bluuebunny/crossref_metadata_2025_split huggingface dataset:
Question–response–evaluation sequences in the home interactions of a bilingual child with autism spectrum disorder
Authors: Bottema‐Beutel Kristen , Oliveira Gabrielle , Cohen Shana R. , Miguel Jessica 
Published: November 2019

AbstractBackgroundPrior research has described the prevalence and utility of questions in children's language learning environment. However, there has been little empirical investigation of the interaction sequences that ensue following caregiver questions. Understanding these interactions may be especially important for children with autism spectrum disorder (ASD), who may have difficulty engaging in reciprocal interactions. Question–response–evaluation sequences (QRE) are a particular type of interaction sequence launched by questions that have been examined primarily in classroom contexts. Less research has been devoted to understanding how caregivers and children with ASD leverage this interactional format in the context of home interactions.AimsWe focus on QRE sequences within interactions between a 5‐year‐old bilingual child with ASD and his parents. In these sequences, the adult poses known‐answer questions, the child responds and the adult evaluates the response. QRE sequences are primarily structured by the questioner (i.e., the parents in our context), and we examine the interactive work done by parents to initiate, maintain and close these sequences. We also examine the child's contributions to these sequences.Methods & ProceduresWe applied conversation analysis (CA) to video recordings of home routines, such as play, book‐reading and schoolwork. Videos were fully transcribed using CA conventions, and 55 QRE segments were isolated from the data corpus for further analysis.Outcomes & ResultsQ‐word questions (i.e., where, what, why, when, how questions) were the most prevalent question format, and repetition of the child's response was the most prevalent form of evaluation. We found that QRE sequences were embedded within a variety of action trajectories that extend beyond pedagogical functions. These included repairing a prior utterance, extending collaborative play routines and engaging in topically connected labelling rituals.Conclusions & ImplicationsQRE sequences appeared to strike a balance in terms of the level of constraint they placed on the child's contributions to interactions, and the affordances they provide for participating in and progressing through interactions. This study can help clinicians understand the types of interactions that can be pursued with QRE sequences in their work with children with ASD. The findings may also aid intervention researchers’ efforts to leverage caregivers’ existing strengths for adapting their interactional overtures to maximize children's engagement. Finally, this study provides an illustration of caregiver–child interactions in a population that is currently under‐represented in the literature.
Continuous subcutaneous insulin infusion reduces the risk of postoperative infection
Authors: Mou Yune , Ma Delin , Zhang Jianhua , Tao Jing , He Wentao , Li Wenjun , Mu Yiming , Yu Xuefeng 
Published: November 2019

AbstractBackgroundPerioperative hyperglycemia was associated with postoperative infection, and proper management of perioperative glucose has become critical in improving the prognosis of patients.MethodsA total of 1015 diabetic patients who underwent surgery and received insulin treatment for their hyperglycemia in our hospital were retrospectively reviewed. According to propensity matching, we obtained 253 pairs of patients from the group which received continuous subcutaneous insulin infusion (CSII) therapy (CSII group) and the group which received insulin injection therapy (non‐CSII group). Perioperative glucose levels and corresponding outcomes were compared between the two groups.ResultsCompared with the non‐CSII group, the CSII group had lower fasting and mean glucose levels, lower incidence of fever (operation day: 18.6% vs 10.2%; P = .014; first postoperative day: 55.1% vs 34.7%; P < .001), a positive rate of postoperative secretion culture (6.3% vs 1.2%; P = .004), and a shorter time of antibiotics use (total antibiotics use: P = .002; postoperative antibiotics use: P < .001) and hospital stays (P < .001). However, there was no difference in the total medical expenditure between the two groups (P = .499). Further analysis showed that CSII therapy was superior to multiple daily insulin injection (MDI) therapy in its effect on infection and other postoperative outcomes when 64 pairs of patients from the CSII group and MDI group were compared.ConclusionsCSII therapy provides better perioperative glucose control and a lower risk of postoperative infection without increasing the total medical expenditure.
pime: A package for discovery of novel differences among microbial communities
Authors: Roesch Luiz Fernando W. , Dobbler Priscila T. , Pylro Victor S. , Kolaczkowski Bryan , Drew Jennifer C. , Triplett Eric W. 
Published: November 2019

AbstractThe data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are lacking. pime (Prevalence Interval for Microbiome Evaluation) was designed to remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of pime were compared against existing methods and tested using 16S rRNA independent data sets. pime filters microbial taxa not shared in a per treatment prevalence interval started at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees were calculated to predict the likelihood of detecting differences in treatments. The best prevalence‐filtered data set was user‐selected by choosing the prevalence interval that kept a large portion of the 16S rRNA sequences in the data set while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence‐filtered data sets, an error detection step based was also included. A pime reanalysis of published data sets uncovered other expected microbial associations than previously reported, which may be masked when only relative abundance was considered.
Copy number variation in plasma as a tool for lung cancer prediction using Extreme Gradient Boosting (XGBoost) classifier
Authors: Yu Daping , Liu Zhidong , Su Chongyu , Han Yi , Duan XinChun , Zhang Rui , Liu Xiaoshuang , Yang Yang , Xu Shaofa 
Published: November 2019

AbstractBackgroundThe main cause of cancer death is lung cancer (LC) which usually presents at an advanced stage, but its early detection would increase the benefits of treatment. Blood is particularly favored in clinical research given the possibility of using it for relatively noninvasive analyses. Copy number variation (CNV) is a common genetic change in tumor genomes, and many studies have indicated that CNV‐derived cell‐free DNA (cfDNA) from plasma could be feasible as a biomarker for cancer diagnosis.MethodsIn this study, we determined the possibility of using chromosomal arm‐level CNV from cfDNA as a biomarker for lung cancer diagnosis in a small cohort of 40 patients and 41 healthy controls. Arm‐level CNV distributions were analyzed based on z score, and the machine‐learning algorithm Extreme Gradient Boosting (XGBoost) was applied for cancer prediction.ResultsThe results showed that amplifications tended to emerge on chromosomes 3q, 8q, 12p, and 7q. Deletions were frequently detected on chromosomes 22q, 3p, 5q, 16q, 10q, and 15q. Upon applying a trained XGBoost classifier, specificity and sensitivity of 100% were finally achieved in the test group (12 patients and 13 healthy controls). In addition, five‐fold cross‐validation proved the stability of the model. Finally, our results suggested that the integration of four arm‐level CNVs and the concentration of cfDNA into the trained XGBoost classifier provides a potential method for detecting lung cancer.ConclusionOur results suggested that the integration of four arm‐level CNVs and the concentration from of cfDNA integrated withinto the trained XGBoost classifier could become provides a potentially method for detecting lung cancer detection.Key pointsSignificant findings of the study:
Healthy individuals have different arm‐level CNV profiles from cancer patients.
Amplifications tend to emerge on chromosome 3q, 8q, 12p, 7q and deletions tend to emerge on chromosome 22q, 3p, 5q, 16q, 10q, 15q.

What this study adds:

CfDNA concentration, arm 10q, 3q, 8q, 3p, and 22q are key features for prediction.
Trained XGBoost classifier is a potential method for lung cancer detection.
Genomic regions influencing intramuscular fat in divergently selected rabbit lines
Authors: Sosa‐Madrid Bolívar S. , Hernández Pilar , Blasco Agustín , Haley Chris S. , Fontanesi Luca , Santacreu María A. , Pena Romi N. , Navarro Pau , Ibáñez‐Escriche Noelia 
Published: November 2019

SummaryIntramuscular fat (IMF) is one of the main meat quality traits for breeding programmes in livestock species. The main objective of this study was to identify genomic regions associated with IMF content comparing two rabbit populations divergently selected for this trait, and to generate a list of putative candidate genes. Animals were genotyped using the Affymetrix Axiom OrcunSNP Array (200k). After quality control, the data involved 477 animals and 93 540 SNPs. Two methods were used in this research: single marker regressions with the data adjusted by genomic relatedness, and a Bayesian multiple marker regression. Associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU8 and OCU13. The highest value for the percentage of the genomic variance explained by a genomic region was found in two consecutive genomic windows on OCU8 (7.34%). Genes in the associated regions of OCU1 and OCU8 presented biological functions related to the control of adipose cell function, lipid binding, transportation and localisation (APOLD1, PLBD1, PDE6H, GPRC5D and GPRC5A) and lipid metabolic processes (MTMR2). The EWSR1 gene, underlying the OCU13 region, is linked to the development of brown adipocytes. The findings suggest that there is a large component of polygenic effect behind the differences in IMF content in these two lines, as the variance explained by most of the windows was low. The genomic regions of OCU1, OCU8 and OCU13 revealed novel candidate genes. Further studies would be needed to validate the associations and explore their possible application in selection programmes.
Aromatase inhibitors and selective estrogen receptor modulators: Unconventional therapies for functional hypogonadism?
Authors: Awouters Marijke , Vanderschueren Dirk , Antonio Leen 
Published: November 2019

AbstractIntroductionFunctional hypogonadism increases in prevalence due to aging as well as an overall increase of obesity. Aromatase inhibitors (AIs) and selective estrogen receptor modulators (SERMs) could be an alternative for testosterone replacement therapy (TRT), but have not yet been established as common clinical practice.MethodsWe conducted a thorough search of the literature published between 2009 and 2018. Only RCTs published in English were included. We assessed the impact of AIs and SERMs on gonadal steroids, sexual function and semen parameters, body composition and glucose homeostasis, physical function, bone mineral density (BMD), anemia, as well as potential adverse effects.ResultsTwelve RCTs were included, with a total number of 645 patients. A total of 145 men were included in RCTs comparing AIs versus placebo or TRT and 476 men in RCTs with SERMs versus placebo or TRT. One RCT compared AIs versus SERMs in 24 men. Inclusion criteria were heterogenic. Most studies only included a small number of patients (range 11‐256) and follow‐up time was relatively short (6 weeks to 12 months). AIs as well as SERMs increased serum testosterone levels. Overall, there was no effect on sexual symptoms nor on semen parameters. Following aromatase inhibition, only minimal improvement of body composition and physical function was observed in some of the trials, but spinal BMD decreased. SERMs only induced a small improvement in body composition. The effect of SERMs on physical function and on BMD was not assessed. No major adverse effects occurred.ConclusionAIs are not recommended as treatment for functional hypogonadism because of insufficient efficacy as well as a decrease in BMD. SERMs might be an alternative for TRT, but more research is needed to evaluate their effect on hypogonadal signs and symptoms, as well as on their long‐term safety profile.
RETURNS TO DEBT AND EQUITY IN FARM PRODUCER ORGANIZATIONS
Authors: GRASHUIS Jasper 
Published: November 2019

ABSTRACTWhile the capital structure irrelevance proposition is the point of departure in corporate finance, it is unknown if debt‐or‐equity decisions matter to farm producer organizations. To inform decisions of capital acquisition, a panel study is conducted to estimate the relationships of different types of debt (current, long‐term) and equity (allocated, unallocated) to the financial performance of 707 farm producer organizations in the United States during the 2005–2011 period. Using 3,120 observations, the panel analysis indicates net sales in period t is increased by $1.97, $9.59, and $4.01 with an addition of $1 in current debt, allocated equity, or unallocated equity in period t‐1. Furthermore, the magnitude of the positive relationship of an additional dollar of allocated (unallocated) equity to net income is estimated at $0.32 ($0.14). We thus reject the notion managers and directors of farm producer organizations should decide to use debt or equity with a coin toss.
Macrophages reprogram after ischemic stroke and promote efferocytosis and inflammation resolution in the mouse brain
Authors: Zhang Wenting , Zhao Jingyan , Wang Rongrong , Jiang Ming , Ye Qing , Smith Amanda D. , Chen Jun , Shi Yejie 
Published: November 2019

AbstractAimsBlood‐borne monocytes/macrophages infiltrate the brain in massive numbers after ischemic stroke, but their impact on poststroke brain injury and recovery remains elusive. This study examined the transcriptomic changes in monocytes/macrophages after ischemic stroke and the functional implications of these changes, particularly with regards to the contribution of these cells to the phagocytic clearance of dead/dying cells (efferocytosis) in the poststroke brain.MethodsWe performed whole‐genome RNA sequencing on the monocyte/macrophage population sorted from mouse brain and peripheral blood 5 days after permanent focal cerebral ischemia. In addition, the spatial and temporal profiles of macrophage efferocytosis were examined in vivo by immunohistochemistry 3‐7 days after brain ischemia.ResultsRobust transcriptomic changes occurred in monocytes/macrophages upon infiltrating the poststroke brain. Functional enrichment analysis revealed a transcriptome of brain macrophages that strongly favored efferocytic activity. A large number of efferocytosis‐related genes were upregulated in brain macrophages, the products of which are essential components involved in various steps of efferocytosis, such as chemotaxis, recognition of dead cells, engulfment, and processing of phagosomes. The efferocytic activity of brain macrophages were verified by immunohistochemistry, wherein Iba1‐labeled microglia/macrophages effectively cleared apoptotic neurons in the infarct during the subacute stage after brain ischemia. We also identified PPARγ and STAT6 as potential upstream regulators that shaped this proefferocytic and inflammation‐resolving transcriptome of macrophages in the poststroke brain.ConclusionMacrophages play a crucial role in the phagocytic clearance of dead neurons after ischemic stroke and promote the resolution of inflammation in the brain. Molecular therapies that enhance macrophage efferocytic capability may be promising treatments for ischemic stroke by facilitating inflammation resolution, brain repair, and recovery of neurological functions.
The impact of conductive hearing loss on balance
Authors: Horowitz Gilad , Ungar Omer J. , Levit Yael , Himmelfarb Mordechai , Handzel Ophir 
Published: November 2019

AbstractBackgroundBalance is a complex process involving the coordinated activities of multiple sensory, motor and biomechanical components. Balance function may be disturbed in subjects suffering from hearing loss but the impairment has been attributed to the pathology underlying the hearing loss.AimThe purpose of the study was to investigate the possible interference of simulated conductive hearing loss with the ability to maintain postural balance.MethodsTwenty normal‐hearing subjects, 20‐30 years old, underwent the computerised dynamic posturography test battery before and after plugging their external ear canals with earplugs, thus simulating a 40dB conductive hearing loss.ResultsEighteen females and two males were tested before and after plugging their ear canals. Average CHL was 40 ± 4.9dB. The composite equilibrium score was significantly diminished after plugging the ears with an average sway score of 73.5% (P < .05, T = 2.27). The fourth test condition was specifically affected with an average sway score of 72.85% with earplugs (P < .05, T = 2.37).ConclusionsConductive hearing loss has a negative effect on balance. This can be theoretically explained by the association between hearing loss and saccular dysfunction.
Long‐term follow‐up of patients undergoing standardized bicycle exercise stress testing: new recommendations for grading of exercise capacity are clinically relevant
Authors: Lindow Thomas , Brudin Lars , Elmberg Viktor , Ekström Magnus 
Published: November 2019

SummaryIntroductionA new grading of exercise capacity during bicycle stress testing has been proposed in Sweden based on the new reference material (‘the Kalmar material’), which has not been validated. We aimed to examine the prognostic information of the new grading of exercise capacity during exercise stress testing.MethodsData on all bicycle exercise tests performed at the Department of Clinical Physiology in Kalmar between May 2005 and October 2016 were cross‐linked with the Causes of Death Register (until 30 April 2019) and the National Patient Register (until 12 December 2017). Exercise capacity was graded based on predicted exercise capacity: ≥120% (good), 75 to <120% (normal), 70 to <75% (mildly reduced), 50 to <70% (moderately reduced) and <50% (severely reduced). Associations with all‐cause mortality, cardiovascular mortality and hospitalization for ischaemic heart disease (IHD) and heart failure were analysed using Cox regression.ResultsA total of 13 887 patients were followed a median of 7·7 years (interquartile range 5·0–10·8); 1809 patients died (546 from cardiovascular disease). Compared to normal exercise capacity, reduction of exercise capacity was strongly associated with increased all‐cause mortality [(hazard ratio; 95% confidence interval): mild (3·0; 2·6–3·5); moderate (4·4; 3·9–4·9); and severe reduction (8·5; 7·2–10·0)]. Reduced exercise capacity was also associated with increased risks of cardiovascular hospitalization and mortality.ConclusionReduced exercise capacity is associated with increased all‐cause and cardiovascular mortality, as well as increased risk of future IHD and heart failure diagnosis and hospitalization. In patients with reduced exercise capacity, mortality is progressively increased with worsening grade of exercise capacity.
Cardiovascular changes in patients with mild‐to‐moderate chronic kidney disease compared with healthy subjects: a 5‐year follow‐up study
Authors: Asp Anna M. , Wallquist Carin , Rickenlund Anette , Hylander Britta , Jacobson Stefan H. , Caidahl Kenneth , Eriksson Maria J. 
Published: November 2019

SummaryBackgroundThere is limited knowledge about how cardiovascular parameters change over time in patients with mild‐to‐moderate chronic kidney disease (CKD). We studied several cardiovascular biomarkers over a 5‐year period in patients with mild‐to‐moderate CKD and in healthy controls.MethodsFifty‐four patients with CKD stages 2–3 and 54 controls were included. The CKD patients were closely monitored and well controlled for hypertension and other cardiovascular risk factors. Ambulatory blood pressure (BP) monitoring, ankle–brachial index (ABI), carotid and cardiac ultrasound (including measurement of the left ventricular mass index (LVMI)), and biochemical analyses were evaluated.ResultsRenal function decreased in both groups, with no significant difference in the change over time. In the CKD patients, none of the BP variables increased over time, but in the controls, average 24‐h and daytime systolic BP increased significantly. ABI increased slightly in the CKD patients (P<0·001), but not in the controls (P = 0·963), and phosphate had a significant positive effect on ABI. Although in the CKD patients, there was no significant increase over time in common carotid artery diameter (P = 0·274), there was a small but significant increase in the controls (P = 0·001). LVMI increased significantly over time in both groups.ConclusionsIn our study of patients with mild‐to‐moderate CKD, the progression of cardiovascular changes over time was relatively slow. Good BP control and treatment of other risk factors may have contributed to slow the progress of cardiovascular involvement, which emphasizes the importance of dedicated care in this population.
Histopathology‐guided mass spectrometry differentiates benign nevi from malignant melanoma
Authors: Lazova Rossitza , Smoot Katy , Anderson Heather , Powell Matthew J. , Rosenberg Arlene S. , Rongioletti Franco , Pilloni Luca , D'Hallewin Sara , Gueorguieva Ralitza , Tantcheva‐Poór Iliana , Obadofin Omobolade , Camacho Christine , Hsi Andy , Kluger Harriet H. , Fadare Oluwole , Seeley Erin H. 
Published: November 2019

AbstractPurposeDistinguishing benign nevi from malignant melanoma using current histopathological criteria may be very challenging and is one the most difficult areas in dermatopathology. The goal of this study was to identify proteomic differences, which would more reliably differentiate between benign and malignant melanocytic lesions.MethodsWe performed histolpathology ‐ guided mass spectrometry (HGMS) profiling analysis on formalin‐fixed, paraffin embedded tissue samples to identify differences at the proteomic level between different types of benign nevi and melanomas. A total of 756 cases, of which 357 cases of melanoma and 399 benign nevi, were included in the study. The specimens originated from both biopsies (376 samples) and tissue microarray (TMA) cores (380 samples). After obtaining mass spectra from each sample, classification models were built using a training set of biopsy specimens from 111 nevi and 100 melanomas. The classification algorithm developed on the training data set was validated on an independent set of 288 nevi and 257 melanomas from both biopsies and TMA cores.ResultsIn the melanoma cohort, 239/257 (93%) cases classified correctly in the validation set, 3/257 (1.2%) classified incorrectly, and 15/257 (5.8%) classified as indeterminate. In the cohort of nevi, 282/288 (98%) cases classified correctly, 1/288 (0.3%) classified incorrectly, and 5/288 (1.7%) were indeterminate. HGMS showed a sensitivity of 98.76% and specificity of 99.65% in determining benign vs malignant.ConclusionHGMS proteomic analysis is an objective and reliable test with minimal tissue requirements, which can be a helpful ancillary test in the diagnosis of challenging melanocytic lesions.