bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case Series and Systematic Review of Treatment Outcomes for Auricular Pseudocysts
Authors: Ungar Omer J. , Oron Yahav , Cavel Oren , Handzel Ophir , Warshavsky Anton , Horowitz Gilad , Matot Sofi 
Published: December 2020

Objective:
Auricular pseudocyst (AP: intracartilaginous cyst, endochondral AP, cystic chondromalacia, and benign idiopathic cystic chondromalacia) is a benign condition of unknown etiology. This report systematically reviews the published demographics, treatment protocols, and outcomes of AP between the various medical disciplines, and compares the findings to a theretofore-unreported 12-patient cohort. Primary outcome measure was AP complete resolution without recurrence.

Data Source:
A systematic literature search of “MEDLINE” via “PubMed” and “Google Scholar” was performed in June, 2020. The 12 new patients were enrolled between January 2016 and December 2020.

Study Selection:
Seventy-four papers met the study inclusion criteria and provided data on sex distribution, surgical approach and outcome, performance of approaches according to medical specialty, and recurrence rates of the reported AP populations.

Data Extraction:
The appropriateness and study design quality were independently assessed by two reviewers.

Data Synthesis:
The primary outcome was therapeutic success. A comparative analysis was also performed on the same extracted information that was retrieved from the medical files of the 12 new patients (10 men, 2 women, average age 24 yrs, range, 17–38).

Conclusions:
AP is not uncommon. In line with the published literature, incision and curettage with excision of the anterior pseudocystic wall (deroofing) resulted in a recurrence rate of less than 17% with good cosmetic outcome among all 12 patients. Aspiration alone was associated with increased recurrence rates. Deroofing emerged as the preferred modality, with good cosmetic outcome and reduced recurrence rate. It was usually performed by otolaryngologists, while dermatologists used more conservative approach more frequently. Incision and drainage combined with compression reduces risk of recurrence.
Training Situational Awareness for Patient Safety in a Room of Horrors: An Evaluation of a Low-Fidelity Simulation Method
Authors: Zimmermann Chantal , Fridrich Annemarie , Schwappach David L. B. 
Published: December 2020

Background
To protect patients from potential hazards of hospitalization, health care professionals need an adequate situational awareness. The Room of Horrors is a simulation-based method to train situational awareness that is little used in Switzerland.

Objectives
This study aimed to evaluate (1) the performance of health care staff in identifying patient safety hazards, (2) the participants’ subjective experiences, and (3) the group interactions in Rooms of Horrors.

Methods
The study was conducted in 13 Swiss hospitals that implemented a Room of Horrors. Health care professionals participated as individuals or in groups and were asked to identify as many errors as possible within a certain time and to complete an evaluation questionnaire. Observations of group interactions were carried out in 8 hospitals. t Tests and χ2 tests were used to examine differences in performance between participants solving the task alone versus in groups.

Results
Data of 959 health care professionals were included in the analysis. Single participants identified on average 4.7 of the 10 errors and additional 10 errors and hazards that were not part of the official scenario. However, they also overestimated their performance, with 58% feeling the errors to be easy to find. Group observations indicated that participants rarely reflected on possible consequences of the hazards for the patient or their daily work. Participants feedback to the method was very positive.

Conclusions
Our findings suggest that the Room of Horrors is a popular and effective method to raise situational awareness for patient safety issues among health care staff. More attention should be given to debriefing after the experience and to benefits of interprofessional trainings.
Comparison of dementia risk after age 50 between individuals with and without HIV infection
Authors: Lam Jennifer O. , Hou Craig E. , Hojilla J. Carlo , Anderson Alexandra N. , Gilsanz Paola , Alexeeff Stacey E. , Levine-Hall Tory , Hood Nicole , Lee Catherine , Satre Derek D. , Silverberg Michael J. 
Published: December 2020

Objective:
To compare risk of dementia after age 50 by HIV status among individuals in a primary care setting.

Design:
Observational cohort study; participants were identified from 2013 to 2017 and followed through 2019.

Methods:
Participants were people with HIV (PWH) on antiretroviral therapy (ART) and demographically similar people without HIV (PWOH), all at least 50 years old and with no prior diagnosis of dementia. The study setting was Kaiser Permanente Northern California, an integrated healthcare delivery system in the United States. Incident dementia diagnoses and baseline data on sociodemographics, smoking, alcohol use, other substance use, and clinical factors were gathered from the electronic health record. Cumulative proportion of incident dementia by HIV status was assessed using Kaplan--Meier curves. Unadjusted and adjusted hazard ratios for incident dementia by HIV status were generated using Cox proportional hazards models with age as the time scale.

Results:
The study included 5381 PWH and 119 022 PWOH (average age at baseline: 57 and 58 years, respectively). Incident dementia was diagnosed in 117 PWH and 2427 PWOH. By age 80, 25.8% of PWH and 13.8% of PWOH had been diagnosed with dementia, corresponding with an unadjusted hazard ratio of 1.98 (95% CI 1.64–2.39). After adjustment for sociodemographic, substance use, and clinical factors, including frequency of outpatient visits, the risk of dementia among PWH remained elevated (vs. PWOH, adjusted hazard ratio = 1.58, 95% CI 1.31–1.92).

Conclusion:
Compared with PWOH, PWH were at 58% higher risk for dementia despite HIV treatment with ART. Research is needed to investigate the potential benefits of targeted risk factor management or earlier cognitive screening in this population.
Impact of HIV infection on baseline characteristics and survival of women with breast cancer
Authors: Brandão Mariana , Bruzzone Marco , Franzoi Maria-Alice , De Angelis Claudia , Eiger Daniel , Caparica Rafael , Piccart-Gebhart Martine , Buisseret Laurence , Ceppi Marcello , Dauby Nicolas , Carrilho Carla , Lunet Nuno , de Azambuja Evandro , Lambertini Matteo 
Published: December 2020

Background:
As women living with HIV (WLWH) become older, their risk of developing breast cancer increases. Nonetheless, literature is conflicting regarding tumor stage, distribution of subtypes and overall survival among WLWH vs. HIV-negative women with breast cancer. We assessed differences in clinicopathological characteristics and overall survival between these two groups.

Methods:
Systematic review and meta-analysis using MEDLINE, Scopus, ISI Web of Knowledge, LILACS, SciELO and conference abstracts up to 1 January 2020. Cross-sectional/cohort studies comparing baseline characteristics (stage and/or subtypes) and/or overall survival of WLWH vs. HIV-negative women with breast cancer were included. We performed random-effects meta-analyses to estimate summary statistics and subgroup analyses according to region of the world.

Results:
Eighteen studies [4 from North America, 14 from sub-Saharan Africa (SSA)] were included, with 3174 WLWH and 2 394 598 HIV-negative women. WLWH from North America and SSA were more likely to present with stage III/IV disease compared with HIV-negative women – pooled odds ratio (pOR) 1.76 [95% confidence interval (CI):1.58–1.95] and pOR 1.23 (95% CI: 1.06–1.42), respectively. WLWH from SSA were also less likely to have estrogen receptor-positive/HER2-negative tumors (pOR 0.81; 95% CI: 0.66–0.99). After adjustment, WLWH had worse overall survival compared with HIV-negative women, both in North America [pooled adjusted hazard ratio (aHR) 2.45; 95% CI: 1.11–5.41] and SSA (aHR 1.43; 95% CI: 1.06–1.92).

Conclusion:
Compared with HIV-negative women, WLWH are diagnosed with breast cancer at a more advanced stage and have a worse overall survival. These results should raise awareness regarding the detection and survival gap among WLWH with breast cancer and further studies are needed to decipher the reasons behind these disparities.
International Core Outcome Set for Acute Simple Appendicitis in Children
Authors: Knaapen Max , Hall Nigel J. , Moulin Darcy , van der Lee Johanna H. , Butcher Nancy J. , Minneci Peter C. , Svensson Jan F. , St. Peter Shawn D. , Adams Susan , Nah Shireen A. , Skarsgard Erik D. , Zani Augusto , Emil Sherif , Suominen Janne S. , Aziz Dayang A. , Rai Rambha , Offringa Martin , van Heurn Ernst W. , Bakx Roel , Gorter Ramon R. ,   On behalf of the pediatric appendicitis COS development group
Published: December 2020

Objective:
To develop an international core outcome set (COS), a minimal collection of outcomes that should be measured and reported in all future clinical trials evaluating treatments of acute simple appendicitis in children.

Summary of Background Data:
A previous systematic review identified 115 outcomes in 60 trials and systematic reviews evaluating treatments for children with appendicitis, suggesting the need for a COS.

Methods:
The development process consisted of 4 phases: (1) an updated systematic review identifying all previously reported outcomes, (2) a 2-stage international Delphi study in which parents with their children and surgeons rated these outcomes for inclusion in the COS, (3) focus groups with young people to identify missing outcomes, and (4) international expert meetings to ratify the final COS.

Results:
The systematic review identified 129 outcomes which were mapped to 43 unique outcome terms for the Delphi survey. The first-round included 137 parents (8 countries) and 245 surgeons (10 countries), the second-round response rates were 61% and 85% respectively, with 10 outcomes emerging with consensus. After 2 young peoples' focus groups, 2 additional outcomes were added to the final COS (12): mortality, bowel obstruction, intraabdominal abscess, recurrent appendicitis, complicated appendicitis, return to baseline health, readmission, reoperation, unplanned appendectomy, adverse events related to treatment, major and minor complications.

Conclusion:
An evidence-informed COS based on international consensus, including patients and parents has been developed. This COS is recommended for all future studies evaluating treatment ofsimple appendicitis in children, to reduce heterogeneity between studies and facilitate data synthesis and evidence-based decision-making.
Changes in traumatic mechanisms of injury in Southern California related to COVID-19: Penetrating trauma as a second pandemic
Authors: Yeates Eric O. , Grigorian Areg , Barrios Cristobal , Schellenberg Morgan , Owattanapanich Natthida , Barmparas Galinos , Margulies Daniel , Juillard Catherine , Garber Kent , Cryer Henry , Tillou Areti , Burruss Sigrid , Penaloza-Villalobos Liz , Lin Ann , Figueras Ryan Arthur , Brenner Megan , Firek Christopher , Costantini Todd , Santorelli Jarrett , Curry Terry , Wintz Diane , Biffl Walter L. , Schaffer Kathryn B. , Duncan Thomas K. , Barbaro Casey , Diaz Graal , Johnson Arianne , Chinn Justine , Naaseh Ariana , Leung Amanda , Grabar Christina , Nahmias Jeffry 
Published: December 2020

BACKGROUND
The COVID-19 pandemic resulted in a statewide stay-at-home (SAH) order in California beginning March 19, 2020, forcing large-scale behavioral changes and taking an emotional and economic toll. The effects of SAH orders on the trauma population remain unknown. We hypothesized an increase in rates of penetrating trauma, gunshot wounds, suicide attempts, and domestic violence in the Southern California trauma population after the SAH order.

METHODS
A multicenter retrospective analysis of all trauma patients presenting to 11 American College of Surgeons levels I and II trauma centers spanning seven counties in California was performed. Demographic data, injury characteristics, clinical data, and outcomes were collected. Patients were divided into three groups based on injury date: before SAH from January 1, 2020, to March 18, 2020 (PRE), after SAH from March 19, 2020, to June 30, 2020 (POST), and a historical control from March 19, 2019, to June 30, 2019 (CONTROL). POST was compared with both PRE and CONTROL in two separate analyses.

RESULTS
Across all periods, 20,448 trauma patients were identified (CONTROL, 7,707; PRE, 6,022; POST, 6,719). POST had a significantly increased rate of penetrating trauma (13.0% vs. 10.3%, p < 0.001 and 13.0% vs. 9.9%, p < 0.001) and gunshot wounds (4.5% vs. 2.4%, p = 0.002 and 4.5% vs. 3.7%, p = 0.025) compared with PRE and CONTROL, respectively. POST had a suicide attempt rate of 1.9% and a domestic violence rate of 0.7%, which were similar to PRE (p = 0.478, p = 0.514) and CONTROL (p = 0.160, p = 0.618).

CONCLUSION
This multicenter Southern California study demonstrated an increased rate of penetrating trauma and gunshot wounds after the COVID-19 SAH orders but no difference in attempted suicide or domestic violence rates. These findings may provide useful information regarding resource utilization and a target for societal intervention during the current or future pandemic(s).

LEVEL OF EVIDENCE
Epidemiological, level IV.
Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture Prior
Authors: Du Jin-Hong , Chen Tianyu , Gao Ming , Wang Jingshu 
Published: December 2020

AbstractTrajectory inference methods are essential for analyzing the developmental paths of cells in single-cell sequencing datasets. It provides insights into cellular differentiation, transitions, and lineage hierarchies, helping unravel the dynamic processes underlying development and disease progression. However, many existing tools lack a coherent statistical model and reliable uncertainty quantification, limiting their utility and robustness. In this paper, we introduce VITAE (VariationalInference forTrajectory byAutoEncoder), a novel statistical approach that integrates a latent hierarchical mixture model with variational autoencoders to infer trajectories. The statistical hierarchical model enhances the interpretability of our framework, while the posterior approximations generated by our variational autoencoder ensure computational efficiency and provide uncertainty quantification of cell projections along trajectories. Specifically, VITAE enables simultaneous trajectory inference and data integration, improving the accuracy of learning a joint trajectory structure in the presence of biological and technical heterogeneity across datasets. We show that VITAE outperforms other state-of-the-art trajectory inference methods on both real and synthetic data under various trajectory topologies. Furthermore, we apply VITAE to jointly analyze three distinct single-cell RNA sequencing datasets of the mouse neocortex, unveiling comprehensive developmental lineages of projection neurons. VITAE effectively reduces batch effects within and across datasets and uncovers finer structures that might be overlooked in individual datasets. Additionally, we showcase VITAE’s efficacy in integrative analyses of multi-omic datasets with continuous cell population structures.
Aligning Bacteria and Synthetic Biomolecules with Engineered DNA Fibers
Authors: Burns Jonathan R. 
Published: December 2020

AbstractDNA nanotechnology enables user-defined structures to be built with unrivalled control. However, the approach is currently restricted across the nanoscale, yet the ability to generate macroscopic DNA structures has enormous potential with applications spanning material, physical and biological science. I have employed DNA nanotechnology[1, 2]and developed a new macromolecular nanoarchitectonic[3]assembly method to produce DNA fibers with customizable properties. The process involves coalescing DNA nanotubes under high salt conditions to yield filament superstructures. Using this strategy, fibers over 100 microns long, with stiffnesses 10 times greater than cytoskeletal actin filaments can be fabricated. The DNA framework enables fibers to be functionalized with advanced synthetic molecules, including, aptamers, origami, nanoparticles and vesicles. In addition, the fibers can act as bacterial extracellular scaffolds and alignE.colicells in a controllable fashion. The results showcase the opportunities offered from DNA nanotechnology across the macroscopic scale. The new biophysical approach should find widespread use, from the generation of hybrid-fabric materials, platforms to study cell-cell interactions, to smart analytical and purification devices in biomedicine.
Blocking plasmodesmata in specific phloem cell types reduces axillary bud growth inArabidopsis thaliana
Authors: Paterlini Andrea , Dorussen Delfi , Fichtner Franziska , van Rongen Martin , Delacruz Ruth , Vojnović Ana , Helariutta Yrjö , Leyser Ottoline 
Published: December 2020

AbstractThe plasticity of above ground plant architecture depends on the regulated re-activation and growth of axillary meristems laid down in the axils of leaves along the stem, which often arrest as dormant buds. Plasmodesmata connecting plant cells might control the movement of regulators involved in this developmental switch. Constructs capable of occluding these structures were employed in phloem cell types, because of the importance of phloem in local and systemic trafficking. We show that over-accumulation of callose within companion cells of the Arabidopsis inflorescence reduces the growth rates of activated buds, but does not affect bud activation. Growth rate reductions were not dependent on the phloem-mobile strigolactone receptor, which regulates bud activation. Furthermore, there was no correlation with early bud sugar profiles, which can also affect bud activity and depend on phloem-mediated delivery. It is therefore possible that an as yet unknown mobile signal is involved in modulating branch growth rate.
ADP-ribosylation of mitochondrial proteins is mediated by Neuralized-like protein 4 (NEURL4)
Authors: Cardamone Maria Dafne , Gao Yuan , Kwan Julian , Hayashi Vanessa , Sheeran Megan , Xu Junxiang , English Justin , Orofino Joseph , Emili Andrew , Perissi Valentina 
Published: December 2020

ADP-ribosylation is a reversible post-translational modification where an ADP-ribose moiety is covalently attached to amino acid side-chains of target proteins either as mono-ADP-ribose (MARylation or MAR) or poly-ADP-ribose chains (PARylation or PAR) by a class of enzymes called ADP-ribosyltransferases (ARTs). Although ADP-ribosylation is best known for its nuclear roles, ADP-ribosylation of extra nuclear proteins is increasingly recognized as a key regulatory strategy across cellular compartments. ADP-ribosylation of mitochondrial proteins, in particular, has been widely reported, even though the extent to which ADP-ribosylation of specific proteins regulates mitochondrial functions is unclear and the exact nature of mitochondrial ART enzymes is debated.Here, we have identified Neuralized-like protein 4 (NEURL4) as a mitochondrial ART enzyme and profiled the NEURL4-dependent ADP-ribosylome in mitochondrial extracts from Hela cells by LC-MS/MS, using isobaric tandem mass tag (TMT) labeling for relative quantification. Comparison of WT and NEURL4-KO cells generated by CRISPR/Cas9 genome editing revealed that most ART activity associated with mitochondria is lost in absence of NEURL4. Putative NEURL4 targets include numerous mitochondrial proteins previously shown to be ADP-ribosylated. In particular, we show that NEURL4 enzymatic activity is required for the regulation of mtDNA integrity via poly-ADP-ribosylation of mitochondrial specific Ligase III (mtLIG3), the rate-limiting enzyme for mitochondrial DNA (mtDNA) Base Excision Repair (BER).Collectively, our studies reveal that NEURL4 acts as the main mitochondrial ART enzyme under physiological conditions and provide novel insights in the regulation of mitochondria homeostasis through ADP-ribosylation.
A high-quality genome of the mangroveAegiceras corniculatumaids investigation of molecular adaptation to intertidal environments
Authors: Feng Xiao , Li Guohong , Xu Shaohua , Wu Weihong , Chen Qipian , Shao Shao , Liu Min , Wang Nan , Zhong Cairong , He Ziwen , Shi Suhua 
Published: December 2020

AbstractMangroves have colonized extreme intertidal environments characterized by high salinity, hypoxia, and other abiotic stresses. During millions of years of evolution, mangroves have adapted to these habitats, evolving a series of highly specialized traits.Aegiceras corniculatum, a pioneer mangrove species that evolved salt secretion and crypto-vivipary, is an attractive ecological model to investigate molecular mechanisms underlying adaptation to intertidal environments. Here we report a high-quality reference genome ofA. corniculatumusing the PacBio SMRT sequencing technology, comprising 827 Megabases (Mb) and containing 32,092 protein-coding genes. The longest scaffold and N50 for the assembled genome are 13.76 Mb and 3.87 Mb. Comparative and evolutionary analyses revealed thatA. corniculatumexperienced a whole-genome duplication (WGD) event around 35 million years ago after the divergence betweenAegicerasandPrimula. We inferred that maintenance of cellular environmental homeostasis is an important adaptive process inA. corniculatum. The 14-3-3 protein-coding genes were retained after the recent WGD event, decoding a calcium signal to regulate Na+homeostasis.A. corniculatumhas more H+-ATPase coding genes, essential for the maintenance of low Na+concentration in the cells, than its relatives. Photosynthesis and oxidative-phosphorylation pathways are overrepresented among significantly expanded gene families and might supply the energy needed for salt secretion. Genes involved in natural antioxidant biosynthesis, contributing to scavenging reactive oxygen species against high salinity, have also increased in copy number. We also found that all homologs ofDELAY OF GERMINATION1(DOG1), a pivotal regulator of seed dormancy, lost their heme-binding ability inA. corniculatum. This loss may contribute to crypto-vivipary. Our study provides a valuable resource to investigate molecular adaptation to extreme environments in mangroves.
Brain dysfunction during warming is caused by oxygen limitation in larval zebrafish
Authors: Andreassen Anna H. , Hall Petter , Khatibzadeh Pouya , Jutfelt Fredrik , Kermen Florence 
Published: December 2020

ABSTRACTUnderstanding the physiological mechanisms that limit animal thermal tolerance is crucial in predicting how animals will respond to increasingly severe heatwaves. Despite its importance for understanding climate change impacts, these mechanisms underlying the upper thermal tolerance limits of animals are largely unknown. It has been hypothesised that the upper thermal tolerance in fish is limited by the thermal tolerance of the brain and that it is ultimately caused by a global brain depolarization. In this study, we developed methods for measuring the upper thermal limit (CTmax) in larval zebrafish (Danio rerio) with simultaneous recordings of brain activity using GCaMP6s calcium imaging in both free-swimming and agar-embedded fish. We discovered that during warming, CTmaxprecedes, and is therefore not caused by, a global brain depolarization. Instead, the CTmaxcoincides with a decline in spontaneous neural activity and a loss of neural response to visual stimuli. By manipulating water oxygen levels, we found that oxygen availability during heating affects both locomotor-related neural activity, the neural response to visual stimuli, and CTmax. Our results suggest that the mechanism limiting the upper thermal tolerance in zebrafish larvae is reduced oxygen availability causing impaired brain function.