kaplunov Julius , Prikazchikov Danila 
Published: February 2020

Near-surface resonance phenomena often arise in semi-infinite solids. For instance, when a moving load with a speed
v
close to the surface wave speed
v

R

is applied to the surface of an elastic half-space, it will give rise to a large-amplitude disturbance inversely proportional to
v
−
v

R

. The latter can be determined by a multiple-scale approach using an extra slow time variable. It has also been shown for isotropic elastic half-spaces that the reduced governing equation thus derived is capable of describing the surface wave contribution even for arbitrary dynamic loading. In this paper, we first derive the analogous evolution equation for a generally anisotropic elastic half-space, and then assess its applicability in the study of travelling waves in a half-space that is coated with a continuous array of spring-like vertical resonators or bonded to an elastic layer of different properties. Our results are validated by comparison with previously known results, and illustrative calculations are carried out for a fibre-reinforced half-space and a coated half-space that is subjected to a finite deformation.
Application of High Resolution Melt analysis (HRM) for screening haplotype variation in non-model plants: a case study of Honeybush (CyclopiaVent.)
Authors: Galuszynski Nicholas C , Potts Alastair J 
Published: February 2020

AbstractAimThis study has three broad aims: a) to develop genus-specific primers for High Resolution Melt analysis (HRM) of members ofCyclopiaVent., b) test the haplotype discrimination of HRM compared to Sanger sequencing, and c) provide a case study using HRM to detect novel haplotype variation in wildC. subternataVogel. populations.LocationThe Cape Floristic Region (CFR), located along the southern Cape of South Africa.MethodsPolymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA regions across 14Cyclopiaspecies. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR, the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM regions were then applied to detect novel haplotypes in wildC. subternatapopulations, and phylogeographic patterns ofC. subternatawere explored.ResultsWe present a framework for applying HRM to non-model systems. HRM accuracy varied across the regions screened using the genus-specific primers developed, ranging between 56 and 100 %. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100 % specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wildC. subternatapopulations with high accuracy (96%). Sensitivity below 100 % (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100 %. Phylogeographic analyses revealed that wildC. subternatapopulations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8 % of genetic variation base on an AMOVA), and genetic differentiation between populations increases with distance (p < 0.05 for IBD analyses).ConclusionsAfter screening for regions with high HRM clustering specificity — akin to the screening process associated with most PCR based markers — the technology was found to be a high throughput tool for detecting genetic variation in non-model plants.
Ecotype Simulation 2: An improved algorithm for efficiently demarcating microbial species from large sequence datasets
Authors: Wood Jason M. , Becraft Eric D. , Krizanc Daniel , Cohan Frederick M. , Ward David M. 
Published: February 2020

AbstractBackgroundMicrobial systematists have used molecular cutoffs to classify the vast diversity present within a natural microbial community without invoking ecological theory. The use of ecological theory is needed to identify whether or not demarcated groups are the ecologically distinct, fundamental units (ecotypes), necessary for understanding the system. Ecotype Simulation, a Monte-Carlo approach to modeling the evolutionary dynamics of a microbial population based on the Stable Ecotype Model of microbial speciation, has proven useful for finding these fundamental units. For instance, predicted ecotypes ofSynechococcusforming microbial mats in Yellowstone National Park hot springs, which were previously considered to be a single species based on phenotype, have been shown to be ecologically distinct, with specialization to different temperature and light levels. Unfortunately, development of high-throughput DNA sequencing methods has outpaced the ability of the program to analyze all of the sequence data produced.ResultsWe developed an improved version of the program called Ecotype Simulation 2, which can rapidly analyze alignments of very large sequence datasets. For instance, while the older version takes days to analyze 200 sequences, the new version can analyze 1.92 × 105sequences in about six hours. The faster simulation identified similar ecotypes as found with the slower version, but from larger amounts of sequence data.ConclusionsBased on ecological theory, Ecotype Simulation 2 provides a much-needed approach that will help guide microbial ecologists and systematists to the natural, fundamental units of bacterial diversity.
Measuring protected-area outcomes with leech iDNA: large-scale quantification of vertebrate biodiversity in Ailaoshan nature reserve
Authors: Baker Christopher CM , Ji Yinqiu , Popescu Viorel D , Wang Jiaxin , Wu Chunying , Wang Zhengyang , Li Yuanheng , Wang Lin , Hua Chaolang , Yang Zhongxing , Yang Chunyan , Xu Charles CY , Diana Alex , Wen Qingzhong , Pierce Naomi E , Yu Douglas W 
Published: February 2020

1AbstractProtected areas are central to meeting biodiversity conservation goals, but measuring their effectiveness is challenging. We address this challenge by using DNA from leech-ingested bloodmeals to estimate vertebrate occupancies across the 677 km2Ailaoshan reserve in Yunnan, China. 163 park rangers collected 30,468 leeches from 172 patrol areas. We identified 86 vertebrate species, including amphibians, mammals, birds, and squamates. Multi-species occupancy modelling showed that species richness increased with elevation and distance to reserve edge, including the distributions of most of the large mammals (e.g. sambar, black bear, serow, tufted deer). The exceptions were the three domestic mammal species (cows, sheep, goats) and muntjak deer, which were more common at lower elevations. eDNA-estimated vertebrate occupancies areGranular, Repeatable, Auditable, Direct, Efficient, andSimple-to-understandmeasures that can be used to assess conservation effectiveness and thus to improve the contributions that protected areas make to achieving global biodiversity goals.
Intron retention as a new pre-symptomatic marker of aging and its recovery to the normal state by a traditional Japanese multi-herbal medicine
Authors: Okada Norihiro , Oshima Kenshiro , Iwasaki Yuki , Maruko Akiko , Matsumura Kenya , Iioka Erica , Vu Trieu-Duc , Fujitsuka Naoki , Nishi Akinori , Sugiyama Aiko , Nishiyama Mitsue , Kaneko Atsushi , Mizoguchi Kazushige , Yamamoto Masahiro , Nishimura Susumu 
Published: February 2020

AbstractIntron retention (IR) is an important regulatory mechanism that affects gene expression and protein functions. Using klotho mice at the pre-symptomatic state, we discovered that retained-introns accumulated in several organs including the liver and that among these retained introns in the liver a subset was recovered to the normal state by a Japanese traditional herbal medicine. This is the first report of IR recovery by a medicine. IR-recovered genes fell into two categories: those involved in liver-specific metabolism and in splicing. Metabolome analysis of the liver showed that the klotho mice were under starvation stress. In addition, our differentially expressed gene analysis showed that liver metabolism was actually recovered by the herbal medicine at the transcriptional level. By analogy with the widespread accumulation of intron-retained pre-mRNAs induced by heat shock stress, we propose a model in which retained-introns in klotho mice were induced by an aging stress and in which this medicine-related IR recovery is indicative of the actual recovery of liver-specific metabolic function to the healthy state. Accumulation of retained-introns was also observed at the pre-symptomatic state of aging in wild-type mice and may be an excellent marker for this state in general.
Predictive features of gene expression variation reveal a mechanistic link between expression variation and differential expression
Authors: Sigalova Olga M. , Shaeiri Amirreza , Forneris Mattia , Furlong Eileen E.M. , Zaugg Judith B 
Published: February 2020

AbstractFor most biological processes, organisms must respond to extrinsic cues, while maintaining essential gene expression programs. Although studied extensively in single cells, it is still unclear how variation is controlled in multicellular organisms. Here, we used a machine-learning approach to identify genomic features that are predictive of genes with high versus low variation in their expression across individuals, using bulk data to remove stochastic cell-to-cell variation. Using embryonic gene expression across 75Drosophilaisogenic lines, we identify features predictive of expression variation, while controlling for expression level. Genes with low variation fall into two classes, indicating they employ different mechanisms to maintain a robust expression. In contrast, genes with high variation seem to lack both types of stabilizing mechanisms. Applying the framework to human tissues from GTEx revealed similar predictive features, indicating that promoter architecture is an ancient mechanism to control expression variation. Remarkably, expression variation features could also predict differential expression upon stress in bothDrosophilaand human. Differential gene expression signatures may therefore be partially explained by genetically encoded gene-specific features, unrelated to the studied treatment.
Biogeochemical variability in the California Current System
Authors: Deutsch Curtis , Frenzel Hartmut , McWilliams James C. , Renault Lionel , Kessouri Faycal , Howard Evan , Liang Jun-Hong , Bianchi Daniele , Yang Simon 
Published: February 2020

AbstractThe biological productivity and diversity of the California Current System (CCS) is at the leading edge of major emerging climate trends, including hypoxia and acidification. We present results from a hindcast simulation (reanalysis) of an eddy-resolving oceanic physical-biogeochemical model of the CCS, to characterize its mean state and its patterns and drivers of variability in marine biogeochemical and ecosystem processes from 1995-2010. This is a companion paper to a physical analysis in Renault et al. (2021). The model reproduces long-term mean distributions of key ecosystem metrics, including surface nutrients and productivity and subsurface O2 and carbonate undersaturation. The spatial patterns of Net Primary Productivity (NPP) are broadly consistent with measured and remotely sensed rates, and they reflect a predominant limitation by nitrogen, with seasonal and episodic limitation by Fe nearshore in the central CCS, and in the open ocean northern CCS. The vertical distribution of NPP is governed by the trade-off between nutrient and light limitation, a balance that reproduces and explains the observed spatial variations in the depth of the deep Chl maximum. The seasonal to interannual variability of biogeochemical properties and rates is also well captured by model simulations. Because of the prevailing nutrient limitation, fluctuations in the depth of the pycnocline and associated nutricline are the leading single factor explaining interannual variability in the interior biogeochemical state, and the relationships between density and biogeochemical rates and tracers are consistent between model and observations. The magnitude and relationship between density structure and biogeochemical processes is illustrated by the 1997-98 El Niño event, which faithfully reproduces the single largest deviation from the mean state in the simulated period. A slower decadal shoaling of the pycnocline also accounts for the concomitant trends in hypoxic and corrosive conditions on the shelf. The resulting variability is key to understanding the vulnerability of marine species to oceanic change, and to the detection of such changes, soon projected to exceed the range of conditions in the past century.
Molecular taxonomy of human ocular outflow tissues defined by single cell transcriptomics
Authors: Patel Gaurang , Fury Wen , Yang Hua , Gomez-Caraballo Maria , Bai Yu , Yang Tao , Adler Christina , Wei Yi , Ni Min , Hu Ying , Yancopoulos George , Stamer W. Daniel , Romano Carmelo 
Published: February 2020

ABSTRACTThe conventional outflow pathway is a complex tissue responsible for maintaining intraocular pressure (IOP) homeostasis. The coordinated effort of multiple cells with differing responsibilities ensure healthy outflow function and IOP maintenance. Dysfunction of one or more resident cell type results in ocular hypertension and risk for glaucoma, a leading cause of blindness. In this study, single cell RNA sequencing was performed to generate a comprehensive cell atlas of human conventional outflow tissues. We obtained 17757 genes expression profiles from 8758 cells from eight eyes of four donors representing the outflow cell transcriptome. Upon clustering analysis, 12 distinct cell types were identified, and region-specific expression of candidate genes were mapped in human tissues. Significantly, we identified two distinct expression patterns (myofibroblast and fibroblast) from cells located in the trabecular meshwork (TM), the primary structural component of the conventional outflow pathway. We also located neuron and macrophage signatures in the TM. The second primary component structure, Schlemm’s canal displayed a unique combination of lymphatic/blood vascular gene expression. Other expression clusters corresponded to cells from neighboring tissues, predominantly in the ciliary muscle/scleral spur, which together correspond to the uveoscleral outflow path. Importantly, the utility of our atlas was demonstrated by mapping glaucoma-relevant genes to outflow cell clusters. Our study provides a comprehensive molecular and cellular classification of conventional and unconventional outflow pathway structures responsible for IOP homeostasis.Significance statementOcular hypertension is the primary, and only modifiable risk factor for glaucoma, the leading cause of irreversible blindness. Intraocular pressure is regulated homeostatically by resistance to aqueous humor outflow through an architecturally complex tissue, the conventional/trabecular pathway. In this study, we generated a comprehensive cell atlas of the human trabecular meshwork and neighboring tissues using single cell, RNA sequencing. We identified 12 distinct cell types, and mapped region-specific expression of candidate genes. The utility of our atlas was demonstrated by mapping glaucoma-relevant genes to conventional outflow cell clusters. Our study provides a comprehensive molecular and cellular classification of tissue structures responsible for intraocular pressure homeostasis in health, and dysregulation in disease.