bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data
Authors: Serra Angela , Coretto Pietro , Fratello Michele , Tagliaferri Roberto 
Published: October 2017

Abstract

Motivation
Microarray technology can be used to study the expression of thousands of genes across a number of different experimental conditions, usually hundreds. The underlying principle is that genes sharing similar expression patterns, across different samples, can be part of the same co-expression system, or they may share the same biological functions. Groups of genes are usually identified based on cluster analysis. Clustering methods rely on the similarity matrix between genes. A common choice to measure similarity is to compute the sample correlation matrix. Dimensionality reduction is another popular data analysis task which is also based on covariance/correlation matrix estimates. Unfortunately, covariance/correlation matrix estimation suffers from the intrinsic noise present in high-dimensional data. Sources of noise are: sampling variations, presents of outlying sample units, and the fact that in most cases the number of units is much larger than the number of genes.

Results
In this paper, we propose a robust correlation matrix estimator that is regularized based on adaptive thresholding. The resulting method jointly tames the effects of the high-dimensionality, and data contamination. Computations are easy to implement and do not require hand tunings. Both simulated and real data are analyzed. A Monte Carlo experiment shows that the proposed method is capable of remarkable performances. Our correlation metric is more robust to outliers compared with the existing alternatives in two gene expression datasets. It is also shown how the regularization allows to automatically detect and filter spurious correlations. The same regularization is also extended to other less robust correlation measures. Finally, we apply the ARACNE algorithm on the SyNTreN gene expression data. Sensitivity and specificity of the reconstructed network is compared with the gold standard. We show that ARACNE performs better when it takes the proposed correlation matrix estimator as input.

Availability and implementation
The R software is available at https://github.com/angy89/RobustSparseCorrelation.

Supplementary information
Supplementary data are available at Bioinformatics online.
SELANSI: a toolbox for simulation of stochastic gene regulatory networks
Authors: Pájaro Manuel , Otero-Muras Irene , Vázquez Carlos , Alonso Antonio A 
Published: October 2017

Abstract

Motivation
Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort.

Results
This work presents SELANSI (SEmi-LAgrangian SImulation of GRNs), a software toolbox for the simulation of stochastic multidimensional gene regulatory networks. SELANSI exploits intrinsic structural properties of gene regulatory networks to accurately approximate the corresponding Chemical Master Equation with a partial integral differential equation that is solved by a semi-lagrangian method with high efficiency. Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors. Moreover, the validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options.

Availability and implementation
SELANSI runs under the MATLAB environment, and is available under GPLv3 license at https://sites.google.com/view/selansi.
Dimensions of Sets Which Uniformly Avoid Arithmetic Progressions
Authors: Fraser Jonathan M , Saito Kota , Yu Han 
Published: October 2017

AbstractWe provide estimates for the dimensions of sets in $\mathbb{R}$ which uniformly avoid finite arithmetic progressions (APs). More precisely, we say $F$ uniformly avoids APs of length $k \geq 3$ if there is an $\epsilon>0$ such that one cannot find an AP of length $k$ and gap length $\Delta>0$ inside the $\epsilon \Delta$ neighbourhood of $F$. Our main result is an explicit upper bound for the Assouad (and thus Hausdorff) dimension of such sets in terms of $k$ and $\epsilon$. In the other direction, we provide examples of sets which uniformly avoid APs of a given length but still have relatively large Hausdorff dimension. We also consider higher dimensional analogues of these problems, where APs are replaced with arithmetic patches lying in a hyperplane. As a consequence, we obtain a discretized version of a “reverse Kakeya problem:” we show that if the dimension of a set in $\mathbb{R}^d$ is sufficiently large, then it closely approximates APs in every direction.
The Inadequate Protection of Human Rights in Unfair Dismissal Law
Authors: Collins Philippa 
Published: October 2017

Abstract
Workers in the private sector have limited legal options if they believe that, by terminating the working relationship, the employer has infringed their human rights. In most cases, they must rely on an existing cause of action, notably the right not to be unfairly dismissed contained in the Employment Rights Act 1996. The provisions of the Human Rights Act 1998 reinforce the argument that unfair dismissal law should play a role in the vindication of human rights in the employment context. Is the law of unfair dismissal capable of fulfilling this role? This article will argue that it is not. It will demonstrate that there are several major obstacles to the vindication of a worker’s human rights through unfair dismissal law. It will be argued that there are three ways in which the law of unfair dismissal is inconsistent with the principles of the European Convention on Human Rights: the narrow personal scope of protection, the lax standard of review applied by the tribunals and the inadequate remedies available to claimants who are successful in their claim.
Navigation-Linked Heads-Up Display in Intracranial Surgery: Early Experience
Authors: Mascitelli Justin R , Schlachter Leslie , Chartrain Alexander G , Oemke Holly , Gilligan Jeffrey , Costa Anthony B , Shrivastava Raj K , Bederson Joshua B 
Published: October 2017

Abstract

BACKGROUND
The use of intraoperative navigation during microscope cases can be limited when attention needs to be divided between the operative field and the navigation screens. Heads-up display (HUD), also referred to as augmented reality, permits visualization of navigation information during surgery workflow.

OBJECTIVE
To detail our initial experience with HUD.

METHODS
We retrospectively reviewed patients who underwent HUD-assisted surgery from April 2016 through April 2017. All lesions were assessed for accuracy and those from the latter half of the study were assessed for utility.

RESULTS
Seventy-nine patients with 84 pathologies were included. Pathologies included aneurysms (14), arteriovenous malformations (6), cavernous malformations (5), intracranial stenosis (3), meningiomas (27), metastasis (4), craniopharygniomas (4), gliomas (4), schwannomas (3), epidermoid/dermoids (3), pituitary adenomas (2) hemangioblastoma (2), choroid plexus papilloma (1), lymphoma (1), osteoblastoma (1), clival chordoma (1), cerebrospinal fluid leak (1), abscess (1), and a cerebellopontine angle Teflon granuloma (1). Fifty-nine lesions were deep and 25 were superficial. Structures identified included the lesion (81), vessels (48), and nerves/brain tissue (31). Accuracy was deemed excellent (71.4%), good (20.2%), or poor (8.3%). Deep lesions were less likely to have excellent accuracy (P = .029). HUD was used during bed/head positioning (50.0%), skin incision (17.3%), craniotomy (23.1%), dural opening (26.9%), corticectomy (13.5%), arachnoid opening (36.5%), and intracranial drilling (13.5%). HUD was deactivated at some point during the surgery in 59.6% of cases. There were no complications related to HUD use.

CONCLUSION
HUD can be safely used for a wide variety of vascular and oncologic intracranial pathologies and can be utilized during multiple stages of surgery.
A history into genetic and epigenetic evolution of food tolerance: how humanity rapidly evolved by drinking milk and eating wheat
Authors: Blanchard Carine 
Published: October 2017

Purpose of review
Human exposure to wheat and milk is almost global worldwide. Yet the introduction of milk and wheat is very recent (5000–10 000 years) when compared to the human evolution. The last 4 decades have seen a rise in food allergy and food intolerance to milk and wheat. Often described as plurifactorial, the cause of allergic diseases is the result from an interplay between genetic predisposition and epigenetic in the context of environmental changes.

Recent findings
Genetic and epigenetic understanding and their contribution to allergy or other antigen-driven diseases have considerably advanced in the last few years. Yet, environmental factors are also quite difficult to identify and associate with disease risk. Can we rethink our old findings and learn from human history and recent genetic studies?

Summary
More than one million years separate Homo habilis to today's mankind, more than 1 million years to develop abilities to obtain food by foraging in diverse environments. One million year to adjust and fine-tune our genetic code and adapt; and only 1% of this time, 10 000 years, to face the three biggest revolutions of the human kind: the agricultural revolution, the industrial revolution and the postindustrial revolution. With big and rapid environmental changes come adaptation but with no time for fine-tuning. Today tolerance and adverse reactions to food may be a testimony of adaptation successes and mistakes.
Disparities in Care for Publicly Insured Women With Pregestational Diabetes
Authors: Easter Sarah Rae , Rosenthal Emily W. , Morton-Eggleston Emma , Nour Nawal , Tuomala Ruth , Zera Chloe A. 
Published: October 2017

OBJECTIVE:
To investigate the association among public health insurance, preconception care, and pregnancy outcomes in pregnant women with pregestational diabetes.

METHODS:
This is a retrospective cohort of pregnant women with pregestational type 1 or type 2 diabetes from 2006 to 2011 in Massachusetts—a state with universal insurance coverage since 2006. Women delivering after 24 weeks of gestation and receiving endocrinology and obstetric care in a multidisciplinary clinic were included. Rates of preconception consultation, our primary outcome of interest, were then compared between publicly and privately insured women. We used univariate analysis followed by logistic regression to compare receipt of preconception consultation and other secondary diabetes care measures and pregnancy outcomes according to insurance status.

RESULTS:
Fifty-four percent (n=106) of 197 women had public insurance. Publicly insured women were younger (median age 30.4 compared with 35.3 years, P<.01) with lower rates of college education (12.3% compared with 45.1%, P<.01). Women with public insurance were less likely to receive a preconception consult (5.7% compared with 31.9%, P<.01), had lower rates of hemoglobin A1C less than 6% at the onset of pregnancy (37.2% compared with 58.4%, P=.01), and experienced higher rates of pregnancies affected by congenital anomalies (10.4% compared with 2.2%, P=.02) compared with those with private insurance. In adjusted analyses controlling for educational attainment, maternal age, and body mass index, women with public insurance were less likely to receive a preconception consult (adjusted odds ratio [OR] 0.21, 95% CI 0.08–0.58), although the odds of achieving the target hemoglobin A1C (adjusted OR 0.45, 95% CI 0.20–1.02) and congenital anomaly (adjusted OR 2.23, 95% CI 0.37–13.41) were similar after adjustment.

CONCLUSION:
Despite continuous access to health insurance, publicly insured women were less likely than privately insured women to receive a preconception consult—an evidence-based intervention known to improve pregnancy outcomes. Improving use of preconception care among publicly insured women with diabetes is critical to reducing disparities in outcomes.
Trial of Labor Compared With Cesarean Delivery in Superobese Women
Authors: Grasch Jennifer L. , Thompson Jennifer L. , Newton J. Michael , Zhai Amy W. , Osmundson Sarah S. 
Published: October 2017

OBJECTIVE:
To examine whether labor compared with planned cesarean delivery is associated with increased maternal and neonatal morbidity.

METHODS:
We conducted a retrospective cohort study of all women with body mass indexes (BMIs) at delivery of 50 or greater delivering a live fetus at 34 weeks of gestation of greater between January 1, 2008, and December 31, 2015. Pregnancies with multiple gestations and major fetal anomalies were excluded. The primary outcome was a composite of maternal and neonatal morbidity and was estimated to be 50% in superobese women based on institutional data. A sample size of 338 women determined the study period and was selected to show a 30% difference in the incidence of the primary outcome between the two groups. Multivariate logistic regression adjusted for potential confounders.

RESULTS:
There were 344 women with BMIs of 50 or greater who met eligibility criteria, of whom 201 (58%) labored and 143 (42%) underwent planned cesarean delivery. Women who labored were younger, more likely to be nulliparous, and less likely to have pre-existing diabetes. Among women who labored, 45% underwent a cesarean delivery, most commonly for labor arrest (61%) or nonreassuring fetal status (28%). Composite maternal and neonatal morbidity was reduced among women who labored even after adjusting for age, parity, pre-existing diabetes, and prior cesarean delivery (adjusted odds ratio 0.42, 95% CI 0.24–0.75). In the subgroup of women (n=234) who underwent a cesarean delivery, whether planned (n=143) or after labor (n=91), there were no differences in maternal and neonatal morbidity except that severe maternal morbidity was increased in women (n=12) who labored (8.8% compared with 2.1%, relative risk 4.2, 95% CI 1.14–15.4).

CONCLUSION:
Despite high rates of cesarean delivery in women with superobesity, labor is associated with lower composite maternal and neonatal morbidity. Severe maternal morbidity may be higher in women who require a cesarean delivery after labor.
Implementing a Systematic Approach to Reduce Cesarean Birth Rates in Nulliparous Women
Authors: Bell Amy D. , Joy Saju , Gullo Susan , Higgins Robert , Stevenson Eleanor 
Published: October 2017

OBJECTIVE:
To implement a systematic approach to safely reduce nulliparous cesarean birth rates.

METHODS:
This is a quality improvement project at two rural community hospitals and one urban community hospital in North Carolina. These facilities implemented a systematic approach to reduce nulliparous cesarean birth rates, aligning with recommendations developed by the Council on Patient Safety in Women's Health Care: Patient Safety Bundle on the Safe Reduction of Primary Cesarean Births. Health care providers and nurses received education on contemporary labor management guidelines developed by the American College of Obstetricians and Gynecologists and the Society for Maternal-Fetal Medicine Obstetric Care Consensus regarding safe prevention of primary cesarean deliveries and nurses were instructed on labor support techniques. The preguideline implementation period was January 1, 2015, to June 30, 2015. The postguideline implementation period was July 1, 2016, to December 31, 2016. The primary outcome measured was the nulliparous, term, singleton, vertex cesarean birth rate. Secondary outcomes included maternal and neonatal outcomes. Standard statistical analysis was used and a P value of <.05 was considered significant.

RESULTS:
There were 434 women identified in the preguideline period and 401 women in the postguideline period. The nulliparous, term, singleton, vertex cesarean birth rate decreased from 27.9% to 19.7% [odds ratio (OR) 0.63, CI 0.46–0.88]. There were improvements in health care provider compliance with following the labor management guidelines from 86.2% to 91.5% (OR 1.73, 95% CI 1.11–2.70), the use of maternal position changes from 78.7% to 87.5% (OR 1.86, 95% CI 1.29–2.68), and use of the peanut birthing ball from 16.8% to 45.2% (OR 3.83, 95% CI 2.84–5.16) as provisions for labor support.

DISCUSSION:
Implementing a systematic approach for care of nulliparous women is associated with a decrease in term, singleton, vertex cesarean birth rates.
Maternal Vascular Malperfusion and Adverse Perinatal Outcomes in Low-Risk Nulliparous Women
Authors: Wright Emily , Audette Melanie C. , Ye Xiang Y. , Keating Sarah , Hoffman Barry , Lye Stephen J. , Shah Prakesh S. , Kingdom John C. 
Published: October 2017

OBJECTIVE:
To evaluate the disease burden of placental maternal vascular malperfusion pathology in a low-risk nulliparous population and test the hypothesis that a multiparameter model in the second trimester can predict maternal vascular malperfusion with high precision.

METHODS:
A single-center, prospective cohort study was conducted in healthy nulliparous women. Maternal vascular malperfusion disease burden was estimated by incidence, relative risk (RR), and population-attributable risk percent. Maternal risk factors, serum biomarkers, Doppler, and placental morphologic ultrasonography were examined in isolation and in combination for prediction of this placental pathology.

RESULTS:
The incidence of maternal vascular malperfusion pathology was 8.4% (72/856). Women with pathology had higher risk of preeclampsia (8.33% compared with 1.79%; RR 4.67, 95% CI 1.85–11.77%; population-attributable risk 23.6%, 95% CI 16.9–31.6%), small for gestational age (SGA) (47.22% compared with 9.45%; RR 5.00, 95% CI 3.6–6.93%; population-attributable risk 25.2%, 95% CI 22.1–28.5%), and the composite of adverse outcomes (defined as SGA or preeclampsia) (47.22% compared with 10.59%; RR 4.46, 95% CI 3.25–6.13; population-attributable risk 22.5%, 95% CI 19.8–25.5%). The combination of parameters was superior to individual modalities alone in predicting maternal vascular malperfusion, but achieved only moderate precision (area under the curve 0.77, 95% CI 0.71–0.84).

CONCLUSION:
One in 12 healthy nulliparous women develop maternal vascular malperfusion placental pathology, and these pregnancies had a 4.5 times higher risk of developing preeclampsia or delivering a SGA neonate compared with those without this pathology. A multiparameter model achieved modest precision to predict placental maternal vascular malperfusion. Importantly, in low-risk pregnancies, maternal vascular malperfusion accounts for one fourth of pregnancy outcomes with SGA or preeclampsia. The low population-attributable risk of this placental pathology for SGA and preeclampsia illustrates the importance of discovering novel associations to reduce the disease burden of these pregnancy complications.
A Medically Supervised Pregnancy Exercise Intervention in Obese Women
Authors: Daly Niamh , Farren Maria , McKeating Aoife , O'Kelly Ruth , Stapleton Mary , Turner Michael J. 
Published: October 2017

OBJECTIVE:
To evaluate whether an intensive, medically supervised exercise intervention improved maternal glycemia and gestational weight gain in obese pregnant women when compared with routine prenatal care.

METHODS:
This randomized controlled trial compared a medically supervised exercise intervention with routine prenatal care. The primary outcome was a reduction in mean maternal fasting plasma glucose in the intervention group by 6.9 mg/dL at the time of a 75-g oral glucose tolerance test at 24–28 weeks of gestation. Secondary outcomes included excessive gestational weight gain. The intervention consisted of 50–60 minutes of exercise: warm-up, resistance or weights, aerobic exercises, and cool-down. All women received routine prenatal care. Power calculation determined that 24 women were required per group to detect a difference of 6.9 mg/dL in fasting plasma glucose between groups based on an independent-sample t test for statistical power of 80% at a type I error rate of 0.05. A sample size of 44 per group was planned to allow a dropout rate of 33%.

RESULTS:
From November 2013 through August 2015, 88 women were randomized: 44 each to the exercise and control groups. Eight women in the control group and 11 in the intervention group did not complete the trial at 6 weeks postpartum (P=.61), but 43 in each group attended the 24- to 28-week glucose screen. There were no baseline maternal differences between groups. Classes commenced at a mean of 13 4/7±1 2/7 weeks of gestation. In early pregnancy, 51.1% (n=45/88) had an elevated fasting plasma glucose (92–125 mg/dL). There was no difference in the mean fasting plasma glucose at 24–28 weeks of gestation: 90.0±9.0 mg/dL (n=43) compared with 93.6±7.2 mg/dL (n=43) (P=.13) or in the incidence of gestational diabetes mellitus at 24–28 weeks of gestation: 48.8% (n=21/43) compared with 58.1% (n=25/43) (P=.51) in the control and exercise groups, respectively. At 36 weeks of gestation, excessive gestational weight gain greater than 9.1 kg was lower in the exercise group, 23.5% compared with 45.2% in the control group (P<.05).

CONCLUSION:
An intensive, medically supervised exercise intervention for obese women from early pregnancy did not improve maternal glycemia. Pregnant women who are obese, however, should be advised to exercise because it attenuates excessive gestational weight gain.

CLINICAL TRIAL REGISTRATION:
International Standard Randomised Controlled Trials (ISRCTN) registry, ISRCTN 31045925.
Early Pregnancy Diabetes Screening and Diagnosis
Authors: Mission John F. , Catov Janet , Deihl Tiffany E. , Feghali Maisa , Scifres Christina 
Published: October 2017

OBJECTIVE:
To evaluate the prevalence of early diabetes screening in pregnancy, rates of abnormal diabetes test results before 24 weeks of gestation, and factors associated with early diabetes screening.

METHODS:
This was a retrospective cohort study of all singleton deliveries from 2012 to 2014 among diverse clinical practices at a large academic medical center. We assessed rates of early (less than 24 weeks of gestation) and routine (at or beyond 24 weeks of gestation) diabetes screening, with abnormal test results defined using the Carpenter-Coustan criteria, a 50-g glucose challenge test result greater than 200 mg/dL, or a hemoglobin A1C level greater than 6.5%. Univariate and multivariate analyses were used to evaluate clinical and demographic determinants of screening and diagnosis.

RESULTS:
Overall, 1,420 of 11,331 (12.5%) women underwent early screening. Increasing body mass index (BMI) category, race, public insurance, history of gestational diabetes mellitus, a family history of diabetes, and chronic hypertension were associated with early screening. Early screening rates rose with increasing BMI category, but only 268 of 551 (48.6%) of women with class III obesity underwent early screening. Among those screened early, 2.0% of normal-weight women, 4.0% of overweight women, 4.2% of class I obese women, 3.8% of class II obese women, and 9.0% of class III obese women had abnormal early test results (P<.001).

CONCLUSION:
Early diabetes screening is used inconsistently, and many women with risk factors do not undergo early screening. A significant proportion of women with class III obesity will test positive for gestational diabetes mellitus before 24 weeks of gestation, and studies are urgently needed to assess the effect of early diabetes screening and diagnosis on perinatal outcomes in high-risk women.