bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Morphological Clock versus Parsimony: An Insight into the Relationships and Dispersal Events of Postvacuum Cricetidae (Rodentia, Mammalia)
Authors: López-Antoñanzas Raquel , Peláez-Campomanes Pablo 
Published: July 2021

Abstract
Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution, and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only data sets. Herein, we present a morphological data set for a group of cricetid rodents to which we apply an array of methods fairly new in paleontology that can be used by paleontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated, and noncalibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our data set, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae, and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes, and diversification in cricetids. [Bayesian tip-dating; Cricetidae; Miocene; morphological clock; paleobiodiversity; paleobiogeography; paleoecology; parsimony; STRAP.]
Effect of Plant Age, Temperature, and Vector Load on ‘Candidatus Liberibacter solanacearum’ in Planta Titer and Shoot Proliferation Symptoms in Carrot
Authors: Keshet-Sitton Atalya , Piasezky Alon , Assoline Nofar , Dror Orit , Bahar Ofir 
Published: July 2021

A decade ago, shoot proliferation symptoms (i.e., witches’ broom) in carrots were believed to be the cause of ‘Candidatus Phytoplasma’ and Spiroplasma infection, yet in recent years this association appeared to have weakened, and a closer association was found with the yet-unculturable, psyllid-transmitted Gram-negative bacterium ‘Candidatus Liberibacter solanacearum’. In Israel, carrots are grown throughout the year, yet shoot proliferation symptoms tend to appear only in mature plants and mostly in late spring to early summer. We hypothesized that factors such as plant age, temperature, and vector load, which vary during the year, have a critical effect on symptom development and examined these factors under controlled conditions. Here we show that young carrot seedlings are as prone as older plants to develop shoot proliferation symptoms after ‘Ca. L. solanacearum’ inoculation. Surprisingly, we found that the local ‘Ca. L. solanacearum’ haplotype was extremely sensitive to constant temperature of 30°C, which led to a significant reduction in bacterial growth and symptom development compared with 18°C, which was very conducive to symptom development. We have also found that inoculations with 10 or 20 psyllids per plant results in faster symptom development compared with inoculations with two psyllids per plant; however, the difference between vector loads in disease progress rate was not significant. These data provide important insights to the effects of plant age, growth temperature, and vector load on ‘Ca. L. solanacearum’ and its associated symptoms and further strengthen the notion that ‘Ca. L. solanacearum’ is the main responsible agent for carrot witches’ broom in Israel. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
CsMYB60 Confers Enhanced Resistance to Fusarium solani by Increasing Proanthocyanidin Biosynthesis in Cucumber
Authors: Li Jialin , Luan Qianqian , Han Jing , Chen Chunhua , Ren Zhonghai 
Published: July 2021

Root rot caused by Fusarium solani is one of the most common fungal diseases in cucumber (Cucumis sativus). Proanthocyanidins (PAs) are known to play important roles in inhibiting the growth of phytopathogens. In addition, CsMYB60 is a known positive regulator of flavonol and PA biosynthesis in cucumber. However, it remains unclear that whether PAs can inhibit the growth of F. solani and whether CsMYB60 serves as a target gene for increasing resistance to phytopathogens in cucumber. In this study, we demonstrated that PAs (or their building block, catechin) could increase the resistance of cucumber seedlings to F. solani both in vitro and in vivo. The addition of catechins, or crude leaf extracts treated with different concentrations of catechins in culture medium, could significantly inhibit the hyphal growth of F. solani. On the other hand, cucumber seedlings treated with catechins showed higher resistance to F. solani than the seedlings of control group. Moreover, transgenic cucumber seedlings overexpressing CsMYB60, with the observed accumulation of PAs, were more resistant to F. solani than the nontransgenic siblings. Therefore, our results suggest that PAs (or catechin) can serve as a biological control agent to protect cucumber plants from the infection of F. solani. More importantly, CsMYB60 holds great promise as a target gene to confer disease resistance during the molecular breeding in cucumber.
Oxidative stress in leukemia and antioxidant treatment
Authors: Dong Chao , Zhang Nai-Jin , Zhang Li-Jun 
Published: July 2021

Abstract
Oxidative stress is caused by the imbalance between the generation of free radicals/reactive oxygen species (ROS) and the antioxidant defense systems, which can activate various transcription factors and affect their transcriptional pathways. Oxidative stress plays an important role in the occurrence and development of leukemia and is closely related to the treatment and prognosis of leukemia. The standard chemotherapy strategies for the pre-treatment of leukemia have many drawbacks. Hence, the usage of antioxidants and oxidants in the treatment of leukemia is being explored and has been preliminarily applied. This article reviews the research progress of oxidative stress and leukemia. In addition, the application of antioxidants treatment in leukemia has been summarized.
MicroRNA miR-215-5p Regulates Doxorubicin-induced Cardiomyocyte Injury by Targeting ZEB2
Authors: Xiong Xiaojv , He Qin , Liu Jinhua , Dai Rui , Zhang Hui , Cao Zhe , Liao Yuanxi , Liu Bo , Zhou Yi , Chen Juan , Chen Manhua , Liu Jijun 
Published: July 2021

Abstract:
Doxorubicin (DOX) is a chemotherapeutic drug for treating various cancers. However, the DOX-induced cardiotoxicity greatly limits its clinical application. MicroRNAs are emerged as critical mediators of cardiomyocyte injury. This work explored the function of miR-215-5p in the regulation of DOX-induced mouse HL-1 cardiomyocyte injury. An in vitro model of DOX-treated cardiotoxicity was established in cardiac mouse cell line HL-1. Gene expression was measured by reverse transcription quantitative polymerase chain reaction. Cell viability was detected using CCK-8. Cell death and apoptosis were tested using transferase-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL), flow cytometry, and caspase-3/7 activity assays. Luciferase reporter assay was used to examine the target of miR-215-5p. We found that DOX induced cardiomyocyte injury and upregulated miR-215-5p in HL-1 cells. Inhibition of miR-215-5p attenuated DOX-induced cardiomyocyte death and apoptosis in vitro. Mechanistical experiments indicated that zinc finger E-box–binding homeobox (ZEB2) was targeted by miR-215-5p. In addition, ZEB2 expression was reduced in DOX-treated HL-1 cells. Rescue assays indicated that ZEB2 knockdown reversed the effects of miR-215-5p inhibition. In conclusion, miR-215-5p inhibition protects HL-1 cells against DOX-induced injury by upregulating ZEB2 expression.
Lower Extremity Nerve Transfers in Acute Flaccid Myelitis Patients: A Case Series
Authors: Moore Amy M. , Bettlach Carrie Roth , Tung Thomas T. , West Julie M. , Russo Stephanie A. 
Published: July 2021

Background:
Acute flaccid myelitis (AFM) is characterized by flaccid paralysis following prodromal symptoms. Complete recovery is rare, and patients typically have residual extremity weakness. This study aimed to describe the technique and outcomes of lower extremity nerve transfers for children with AFM.

Methods:
A retrospective review of eight children who developed AFM in 2016 and had lower extremity nerve transfers was performed. Principles of nerve transfer were applied to develop novel nerve transfer procedures to restore function for this patient population. Pre- and postoperative muscle strength grades were reviewed, and qualitative improvements in function were recorded.

Results:
A variety of nerve transfers were utilized in eight patients with average time to surgery from AFM diagnosis of 15.7 months. Restoration of gluteal, femoral, hamstring, and gastrocnemius function was attempted. Variable MRC grade improvement was achieved (range MRC grade 0–4). All patients reported subjective improvements in function. Four of five patients with follow-up who underwent nerve transfers for restoration of gluteal function transitioned from wheelchair use to walking with assistive devices as their primary modes of ambulation. No donor site complications occurred.

Conclusions:
The unique needs of this patient population and variable patterns of residual weakness require meticulous assessment and development of individualized surgical plans. With appropriate goals and expectations in mind, functional improvement may be achieved, including return to ambulation.
LONGITUDINAL FOVEAL FLUORESCENCE LIFETIME CHARACTERISTICS IN GEOGRAPHIC ATROPHY USING FLUORESCENCE LIFETIME IMAGING OPHTHALMOSCOPY
Authors: Lincke Joel-Benjamin , Dysli Chantal , Jaggi Damian , Solberg Yasmin , Wolf Sebastian , Zinkernagel Martin S. 
Published: July 2021

Purpose:
Short foveal fluorescence lifetimes (fFLT) in geographic atrophy are typically found in eyes with foveal sparing (FS) but may also occur in eyes without FS. We investigated whether short fFLT could serve as a functional biomarker for disease progression in geographic atrophy.

Methods:
Thirty three eyes were followed over the course of 4 to 6 years. Foveal sparing was assessed using fluorescence lifetime imaging ophthalmoscopy, optical coherence tomography, fundus Autofluorescence, and macular pigment optical density.

Results:
Eyes with FS exhibited shorter fFLT compared with eyes without FS. Short fFLT (<600 ps) were measured in all eyes with FS and half of the eyes without FS. Eyes with FS showed a bigger increase in fFLT per year (+39/+30 ps (short spectral channel/long spectral channel) in FS versus +29/+22 ps (short spectral channel/long spectral channel) in non FS). The best-corrected distance visual acuity correlated significantly with fFLT (P = 0.018 and P = 0.005 for short spectral channel/long spectral channel). Macular pigment optical density measurements correlated significantly with fFLT but not in all spectral channels (P ranging from 0.018 to 0.077).

Conclusion:
In geographic atrophy, shorter fFLT are associated with FS but they can also be observed in eyes without FS. Our longitudinal data suggest that shorter fFLT features in eyes with loss of FS represent an earlier stage of disease and may be more prone to loss of the visual acuity.
Botulinum Toxin A for Chronic Exertional Compartment Syndrome: A Retrospective Study of 16 Upper- and Lower-Limb Cases
Authors: Charvin Marion , Orta Cyril , Davy Laroche , Raumel Marc-Antoine , Petit Julien , Casillas Jean-Marie , Gremeaux Vincent , Gouteron Anaïs 
Published: July 2021

Objective:
To assess initial and mid-term efficacy of botulinum toxin A (BoNT-A) injections in patients with chronic exertional compartment syndrome (CECS) in the lower and upper limbs.

Design:
Retrospective monocentric study.

Setting:
A University Hospital Department of Physical Medicine and Rehabilitation.

Patients:
Sixteen patients with CECS of the lower and upper limbs treated with BoNT-A injections (first-line treatment) were included.

Interventions, Main Outcome Measures:
We collected data from a follow-up consultation (initial pain reduction [complete, partial, or ineffective] and specific activities triggering CECS) and a subsequent phone questionnaire (mid-term efficacy, pain recurrence, and adverse effects).

Results:
Sixteen patients were included (median age: 25.5 years), and 68.75% reported initial efficacy (4 partial and 7 complete); 8/16 patients were able to resume the activity that triggered CECS. All the patients with initial partial efficacy had pain recurrence (median time of 2.25 months). Among patients with initial complete efficacy, 57.14% had recurrence (median time of 5 months). Minor adverse effects were observed, but with no functional impact.

Conclusion:
In 16 individuals with CECS treated with BoNT-A injections, we observed moderate efficacy without major adverse effects, but an initial improvement was often followed by recurrence, especially among those with partial initial efficacy.
Flexible Bronchoscopy Diagnosis of Uncommon Congenital H-type Tracheoesophageal Fistula, Dual Fistulae, Bronchoesophageal Fistula, and Recurrence of Fistula in Children
Authors: Wong Matthew D. , Thomas Rahul J. , Powell Jennifer , Masters Ian Brent 
Published: July 2021

Background:
Interventional pediatric flexible bronchoscopy has many advantages over radiologic investigations in diagnosing uncommon congenital H-type tracheoesophageal fistula (TEF), dual TEF, bronchoesophageal fistula (BEF) and fistula recurrence including higher rates of identification and anatomic localization with guide wire cannulation. We compare the diagnostic utility of flexible bronchoscopy to radiologic techniques for congenital aerodigestive fistula.

Methods:
A single center retrospective review was completed of all cases of pediatric TEF and BEF diagnosed with flexible bronchoscopy between January 2000 and November 2020.

Results:
Fistulae were diagnosed 21 times in 18 patients at a median age of 1.22 years (interquartile range: 0.50 to 2.99). The median time from diagnosis to repair was 17.5 days (interquartile range: 5.5 to 43). Symptoms commonly related to fistula were found in all patients. Uncommon fistulae included single H-type TEF (n=10, 47.6%), dual H-type TEF (n=2, 9.5%), dual proximal and distal TEF with esophageal atresia (n=5, 23.8%), TEF recurrence (n=2, 14.3%), BEF (n=1, 4.8%), and a BEF recurrence (n=1, 4.8%). Flexible bronchoscopy confirmed the diagnosis in all fistulae using a guide wire cannulation or methylene blue dye injection. A combined procedure with simultaneous bronchoscopy and esophagoscopy was used for 6 fistulae. The positive examination rate was 75% for bronchoscopy compared with 2.6% for contrast swallow studies and 28.6% for tube esophagograms.

Conclusions:
Flexible bronchoscopy should be considered as a first line investigation in uncommon aerodigestive fistulae. In the absence of a skilled bronchoscopist, the best radiologic investigation is a pull-back tube esophagogram but may still require endoscopic confirmation at the time of fistula repair.
On the Accuracy of Clinical Insertion Angle Predictions With a Surgical Planning Platform for Cochlear Implantation
Authors: Avallone Emilio , Lenarz Thomas , Timm Max E. 
Published: July 2021

Hypothesis:
Various studies over the last few decades have shown that the cochlea is not a uniform structure, but that its size and shape may vary quite substantially in between subjects. The surgical planning platform enables the user to quickly approximate the size of a cochlea within clinical imaging data by measuring the basal cochlear diameters A and B. It also allows for contact specific insertion angle predictions for MED-EL cochlear implant electrode arrays based on this individual anatomy approximation. The proposed, retrospective study was performed to evaluate the accuracy of these predictions.

Methods:
Preoperative CBCT scans of N = 91 MED-EL cochlear implant patients with different types of FLEX electrode arrays (flexible, thin, and straight arrays) were evaluated using a planning module. Both the initial version (based on an equation proposed by Escudé et al.) as well as a novel, recently proposed approach (called elliptic-circular approximation) was employed. All predictions were then compared to the actual insertion angles which were derived from postoperative CBCT images of the same patient.

Results:
Most prediction deviations of the investigated cases stayed below 45deg for all electrode arrays and both prediction methods. In general, prediction deviations increased from base to apex were found to be larger for longer electrode arrays. Hardly any significant differences between the two prediction methods were observed. However, particularly large deviations were found for the Escudé method and could be substantially deceased with the updated elliptic-circular approximation approach.

Conclusions:
The new platform version with its updated prediction module allows to reliably predict insertion angles even for cochlear anatomies with slightly unusual features and shapes.
Characteristics and Outcomes of Children With Necrotizing Pneumonia
Authors: Ness-Cochinwala Manette , Kobaitri Kaitlin , Totapally Balagangadhar R. 
Published: July 2021

OBJECTIVES:
In this study, we describe the characteristics and outcomes of pediatric necrotizing pneumonia in the United States.

Design and Setting:
A retrospective analysis of the Healthcare Cost and Utilization Project 2016 Kids Inpatient Database was performed. The Kids Inpatient Database is a large deidentified hospital discharge database of pediatric patients in the United States.

PATIENTS:
The database was filtered using International Classification of Diseases, 10th Edition code J85.0 to identify necrotizing pneumonia in children 28 days to 20 years old.

INTERVENTIONS:
Children with necrotizing pneumonia with and without bacterial isolation and with and without complex chronic conditions were compared. Sample weighting was employed to produce national estimates.

MEASUREMENTS AND MAIN RESULTS:
Of the 2,296,220 discharges, 746 patients had necrotizing pneumonia (prevalence: 3.2/10,000 discharges). In patients with necrotizing pneumonia, 46.6% required chest tubes, 6.1% underwent video-assisted thoracoscopic surgery, and 27.6% were mechanically ventilated. Pneumothorax was identified in 16.7% and pyothorax in 27.4%. The overall mortality rate was 4.1% (n = 31). Bacterial isolation was documented in 40.9%. The leading organisms identified in patients without a complex chronic condition were Streptococcus pneumoniae (12.6%) and Staphylococcus aureus (9.2%) and in patients with a complex chronic condition were S. aureus (13.4%) and Pseudomonas aeruginosa (12.8%). Patients with bacterial isolation were significantly more likely to develop pneumothorax (odds ratio, 2.6; CI, 1.6–4.2) or septic shock (odds ratio, 3.2; CI, 1.9–5.4) and require a chest tube (odds ratio, 2.5; CI, 1.7–3.5) or mechanical ventilation (odds ratio, 2.3; CI, 1.5–3.3) than patients without bacterial isolation.

CONCLUSIONS:
Bacterial etiology of necrotizing pneumonia in children varied with the presence or absence of a complex chronic condition. Bacterial isolation is associated with increased invasive procedures and complications. The mortality rate is higher in children with complex chronic conditions. This study provides national data on necrotizing pneumonia among hospitalized children.
Assessment of the effect of amantadine in patients with traumatic brain injury: A meta-analysis
Authors: Mohamed Mona Salah , El Sayed Iman , Zaki Adel , Abdelmonem Sherif 
Published: July 2021

BACKGROUND
Traumatic brain injury is a global burden. We aimed to perform a meta-analysis to determine the efficacy of amantadine for cognitive performance after traumatic brain injury.

METHODS
The systematic review was prospectively registered on the International Prospective Register of Systematic Reviews website under the registration number CRD42017080044. We used Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines to report the steps of meta-analysis. The search included electronic databases (PubMed, PsycINFO, Embase, Cochrane Library databases, CENTRAL, ProQuest and ClinicalTrials.gov trial registry). Critical care medicine journals and clinical neurology specialty were searched using www.scimagojr.com. There was no publication date restriction. Two authors assessed studies’ relevance and extracted data. Studies were assessed for quality using the Cochrane risk of bias tool. Data were analyzed using Comprehensive Meta-analysis Program versions 2.0 and 3.0.

RESULTS
Twenty-six studies out of 3,440 records were included in the systematic review, of which only 14 clinical trials and 6 observational studies were included in the meta-analysis. Amantadine significantly enhanced the cognitive function relative to control group (mean difference [MD], 0.50; 95% confidence interval [CI], 0.33–0.66; p < 0.001, 16 studies, 1,127 participants, low certainty evidence). Consistent significant difference in favor of amantadine relative to control group was found (MD of 0.79 [95% CI, 0.34–1.24], very low certainty evidence, for cohort studies vs. MD of 0.40 [95% CI, 0.25–0.56], moderate certainty evidence, for RCTS). Starting amantadine in the first week after TBI had a significant effect on improving cognitive function (MD, 0.97; 95% CI, 0.45–1.49; 16 studies, 1,127 participants, low certainty). Amantadine showed a better effect when administered for less than 1 month (MD, 0.83; 95% CI, 0.56–1.11; low certainty) and to patients below 18 years of age (MD, 0.66; 95% CI, 0.32–0.99; low certainty) or to patients with less severe traumatic brain injury (MD, 0.40; 95% CI, 0.18–0.62; low certainty). No statistically significant difference existed between amantadine and the control concerning the adverse events (OR, 1.74; 95% CI, 0.88–3.44; p = 0.11, moderate certainty). Metaregression of the different clinical parameters, which are onset of treatment, age, and severity of traumatic brain injury, showed a statistically significant relation between onset of treatment and the effect size of amantadine. The relation between the other two parameters and the effect size of amantadine showed a marginal statistical significance.

CONCLUSION
Amantadine may improve the cognitive function when used after TBI. Further research with high validity is needed to reach a solid conclusion about the use of amantadine in traumatic brain injury.

LEVEL OF EVIDENCE
Systematic review/meta-analysis, level III.