bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Benchmarks for Global Surgery: Nationwide Enumeration of Operations Performed in Ghana
Authors: Gyedu Adam , Stewart Barclay , Gaskill Cameron , Boakye Godfred , Appiah-Denkyira Ebenezer , Donkor Peter , Maier Ronald , Quansah Robert , Mock Charles 
Published: August 2017

Objective:
To evaluate the operation rate in Ghana and characterize it by types of procedures and hospital level.

Background:
The Lancet Commission on Global Surgery recommended an annual rate of 5000 operations/100,000 people as a benchmark at which low- and middle-income countries could achieve most of the population-wide benefits of surgery, but did not define procedure-type benchmarks.

Methods:
Data on operations performed from June 2014 to May 2015 were obtained from representative samples of 48 of 124 district-level (first-level) hospitals, 9 of 11 regional (referral) hospitals, and 3 of 5 tertiary hospitals, and scaled-up to nationwide estimates. Operations were categorized into those deemed as essential procedures (most cost-effective, highest population impact) by the World Bank's Disease Control Priorities Project versus other.

Results:
An estimated 232,776 [95% uncertainty interval (95% UI) 178,004 to 287,549] operations were performed nationally. The annual rate of operations was 869 of 100,000 (95% UI 664 to 1073). The rate fell well short of the benchmark. 77% of the estimated annual national surgical output was in the essential procedure category. Most operations (62%) were performed at district-level hospitals. Most district-level hospitals (54%) did not have fully trained surgeons, but nonetheless performed 36% of district-level hospital operations.

Conclusion:
The operation rate was short of the Lancet Commission benchmark, indicating large unmet need, although most operations were in the essential procedure category. Future global surgery benchmarking should consider both total numbers and priority levels. Most surgical care was delivered at district-level hospitals, many without fully trained surgeons. Benchmarking to improve surgical care needs to address both access deficiencies and hospital and provider level.
Surgery for Primary Hyperparathyroidism
Authors: Kuo Eric J. , Al-Alusi Mostafa A. , Du Lin , Shieh Albert , Livhits Masha J. , Leung Angela M. , Yeh Michael W. 
Published: August 2017

Objective:
To determine the extent to which consensus guidelines for surgery in patients with primary hyperparathyroidism (PHPT) are followed within an academic health system.

Background:
Previous studies have shown that adherence to consensus guidelines in community practice is low.

Methods:
Adults with biochemically confirmed PHPT who received primary care within an academic health system were identified from 2005 to 2015. Multivariable logistic regression was used to analyze predictors of parathyroidectomy (PTx).

Results:
In 617 patients, the overall PTx rate was 30.8%. When individual consensus criteria were examined, age <50 (P<0.01), serum calcium >11.3 mg/dL (P < 0.01), and hypercalciuria (P = 0.02) were associated with PTx; while nephrolithiasis (P = 0.07) and osteoporosis (P = 0.34) did not affect the PTx rate. The PTx rate increased with the number of consensus criteria satisfied (1 criterion, 33%; 2 criteria, 45%; 3 or more criteria, 82%, P < 0.01). Independent predictors of PTx included male sex [odds ratio (OR) 1.7, 95% confidence interval (CI) 1.1–2.8], increasing serum parathyroid hormone (OR 1.1 per 10 pg/mL 95% CI 1.05–1.13), and endocrinologist evaluation (OR 1.6, 95% CI 1.1–2.4); while Black race (OR 0.4, 95% CI 0.2–0.8), lack of 24-hour urine calcium measurement (OR 0.5, 95% CI 0.3–0.8), Charlson Comorbidity Index ≥ 2 (OR 0.6, 95% CI 0.4–0.9), and age ≥80 years (OR 0.2, 95% CI 0.1–0.4) predicted against PTx.

Conclusion:
Within an academic health system, consensus guidelines do appear to influence the decision for surgery in patients with PHPT. However, the level of compliance is generally low, and similar to that observed in community practice.
Peritoneal cavity lavage reduces the presence of mitochondrial damage associated molecular patterns in open abdomen patients
Authors: Martinez-Quinones Patricia A. , McCarthy Cameron G. , Mentzer Caleb J. , Wenceslau Camilla F. , Holsten Steven B. , Webb R Clinton , O’Malley Keith 
Published: August 2017

BACKGROUND
Mitochondrial damage-associated molecular patterns (mtDAMPs), such as mitochondrial DNA and N-formylated peptides, are endogenous molecules released from tissue after traumatic injury. mtDAMPs are potent activators of the innate immune system. They have similarities with bacteria, which allow mtDAMPs to interact with the same pattern recognition receptors and mediate the development of systemic inflammatory response syndrome (SIRS). Current recommendations for management of an open abdomen include returning to the operating room every 48 hours for peritoneal cavity lavage until definitive procedure. These patients are often critically ill and develop SIRS. We hypothesized that mitochondrial DAMPs are present in the peritoneal cavity fluid in this setting, and that they accumulate in the interval between washouts.

METHODS
We conducted a prospective pilot study of critically ill adult patients undergoing open abdomen management in the surgical and trauma intensive care units. Peritoneal fluid was collected daily from 10 open abdomen patients. Specimens were analyzed via quantitative polymerase chain reaction (qPCR) for mitochondrial DNA (mtDNA), via enzyme immunoassay for DNAse activity and via Western blot analysis for the ND6 subunit of the NADH: ubiquinone oxidoreductase, an N-formylated peptide.

RESULTS
We observed a reduction in the expression of ND6 the day after lavage of the peritoneal cavity, that was statistically different from the days with no lavage (% change in ND6 expression, postoperative from washout: −50 ± 11 vs. no washout day, 42 ± 9; p < 0.05). Contrary to expectation, the mtDNA levels remained relatively constant from sample to sample. We then hypothesized that DNAse present in the effluent may be degrading mtDNA.

CONCLUSION
These results indicate that the peritoneal cavity irrigation reduces the presence of mitochondrial DAMPs in the open abdomen. It is possible that increased frequency of peritoneal cavity lavage may lead to decreased systemic absorption of mtDAMPs, thereby reducing the risk of SIRS.

LEVEL OF EVIDENCE
Prospective study, Case Series, Level V.
Is extracorporeal cardiopulmonary resuscitation practical in severe chest trauma? A systematic review in single center of developing country
Authors: Huh Up , Song Seunghwan , Chung Sung Woon , Kim Sang-pil , Lee Chung Won , Ahn Hyo Young , Bae Miju , Kim Seon Hee 
Published: August 2017

BACKGROUND
We report our experience with extracorporeal cardiopulmonary resuscitation (ECPR) in patients with rupture of heart and major vessels caused by severe chest trauma.

METHODS
From April 2015 to May 2016, 10 patients with suspected injuries to the heart and major vessels after focused assessment with sonography in trauma or computed tomography were selected from patients admitted at a Level I trauma center presenting with cardiac tamponade and tension hemothorax due to severe chest trauma. Patients were divided as follow: group A (n = 3), patients without cardiac arrest before entering the operating theatre; group B (n = 5), patients with cardiac arrest for whom ECPR was applied, and group C (n = 2), patients with cardiac arrest for whom ECPR was not applied.

RESULTS
All patients underwent exploratory thoracotomy or sternotomy. Injuries included cardiac chamber ruptures (n = 8), lesions in the internal mammary arteries (n = 1), and lesions of the bronchial arteries (n = 1). In group B, extracorporeal membrane oxygenation (ECMO) was initiated and circulation was restored promptly with adequate extracorporeal blood flow in all five cases. These patients were weaned off ECMO uneventfully after controlling the bleeding in the operating theatre. Mean ECMO time was 142 ± 48.2 minutes. Conversely, both patients in group C died, one due to low cardiac output on postoperative day 1, and the other due to multiple-organ failure on postoperative day 7.

CONCLUSION
ECPR may be an option to rescue and stabilize patients with cardiac arrest due to severe chest trauma.

LEVELS OF EVIDENCE
Therapeutic/Care Management, Level V.
Developing a 3- to 6-state EEG-based brain-computer interface for a robotic manipulator control
Authors: Mishchenko Yuriy , Kaya Murat , Ozbay Erkan , Yanar Hilmi 
Published: August 2017

AbstractRecent developments in BCI techniques have demonstrated high-performance control of robotic prosthetic systems primarily via invasive methods. In this work we develop an electroencephalography (EEG) based noninvasive BCI system that can be used for a similar, albeit lower-speed robotic control, and a signal processing system for detecting user’s mental intent from EEG data based on up to 6-state motor-imagery BCI communication paradigm. We examine the performance of that system on experimental data collected from 12 healthy participants and analyzed offline. We show that our EEG BCI system can correctly identify different motor imageries in EEG data with high accuracy: 3 out of 12 participants achieved accuracy of 6-state communication in 80-90% range, while 2 participants could not achieve a satisfactory accuracy. We further implement an online BCI system for control of a virtual 3 degree-of-freedom prosthetic manipulator and test it with our 3 best participants. The participants’ ability to control the BCI is quantified by using the percentage of successfully completed BCI tasks, the time required to complete a task, and the error rate. 2 participants were able to successfully complete 100% of the test tasks, demonstrating on average the error rate of 80% and requiring 5-10 seconds to execute a manipulator move. 1 participant failed to demonstrate a satisfactory performance in online trials. Our results lay a foundation for further development of EEG BCI-based robotic assistive systems and demonstrate that EEG-based BCI may be feasible for robotic control by paralyzed and immobilized individuals.
qDSB-Seq: quantitative DNA double-strand break sequencing
Authors: Zhu Yingjie , Biernacka Anna , Pardo Benjamin , Dojer Norbert , Forey Romain , Skrzypczak Magdalena , Fongang Bernard , Nde Jules , Yousefi Raziyeh , Pasero Philippe , Ginalski Krzysztof , Rowicka Maga 
Published: August 2017

AbstractSequencing-based methods for mapping DNA double-strand breaks (DSBs) allow measurement only of relative frequencies of DSBs between loci, which limits our understanding of the physiological relevance of detected DSBs. We propose quantitative DSB sequencing (qDSB-Seq), a method providing both DSB frequencies per cell and their precise genomic coordinates. We induced spike-in DSBs by a site-specific endonuclease and used them to quantify labeled DSBs (e.g. using i-BLESS). Utilizing qDSB-Seq, we determined numbers of DSBs induced by a radiomimetic drug and various forms of replication stress, and revealed several orders of magnitude differences in DSB frequencies. We also measured for the first time Top1-dependent absolute DSB frequencies at replication fork barriers. qDSB-Seq is compatible with various DSB labeling methods in different organisms and allows accurate comparisons of absolute DSB frequencies across samples.
X10 Expansion Microscopy Enables 25 nm Resolution on Conventional Microscopes
Authors: Truckenbrodt Sven , Maidorn Manuel , Crzan Dagmar , Wildhagen Hanna , Kabatas Selda , Rizzoli Silvio O. 
Published: August 2017

ABSTRACTExpansion microscopy is a recently introduced imaging technique that achieves super-resolution through physically expanding the specimen by ~4x, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately 4-fold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20-30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10x in each dimension, which corresponds to an expansion of the sample volume by more than 1000-fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25-30 nm on conventional epifluorescence microscopes. X10 provides multi-color images similar or even superior to those produced with more challenging methods, such as STED, STORM and iterative expansion microscopy (iExM), in both cell cultures and tissues.
Chemosensory proteins in the CSP4 clade evolved as plant immunity suppressors before two suborders of plant-feeding hemipteran insects diverged
Authors: Drurey Claire , Mathers Thomas C. , Prince David C. , Wilson Christine , Caceres-Moreno Carlos , Mugford Sam T. , Hogenhout Saskia A. 
Published: August 2017

AbstractChemosensory proteins (CSPs) are small globular proteins with hydrophobic binding pockets that have a role in detection of chemicals, regulation of development and growth and host seeking behaviour and feeding of arthropods. Here, we show that a CSP has evolved to modulate plant immune responses. Firstly, we found that the green peach aphidMyzus persicaeCSP Mp10, which is delivered into the cytoplasm of plant cells, suppresses the reactive oxygen species (ROS) bursts to both aphid and bacterial elicitors inArabidopsis thalianaandNicotiana benthamiana. Aphid RNA interference studies demonstrated that Mp10 modulates the first layer of the plant defence response, specifically the BAK1 pathway. We identified Mp10 homologs in diverse plant-sucking insect species, including aphids, whiteflies, psyllids and leafhoppers, but not in other insect species, including blood-feeding hemipteran insects. We found that Mp10 homologs from other splant-sucking insect species are also capable of suppressing plant ROS. Together, these data and phylogenetic analyses provides evidence that an ancestral Mp10-like sequence acquired plant ROS suppression activity before the divergence of plant-sucking insect species over 250 million years ago.SignificanceAphids, whiteflies, psyllids, leafhoppers and planthoppers are plant-sucking insects of the order Hemiptera that cause dramatic crop losses via direct feeding damage and vectoring of plant pathogens. Chemosensory proteins (CSPs) regulate behavioural and developmental processes in arthropods. Here we show that the CSP Mp10 of the green peach aphidMyzus persicaeis an effector that suppresses plant reactive oxygen species (ROS) bursts and the first layer of plant defence responses. Surprisingly, Mp10 homologs are present in diverse plant-feeding hemipteran species, but not blood-feeding ones. An ancestral Mp10-like sequence most likely acquired ROS suppression activity before the divergence of plant-sucking insect species 250 million years ago.
On the relative role of different age groups during epidemics associated with the respiratory syncytial virus
Authors: Goldstein E. , Nguyen H. H. , Liu P. , Viboud C. , Steiner C.A. , Worby C. J. , Lipsitch M. 
Published: August 2017

AbstractBackgroundWhile RSV circulation results in high burden of hospitalization, particularly among infants, young children and the elderly, little is known about the role of different age groups in propagating annual RSV epidemics in the community.MethodsDuring a communicable disease outbreak, some subpopulations may play a disproportionate role during the outbreak's ascent due to increased susceptibility and/or contact rates. Such subpopulations can be identified by considering the proportion that cases in a subpopulation represent among all cases in the population occurring before (Bp) and after the epidemic peak (Ap) to calculate the subpopulation's relative risk, RR=Bp/Ap. We estimated RR for several age groups using data on RSV hospitalizations in the US between 2001-2012 from the Healthcare Cost and Utilization Project (HCUP).ResultsChildren aged 3-4y and 5-6y each had the highest RR estimate for 5/11 seasons in the data, with RSV hospitalization rates in infants being generally higher during seasons when children aged 5-6y had the highest RR estimates. Children aged 2y had the highest RR estimate during one season. RR estimates in infants and individuals aged 11y and older were mostly lower than in children aged 1-10y.ConclusionsThe RR estimates suggest that preschool and young school-age children have the leading relative roles during RSV epidemics. We hope that those results will aid in the design of RSV vaccination policies.
Predictors of intestinal inflammation in asymptomatic first-degree relatives of patients with Crohn’s disease
Authors: Taylor Kirstin M. , Hanscombe Ken B. , Iniesta Raquel , Traylor Matthew , Taylor Nicola S. , Powell Nicholas , Irving Peter M. , Anderson Simon H. , Prescott Natalie J. , Mathew Christopher G. , Lewis Cathryn M. , Sanderson Jeremy D. 
Published: August 2017

AbstractObjectiveRelatives of individuals with Crohn’s disease (CD) carry an increased number of CD-associated genetic variants and are at increased risk of developing the disease. Multiple environmental and genetic factors contribute to this increased risk. We aimed to estimate the utility of genotype, smoking, family history, and a panel of biomarkers to predict risk in asymptomatic first-degree relatives (FDRs) of CD patients.DesignWe calculated a combined genotype (72 CD-associated genetic markers) and smoking relative risk score in 454 FDRs, and performed capsule endoscopy and collected 22 biomarkers in individuals from the highest and lowest risk quartiles. We then predicted small intestinal inflammation using genetic risk score, smoking status, number of relatives with CD, capsule transit time, and the panel of biomarkers in 124 individuals with complete data. Our principal analysis was to calculate the predictive utility from two machine learning classifiers: an elastic net and a random forest.ResultsBoth classifiers successfully predicted FDRs with intestinal inflammation: elastic net (AUC=0.80, 95% CI: 0.62-0.98), random forest (AUC=0.87, 95% CI: 0.75-1.00). The elastic net selected a 3-predictor solution: CD family history (OR=1.31), genetic risk score (OR=1.14), and faecal calprotectin (OR=1.04). The same 3 variables were among the top 5 most important predictors as ranked by the random forest.ConclusionA readily collectable panel of genetic risk variants, added to family history and faecal calprotectin, predicts those at greatest risk for developing CD with a good degree of accuracy.
A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila
Authors: Mallard François , Nolte Viola , Tobler Ray , Kapun Martin , Schlötterer Christian 
Published: August 2017

AbstractPopulation genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. To investigate the genetic architecture of thermal adaptation - a highly complex trait - we performed experimental evolution on a naturalDrosophila simulanspopulation. Transcriptome and respiration measurements revealed extensive metabolic rewiring after only ∼60 generations in a hot environment. Analysis of genome-wide polymorphisms identified two interacting selection targets,SestrinandSNF4Aγ, pointing to AMPK, a central metabolic switch, as a key factor for thermal adaptation. Our results demonstrate that large-effect loci segregating at intermediate allele frequencies can allow natural populations to rapidly respond to selection. BecauseSNF4Aγalso exhibits clinal variation in variousDrosophilaspecies, we suggest that this large effect polymorphism is maintained by temporal and spatial temperature variation in natural environments.
Spring flowering habit in field pennycress (Thlaspi arvense) has arisen multiple independent times
Authors: Dorn Kevin M. , Johnson Evan B. , Daniels Erin , Wyse Donald L. , David Marks M. 
Published: August 2017

Summary- Pennycress (Thlaspi arvenseL.) is currently being developed as a new cold-season oilseed crop. Like many Brassicaceae, pennycress can exhibit either a winter or spring annual phenotype. In Arabidopsis, mutations in negative regulators of flowering, including FLOWERING LOCUS C (FLC) and FRIGIDA can cause the transition to a spring annual habit. The genetics underlying the difference between spring and winter annual pennycress are currently unknown.- Using whole genome sequencing across wild spring annual pennycress accessions, co-segregation analyses, and comparative genomics approaches, we identify new alleles of TaFLC and explore their geographic distribution.- We report that loss of function mutations in TaFLC confer the spring annual phenotype in pennycress. We have also identified four natural alleles of TaFLC that confer a spring annual growth habit. The two spring annual FLC alleles present in European accessions were only identified in accessions collected in Montana, USA.- In pennycress, the spring annual habit has arisen several independent times. Accessions harboring the two European alleles were introduced to North America, likely after the species became a widespread on the continent. These findings provide new information on the natural history of the introduction and spread of the spring annual phenotype in pennycress.
Transmission Expression Signature in NascentPlasmodium vivaxBlood Stage Infection
Authors: Adapa Swamy Rakesh , Taylor Rachel A. , Wang Chengqi , Thomson-Luque Richard , Johnson Leah R. , Jiang Rays H.Y. 
Published: August 2017

AbstractThe lack of a continuousin vitroculture system forPlasmodium vivaxseverely limits our knowledge of pathophysiology of the most widespread malaria parasite. To gain direct understanding ofP. vivaxhuman infections, we used Next Generation Sequencing data mining to unravel parasitein vivoexpression profiles forP. vivax,andP. falciparumas comparison. We performed cloud and local computing to extract parasite transcriptomes from publicly available raw data of human blood samples. We developed a Poisson Modelling (PM) method to confidently identify parasite derived transcripts in mixed RNAseq signals of infected host tissues. We successfully retrieved and reconstructed parasite transcriptomes from infected patient blood as early as the first blood stage cycle; and the same methodology did not recover any significant signal from controls. Surprisingly, these first generation blood parasites already show strong signature of transmission, which indicates the commitment from asexual-to-sexual stages. Further, we develop mathematical models forP. vivaxandP. falciparumto assess the epidemiological impact of possible 7-day early stage transmission andP. vivaxcomplex life cycle. The study uncovers the earliest onset ofP. vivaxblood pathogenesis and highlights the challenges ofP. vivaxeradication programs.Author summaryWe discovered thatP. vivax in vivoparasitemia is associated with gametocytogenesis expression signature within the first blood stage cycle, that is, eight days from a mosquito bite. Our results suggest that asexual-to-sexual commitment may happen with first generation merozoite infection. This allows for the possibility of transmission at this early stage, much earlier than forP. falciparum. Our novel mathematical model accounts for multiple unique aspects ofP. vivaxbiology to advance our understanding of expected disease prevalence, and compares the results to those ofP. falciparum. We demonstrate that given the presence of asymptotical carriers and the possibility of relapses, earlier parasite transmission is capable of increasing the spread of disease within human populations. In summary,P. vivaxgametogenesis has the potential to fast track the transmission cycle, which will drive enhanced propagation of the disease during the transmission season and clinical relapses.