bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clustering of samples with a tree-shaped dependence structure, with an application to microscopic time lapse imaging
Authors: Failmezger Henrik , Dursun Ezgi , Dümcke Sebastian , Endele Max , Poron Don , Schroeder Timm , Krug Anne , Tresch Achim 
Published: November 2018

Abstract

Motivation
Recent imaging technologies allow for high-throughput tracking of cells as they migrate, divide, express fluorescent markers and change their morphology. The interpretation of these data requires unbiased, efficient statistical methods that model the dynamics of cell phenotypes.

Results
We introduce treeHFM, a probabilistic model which generalizes the theory of hidden Markov models to tree structured data. While accounting for the entire genealogy of a cell, treeHFM categorizes cells according to their primary phenotypic features. It models all relevant events in a cell’s life, including cell division, and thereby enables the analysis of event order and cell fate heterogeneity. Simulations show higher accuracy in predicting correct state labels when modeling the more complex, tree-shaped dependency of samples over standard HMM modeling. Applying treeHFM to time lapse images of hematopoietic progenitor cell differentiation, we demonstrate that progenitor cells undergo a well-ordered sequence of differentiation events.

Availability and implementation
The treeHFM is implemented in C++. We provide wrapper functions for the programming languages R (CRAN package, https://CRAN.R-project.org/package=treeHFM) and Matlab (available at Mathworks Central, http://se.mathworks.com/matlabcentral/fileexchange/57575-treehfml).

Supplementary information
Supplementary data are available at Bioinformatics online.
DiPhiSeq: robust comparison of expression levels on RNA-Seq data with large sample sizes
Authors: Li Jun , Lamere Alicia T 
Published: November 2018

AbstractMotivationIn the analysis of RNA-Seq data, detecting differentially expressed (DE) genes has been a hot research area in recent years and many methods have been proposed. DE genes show different average expression levels in different sample groups, and thus can be important biological markers. While generally very successful, these methods need to be further tailored and improved for cancerous data, which often features quite diverse expression in the samples from the cancer group, and this diversity is much larger than that in the control group.ResultsWe propose a statistical method that can detect not only genes that show different average expressions, but also genes that show different diversities of expressions in different groups. These ‘differentially dispersed’ genes can be important clinical markers. Our method uses a redescending penalty on the quasi-likelihood function, and thus has superior robustness against outliers and other noise. Simulations and real data analysis demonstrate that DiPhiSeq outperforms existing methods in the presence of outliers, and identifies unique sets of genes.Availability and implementationDiPhiSeq is publicly available as an R package on CRAN: https://cran.r-project.org/package=DiPhiSeq.Supplementary informationSupplementary data are available at Bioinformatics online.
The British West India Interest and Its Allies, 1823–1833
Authors: Taylor Michael 
Published: November 2018

Abstract
Between the foundation of the Anti-Slavery Society in 1823 and the passage of the Slave Emancipation Act in 1833, the British West India interest mounted a pervasive and influential campaign in defence of colonial slavery. This article gives the fullest account yet of the strength and activities of the West India interest during that decade of debate and argument. Moreover, this article demonstrates that the West Indians—far from a reactionary political rump—successfully created a broader pro-slavery lobby. First, the West Indians cultivated the support of numerous leading conservative periodicals such as Blackwood’s Edinburgh Magazine, the Quarterly Review, and Fraser’s Magazine. Secondly, the West Indians courted the political favour of several leading Tories of the day, among them Canning, Huskisson, Peel and Wellington. Consequently, this article shows that pro-slavery sympathies were prevalent and influential with British print and political culture until 1833. It concludes that, for many Britons and especially British conservatives, colonial slavery—as much as the monarchy, the aristocracy and the Established Church—was an essential element of national life.
Local environment affecting northern shrimp recruitment: a comparative study of Gulf of St. Lawrence stocks
Authors: Brosset Pablo , Bourdages Hugo , Blais Marjolaine , Scarratt Michael , Plourde Stéphane 
Published: November 2018

Abstract
Climate and density-dependent effects are important drivers of recruitment (R). In the Gulf of St. Lawrence (GSL), recent years indicated an exceptional warming of water associated with variations in plankton phenology and fish abundance. At the same time, northern shrimp (Pandalus borealis) recruitment and stock dynamics fluctuated greatly, but the underlying mechanisms remain poorly understood. We estimated recruitment from yearly fisheries independent abundance estimates for three different northern shrimp stocks in the GSL (Sept-Iles, Anticosti, and Esquiman). For 2001–2016, we quantified how northern shrimp R changed in relation to physical variables, phytoplankton bloom characteristics, zooplankton abundance and phenology, and predator biomass. Results indicated that northern shrimp R seemed related to phytoplankton bloom characteristics and resulting zooplankton phenology in addition to northern shrimp adult abundance, rather than to fish predator biomass. Importantly, the significant variables explaining the R were stock specific, implying that environmental variability and stock abundance effects depend on the area considered. In future, Esquiman area might show increasing northern shrimp R under moderate warming but northern shrimp Sept-Iles R might be impaired. These results improve our understanding of stock-specific northern shrimp recruitment dynamics in a changing environment and can ultimately improve its management in the GSL.
Highest Weights for Categorical Representations
Authors: Ben-Zvi David , Gunningham Sam , Orem Hendrik 
Published: November 2018

Abstract
We present a criterion for establishing Morita equivalence of monoidal categories and apply it to the categorical representation theory of reductive groups $G$. We show that the “de Rham group algebra” $\mathcal D(G)$ (the monoidal category of $\mathcal D$-modules on $G$) is Morita equivalent to the universal Hecke category $\mathcal D({N}\backslash{G}/{N})$ and to its monodromic variant $\widetilde{\mathcal D}({B}\backslash{G}/{B})$. In other words, de Rham $G$-categories, that is, module categories for $\mathcal D(G)$, satisfy a “highest weight theorem”—they all appear in the decomposition of the universal principal series representation $\mathcal D(G/N)$ or in twisted $\mathcal D$-modules on the flag variety $\widetilde{\mathcal D}(G/B)$.
Estimating Lactase Nonpersistence Distributions in the Multi-Ethnic Canadian Demographic: A Population-Based Study
Authors: Fung Manyan , Xue Xiaoqing , Szilagyi Andrew 
Published: November 2018

AbstractObjectivesThe lactase persistence/nonpersistence (LP/LNP) phenotypes follow a geographic pattern that is rooted in the gene-culture coevolution observed throughout the history of human migrations. The immense size and relatively open immigration policy have drawn migrants of diverse ethnicities to Canada. Among the multicultural demographic, two-thirds of the population are derived from the British Isles and northwestern France. A recent assessment of worldwide lactase distributions found Canada to have an LNP rate of 59% (confidence interval [CI] 44%–74%). This estimate is rather high compared with earlier reports that listed Canada as a country with a 10% LNP rate; the authors had also noted that biases were likely because their calculations were based largely on Aboriginal studies. We hereby present an alternate LNP prevalence estimate at the national, provincial and territorial level.MethodsWe applied the referenced LNP frequency distribution data to the 2016 population census to account for the current multi-ethnic distributions in Canada. Prevalence rates for Canada, the provinces and territories were calculated.ResultsThe national LNP rate is estimated at 44% (CI 41%–47%) after accounting for the 254 ethnic groups, with the lowest rates found in the eastern provinces and the highest rates in the Northwest Territories (57%) and Nunavut (66%), respectively.ConclusionDespite the heterogeneous nature of the referenced data and the inference measures taken, evidently, the validity of our LNP estimate is anchored on the inclusion of multi-ethnic groups representing the current Canadian demographic.
Assembly of a parts list of the human mitotic cell cycle machinery
Authors: Giotti Bruno , Chen Sz-Hau , Barnett Mark W , Regan Tim , Ly Tony , Wiemann Stefan , Hume David A , Freeman Tom C 
Published: November 2018

AbstractThe set of proteins required for mitotic division remains poorly characterized. Here, an extensive series of correlation analyses of human and mouse transcriptomics data were performed to identify genes strongly and reproducibly associated with cells undergoing S/G2-M phases of the cell cycle. In so doing, 701 cell cycle-associated genes were defined and while it was shown that many are only expressed during these phases, the expression of others is also driven by alternative promoters. Of this list, 496 genes have known cell cycle functions, whereas 205 were assigned as putative cell cycle genes, 53 of which are functionally uncharacterized. Among these, 27 were screened for subcellular localization revealing many to be nuclear localized and at least three to be novel centrosomal proteins. Furthermore, 10 others inhibited cell proliferation upon siRNA knockdown. This study presents the first comprehensive list of human cell cycle proteins, identifying many new candidate proteins.
Glomerular filtration rate: when to measure and in which patients?
Authors: Agarwal Rajiv , Delanaye Pierre 
Published: November 2018

AbstractOf the glomerular, tubular and endocrine functions of the kidney, nephrologists have mostly focused their attention on the glomerular functions—albuminuria and glomerular filtration rate (GFR)—to grade the severity of chronic kidney disease (CKD). Although both albuminuria and GFR are associated with renal and cardiovascular morbidity and mortality, the utility of measured GFR (mGFR) has been questioned. GFR when measured adequately is the most precise measure of glomerular function and can be useful to individualize therapy among patients with CKD. In situations where estimated GFR is known to provide imprecise estimates of glomerular function, for example, sarcopenia and advanced cirrhosis, the measurement of GFR may be especially important. We discuss several clinical situations where mGFR can potentially influence the quality of life or complications of therapy because of interventions based on imperfect knowledge of GFR. We reason that although large databases may not detect the benefits of mGFR at the population level, precision medicine requires that therapy be individualized based on the best estimate of GFR that can be obtained particularly when the risk of harm is increased. The recent standardization of mGFRs is a step in the right direction and may help in treating the individual patient with CKD with a lower risk of complications and a better quality of life. We call for research in these subgroups of patients where it is clinically felt that mGFR is useful for clinical decision-making.
International Consensus Statement on the Management of Hypotension With Vasopressors During Caesarean Section Under Spinal Anaesthesia
Authors: Kinsella S.M. , Carvalho B. , Dyer R.A. , Fernando R. , McDonnell N. , Mercier F.J. , Palanisamy A. , Sia A.T.H. , Van de Velde M. , Vercueil A. 
Published: November 2018

(Anaesthesia. 2018;73:71–92)
The objective of this comprehensive consensus statement was to provide practical and independent advice to physicians for treating and managing spinal anesthesia-induced maternal hypotension in both resource-rich and resource-poor environments. This clinical best practices summary was necessary as there has been much variation in the methods used to manage spinal anesthesia-induced hypotension during cesarean section, and maternal hypotension increases risks to both maternal and fetal/neonatal health. While generalized recommendations have been made for the management of this problem by professional organizations, the authors indicated this was the first consensus statement providing specific, pragmatic recommendations for managing spinal anesthesia-induced hypotension.
A Randomized Comparison of Bolus Phenylephrine and Ephedrine for the Management of Spinal Hypotension in Patients With Severe Preeclampsia and Fetal Compromise
Authors: Dyer R.A. , Emmanuel A. , Adams S.C. , Lombard C.J. , Arcache M.J. , Vorster A. , Wong C.A. , Higgins N. , Reed A.R. , James M.F. , Joolay Y. , Schulein S. , van Dyk D. 
Published: November 2018

(Int J Obstet Anesth. 2018;33:23–31)
Ephedrine and phenylephrine have both been used to prevent and treat the spinal hypotension that is common during cesarean delivery. When compared with phenylephrine, ephedrine is associated with greater fetal acidosis in healthy parturients. However, there are limited data regarding the relative efficacy of these 2 drugs for managing hypotension in women with fetal compromise. The present trial examined the effects of bolus ephedrine versus phenylephrine for the treatment of spinal hypotension in women with severe preeclampsia and a nonreassuring fetal heart tracing who were undergoing cesarean delivery.
Maternal Cardiac Output Response to Colloid Preload and Vasopressor Therapy During Spinal Anesthesia for Cesarean Section in Patients With Severe Preeclampsia: A Randomized, Controlled Trial
Authors: Dyer R.A. , Daniels A. , Vorster A. , Emmanuel A. , Arcache M.J. , Schulein S. , Reed A.R. , Lombard C.J. , James M.F. , van Dyk D. 
Published: November 2018

(Anaesthesia. 2018;73:23–31)
Minimally invasive cardiac output monitors have been used in parturients to assess the hemodynamic effects of spinal anesthesia and the commonly used vasopressors phenylephrine and ephedrine. However, studies utilizing these devices have been performed mostly in healthy parturients, with data lacking for those with severe preeclampsia. This randomized study’s objective was to compare the cardiac output response to phenylephrine or ephedrine administered for spinal hypotension during cesarean delivery in women with severe early-onset preeclampsia as well as to measure the stroke volume response to administration of a colloid preload.
Learning From the Law: A Review of 21 Years of Litigation for Pain During Cesarean Section
Authors: McCombe K. , Bogod D.G. 
Published: November 2018

(Anaesthesia. 2018;73:223–230)
In the United Kingdom, the majority of cesarean deliveries are now performed under neuraxial anesthesia instead of general anesthesia, thereby mitigating the increased anesthetic risks associated with general anesthesia in pregnant women. However, as the use of neuraxial anesthesia for cesarean delivery has increased so has the risk of patients experiencing pain during surgery. As a result, pain during cesarean delivery has now become the most common reason for negligence claims relating to regional anesthesia against obstetric anesthesiologists in the UK. This article examined common themes (relating to consent, checking the block, managing intraoperative pain, and professionalism) that emerged from an analysis of these claims and highlighted the lessons to be learned for practicing anesthesiologists.
The Need for an Epidural “Window of Opportunity” in Pregnant Women With a Lumbar Tattoo
Authors: Zipori Y. , Jakobi P. , Solt I. , Abecassis P. 
Published: November 2018

(Int J Obstet Anesth. 2018;33:53–56)
Anesthesiologists face a dilemma when pregnant women with lower back tattoos request epidural analgesia during labor, as clear guidelines have not been established regarding the performance of epidural procedures through a tattoo on the lower back. In the United States ∼25% of people between the ages of 18 and 50 report having a tattoo. The opinions of anesthesiologists vary widely as to how to approach this scenario. In surveys performed addressing the issue, 40% of survey respondents indicated they would not perform an epidural technique through a lumbar tattoo and 70% reported the lack of a departmental policy for how to manage these patients.
Vitamin D Supplementation During Pregnancy: State of the Evidence From a Systematic Review of Randomized Trials
Authors: Hollis B.W. , Johnson D. , Thomas C. , Hulsey T.C. , Wagner C.L. 
Published: November 2018

(BMJ. 2017;359:j5237)
Vitamin D affects bone growth and calcium homeostasis but more far reaching effects have been proposed, including effects on pregnancy and birth outcomes. Dietary and supplementation recommendations for vitamin D vary across medical and professional organizations in spite of growing concern regarding the high prevalence of vitamin D deficiency in pregnant women and newborns. This study was a systematic review and meta-analysis of randomized controlled trials of prenatal vitamin D supplementation that was undertaken with the goal of estimating the effects of vitamin D supplementation during pregnancy on maternal, neonatal, and infant outcomes.
Very Tight Versus Tight Control: What Should be the Criteria for Pharmacologic Therapy Dose Adjustment in Diabetes in Pregnancy? Evidence From Randomized Controlled Trials
Authors: Caissutti C. , Saccone G. , Ciardulli A. , Berghella V. 
Published: November 2018

(Acta Obstet Gynecol Scand. 2018;97:235–247)
Management for women with gestational diabetes mellitus (GDM) and pregestational diabetes mellitus (DM), includes diet, physical activity, and oral hypoglycemic agents or insulin as needed. However, the optimal schedule, frequency, and timing of glucose monitoring as well as the ideal therapeutic glucose level remain inconclusive. Results from randomized controlled trials (RCTs) have not been able to define any specific criteria for pharmacologic therapy dose adjustment. Therefore, these investigators undertook a systematic review of RCTs in order to analyze the criteria being used for pharmacologic therapy dose adjustment.
A Survey of International Antisepsis Procedures for Neuraxial Catheterization in Labor
Authors: Fayman K. , Allan A. , Hudson C. , Logarta M. 
Published: November 2018

(Int J Obstet Anesth. 2018;33:8–16)
Neuraxial analgesia during labor is commonly performed, but serious complications may arise due to infection of the neuraxial space. Although adherence to antisepsis precautions is mandatory, what appropriate antisepsis practice entails varies widely among countries and even hospitals within the same country. In view of this, the current study was undertaken with the primary aim of clarifying international antisepsis practices for neuraxial analgesia during labor.
Eroding Access and Quality of Childbirth Care in Rural US Counties
Authors: Shah N.T. 
Published: November 2018

(JAMA. 2018;319(12):1203–1204)
Compared with other high-income nations, the United States is lagging in birth outcomes. Hospitals often lose money on maternity care as obstetric services have high fixed costs and low reimbursements. As a result, many hospital obstetric units with small volumes and large shares of Medicaid recipients have closed. This has particularly impacted hospitals in rural counties.
Prediction of Outliers in Pain, Analgesia Requirement, and Recovery of Function After Childbirth: A Prospective Observational Cohort Study
Authors: Komatsu R. , Carvalho B. , Flood P. 
Published: November 2018

(Br J Anaesth. 2018;121:417–426)
Most women report opioid-free functional recovery ∼3 to 4 weeks after childbirth. However, a minority of women report severe pain and remain on opioids for a prolonged period after childbirth, which has potential for long-term harm. There is limited information available to predict which women will have poor recovery or require opioids for a protracted period. Consequently, the authors of the present study identified demographic, obstetrical, and psychological factors associated with parturients who are likely to have a difficult postpartum recovery with respect to pain, opioid use, and recovery of function.
Perinatal and Maternal Morbidity and Mortality Among Term Singletons Following Midcavity Operative Vaginal Delivery Versus Cesarean Delivery
Authors: Muraca G.M. , Skoll A. , Lisonkova S. , Sabr Y. , Brant R. , Cundiff G.W. , Joseph K.S. 
Published: November 2018

(BJOG. 2018;125:693–702)
Recently, to reduce the cesarean delivery rate, the use of operative vaginal delivery has been advocated by the American College of Obstetricians and Gynecologists and the Society for Maternal-Fetal Medicine. There is uncertainty, however, in the balance of risks and benefits between cesarean delivery and operative vaginal delivery. Previous research has lacked information on pelvic station, a measure of the descent of the fetal head with respect to the maternal ischial spines. Operating at the midcavity station requires the greatest skill compared with outlet or lowcavity forceps procedures. This study aimed to quantify the effect of operative vaginal delivery at midcavity station on maternal and perinatal mortality and morbidity compared with cesarean delivery.
Gastric Ultrasound in the Third Trimester of Pregnancy: A Randomized Controlled Trial to Develop a Predictive Model of Volume Assessment
Authors: Arzola C. , Perlas A. , Siddiqui N.T. , Downey K. , Ye X.Y. , Carvalho J.C.A. 
Published: November 2018

(Anaesthesia. 2018;73:295–303)
Bedside gastric ultrasound is used in diverse patient groups for the assessment of gastric content and volume. Using qualitative assessment, a distinction can be made between an empty stomach and one containing solid/thick fluid contents or clear fluids. In addition, quantitative assessment of gastric volume can be estimated using the cross-sectional area of the gastric antrum when clear fluid contents are present in the stomach. Small volumes ≤1.5 mL/kg1 are consistent with baseline gastric secretions, whereas higher volumes suggest patient ingestion that may increase aspiration risk. The primary objective of this study was to evaluate the relationship between gastric antral cross-sectional area as measured by ultrasound and the volume of clear fluids ingested by pregnant women.
A Prospective Cohort Study of Fetal Heart Rate Monitoring: Deceleration Area is Predictive of Fetal Acidemia
Authors: Cahill A.G. , Tuuli M.G. , Stout M.J. , López J.D. , Macones G.A. 
Published: November 2018

(Am J Obstet Gynecol. 2018;218:523.e1–523.e12)
While intrapartum electronic fetal monitoring (EFM) is commonly used and promises to reduce adverse neonatal outcomes by predicting acidemia, there is a lack of data regarding an association between EFM patterns and acidemia. This study aimed to assess EFM patterns and their association with acidemia and neonatal morbidity and determine which visually interpreted EFM patterns were associated with acidemia and neonatal morbidity.