bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of undetected recombination on genealogy sampling and inference under an isolation‐with‐migration model
Authors: Hey Jody , Wang Katherine 
Published: September 2019

AbstractMany methods for fitting demographic models to data sets of aligned sequences rely upon an assumption that the data have a branching coalescent history without recombination within regions or loci. To mitigate the effects of the failure of this assumption, a common approach is to filter data and sample regions that pass the four‐gamete criterion for recombination, an approach that allows data to run, but that is expected to detect only a minority of recombination events. A series of empirical tests of this approach were conducted using computer simulations with and without recombination for a variety of isolation‐with‐migration (IM) model for two and three populations. Only the IMa3 program was used, but the general results should apply to related genealogy‐sampling‐based methods for IM models or subsets of IM models. It was found that the details of sampling intervals that pass a four‐gamete filter have a moderate effect, and that schemes that use the longest intervals, or that use overlapping intervals, gave poorer results. A simple approach of using a random nonoverlapping interval returned the smallest difference between results with and without recombination, with the mean difference between parameter estimates usually less than 20% of the true value (usually much less). However, the posterior probability distributions for migration rates were flatter with recombination, suggesting that filtering based on the four‐gamete criterion, while necessary for methods like these, leads to reduced resolution on migration. A distinct, alternative approach, of using a finite sites mutation model and not filtering the data, performed quite poorly.
Evaluation of the smartphone for measurement of femoral rotational deformity
Authors: Shen Yi‐Fan , Huang Jing‐Huan , Li Xiao‐Lin , Gao Hong 
Published: September 2019

AbstractBackgroundA novel measurement technique has been designed to assess femoral rotation deformation. The purpose of this study was to evaluate smartphone‐aided measurement, including measurement software, intra‐observer differences and the occurrence frequency of the unacceptable outliers.MethodsFive positions (intact bone, external and internal rotations of 20° and 40° of the distal blocks after dividing the femoral shafts using a saw) were used in each of the five artificial femora. Guide wires were separately inserted into the proximal and distal ends of the model femora with a navigation system and the intersection angles between the guide wires were measured with a smartphone. The values obtained by two measurement software packages (Smart Tools and Super Swiss Army Knife) were compared with that measured on the overlapped computed tomography images.ResultsThere were no significant differences between the intersection angles measured by smartphone and that measured on the overlapped images (P = 0.24). The mean absolute difference between pairs of measurements of the two software packages for all guide wire angles was 2.33 ± 2.34°, without statistically significant difference (P = 0.33). There was a significant correlation (r = 0.99) between the first and second (1 week apart) measurements with the same measurement tool. The values of offset capability index of the Smart Tools and the Super Swiss Army Knife measurement tools were 1.62 and 1.13, respectively.ConclusionSmartphone‐aided measurement technique could reliably assess femoral rotation deformation with more accurate angle measurement for software with zero calibration function.
Biomechanical performance of an intramedullary Echidna pin for fixation of comminuted mid‐shaft clavicle fractures
Authors: Sidhu Navjit , Huntington Lachlan S. , Richardson Martin , Ackland David C. 
Published: September 2019

AbstractBackgroundSurgical fixation of comminuted mid‐shaft clavicle fractures commonly employs intramedullary devices; however, pins with smooth surfaces are prone to migration, whilst threaded pins can be challenging to remove post‐operatively. The aim of this study was to evaluate the biomechanical performance of fractured clavicles repaired using a novel intramedullary Echidna pin device and a non‐threaded Knowles pin. The Echidna pin features retractable spines that engage with the bone to minimize migration and facilitate ease of device removal.MethodsA total of 28 cadaveric clavicle specimens were harvested and a mid‐shaft wedge‐shaped osteotomy was performed to simulate a comminuted butterfly fragment. Specimens were allocated randomly to either the Echidna pin or Knowles pin fracture repair groups. Following surgery, eight specimens in each group underwent 200 cycles of four‐point bending, whilst six specimens in each group underwent torsional testing and pull‐out. Cyclic construct bending stiffness, torsional stiffness and ultimate strength were recorded.ResultsEchidna pin intramedullary repair constructs showed significantly greater bending stiffness (mean difference 0.55 N.m/°, 95% confidence interval −0.96, −0.14, P = 0.01) and pull‐out strength (mean difference 146.03 N, 95% confidence interval 29.14, 262.92, P = 0.019) in comparison to Knowles pin constructs. There was no significant difference in torsional stiffness between Echidna pin and Knowles pin repair constructs (P > 0.05).ConclusionThe intramedullary Echidna pin device, which exhibits greater bending strength and pull‐out strength than that of the Knowles pin, may produce a more stable clavicle fracture reduction compared to that of commercially available threadless intramedullary pins.
Modifiable risk factors for multidrug‐resistant Gram‐negative infection in critically ill burn patients: a systematic review and meta‐analysis
Authors: Vickers Mark L. , Malacova Eva , Milinovich Gabriel J. , Harris Patrick , Eriksson Lars , Dulhunty Joel M. , Cotta Menino O. 
Published: September 2019

AbstractBackgroundWe conducted a systematic review and meta‐analysis to identify potentially modifiable risk factors for multidrug‐resistant Gram‐negative colonization or infection in critically ill burn patients.MethodsA systematic search was conducted of PubMed, Embase, CINAHL, Web of Science and Central (Cochrane). Risk factors including antibiotic use and hospital interventions were summarized in a random‐effects meta‐analysis. Risk of publication bias was assessed using the Grading of Recommendations Assessment, Development and Evaluation method and funnel plots.ResultsA total of 11 studies met the inclusion criteria. We identified several potentially modifiable risk factors and were able to grade their importance based on effect size. Related to prior antibiotic exposure, extended‐spectrum cephalosporins (pooled odds ratio (OR) 7.00, 95% confidence interval (CI) 2.77–17.67), carbapenems (pooled OR 6.65, 95% CI 3.49–12.69), anti‐pseudomonal penicillins (pooled OR 4.23, 95% CI 1.23–14.61) and aminoglycosides (pooled OR 4.20, 95% CI 2.10–8.39) were most significant. Related to hospital intervention, urinary catheters (pooled OR 11.76, 95% CI 5.03–27.51), arterial catheters (pooled OR 8.99, 95% CI 3.84–21.04), mechanical ventilation (pooled OR 5.49, 95% CI 2.59–11.63), central venous catheters (pooled OR 4.26, 95% CI 1.03–17.59), transfusion or blood product administration (pooled OR 4.19, 95% CI 1.48–11.89) and hydrotherapy (pooled OR 3.29, 95% CI 1.64–6.63) were most significant.ConclusionPrior exposure to extended‐spectrum cephalosporins and carbapenems, as well as the use of urinary catheters and arterial catheters pose the greatest threat for infection or colonization with multidrug‐resistant Gram‐negative organisms in the critically ill burn patient population.
Early laparoscopic cholecystectomy by a dedicated emergency surgical unit confers excellent outcomes in acute cholecystitis presenting beyond 72 hours
Authors: Chia Clement L. K. , Lu Junde , Goh Serene S. N. , Lee Daniel J. K. , Rao Anil D. , Lim Woan Wui , Tan Kok‐Yang , Goo Jerry T. T. 
Published: September 2019

AbstractBackgroundEarly laparoscopic cholecystectomy (ELC) within 72 h of symptom onset is preferred for management of acute cholecystitis (AC). Beyond 72 h, acute‐on‐chronic fibrosis sets in rendering surgery challenging. This study aims to compare the outcomes of ELC for AC within and beyond 72 h of symptom onset by a dedicated acute surgical unit.MethodsThis is a single‐centre retrospective study of 217 patients with AC who underwent ELC by an acute surgical unit from January 2017 to August 2018. Outcomes collected include post‐operative morbidity, length of hospitalization and operation duration. A subgroup analysis for the same outcomes was performed for elderly patients.ResultsOf the 217 patients, 88 were operated within 72 h of symptom onset while 129 were operated beyond 72 h. Twenty‐six patients received ELC after 7 days. There was no occurrence of bile duct injury. There was no statistical difference in conversion rates, wound infections and post‐operative collections. Patients receiving ELC beyond 72 h had longer duration of operation (125.4 versus 116 min,P= 0.035) and length of hospitalization (4.59 versus 3.09 days,P= 0.001) without increase in morbidity. Patients older than 75 years had a higher incidence of post‐operative collection (P < 0.001).ConclusionPatients with AC undergoing ELC by a dedicated acute surgical unit can have good outcomes even beyond 72 h of symptom onset. Meticulous haemostasis should be performed for the elderly subgroup of patients.
Mothers' perspectives of the experience and impact of caring for their child with a life‐limiting neurodevelopmental disability
Authors: Courtney E. , Kiernan G. , Guerin S. , Ryan K. , McQuillan R. 
Published: September 2019

AbstractBackgroundThis study explored mothers' perspectives of the experiences and impact on themselves and their family when their child has a life‐limiting neurodevelopmental disability.MethodsTwelve mothers were interviewed and topics included mothers' experiences of caring, the impact on themselves and their family of care provision, and the management of day‐to‐day life. Data were analysed using thematic analysis.ResultsFour themes were identified. “Starting Out” relates to mothers' experiences of the birth of their child and the aftermath. “Keeping the Show on the Road” describes the strategies families employ to manage life day to day and the resources they use. “Shouldering the Burden” describes the range of physical, psychological, and social consequences of the situation for mothers and the family. “The Bigger Picture” relates to the world outside the family and how this is navigated.ConclusionsFindings suggest mothers' overall experiences are characterized by a constant struggle, with evidence of negative impacts on family life, though there is also evidence of resilience and coping. Implications regarding the provision of services are discussed.
Inferring Mental States From Dynamic Faces in Adolescents With Autism Spectrum Disorder: Insights From Eye Tracking
Authors: Back Elisa 
Published: September 2019

There is mixed evidence concerning whether individuals with autism spectrum disorder (ASD) can infer mental states from the eyes. This study aims to elucidate whether they use less efficient strategies. Sixteen adolescents with ASD (11–16 year olds) were compared to a chronological age‐ and IQ‐matched sample of 16 typically developing (TD) adolescents. Eight mental states were presented as full dynamic faces and in conditions altering the presence of expressive dynamic information from the eyes and mouth. Bayes factors revealed that adolescents with ASD had similar accuracy, response times (less conclusive), and fixations to TD adolescents. Findings imply that adolescents with ASD spontaneously fixate on the eyes, and not all individuals with ASD have difficulties inferring mental states from faces.
Long bone failure after intraosseous regional perfusion
Authors: Slack‐Smith V. , Davies H. M. S. , Hilbert B. J. 
Published: September 2019

SummaryA 5‐year‐old Australian Stock Horse gelding was initially referred to the Charles Sturt University Veterinary Clinical Centre (CSUVCC) for assessment of a penetrating laceration over the medial splint bone (second metacarpal bone) of the left foreleg. Clinical examination failed to reveal a communication with a synovial structure, but radiographs showed a palisading bone reaction on the proximal aspect of the medial splint bone which was thought to be a characteristic of infection. Soft tissue swelling precluded access to a peripheral vein, so a decision was made to use intraosseous regional limb perfusion. This was achieved through an access portal in the lateral diaphysis of the third metacarpal bone (McIII). Subsequently, the horse developed lameness and further investigation revealed a nondisplaced longitudinal fracture of McIII propagating from the intraosseous regional perfusion access portal.
A new weight function for one‐dimensional subsurface cracks under general loading
Authors: Abdoli Ali , Khezri Jamal , Alizadeh Kaklar Javad 
Published: September 2019

AbstractIn the present study, weight functions (WFs) of a subsurface crack were derived by proposing a new general form for approximate one‐dimensional WF. The WFs coefficients were considered as a function of crack length to depth ratio and were obtained using reference stress intensity factors (SIFs) of 16 cracks under uniform, linear, and parabolic normal and shearing loadings. The verification was performed by comparison of the straight and coupled SIFs calculated by WF and finite element modelling under some complicated loadings. In conclusion, the WFs can be simply and effectively employed for evaluating the cracks under any complex stress distributions.
A changed post‐flood management strategy enables the culture‐based fishery of the Liangzi Lake, Yangtze River Basin, China, to remain economically and environmentally viable
Authors: Wang Qidong , Li Zhongjie , Lin Mingli , Ye Shaowe , Li Wei , Guo Chuanbo , Huang Geng , Yuan Jing , Liu Jiashou , De Silva Sena S. 
Published: September 2019

AbstractThe culture‐based fishery of Liangzi Lake, Yangtze River Basin, established in 1992, yielded 2,652 t/year (±167) between 2005 and 2015, dominated by stocked carps [Hypophthalmichthys molitrix (Val.) and Hypophthalmichthys nobilis (Richardson)] and mitten crab Eriocheir sinensis (Milne Edwards), accounting for 53% and 23% of the production and 20% and 52% in value, respectively. The lake had a macrophyte cover dominated by Vallisneria natans (Lour.) Hara with a cumulative biomass of 10,647 g/m2 that disappeared after a major flood in 2010 and changed its ecology. Management changes in stocking strategies introduced in the post‐flood period enabled the culture‐based fishery to maintain viability and sustainability to combat the major ecological change in the lake. The stocked species contributed significantly to nutrient removal of 24.71 ± 5.12 t/yr and 6.29 ± 0.87 t/yr of total nitrogen and total phosphorus, respectively.
Recognition of the microbiota by Nod2 contributes to the oral adjuvant activity of cholera toxin through the induction of interleukin‐1β
Authors: Kim Donghyun , Kim Yu‐Mi , Kim Wan‐Uk , Park Jong‐Hwan , Núñez Gabriel , Seo Sang‐Uk 
Published: September 2019

SummaryThe role of symbiotic bacteria in the development of antigen‐specific immunity remains poorly understood. Previous studies showed that sensing of symbiotic bacteria by nucleotide‐binding oligomerization domain‐containing protein 2 (Nod2) regulates antibody responses in response to nasal immunization with antigen and cholera toxin (CT). In this study, we examined the role of the microbiota in the adjuvant activity of CT induced after oral immunization with antigen. Germ‐free (GF) mice showed impaired production of antibody responses and T‐cell‐specific cytokines after oral immunization when compared with that observed in conventionally raised mice. Similar to GF mice, Nod2‐deficient mice showed reduced humoral responses upon oral immunization with antigen and CT. Treatment with CT enhanced the production of interleukin‐1β (IL‐1β), but not tumor necrosis factor‐α or IL‐12p40, induced by stimulation of dendritic cells with muramyl dipeptide, the Nod2 ligand. Mechanistically, the enhanced production of IL‐1β induced by muramyl dipeptide and CT stimulation required Nod2 and was mediated by both increased synthesis of pro‐IL‐1β and caspase‐1 activation. Furthermore, antigen‐specific antibody and cytokine responses induced by CT were impaired in orally immunized IL‐1β‐deficient mice. Collectively, our results indicate that Nod2 stimulation by symbiotic bacteria contributes to optimal CT‐mediated antigen‐specific oral vaccination through the induction of IL‐1β production.
In vitro responses of multiple cytokines to purified protein derivative in healthy and naturally Mycobacterium tuberculosis‐infected rhesus monkeys (Macaca mulatta)
Authors: Min Fangui , Wang Jing , Huang Shuwu , Pan Jinchun , Zhang Lan 
Published: September 2019

AbstractBackgroundAs the widely used biomarker of whole‐blood stimulation assays for tuberculosis diagnosis, the release of IFN‐γ might be affected by multiple factors, such as immunosuppression and some infectious agents. Here, we evaluated additional cytokines as diagnostic biomarkers.MethodsForty‐three cytokines were measured by Luminex xMAP technologies in 30 healthy and 10 naturally Mycobacterium tuberculosis (MTB)‐infected rhesus monkeys pre‐ and post‐stimulation by purified protein derivative (PPD).ResultsAfter stimulation, production of 23 and 38 cytokines was markedly increased in healthy and MTB‐infected macaques, respectively. A comparison of the stimulation index (SI) between MTB infections and healthy macaques showed that the SIs of 32 cytokines in MTB‐infected macaques were significantly higher than those in healthy macaques. Pooling the results, eight cytokines were suggested as ideal biomarkers for a whole‐blood stimulation assay for MTB diagnosis.ConclusionPPD could induce multiple cytokine responses in either healthy or MTB‐infected monkeys, and eight cytokines had reliable predictive capacity as diagnostic biomarkers of MTB infection.
Spontaneous resolution of prenatally diagnosed isolated pleural effusion: An unusual early sign of a newborn disease
Authors: Kajdy Anna , Materny Anna , Modzelewski Jan , Baszczeska Jolanta , Rabijewski Michał , Szymkiewicz‐Dangel Joanna 
Published: September 2019

AbstractWe present a case report of a fetus with a diagnosed pleural effusion in the first trimester on nuchal translucency scan. The effusion resolved spontaneously by 17 weeks of pregnancy. Toxoplasmosis, rubella, cytomegalovirus, herpes simplex (TORCH) – negative. Array comparative genomic hybridization (aCGH) – normal. Serial Doppler scans normal – no prenatal signs of anemia. Maternal antibodies against red cell antigens – negative. Delivery at term by cesarean section because of macrosomia. Neonate suffered from prolonged jaundice. At 3 weeks of life diagnosed with hereditary spherocytosis. Literature review shows that this may be the first connection between this disease and prenatal life.
Methadone versus morphine treatment outcomes in neonatal abstinence syndrome: A meta‐analysis
Authors: Xiao Feifan , Yan Kai , Zhou Wenhao 
Published: September 2019

AimTo determine whether morphine has better outcomes for neonatal abstinence syndrome treatment than methadone.MethodsStudies published before 1 January 2019 were identified using the PubMed, Web of Science, Scopus, Cochrane Library and ClinicalTrials.gov databases. The Cochrane Collaboration Risk of Bias Tool was used to assess the risk of bias for randomised clinical trials. In addition, the risk of bias for non‐randomised studies was evaluated by a non‐randomised studies of interventions tool.ResultsWe identified 1020 published studies, and 5 were included in the final analysis. Results showed no significant difference in opioid treatment days (standardised mean difference (SMD) = 0.32, 95% confidence interval (CI) = −0.16, 0.80), length of hospital stay (SMD = −0.33, 95% CI = −1.21, 0.56) and duration of treatment (SMD = −0.83 95% CI = −2.09, 0.43) between morphine or methadone treatment.ConclusionsOur meta‐analysis of current evidence demonstrated that neonatal abstinence syndrome treatment with morphine was not associated with better outcomes in infants compared with methadone treatment.
Recommendations on terminology and experimental best practice associated with plant nitric oxide research
Authors: Gupta Kapuganti Jagadis , Hancock John T. , Petrivalsky Marek , Kolbert Zsuzsanna , Lindermayr Christian , Durner Jorg , Barroso Juan B. , Palma José M. , Brouquisse Renaud , Wendehenne David , Corpas Francisco J. , Loake Gary J. 
Published: September 2019

SummaryNitric oxide (NO) emerged as a key signal molecule in plants. During the last two decades impressive progress has been made in plant NO research. This small, redox‐active molecule is now known to play an important role in plant immunity, stress responses, environmental interactions, plant growth and development. To more accurately and robustly establish the full spectrum of NO bioactivity in plants, it will be essential to apply methodological best practice. In addition, there are some instances of conflicting nomenclature within the field, which would benefit from standardization. In this context, we attempt to provide some helpful guidance for best practice associated with NO research and also suggestions for the cognate terminology.
Study of Temperature Effects on Economic Performance of CO2 Enhanced Shale Gas Recovery
Authors: Sui Hao , Pei Peng , Su Qian , Ding Weige , Mao Ruiyong 
Published: September 2019

Abstract
CO2 displacement has been proposed to enhance shale gas recovery and unlock a big potential market for CO2 beneficial utilization. Theoretically, gas adsorption is inversely related to the temperature, so gas can be desorbed by elevating the temperature. This paper investigates the economic performance of enhancing shale gas recovery by injecting CO2 at high temperatures through displacement as well as desorption by rising temperatures. Influences of operation temperature and injection pressure were studied for three potential shale plays in China. Study results show that both factors exerted obvious impacts, and CO2 procurement was the largest cost component. It is found that the net revenue was not always proportional to the operation temperature, but more controlled by the injection–production ratio. This is because of the different temperature impacts to the various patterns of adsorbed CH4 and CO2 contents. Consequently, in some cases, more CO2 is needed to displace CH4 when operation temperature is raised, resulting a higher cost. The modeling results demonstrate that based on the adsorption characters of reservoirs, the productivity and profitability of CO2 enhanced gas recovery can be further improved by choosing appropriate operation temperatures.