bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Gene Introgression Approach and the Potential Cost of Genes that Confer Strong Phosphine Resistance in Red Flour Beetle (Coleoptera: Tenebrionidae)
Authors: Daglish Gregory J , Jagadeesan Rajeswaran , Nayak Manoj K , McCulloch Graham A , Singarayan Virgine T , Walter Gimme H 
Published: February 2020

AbstractResistance in pest insects to the grain fumigant phosphine (PH3) poses a threat to trade and food security. The possible pleiotropic effects of PH3 resistance on development and reproduction were investigated in the red flour beetle, Tribolium castaneum (Herbst), by introgressing two genes known to be major contributors to strong resistance (tc_rph1 and tc_rph2) into a susceptible background. The tc_rph2 allele was the G135S variant, whereas the identity of tc_rph1 allele was unknown but could have been one of the three known variants (L119W, V123F, or S349G). The introgressed resistant strain was 288× more resistant than the susceptible strain, based on mortality after a 20 h fumigation with PH3. Molecular screening confirmed that the introgressed strain was homozygous for the resistance genes, but was otherwise indistinguishable from the susceptible strain based on screening with 12 neutral DNA markers. We found no differences of consequence in developmental time between the susceptible and introgressed resistant strains. Similarly, the number of F1 adults produced by these strains was more or less equal, as was the weight of individual F1 adults. The conclusions remained the same regardless of whether the experiments were conducted on a flour-based medium or wheat. Thus, we found no evidence that being fully strongly PH3 resistant (i.e., homozygous for tc_rph1 and tc_rph2) has major consequences in terms of development or reproduction in T. castaneum.
Metabolic Regulation of Hippocampal Neuroprogenitor Apoptosis After Irradiation
Authors: Li Yu-Qing , Koritzinsky Marianne , Wong C Shun 
Published: February 2020

Abstract
The tumor suppressor p53 is an important regulator of cell fate response after DNA damage. Cell fate response following metabolic stresses has also been linked to p53-dependent pathways. In this study, we asked if 5′-adenosine monophosphate-activated protein kinase (AMPK), the master sensor of cellular energy balance, played a role in p53-dependent apoptosis of neural progenitor cells (NPCs) in the hippocampus after irradiation. Adult mice with targeted disruption of p53 or prkaa2 (gene that encodes AMPKα) in the brain were used to determine the role of p53 and AMPK, respectively, in radiation-induced apoptosis of NPCs in the hippocampus. The p53-dependent apoptosis of NPCs was associated with an increase in phospho-AMPK expression in the dentate gyrus at 8 hours after irradiation. Activation of AMPK was seen in granule neurons and subgranular NPCs. Compared with wildtype mice, apoptosis of NPCs was significantly attenuated in AMPK deficient (nestinCre: prkaa2fl/fl) mice after irradiation. AMPK deficiency did not however alter p53 activation in NPCs after irradiation. We conclude that AMPK may regulate apoptosis of hippocampal NPCs after irradiation. These findings suggest that cellular metabolism may play a role in determining cell fate response such as apoptosis after DNA damage in NPCs.
Mortality and Functional Outcome Predictors in Combat-Related Penetrating Brain Injury Treatment in a Specialty Civilian Medical Facility
Authors: Sirko Andrii , Pilipenko Grigoriy , Romanukha Dmytro , Skrypnik Alexander 
Published: February 2020

Abstract

Introduction
The combined use of new types of weapons and new types of personal protective equipment has led to changes in the occurrence, nature, and severity of penetrating brain wounds. The availability of modern equipment, methods of treatment, and trained medical personnel in a civilian hospital, as well as advanced specialty medical care, has improved treatment outcomes. There have been a limited number of publications regarding analysis and predictors of treatment outcomes in patients with combat-related penetrating brain injury in contemporary armed conflicts. The purpose of this study was to analyze the results of surgical treatment of patients with penetrating brain injury and to identify significant outcome predictors in these patients.

Materials and Methods
This was a prospective analysis of penetrating brain injury in patients who were admitted to Mechnikov Dnipropetrovsk Regional Clinical Hospital, Ukraine, from May 9, 2014, to December 31, 2017. All wounds were sustained during local armed conflict in Eastern Ukraine. The primary outcomes of interest were mortality rate at 1 month and Glasgow Outcome Scale score at 12 months after the injury.

Results
In total, 184 patients were identified with combat-related brain injury; of those, 121 patients with penetrating brain injury were included in our study. All patients were male soldiers with a mean age of 34.1 years (standard deviation [SD], 9.1 years). Mean admission Glasgow Coma Scale score was 10 (SD, 4), and mean admission Injury Severity Score was 27.7 (SD, 7.6). Mortality within 1 month was 20.7%, and intracranial purulent-septic complications were diagnosed in 11.6% of the patients. Overall, 65.3% of the patients had favorable outcome (good recovery or moderate disability) based on Glasgow Outcome Scale score at 12 months after the injury. The following were predictors of mortality or poor functional outcome at 1 year after the injury: low Glasgow Coma Scale score on admission, gunshot wound to the head, dural venous sinuses wound, presence of intracerebral hematomas, intraventricular and subarachnoid hemorrhage accompanied by lateral or axial dislocation, and presence of intracranial purulent-septic complications.

Conclusions
Generally, combat-related penetrating brain injuries had satisfactory treatment outcomes. Treatment outcomes in this study were comparable to those previously reported by other authors in military populations and significantly better than outcomes of peacetime penetrating brain injury treatment.
An intergenic “safe haven” region in Aspergillus fumigatus
Authors: Pham Tuyetnhu , Xie Xiaofeng , Lin Xiaorong 
Published: February 2020

Abstract
Aspergillus fumigatus is the most common opportunistic human fungal pathogen responsible for invasive aspergillosis. Gene manipulation is critical for the investigation of A. fumigatus biology and pathogenesis at the molecular level, and it often requires integration of the introduced DNA into the fungal genome. Here we have searched and identified two potential “safe haven” regions, SH1 and SH2, based on A. fumigatus genome annotation and transcriptome data. When a DNA fragment carrying a fluorescent protein gene mNeonGreen (mNG) and a drug selection marker was inserted into SH1 or SH2, the expression of mNeonGreen was easily detected, indicating that SH1 and SH2 are not surpressive genetic regions. We found that insertion of this DNA fragment into SH1 did not cause any significant changes in the expression of neighboring genes. Insertion of this DNA into either SH1 or SH2 did not significantly alter any of the phenotypes that we analyzed comparing to the wild type control. By comparison, transformants with random ectopic integration of the same DNA fragment showed a wider range of variation in mNeonGreen expression and in virulence in an insect infection model. Having identified predetermined “safe-haven” regions in A. fumigatus could therefore help reduce experimental variations and increase reproducibility, as it has been for the C. neoformans field.
Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction
Authors: Gill Mandev S , Lemey Philippe , Suchard Marc A , Rambaut Andrew , Baele Guy 
Published: February 2020

AbstractReconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing inference in an “online” fashion. Widely used Bayesian phylogenetic inference packages are not set up for this purpose, generally requiring one to recompute trees and evolutionary model parameters de novo when new data arrive. To accommodate increasing data flow in a Bayesian phylogenetic framework, we introduce a methodology to efficiently update the posterior distribution with newly available genetic data. Our procedure is implemented in the BEAST 1.10 software package, and relies on a distance-based measure to insert new taxa into the current estimate of the phylogeny and imputes plausible values for new model parameters to accommodate growing dimensionality. This augmentation creates informed starting values and re-uses optimally tuned transition kernels for posterior exploration of growing data sets, reducing the time necessary to converge to target posterior distributions. We apply our framework to data from the recent West African Ebola virus epidemic and demonstrate a considerable reduction in time required to obtain posterior estimates at different time points of the outbreak. Beyond epidemic monitoring, this framework easily finds other applications within the phylogenetics community, where changes in the data—in terms of alignment changes, sequence addition or removal—present common scenarios that can benefit from online inference.
The Volta: A Galant Gesture of Culmination
Authors: Mitchell Nathaniel 
Published: February 2020

AbstractThis article presents an overview of a new pre-cadential schema in the galant style: the Volta. The Volta is a two-part schema featuring a prominent chromatic reversal: stage one charges up the dominant with a ♯4^–5^ melodic string, while stage two releases to the tonic using a ♮4^–3^ string. The schema sheds light on many aspects of galant music-making: its variants illustrate how central features of a schematic prototype motivate or constrain plausible manipulations, its pre-cadential function reveals the intimate communion between surface schemas and the harmonic patterns inscribed within the style’s formal scripts, and, finally, its use as a climactic gesture in opera seria calls attention to the semantic possibilities of schemas beyond their role in defining musical topics. These and other aspects of the Volta are illustrated using representative excerpts from eighteenth-century masters like Leonardo Vinci, Giovanni Battista Pergolesi, Johann Adolf Hasse, Baldassare Galuppi, Joseph Haydn, and Wolfgang Amadeus Mozart.
Legal, Moral and Political Determinants within the Social Determinants of Health: Approaching Transdisciplinary Challenges through Intradisciplinary Reflection
Authors: Coggon John 
Published: February 2020

AbstractThis article provides a critical analysis of ‘the legal’ in the legal determinants of health, with reference to the Lancet–O’Neill report on that topic. The analysis shows how law is framed as a fluid and porous concept, with legal measures and instruments being conceived as sociopolitical phenomena. I argue that the way that laws are grounded practically as part of a broader concept of politics and evaluated normatively for their instrumental value has important implications for the study of law itself. This, in turn, has implications for how we approach the transdisciplinary ambitions that form a key part of the report’s recommendations to enhance law’s capacity to promote better, more equitable population health at local, national, international and global levels.
Opioid Utilization in Geriatric Patients After Operation for Degenerative Spine Disease
Authors: Nguyen Anthony V. , Ross Evan , Westra Jordan , Huang Nicole , Nguyen Christine Y. , Raji Mukaila , Lall Rishi , Kuo Yong-Fang 
Published: February 2020

Background:
Few studies have investigated opioid utilization by geriatric patients after spinal surgery, a population in whom degenerative spine disease (DSD) is highly prevalent. We aimed to quantify rates of chronic, continuous opioid utilization by geriatric patients following spine surgery for DSD-related diagnoses.

Materials and Methods:
Utilizing a national 5% Medicare sample database, we investigated individuals aged above 66 years who underwent spinal surgery for a DSD-related diagnosis between the years of 2008 and 2014. The outcomes of interest were the rate of and risk factors for continuous opioid utilization at 1-year following anterior cervical discectomy and fusion, posterior cervical fusion, 360-degree cervical fusion, lumbar microdiscectomy, lumbar laminectomy, posterior lumbar fusion, anterior lumbar fusion, or 360-degree lumbar fusion for a DSD-related diagnosis.

Results:
Of the 14,583 Medicare enrollees who met study criteria, 6.0% continuously utilized opioids 1-year after spinal surgery. When stratified by preoperative opioid utilization (with the prior year divided into 4 quarters), the rates of continuous utilization at 1-year postsurgery were 0.3% of opioid-naive patients and 23.6% of patients with opioid use in all 4 quarters before surgery. Anxiety, benzodiazepine use within the year before surgery, and Medicaid dual-eligibility were associated with prolonged opioid utilization.

Conclusions:
Of opioid-naive geriatric patients who underwent surgery for DSD, 0.3% developed chronic, continuous opioid use. Preoperative opioid use was the strongest predictor of prolonged utilization, which may represent suboptimal use of nonopioid alternatives, pre-existing opioid use disorders, delayed referral for surgical evaluation, or over-prescription of opioids for noncancer pain.
Improving Microbe Detection and Optimizing Antibiotic Use in Neonatal Sepsis With Multiplex Polymerase Chain Reaction
Authors: Raju Vivek , Pournami Femitha , Nandakumar Anand , Prabhakar Jyothi , Nair PMC , Jain Naveen 
Published: February 2020

Background
Polymerase chain reaction (PCR) can overcome the drawbacks of culture in diagnosis of neonatal sepsis. Many reports have shown potential benefit.

Aim
We compared microbe detection rate between 2 groups—when PCR was used along with blood culture (culture + PCR, CP) versus when culture alone was used. We also sought to describe, in CP, the causal organisms and their resistance patterns and to study duration of antibiotic therapy in CP versus culture alone groups.

Methods
We studied a prospective cohort of babies where both culture and PCR could be sent and a retrospective cohort when only culture was used; in those who required antibiotic for suspected health care–associated infection.

Results
When PCR was used along with culture, microbes were detected in 40.3% samples, as against only 24.6% with culture alone. Gram-negative bacilli were the most common organism detected (56.5% of positive samples) followed by Candida species. Resistance was reported in only 3 of the tested gram-negative organisms. Empiric antibiotics were stopped significantly earlier in the cohort where PCR was also used as compared with when culture alone was relied upon (median duration of therapy 3 vs 7 days, respectively).

Conclusions
Polymerase chain reaction improves diagnostic yield in neonatal health care–associated infection and can help decrease duration of antibiotic therapy. Resistance to broad spectrum antibiotics is uncommon.
New method to assess the accuracy of intraocular lens power calculation formulas according to ocular biometric parameters
Authors: Fernández Joaquín , Rodríguez-Vallejo Manuel , Poyales Francisco , Burguera Noemí , Garzón Nuria 
Published: February 2020

Purpose:
To develop a new method that makes it easy to detect accuracy deficiencies of any intraocular lens (IOL) power calculation formulas and to test it on 9 different formulas.

Setting:
IOA, Madrid, Spain.

Design:
Retrospective observational case series.

Methods:
This study's first stage included 3519 eyes from 3519 candidates for cataract surgery for which frequency distributions for the following biometric eye parameters were computed: axial length (AL), anterior chamber depth (ACD), lens thickness (LT), white-to-white (WTW), and mean corneal radius (Rm). The resulting data for each parameter were fifth, 25th, 75th and 95th percentiles, which allowed definition of the corresponding normality range. In a second stage, the new graphic-representation method was tested for 9 different formulas in a sample of 70 eyes undergoing cataract surgery with multifocal IOL (mIOL) implantation.

Results:
Normality ranges (defined as the 25th to 75th percentile interval) were 22.84 to 24.42 mm for AL, 2.86 to 3.39 mm for ACD, 4.36 to 4.88 mm for LT, 11.64 to 12.19 mm for WTW, and 7.52 to 7.87 mm for Rm, with lower sizes in women. No significant differences were found among the 9 formulas for percentage of eyes in ±0.50 diopters (D) (P = .82) or ±1.00 D (P = .97). The graphical method showed less accuracy in ±0.50 D for ACDs from 2.46 to 2.85 mm (5th to 25th percentile) for several formulas (P < .05).

Conclusions:
Nine formulas showed nonsignificant differences in the general predictability for a sample of eyes that were candidates to mIOL implantation. Predictability in this sample decreased for short ACDs.
Experimental and analytical quantification of light scattering from vacuoles in intraocular lenses
Authors: Spiezio Vincent , Walker Bennett N. , Calogero Don , Ilev Ilko K. 
Published: February 2020

Purpose:To develop an advanced test methodology for quantification of scattered light from intraocular lenses (IOLs) and to evaluate the correlation between IOL vacuole characteristics and measured scattered light.Setting:U.S. Food and Drug Administration, Optical Therapeutics and Medical Nanophotonics Laboratory, Silver Spring, Maryland, USA.Design:Experimental and analytical study.Methods:Twenty-four IOLs containing vacuoles were evaluated using a digital microscopy approach for identifying and characterizing the vacuoles present. A scanning light scattering profiler (SLSP) was used to evaluate and quantify the amount of scattered light from each IOL and from a 25th control IOL without any vacuoles. A variety of IOLs and vacuoles were also modeled in a Zemax simulation of the SLSP, and the simulated scattered light was modeled.Results:The scattered light as measured with SLSP was well correlated with vacuole characteristics, specifically density and size, as measured under the digital microscope for the 24 vacuole-containing IOLs. Additional correlations were found between vacuole sizes, orientations, and the angle at which light was scattered most severely. These correlations were also present in the Zemax model.Conclusions:Vacuole optical characteristics can be well correlated with measured scatter, demonstrating an ability to predict scattered light based solely on microscope evaluation. Furthermore, the quantitative amount of scatter predicted with Zemax simulations trended closely with the experimentally measured trends.
The Language of Electricity
Authors: Kivnick Alexandra R. , Limone Brittanya , Jacob Sharon E. 
Published: February 2020

ABSTRACT
Electrical devices are commonly used within the field of dermatologic surgery. With the growing role of nursing providers in the dermatologic setting, it is essential to provide education and training regarding electrical devices and concepts within the nursing community. This installment introduces electricity principles and reviews terminology associated with the electrical devices used in dermatologic procedures.
Nonalcoholic fatty liver disease is associated with intrahepatic cholangiocarcinoma and not with extrahepatic form: definitive evidence from meta-analysis and trial sequential analysis
Authors: Corrao Salvatore , Natoli Giuseppe , Argano Christiano 
Published: February 2020

Background
Cholangiocarcinoma is a cancer with poor prognosis. The detection of risk factors is fundamental to identify subjects at higher risk of cholangiocarcinoma. Nonalcoholic fatty liver disease (NAFLD) represents a leading cause of chronic liver disease worldwide. Recent data suggested that NAFLD increases the risk of cholangiocarcinoma development. However, it is necessary to better explain the strength of association between NAFLD and cholangiocarcinoma.

Methods
A systematic research of current case-control, cohort, clinical trial and meta-analysis on the main electronic databases was made. A recent systematic review was recognized. We performed cumulative meta-analyses with sensitivity analysis excluding studies with large sample size and with great clinical heterogeneity, then we checked for further studies. At the final step, three trial sequential analyses were done as well.

Results
NAFLD determines an increased risk of total cholangiocarcinoma and intrahepatic cholangiocarcinoma (iCCA) development: odds ratio (OR) (95% confidence interval [CI]): 1.88 (1.25–2.83), OR (95% CI): 2.19 (1.48–3.25), respectively. On the contrary, NAFLD does not show a significant effect on extrahepatic cholangiocarcinoma (eCCA) (OR (95% CI): 1.48 (0.93–2.36). The trial sequential analyses regarding total cholangiocarcinoma and iCCA showed that z-curve was outside computed alpha boundaries, proving that the positive association was conclusive. The trial sequential analysis about eCCA showed that z-curve was inside computed futile boundaries, proving that negative results were conclusive.

Conclusion
The performance of new sensitive analyses and the respective trial sequential analyses, after withdraw of confounding factors, suggested the existence of definitive association only between NAFLD and iCCA development and not with eCCA.
Immunologic Clearance of a BK Virus-associated Metastatic Renal Allograft Carcinoma
Authors: Meier Raphael P.H. , Muller Yannick D. , Dietrich Pierre-Yves , Tille Jean-Christophe , Nikolaev Sergey , Sartori Ambra , Labidi-Galy Intidhar , Ernandez Thomas , Kaur Amandeep , Hirsch Hans H. , McKee Thomas A. , Toso Christian , Villard Jean , Berney Thierry 
Published: February 2020

Background.
Metastatic carcinoma of a renal allograft is a rare but life threatening event with a difficult clinical management. Recent reports suggested a potential role of BK polyomavirus (BKPyV) in the development of urologic tract malignancies in kidney transplant recipients.

Methods.
We investigated a kidney-pancreas female recipient with an history of BKPyV nephritis who developed a rapidly progressive and widely metastatic donor-derived renal carcinoma 9 years after transplantation.

Results.
Histology and fluorescence in situ hybridization analysis revealed a donor-derived (XY tumor cells) collecting (Bellini) duct carcinoma. The presence of BKPyV oncogenic large tumor antigen was identified in large amount within the kidney tumor and the bowel metastases. Whole genome sequencing of the tumor confirmed multiple genome BKPyV integrations. The transplanted kidney was removed, immunosuppression was withdrawn, and recombinant interleukin-2 (IL-2) was administered for 3 months, inducing a complete tumor clearance, with no evidence of disease at 6-year follow-up. The immunological profiling during IL-2 therapy revealed the presence of donor-specific T cells and expanded cytokine-producing bright natural killer cells but no donor-specific antibodies. Finally, we found persistently elevated anti-BK virus IgG titers and a specific anti-BKPyV T cell response.

Conclusions.
This investigation showed evidence for the potential oncogenic role of BKPyV in collecting duct carcinoma in renal allografts and demonstrated that immunosuppression withdrawal and IL-2 therapy can lead to an efficient antitumor cellular mediated rejection possibly via 3 distinct mechanisms including (1) host-versus-graft, (2) host-versus-tumor, and (3) anti-BKPyV responses.