bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-Dimensional Planning of the Mandibular Margin in Hemifacial Microsomia Using a Printed Patient-Specific Implant
Authors: Igelbrink Sebastian , Zanettini Leonardo Matos Santolim , Bohner Lauren , Kleinheinz Johannes , Jung Susanne 
Published: October 2020

Abstract
Hemifacial microsomia (HFM) is also known as malformation of the first and second branchial arches (BAs), oculoauriculovertebral dysplasia syndrome, and Goldenhar syndrome. Possibilities resulting from CAD/CAM may be a valuable tool to existing procedures to treat these abnormalities. The aim of this study was to report a case where the planning and implementation of an intraorally inserted 2-part patient-specific mandible implant was used for the treatment of HFM esthetic remained problem after orthognathic surgery. A 20-year-old female patient who continued to suffer from the esthetic defect of the unilateral hypoplastic mandible after completion of the orthognathic surgery attended for consultation. Using CT scan and the software Geomagic Freeform (3D Systems, USA), a 2-piece titanium implant was designed and printed to restore the osseous frame of the basal border of the mandible. The base was made of solid polished titanium to minimize soft tissue abrasion. Due to its split design, the implant could be placed anatomically exactly at the mandibular margin via an intraoral access and to avoid damage of the mental nerve. There were no postoperative complications such as infections, soft tissue reactions to the implant, sensitivity disorders, or dehiscence. The occlusion was regular. A measurement of the postoperative x-rays showed a clear increase in bony symmetry. No postoperative pain or trismus was seen. Functionally, the therapy ended with the completion of wound healing and the jaw was fully resilient again. A combined treatment using PSI and additional autogenous fat grafting may represent a valid treatment option for the treatment of facial asymmetry in patients with HFM.
Liver Resection Versus Local Ablation Therapies for Hepatocellular Carcinoma Within the Milan Criteria
Authors: Shin Seong Wook , Ahn Keun Soo , Kim Sang Woo , Kim Tae-Seok , Kim Yong Hoon , Kang Koo Jeong 
Published: October 2020

Objective:
To compare the oncologic outcomes of liver resection (LR) and local ablation therapies for HCC.

Summary of Background Data:
Although several studies have compared LR and local ablation therapies, the optimal treatment of choice for HCC within the Milan criteria remains controversial.

Methods:
We systemically searched the MEDLINE, Embase, and Cochrane Library databases for randomized control trials (RCTs) and matched nonrandomized trials (NRTs) that compared LR and local ablation therapies for HCC within the Milan criteria. The primary outcome was overall survival (OS). Secondary outcomes were recurrence free survival (RFS) and recurrence pattern.

Results:
A total of 7 RCTs and 18 matched NRTs, involving 2865 patients in the LR group and 2764 patients in the local ablation therapy group [RFA, MWA, RFA plus trans-arterial chemoembolization (TACE)], were included. Although there was no significant difference in OS between LR and RFA, LR showed a significantly better 5-year RFS than RFA in the analysis of RCTs (hazards ratio: 0.75; 95% confidence interval: 0.62–0.92; P = 0.006). The RFA group showed a significantly higher local recurrence than the LR group in both analyses of RCTs and NRTs. Additionally, the LR group showed better OS and RFS than the MWA or RFA plus TACE groups.

Conclusion:
Our meta-analysis showed that LR was superior to RFA in terms of RFS and incidence of local recurrence. Moreover, LR showed better oncologic outcomes than MWA or RFA plus TACE.
Stereotactic Body Radiotherapy Versus Delayed Surgery for Early-stage Non-small-cell Lung Cancer
Authors: Mayne Nicholas R. , Lin Belle K. , Darling Alice J. , Raman Vignesh , Patel Deven C. , Liou Douglas Z. , D’Amico Thomas A. , Yang Chi-Fu Jeffrey 
Published: October 2020

Objective:To evaluate the overall survival of patients with operable stage IA non-small-cell lung cancer (NSCLC) who undergo “early” SBRT (within 0–30 days after diagnosis) versus “delayed” surgery (90–120 days after diagnosis).Summary of Background Data:During the COVID-19 pandemic, national guidelines have recommended patients with operable stage IA NSCLC to consider delaying surgery by at least 3 months or, alternatively, to undergo SBRT without delay. It is unknown which strategy is associated with better short- and long-term outcomes.Methods:Multivariable Cox proportional hazards modeling and propensity score-matched analysis was used to compare the overall survival of patients with stage IA NSCLC in the National Cancer Data Base from 2004 to 2015 who underwent “early” SBRT (0–30 days after diagnosis) versus that of patients who underwent “delayed” wedge resection (90–120 days after diagnosis).Results:During the study period, 570 (55%) patients underwent early SBRT and 475 (45%) underwent delayed wedge resection. In multivariable analysis, delayed resection was associated with improved survival [adjusted hazard ratio 0.61; (95% confidence interval (CI): 0.50–0.76)]. Propensity-score matching was used to create 2 groups of 279 patients each who received early SBRT or delayed resection that were well-matched with regard to baseline characteristics. The 5-year survival associated with delayed resection was 53% (95% CI: 45%–61%) which was better than the 5-year survival associated with early SBRT (31% [95% CI: 24%–37%]).Conclusion:In this national analysis, for patients with stage IA NSCLC, extended delay of surgery was associated with improved survival when compared to early treatment with SBRT.
Barriers to the Use of Active Surveillance for Thyroid Cancer Results of a Physician Survey
Authors: Hughes David T. , Reyes-Gastelum David , Ward Kevin C. , Hamilton Ann S. , Haymart Megan R. 
Published: October 2020

Objective:
The aim of this study was to determine physician-reported use of and barriers to active surveillance for thyroid cancer.

Summary Background Data:
It is not clear whether active surveillance for thyroid cancer is widely used.

Methods:
Surgeons and endocrinologists identified by thyroid cancer patients from the Surveillance, Epidemiology, and End Results (SEER) registries of Georgia and Los Angeles County were surveyed between 2018 and 2019. Multivariable weighted logistic regression analyses were conducted to determine physician acceptance and use of active surveillance. Results: Of the 654 eligible physicians identified, 448 responded to the survey (69% response rate). The majority (76%) believed that active surveillance was an appropriate management option, but only 44% used it in their practice. Characteristics of physicians who stated that active surveillance was appropriate management, but did not report using it included more years in practice (reference group <10 years in practice): 10 to 19 years [odds ratio, OR 0.50 [95% confidence interval, CI 0.28–0.92]; 20 to 29 years [OR 0.31 (95% CI 0.15–0.62)]; >30 years [OR 0.30 (95% CI 0.15–0.61)] and higher patient volume 11 to 30 patients per year [OR 0.39 (95% CI 0.21 –0.70)] and >50 patients per year [OR 0.33 (95% CI 0.16–0.71)] compared to < 10, with no significant difference in those seeing 31 to 50 patients. Physicians reported multiple barriers to implementing active surveillance including patient does not want (80.3%), loss to follow-up concern (78.4%), more patient worry (57.6%), and malpractice lawsuit concern (50.9%).

Conclusion and Relevance:
Despite most physicians considering active surveillance to be appropriate management, more than half are not using it. Addressing existing barriers is key to improving uptake.
Perioperative Morbidity and Mortality of Patients With COVID-19 Who Undergo Urgent and Emergent Surgical Procedures
Authors: Knisely Anne , Zhou Zhen Ni , Wu Jenny , Huang Yongmei , Holcomb Kevin , Melamed Alexander , Advincula Arnold P. , Lalwani Anil , Khoury-Collado Fady , Tergas Ana I. , St. Clair Caryn M. , Hou June Y. , Hershman Dawn L. , D’Alton Mary E. , Huang Yolanda Ya-Chin , Wright Jason D. 
Published: October 2020

Objective:
To evaluate the perioperative morbidity and mortality of patients with COVID-19 who undergo urgent and emergent surgery.

Summary Background Data:
Although COVID-19 infection is usually associated with mild disease, it can lead to severe respiratory complications. Little is known about the perioperative outcomes of patients with COVID-19.

Methods:
We examined patients who underwent urgent and emergent surgery at 2 hospitals in New York City from March 17 to April 15, 2020. Elective surgical procedures were cancelled throughout and routine, laboratory based COVID-19 screening was instituted on April 1. Mortality, complications, and admission to the intensive care unit were compared between patients with COVID-19 detected perioperatively and controls.

Results:
Among 468 subjects, 36 (7.7%) had confirmed COVID-19. Among those with COVID-19, 55.6% were detected preoperatively and 44.4% postoperatively. Before the routine preoperative COVID-19 laboratory screening, 7.7% of cases were diagnosed preoperatively compared to 65.2% after institution of screening (P = 0.0008). The perioperative mortality rate was 16.7% in those with COVID-19 compared to 1.4% in COVID-19 negative subjects [aRR = 9.29; 95% confidence interval (CI), 5.68–15.21]. Serious complications were identified in 58.3% of COVID-19 subjects versus 6.0% of controls (aRR = 7.02; 95%CI, 4.96–9.92). Cardiac arrest, sepsis/shock, respiratory failure, pneumonia, acute respiratory distress syndrome, and acute kidney injury were more common in those with COVID-19. The intensive care unit admission rate was 36.1% in those with COVID-19 compared to 16.4% of controls (aRR = 1.34; 95%CI, 0.86–2.09).

Conclusions:
COVID-19 is associated with an increased risk for serious perioperative morbidity and mortality. A substantial number of patients with COVID-19 are not identified until after surgery.
Growth–fragmentation–coagulation equations with unbounded coagulation kernels
Authors: Banasiak J. , Lamb W. 
Published: October 2020

In this paper, we prove the global in time solvability of the continuous growth–fragmentation–coagulation equation with unbounded coagulation kernels, in spaces of functions having finite moments of sufficiently high order. The main tool is the recently established result on moment regularization of the linear growth–fragmentation semigroup that allows us to consider coagulation kernels whose growth for large clusters is controlled by how good the regularization is, in a similar manner to the case when the semigroup is analytic.
This article is part of the theme issue ‘Semigroup applications everywhere’.
Towards a Koopman theory for dynamical systems on completely regular spaces
Authors: Farkas Bálint , Kreidler Henrik 
Published: October 2020

The Koopman linearization of measure-preserving systems or topological dynamical systems on compact spaces has proven to be extremely useful. In this article, we look at dynamics given by continuous semiflows on completely regular spaces, which arise naturally from solutions of PDEs. We introduce Koopman semigroups for these semiflows on spaces of bounded continuous functions. As a first step we study their continuity properties as well as their infinitesimal generators. We then characterize them algebraically (via derivations) and lattice theoretically (via Kato’s equality). Finally, we demonstrate—using the example of attractors—how this Koopman approach can be used to examine properties of dynamical systems.This article is part of the theme issue ‘Semigroup applications everywhere’.
Semigroups for dynamical processes on metric graphs
Authors: Kramar Fijavž Marjeta , Puchalska Aleksandra 
Published: October 2020

We present the operator semigroups approach to the first- and second-order dynamical systems taking place on metric graphs. We briefly survey the existing results and focus on the well-posedness of the problems with standard vertex conditions. Finally, we show two applications to biological models.
This article is part of the theme issue ‘Semigroup applications everywhere’.
Yeosuana marina sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island
Authors: Zhang Qingfeng , Lin Dan , Ye Jianing , Lin Ta-Hui , Li Chenlan , Lin Huaying , Sun Xueqiong , Tang Kai 
Published: October 2020

A novel Gram-stain-negative, non-flagellated, non-motile, rod-shaped (0.4–0.6×1.8–2.5 µm), aerobic bacterial strain, designated JLT21T, was isolated from seawater of a shallow-sea hydrothermal system. Growth occurred with 0–4.0 % (w/v) NaCl (optimum, 2.0 % NaCl), at 8–45 °C (optimum, 25 °C) and at pH 3.0–10.0 (optimum, pH 7.0). Analysis of 16S rRNA gene sequences revealed that strain JLT21T showed the highest 16S rRNA gene sequence similarity to

Gaetbulibacter aquiaggeris

KEM-8T (97.2 %),

Gaetbulibacter marinus

IMCC1914T (96.9 %) and

Yeosuana aromativorans

GW1-1T (96.9 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JLT21T clustered with

Y. aromativorans

GW1-1T. The predominant respiratory quinone of strain JLT21T was menaquinone-6 (MK-6). Polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids and four unidentified lipids. The major fatty acids of strain JLT21T were iso-C15 : 0 (21.7 %), C16 : 1
ω6c/ω7c (11.5 %) and iso-C17 : 0 3-OH (10.9 %). The DNA G+C content of strain JLT21T was 32.6 %. On the basis of polyphasic analysis, strain JLT21T is considered to represent a novel species of the genus

Yeosuana

, for which the name Yeosuana marina sp. nov. is proposed. The type strain of Yeosuana marina is JLT21T (=CGMCC 1.15787T=JCM 31511T). The study helps us better understand the bacterial species in the shallow-sea hydrothermal system and their adaptations to the hydrothermal environment.
Estimating divergence times from DNA sequences
Authors: Sjödin Per , McKenna James , Jakobsson Mattias 
Published: October 2020

ABSTRACTThe patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the ‘Two-Two (TT)’ and the ‘Two-Two-outgroup (TTo)’ methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split-times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo-method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.
Metagenomics and quantitative stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater
Authors: Sieradzki Ella T. , Morando Michael , Fuhrman Jed A. 
Published: October 2020

AbstractBacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by low chronic inputs can respond to acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We demonstrate the ability of a local seed community of degraders at the Port of LA to incorporate carbon from naphthalene, leading to a quick shift in the microbial community composition to be dominated by these normally rare taxa. We were able to directly show that assembled genomes belonged to naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes and even when combining genes from the entire microbial community. We analyze metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate metagenomic-based recommendations for future optimization of PAHs bioremediation.ImportanceOil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil, and have a significant role in degradation of oil spills. The most recalcitrant and toxic component of oil is polycyclic aromatic hydrocarbons. Therefore, the bacteria who can break those molecules down are of particular importance. We identified such bacteria at the port of Los Angeles, one of the busiest ports worldwide, and characterized their metabolic capabilities. Based on those analyses we proposed chemical targets to stimulate the activity of these bacteria in case of an oil spill in the port of LA.
Cysteine residues in the C-terminal tail of connexin32 regulate its trafficking
Authors: Ray Anuttoma , Mehta Parmender P. 
Published: October 2020

ABSTRACTGap junctions (GJ)s are formed by the assembly of constituent transmembrane proteins called connexins (Cxs). Aberrations in this assembly of Cxs are observed in several genetic diseases as well as in cancers. Hence it becomes imperative to understand the molecular mechanisms underlying such assembly defect. The polarized cells in the epithelia express Connexin32 (Cx32). The carboxyl-terminal tail (CT) of Cx32 orchestrates several aspects of GJ dynamics, function and growth. The study here was aimed at determining if post-translational modifications, specifically, palmitoylation of cysteine residues, present in the CT of Cx32, has any effect on GJ assembly. The CT of Cx32 was found to harbor three cysteine residues, which are likely to be modified by palmitoylation. The study here has revealed for the first time that Cx32 is palmitoylated at cysteine 217 (C217). However, it was found that mutating C217 to alanine affected neither the trafficking nor the ability of Cx32 to assemble into GJs. Intriguingly, it was discovered that mutating cysteine 280 and 283 in combination, blocked the transport of Cx32 from the Golgi to the cell surface. Overall, the findings reveal the importance of the two terminal cysteine residues of Cx32 in regulating its trafficking and stability and hence is ability to assemble into GJs, possibly as being part of a CAAX motif in its CT.
RNA-Seq Time Series ofVitis viniferaBud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile
Authors: Pucker Boas , Schwandner Anna , Becker Sarah , Hausmann Ludger , Viehöver Prisca , Töpfer Reinhard , Weisshaar Bernd , Holtgräwe Daniela 
Published: October 2020

AbstractPlants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine (Vitis vinifera) early bud development. The expression of the developmental regulatorVviAP1served as an indicator for progress of development. We investigated the impact of changing temperatures on gene expression levels during the time series and detected a correlation between increased temperatures and a high expression level of genes encoding heat-shock proteins. The data set also allowed the exemplary investigation of expression patterns of genes from three transcription factor (TF) gene families, namely MADS-box, WRKY, and R2R3-MYB genes. Inspection of the expression profiles from all three TF gene families indicated that a switch in the developmental program takes place in July which coincides with increased expression of the bud dormancy marker geneVviDRM1.
Feeding habits and novel prey of larval fishes in the northern San Francisco Estuary
Authors: Jungbluth Michelle J. , Burns Jillian , Grimaldo Lenny , Slaughter Anne , Katla Aspen , Kimmerer Wim 
Published: October 2020

AbstractFood limitation can dampen survival and growth of fish during early development. To investigate prey diversity important to the planktivorous larval longfin smelt (Spirinchus thaleichthys) and Pacific herring (Clupea pallasii) from the San Francisco Estuary, we used DNA metabarcoding analysis of the cytochrome oxidase I gene on the guts of these fishes and on environmental zooplankton samples. Differential abundance analysis suggested that both species consumed the most abundant zooplankton at a lower rate than their availability in the environment. Both fish consumed the prey that were commonly available and relatively abundant. Prey taxa substantially overlapped between the two species (Schoener’s index = 0.66), and alpha diversity analysis suggested high variability in the content of individual guts. Abundant prey taxa in both fish species included the copepodsEurytemora carolleeae, Acanthocyclops americanus, andA. robustus; theAcanthocyclopsspp. are difficult to identify morphologically. A few uncommon prey in the diets hint at variable feeding strategies, such as herring (presumably egg) DNA in the longfin smelt diets, which suggests feeding near substrates. Herring consumed the small (<0.5 mm) copepodLimnoithona tetraspinamore frequently (30%) than did smelt (2%), possibly indicating differences in foraging behavior or sensory abilities. Among the unexpected prey found in the diets was the cnidarianHydra oligactis, the polychaeteDasybranchussp., and a newly identified speciesMesocyclops pehpeiensis. “Unknown” DNA was in 56% of longfin smelt diets and 57% of herring diets, and made up 17% and 21% of the relative read abundance in the two species, respectively. Our results suggest that these two fishes, which overlap in nursery habitat, also largely overlap in food resources necessary for larval survival.