bluuebunny/crossref_metadata_2025_split huggingface dataset:
M Statistic Commands: Interpoint Distance Distribution Analysis
Authors: Tebaldi Pietro , Bonetti Marco , Pagano Marcello 
Published: November 2018

We implement the commands mstat and mtest to perform inference based on the M statistic, a statistic that can be used to compare the interpoint distance distribution across groups of observations. The analyses are based on the study of the interpoint distances between n points in a k-dimensional setting to produce a one-dimensional real-valued test statistic. The locations are distributed in a region of the plane. When we consider all ( n2) interpoint distances, the dependencies among them are difficult to express analytically, but their distribution is informative, and the M statistic can be built to summarize one aspect of this information. The two commands can be used on a wide class of data sets to test the null hypothesis that two groups have the same (spatial) distribution. mstat and mtest return the exact M test statistic. Moreover, mtest executes a Monte Carlo–type permutation test, which returns the empirical p-value together with its confidence interval. This is the command to use in most situations, because the convergence of M to its asymptotic chi-squared distribution is slow. Both commands can be used to obtain graphical output of the empirical density function of the interpoint distance distributions in the two groups and the two-dimensional map of the n observations in the plane. The descriptions of the commands are accompanied by examples of applications with real and simulated data. We run the test on the Alt and Vach grave site dataset (Manjourides and Pagano, forthcoming, Statistics in Medicine) and reject the null hypothesis, in contradiction to other published analyses. We also show how to adapt the techniques to discrete datasets with more than one unit in each location. Finally, we report an extensive application on breast cancer data in Massachusetts; in the application, we show the compatibility of the M commands with Pisati's spmap package.
Goodness-of-Fit Tests for Categorical Data
Authors: Bellocco Rino , Algeri Sara 
Published: November 2018

A significant aspect of data modeling with categorical predictors is the definition of a saturated model. In fact, there are different ways of specifying it—the casewise, the contingency table, and the collapsing approaches—and they strictly depend on the unit of analysis considered. The analytical units of reference could be the subjects or, alternatively, groups of subjects that have the same covariate pattern. In the first case, the goal is to predict the probability of success (failure) for each individual; in the second case, the goal is to predict the proportion of successes (failures) in each group. The analytical unit adopted does not affect the estimation process; however, it does affect the definition of a saturated model. Consequently, measures and tests of goodness of fit can lead to different results and interpretations. Thus one must carefully consider which approach to choose. In this article, we focus on the deviance test for logistic regression models. However, the results and the conclusions are easily applicable to other linear models involving categorical regressors. We show how Stata 12.1 performs when implementing goodness of fit. In this situation, it is important to clarify which one of the three approaches is implemented as default. Furthermore, a prominent role is played by the shape of the dataset considered (individual format or events–trials format) in accordance with the analytical unit choice. In fact, the same procedure applied to different data structures leads to different approaches to a saturated model. Thus one must attend to practical and theoretical statistical issues to avoid inappropriate analyses.
Speaking Stata: Logarithmic Binning and Labeling
Authors: Cox Nicholas J. 
Published: November 2018

Histograms on logarithmic scale cannot be produced by an option like xscale(log). You need first to transform the variable concerned with a logarithm function. That raises small choices: how to select bin start, bin width, and informative axis labels and titles? Problems and solutions are discussed here in detail. In contrast, for logarithmic scales on other graphs, options xscale(log) and yscale(log) may do most of what you want. But there is usually still scope for “nicer” axis labels than are given by default and indeed scope for differing tastes on what “nice” means. This column introduces the niceloglabels command for helping (even automating) label choice. Historical notes and references are sprinkled throughout.
Arteriovenous fistulas ipsilateral to internal jugular catheters for hemodialysis have decreased patency rates
Authors: Ozpak Berkan , Yilmaz Yeliz 
Published: November 2018

Purpose This study aimed to evaluate the effects of hemodialysis catheters on the survival of subsequent arteriovenous fistulas, according to the relative localization to the catheters. Methods A total of 201 patients who initiated dialysis therapy using a hemodialysis catheter were eligible for this retrospective study. Arteriovenous fistulas were created on the nondominant upper extremity after the placement of hemodialysis catheters. The catheters were removed after four consecutive successful dialyses via arteriovenous fistulas. The effective factors on arteriovenous fistula failure were determined in and the prognostic factors for survival were modeled by regression analysis. Results The relative placement of catheters as ipsi- or contralateral was found to significantly affect the survival of the arteriovenous fistulas. The overall survival was significantly longer in the contralateral arteriovenous fistula group (778.7 ± 28.8 vs. 247.3 ± 26.1 days; p < 0.001). The independent predictors of arteriovenous fistula survival were found to be relative side of arteriovenous fistula and hemodialysis catheter, age, and the presence of hypertension in multivariate analyses. Conclusion This study showed that ipsilateral localization of the catheters and arteriovenous fistulas negatively affect the cumulative arteriovenous fistula survival. Therefore, to improve vascular access survival, side of catheters or arteriovenous fistulas should always be considered.
Minimum standards of clinical practice for physiotherapists working in critical care settings in the United Kingdom: A modified Delphi technique
Authors: Twose Paul , Jones Una , Cornell Gareth 
Published: November 2018

Introduction Across the United Kingdom, physiotherapy for critical care patients is provided 24 h a day, 7 days per week. There is a national drive to standardise the knowledge and skills of physiotherapists which will support training and reduce variability in clinical practice. Methods A modified Delphi technique using a questionnaire was used. The questionnaire, originally containing 214 items, was completed over three rounds. Items with no consensus were included in later rounds along with any additional items suggested. Results In all, 114 physiotherapists from across the United Kingdom participated in the first round, with 102 and 92 completing rounds 2 and 3, respectively. In total, 224 items were included: 107 were deemed essential as a minimum standard of clinical practice; 83 were not essential and consensus was not reached for 34 items. Analysis/Conclusion This study identified 107 items of knowledge and skills that are essential as a minimum standard for clinical practice by physiotherapists working in United Kingdom critical care units.
Origins of Intraindividual Genetic Variation in Human Fetuses
Authors: Bazrgar Masood , Gourabi Hamid , Karimpour-Fard Anis , Boroujeni Parnaz Borjian , Anisi Khadije , Movaghar Bahar , Valojerdi Mojtaba Rezazadeh 
Published: November 2018

Background:Intraindividual copy number variation (CNV) origin is largely unknown. They might be due to aging and/or common genome instability at the preimplantation stage while contribution of preimplantation in human intraindividual CNVs occurrence is unknown. To address this question, we investigated mosaicism and its origin in the fetuses of natural conception.Methods:We studied normal fetuses following therapeutic abortion due to maternal indications. We analyzed the genome of 22 tissues of each fetus by array comparative genomic hybridization for intraindividual CNVs. Each tissue was studied in 2 microarray experiments; the reciprocal aberrations larger than 40 Kb, identified by comparing tissues of each fetus, were subsequently validated using quantitative polymerase chain reaction.Results:Through intraindividual comparison, frequency of reciprocal events varied from 2 to 9. According to the distribution pattern of the frequent CNV in derivatives of different germ layers, we found that its origin is early development including preimplantation, whereas CNVs with low frequency have occurred in later stages. Shared CNVs in both fetuses were belonged to thymus and related to the functional role of genes located in these CNVs.Conclusions:The origin of some of fetal CNVs is preimplantation stage. Each organ might inherit CNVs with an unpredictable pattern due to the extensive cell mixing/migration in embryonic development.
A Ciliary Motility Index for Activity Measurement in Cell Cultures With Respiratory Syncytial Virus
Authors: Parrilla Eduardo , Armengot Miguel , Mata Manuel , Carda Carmen , Cortijo Juilo , Moratal David , Ginestar Damián , Hueso José L. , Riera Jaime 
Published: November 2018

Background The respiratory epithelium is frequently infected by the respiratory syncytial virus, resulting in inflammation, a reduction in cilia activity and an increase in the production of mucus. Methods In this study, an automatic method has been proposed to characterize the ciliary motility from cell cultures by means of a motility index using a dense optical flow algorithm. This method allows us to determine the ciliary beat frequency (CBF) together with a ciliary motility index of the cells in the cultures. The object of this analysis is to automatically distinguish between normal and infected cells in a culture. Results The method was applied in 2 stages. It was concluded from the first stage that the CBF is not a good enough indicator to discriminate between the control and infected cultures. However, the ciliary motility index does succeed in discriminating between the control and infected cultures using the t test with a value t = 6.46 and P < .001. In the second stage, it has been shown that the ciliary motility index did not differ significantly between patients, and the analysis of variance test gives α = 0.05, F = 1.61, P = .20. A threshold for this index has been determined using a receiver operating characteristics analysis that gives an area under the curve of 0.93. Conclusions We have obtained a ciliary motility index that is able to discriminate between control and infected cultures after the eighth postinfection day. After infection, there is a rapid cilia loss of the cells and the measured CBF corresponds to the remaining noninfected cells. This is why the CBF does not discriminate between the control and the infected cells.
Absence of functional compensation between coagulation factor VIII and plasminogen in double-knockout mice
Authors: Stagaard Rikke , Ley Carsten Dan , Almholt Kasper , Olsen Lisbeth Høier , Knudsen Tom , Flick Matthew J. 
Published: November 2018

Abstract
Plasminogen deficiency is associated with severely compromised fibrinolysis and extravascular deposition of fibrin. In contrast, coagulation factor VIII (FVIII) deficiency leads to prolonged and excessive bleeding. Based on opposing biological functions of plasminogen and FVIII deficiencies, we hypothesized that genetic elimination of FVIII would alleviate the systemic formation of fibrin deposits associated with plasminogen deficiency and, in turn, elimination of plasminogen would limit bleeding symptoms associated with FVIII deficiency. Mice with single and combined deficiencies of FVIII (F8−/−) and plasminogen (Plg−/−) were evaluated for phenotypic characteristics of plasminogen deficiency, including wasting disease, shortened lifespan, rectal prolapse, and multiorgan fibrin deposition. Conversely, to specifically examine the role of plasmin-mediated fibrinolysis on bleeding caused by FVIII deficiency, F8−/− and F8−/−/Plg−/− mice were subjected to a bleeding challenge. Mice with a combined deficiency in FVIII and plasminogen displayed no phenotypic differences relative to mice with single FVIII or plasminogen deficiency. Plg−/− and F8−/−/Plg−/− mice exhibited the same penetrance and severity of wasting disease, rectal prolapse, extravascular fibrin deposits, and reduced viability. Furthermore, following a tail vein–bleeding challenge, no significant differences in bleeding times or total blood loss could be detected between F8−/− and F8−/−/Plg−/− mice. Moreover, F8−/− and F8−/−/Plg−/− mice responded similarly to recombinant FVIII (rFVIII) therapy. In summary, the pathological phenotype of Plg−/− mice developed independently of FVIII-dependent coagulation, and elimination of plasmin-driven fibrinolysis did not play a significant role in a nonmucosal bleeding model in hemophilia A mice.
Dynamics of respiratory symptoms during infancy and associations with wheezing at school age
Authors: Usemann Jakob , Xu Binbin , Delgado-Eckert Edgar , Korten Insa , Anagnostopoulou Pinelopi , Gorlanova Olga , Kuehni Claudia , Röösli Martin , Latzin Philipp , Frey Urs 
Published: November 2018

Children with frequent respiratory symptoms in infancy have an increased risk for later wheezing, but the association with symptom dynamics is unknown. We developed an observer-independent method to characterise symptom dynamics and tested their association with subsequent respiratory morbidity.In this birth-cohort of healthy neonates, we prospectively assessed weekly respiratory symptoms during infancy, resulting in a time series of 52 symptom scores. For each infant, we calculated the transition probability between two consecutive symptom scores. We used these transition probabilities to construct a Markov matrix, which characterised symptom dynamics quantitatively using an entropy parameter. Using this parameter, we determined phenotypes by hierarchical clustering. We then studied the association between phenotypes and wheezing at 6 years.In 322 children with complete data for symptom scores during infancy (16 864 observations), we identified three dynamic phenotypes. Compared to the low-risk phenotype, the high-risk phenotype, defined by the highest entropy parameter, was associated with an increased risk of wheezing (odds ratio (OR) 3.01, 95% CI 1.15–7.88) at 6 years. In this phenotype, infants were more often male (64%) and had been exposed to environmental tobacco smoke (31%). In addition, more infants had siblings (67%) and attended childcare (38%).We describe a novel method to objectively characterise dynamics of respiratory symptoms in infancy, which helps identify abnormal clinical susceptibility and recovery patterns of infant airways associated with persistent wheezing.
Effectiveness of discovery learning using a mobile otoscopy simulator on knowledge acquisition and retention in medical students: A randomized controlled trial
Authors: Xu Josie , Campisi Paolo , Forte Vito , Carrillo Brian , Vescan Allan , Brydges Ryan 
Published: November 2018

Background Portable educational technologies, like simulators, afford students the opportunity to learn independently. A key question in education, is how to pair self-regulated learning (SRL) with direct instruction. A cloud-based portable otoscopy simulator was employed to compare two curricula involving SRL. Pre-clerkship medical students used a prototype smartphone application, a 3D ear attachment and an otoscope to complete either otoscopy curriculum. Methods Pre-clerkship medical students were recruited and randomized to two curriculum designs. The “Discovery then Instruction” group received the simulator one week before a traditional lecture, while the “Instruction then Discovery” group received it after the lecture. To assess participants’ ability to identify otoscopic pathology, we used a 100-item test at baseline, post-intervention and 2-week retention time points. Secondary outcomes included self-reported comfort, time spent using the device, and a survey on learning preferences. Results Thirty-four students completed the study. Analysis of knowledge acquisition and retention showed improvement in scores of both groups and no significant effects of group (F1,31 = 0.53, p = 0.47). An analysis of participants’ self-reported comfort showed a significant group x test interaction (F1,36 = 4.61, p = 0.04), where only the discovery then instruction group's comfort improved significantly. Overall device usage was low, as the discovery then instruction group spent 21.47 ± 26.28 min, while the instruction then discovery group spent 13.84 ± 18.71 min. The discovery first group's time spent with the simulator correlated moderately with their post-test score ( r = 0.42, p = 0.07). After the intervention, most participants in both groups (63–68%) stated that they would prefer the instruction then discovery sequence. Conclusions Both curricular sequences led to improved knowledge scores with no statistically significant knowledge differences. When given minimal guidance, students engaged in discovery learning minimally. There is value in SRL in simulation education, and we plan to further improve our curricular design by considering learner behaviours identified in this study.
Novel multiplex assay for profiling influenza antibodies in breast milk and serum of mother-infant pairs
Authors: Järvinen Kirsi M. , Wang Jiong , Seppo Antti E. , Zand Martin 
Published: November 2018

Background: During early life, systemic protection to influenza is passively provided by transplacental transfer of IgG antibodies and oral and gastrointestinal mucosal protection via breast milk (BM) containing predominantly IgA. Immune imprinting, influenced by initial exposure of the infant immune system to influenza, has recently been recognized as an important determinant of future influenza immune responses. Methods: We utilized stored frozen BM from a prospective birth cohort to assess immune factors in human milk. The earliest available BM and a paired, timed serum sample was assessed from each of 7 mothers. Paired infant serum samples were assayed at up to three time points during the first 12 months of life, one prior to assumed disappearance of transplacentally transferred IgG, and one after. We utilized a novel multiplex assay to assess mothers’ and infants’ IgG and IgA antibodies in serum to a panel of 30 individual recombinant hemagglutinin (rHA) proteins of influenza virus strains and chimeric rHAs. We also characterized IgA and IgG antibody levels in breast milk providing mucosal protection. Results: Our pilot results, analyzing a small number of samples demonstrate the feasibility of this method for studying paired maternal-infant IgG and IgA anti-influenza immunity patterns. Unlike IgG antibodies, breast milk influenza virus HA-specific IgA antibody levels and patterns were mostly discordant compared to serum. As expected, there was a steady decay of infant influenza specific IgG levels by 6 to 8 months of age, which was not, however, comparable in all infants. In contrast, most of the infants showed an increase in IgA responses throughout the first year of life Conclusions: This new analytical method can be applied in a larger study to understand the impact of maternal imprinting on influenza immunity.
Do age and mating status affect olfactory response of the parasitoid, Microplitis croceipes (Hymenoptera: Braconidae) to host-related plant odors?
Authors: Burrows Matthew , Morawo Tolulope , Fadamiro Henry 
Published: November 2018

Background: Parasitic wasps (parasitoids) use volatile organic compounds released by herbivore-infested plants to locate their hosts. Response of parasitoids to plant odors may be plastic and dependent on their physiological state. Using Microplitis croceipes (Hymenoptera: Braconidae), a relatively specialized larval endoparasitoid of Heliothis virescens (Lepidoptera: Noctuidae), we asked whether age and mating status of parasitoids affect their olfactory response to host-related odors. Methods: Four odor stimuli of varying complexity were selected based on previous reports of parasitoid response to cotton volatiles: cis-3-hexenol (a green leaf volatile), α-pinene (a constitutive monoterpene), a 50/50 v/v binary mixture (cis-3-hexenol + α-pinene), and H. virescens-infested cotton odors. Female M. croceipes used in Y-tube olfactometer bioassays were either mated or unmated, and grouped 1–3, 4–6, and 7–9 d-old. Female parasitoids used in electroantennogram (EAG) recording were mated and grouped 1–3, 4–6, 7–9 and 10–12 d-old. Results: In Y-tube olfactometer bioassays, neither age nor mating status played a major role in the attraction of parasitoids to test odor stimuli, with two exceptions: 4–6 d-old mated parasitoids showed attraction to the binary mixture, and 1–3 d-old mated parasitoids showed attraction to H. virescens-infested cotton. Age did not affect EAG response of parasitoids to test stimuli. Conclusions: The present results suggest that age and mating status do not play a major role in modulating olfactory responses of M. croceipes to host-related plant odors. Instead, plasticity of olfactory response may be limited in M. croceipes due to strong innate sensitivity to host-related odor cues.
Prevalence and associated risk factors of HIV in prisons in Balochistan, Pakistan: a cross-sectional study
Authors: Khan Muhammad Dawood , Wali Ahmad , Fatima Razia , Yaqoob Aashifa , Aziz Shoaib 
Published: November 2018

Background: The prevalence of HIV is 0.1% in Pakistan, with epidemicity in high-risk groups. The infection is on verge of transmission from key populations to the general population through people who inject drugs and sexual transmission. Prisoners are vulnerable to infectious diseases like HIV. This study was conducted in four prisons in Balochistan. Pakistan to determine the prevalence of HIV and associated risk factors. Methods: This cross sectional study was conducted from March to June 2018, in the prisons of Balochistan. WHO-approved rapid diagnostic kits were used for determining the prevalence of HIV and structured interviews were conducted for the assessment of risk factors. Results: Out of 2084 screened prisoners, 33 (1.6%) were found to be positive. A subset of 104 interviews were analysed for risk factors of HIV. Among HIV-infected prisoners 68.8% (OR 4.48; 95% CI 1.41-14.2) had extramarital sex, 43.8% (OR 2.09 95% CI 0.69-6.28) had homosexual experience, and 50% had history of needle sharing (OR 43; 95% CI 7.77-237). About 94% (OR 16.42; 95% CI 2.09-129.81) of prisoners had history of drug addiction of any type while 50% (OR 13; 95% CI 2.82-60.01) of those infected with HIV had a history of using injectable drugs. Around 75% of HIV-infected prisoners had spent 1-5 years in prison, and 25% had spent more than 10 years. Conclusion: The high prevalence of HIV in prisons of Balochistan demands that preventive and treatment strategies should be designed and implemented carefully, allowing early diagnosis and treatment initiation to minimize the spread of infection among the prisons and ultimately their onward transmission into the community.