bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Artificial Nipples Among Brazilian Infants and Associated Factors
Authors: Miranda Cristianny , de Sousa Taciana Maia , do Carmo Ariene Silva , Pereira Simone Cardoso Lisboa , Notaro Karine Antunes Marques , dos Santos Luana Caroline 
Published: January 2020

Abstract
Transversal study conducted in a Human Milk Bank to evaluate the factors associated with the use of artificial nipples (pacifier and/or nursing bottle) among Brazilian infants. Analyses were performed using the χ2 test and logistic regression analysis. A total of 6017 nursing mothers were evaluated and the use of artificial nipples was reported by 31.3%. The chance of using artificial nipples was higher among infants whose mothers attended antenatal care in private hospitals [odds ratio (OR): 1.61, 95% confidence interval (CI) 1.21–2.14], born in maternities without the Baby-Friendly Hospital Initiative (BFHI) (OR: 18.38, 95% CI 13.50–25.04) and those with adequate birth weight (OR: 2.83, 95% CI 1.99–4.03). A lower chance of using artificial nipples was observed among infants whose mothers had previous breastfeeding experience (OR: 0.76, 95% CI 0.61–0.95), received guidance on breastfeeding during antenatal care (OR: 0.80, 95% CI 0.65–0.98), practiced exclusive breastfeeding (OR: 0.36, 95% CI 0.28–0.45), breastfeeding on demand (OR: 0.66, 95% CI 0.52–0.85) and residents of inland cities/towns (OR: 0.38, 95% CI 0.20–0.72). The findings highlight the importance of breastfeeding guidance during antenatal care and the role of BFHI in clarifying risks associated with artificial nipple use.
Observational human studies in allergic diseases: design concepts and highlights of recent National Institute of Allergy and Infectious Diseases-funded research
Authors: Rudman Spergel Amanda K. , Togias Alkis 
Published: January 2020

Purpose of review
To present and discuss key design concepts for optimizing the impact of observational studies in the field of allergy and to highlight recent findings from NIAID-funded research networks.

Recent findings
We discuss three concepts. First, the benefit of prospective, longitudinal observational studies exemplified by recent findings on the seasonal nature of all rhinitis phenotypes in children with asthma and the protective effects of high house dust allergen content during the first year of life on the development of asthma at age 7 years. Second, the benefit of detailed (deep) phenotyping exemplified by the identification of a MALT1 gene variant as a strong genetic link to peanut allergy and the determination that atopic dermatitis with food allergy constitutes a distinct cutaneous endotype, compared with atopic dermatitis alone. Third, the benefit of hypothesis-generating research combined with prospective design and deep phenotyping as exemplified by the unveiling of potential pathophysiologic pathways leading to asthma exacerbations in children, after a ‘cold’.

Summary
Observational studies can be highly impactful if designed well. Longitudinal study design, deep phenotyping, and hypothesis-generating research are three major design concepts that should be considered in the development of these studies.
Development and Validation of an UHPLC-MS/MS Assay for the Therapeutic Monitoring of Brivaracetam Plasma Concentrations in Patients with Epilepsy
Authors: Mohamed Susan , Riva Roberto , Contin Manuela 
Published: January 2020

Background:
Brivaracetam is an antiepileptic drug used as an add-on therapy for partial-onset seizures in subjects aged 4 years and older. Owing to potential drug interactions and intersubject variability in plasma concentrations, therapeutic monitoring for brivaracetam may be useful. The aim of this study was to develop a simplified method for measuring brivaracetam plasma concentrations applicable to therapeutic drug monitoring in epilepsy.

Methods:
An ultra high-pressure liquid chromatography–tandem mass spectrometry method was developed and validated according to current guidelines for bioanalytical methods. Sample preparation (100 µL) involved only a simple precipitation step by acetonitrile. Brivaracetam-d7 was used as internal standard. The chromatographic analysis was performed by a Synergi Fusion column using 0.1% formic acid in water/acetonitrile as a binary gradient mobile phase, at a flow rate of 0.3 mL/min. Both brivaracetam and the internal standard eluted at 1.01 minutes. This method was applied to measure trough and 1-hour postmorning dose brivaracetam plasma concentrations of 11 patients with epilepsy.

Results:
The method was validated over a concentration range of 0.10–10 mcg/mL. The mean recovery was 95%. Both intra- and inter-assay imprecision and inaccuracy were <15% for all quality control samples. The lower limit of quantitation and detection was 0.10 and 0.05 mcg/mL, respectively. No interferences or carry-over was observed. Median (25%–75% quartiles) trough and 1-hour postdosing brivaracetam plasma concentrations were 0.61 mcg/mL (0.47–0.83 mcg/mL) and 1.55 mcg/mL (1.24–2.12 mcg/mL), respectively, at a median dose of 80 mg/d (50–150 mg/d). Large, up to 8-fold, intrasubject fluctuations of brivaracetam concentrations between trough and 1-hour postdosing were observed.

Conclusions:
The present assay is faster and simpler than previously published analytical reports for brivaracetam in human plasma and is suitable for therapeutic drug monitoring.
Is it possible to investigate menopausal age? A comparative cross-sectional study of five cohorts between 1968 and 2017 from the Population Study of Women in Gothenburg, Sweden
Authors: Rödström Kerstin , Weman Lilian , Sandin Linda , Hange Dominique , Björkelund Cecilia 
Published: January 2020

Abstract

Objective:
The aim of this study was to examine if the previously found trend of increasing menopausal age is continuing, taking into consideration hormonal use and surgical menopause in both 38- and 50-year-old women of today.

Methods:
Cohort comparisons of five generations of population-based samples of 38- and 50-year-old women from the Prospective Population Study of Women in Gothenburg with start in 1968/1969, and with follow-ups in 1980/1981, 1992/1993, 2004/2005, and 2016/2017. Across the time periods newly recruited women as well as earlier participants were included. Use of hormonal contraceptives, estrogen plus progestogen therapy (EPT), and time for menopause was registered. Changes between different generations of 38- and 50-year-old women from 1968/1969 until today were studied. The overall sample size across the time periods was 1,873 individuals.

Results:
The prevalence of oral contraceptives in 38-year-old women was about 10% in 1968/1969, increasing from 16% in 2004/2005 to almost 22% in 2016/2017. From 2004/2005 the use of hormonal intrauterine contraceptive method (the Levonorgestrel-releasing intrauterine system [LNG-IUS]) increased from about 11% to 14% in 2016/2017. The same pattern was found in 50-year-old women using LNG-IUS, increasing from 6% to 15.5% between 2004/2005 and 2016/2017. The total hormonal use, including LNG-IUS, oral contraceptives, and EPT, was 28% in 50-year-old women in 2016/2017. The total proportion of hormone use in 50-year-old women increased over the years and together with surgical menopause it reached over 37% in the 2016/2017 survey.

Conclusions:
This study has shown an increase in the hormonal use, in both 38- and 50-year-old women, making it difficult to determine when the actual menopause occurs. Thus, the previously found increasing secular trend in menopausal age will be more complicated to assess in female generations of today and tomorrow.
Evaluation and Treatment Patterns of New Low Back Pain Episodes for Elderly Adults in the United States, 2011–2014
Authors: Ly Dan P. 
Published: January 2020

Introduction:
New low back pain (LBP) is a common outpatient complaint. Little is known about how care is delivered over the course of a year to patients who develop new LBP and whether such care patterns are guideline-concordant.

Methods:
This retrospective analysis included Medicare claims of 162,238 opioid-naïve beneficiaries with new LBP from January 1, 2011, through December 31, 2014. Simple rates of modality use [computed tomography and magnetic resonance imaging (advanced imaging), physical therapy (PT), opioid and nonopioid medications] and percentiles (5th percentile, 25th percentile, median, 75th percentile, and 95th percentile) were reported.

Results:
Within the first year, 29.4% [95% confidence interval (CI), 29.1–29.8] of patients with ≥2 visits for new LBP received advanced imaging, and 48.4% (95% CI, 47.7–49.0) of these patients received advanced imaging within 6 weeks of the first visit; 17.3% (95% CI, 17.1–17.6) of patients with ≥2 visits received PT; 42.2% (95% CI, 41.8–42.5) of patients with ≥2 visits received non–steroidal anti-inflammatory drugs (NSAIDs), 16.9% (95% CI, 16.6–17.1) received a muscle relaxant, and 26.2% (95% CI, 25.9–26.6) received tramadol; 32.3% (95% CI, 31.9–32.6) of patients with ≥2 visits received opioids; 52.4% (95% CI, 51.7–53.0) of these patients had not received a prescription NSAID, and 82.2% (95% CI, 81.7–82.7) of these patients had not received PT.

Conclusions:
Many patients who develop new LBP receive guideline nonconcordant care such as early advanced imaging and opioids before other modalities like PT and prescription NSAIDs.
Cancer-associated fibroblasts in cholangiocarcinoma
Authors: Vaquero Javier , Aoudjehane Lynda , Fouassier Laura 
Published: January 2020

Purpose of review
To give a state-of-art knowledge regarding cancer-associated fibroblasts (CAF) in cholangiocarcinoma (CCA) based both on direct evidence and studies on other desmoplastic cancers. High contingency of CAF characterizes CCA, a tumor with a biliary epithelial phenotype that can emerge anywhere in the biliary tree. Current treatments are very limited, the surgical resection being the only effective treatment but restricted to a minority of patients, whereas the remaining patients undergo palliative chemotherapy regimens. In cancer, CAF shape the tumor microenvironment, drive cancer growth and progression, and contribute to drug resistance. All these functions are accomplished through an interplay network between CAF and surrounding cells including tumor and other stromal cells, i.e. immune and endothelial cells.

Recent findings
Several studies have pointed out the existence of CAF sub-populations carrying out several and opposite functions, cancer-promoting or cancer-restraining as shown in pancreatic cancer, another prototypic desmoplastic tumor in which heterogeneity of CAF is well demonstrated.

Summary
New CAF functions are now emerging in pancreatic and breast cancers like the modulation of immune responses or tumor metabolism, opening new area for treatments.
Environmental mixtures and children's health: identifying appropriate statistical approaches
Authors: Tanner Eva , Lee Alison , Colicino Elena 
Published: January 2020

Purpose of reviewBiomonitoring studies have shown that children are constantly exposed to complex patterns of chemical and nonchemical exposures. Here, we briefly summarize the rationale for studying multiple exposures, also called mixture, in relation to child health and key statistical approaches that can be used. We discuss advantages over traditional methods, limitations and appropriateness of the context.Recent findingsNew approaches allow pediatric researchers to answer increasingly complex questions related to environmental mixtures. We present methods to identify the most relevant exposures among a high-multitude of variables, via shrinkage and variable selection techniques, and identify the overall mixture effect, via Weighted Quantile Sum and Bayesian Kernel Machine regressions. We then describe novel extensions that handle high-dimensional exposure data and allow identification of critical exposure windows.SummaryRecent advances in statistics and machine learning enable researchers to identify important mixture components, estimate joint mixture effects and pinpoint critical windows of exposure. Despite many advantages over single chemical approaches, measurement error and biases may be amplified in mixtures research, requiring careful study planning and design. Future research requires increased collaboration between epidemiologists, statisticians and data scientists, and further integration with causal inference methods.
Evaluating the Anatomical Traits of Lip on Three-Dimensional Computed Tomography Images
Authors: Babacan Serdar , Işiklar Sefa , Kafa Ilker Mustafa , Gökalp Gökhan 
Published: January 2020

Background:
Lips and mouth are the most recognizable parts of the lower face. The morphometry of the facial organs is important for the balance of the face. Besides congenital anomalies occur on the lips, some kinds of deformities might be seen because of trauma or carcinoma. In this respect, lips are in the study of plastic surgery, maxillofacial surgery and orthodontics. Lip morphology also takes an important role in forensic facial reconstruction (facial approximation).

Materials and Methods:
Twenty parameters on the soft tissue and 12 parameters on the hard tissue were measured on three dimensional (3D) computed tomography (CT) images belonging 50 individuals (25 female, mean age 35.40 ± 9.97; 25 male, mean age 34.32 ± 11.06).

Results:
Statistical significance was observed on 4 parameters measured at soft tissue and 6 parameters measured in hard tissue. Statistical significance was not seen between the measurements taken bilaterally. Fourteen equations were developed in order to estimate the lip morphometry using the morphometric traits of hard tissue.

Conclusion:
We hope that the results of current study will be useful at surgery and forensic sciences.
Effect of Induced Membrane on Guided Bone Regeneration in an Experimental Calvarial Model
Authors: Altiparmak Nur , Akdeniz Sidika Sinem , Akcay Eda Yilmaz , Bayram Burak , Araz Kenan 
Published: January 2020

Objective:
The aim of this study was to evaluate the effect of induced membrane on guided bone regeneration and to compare its effect with poly-tetra-flourur-ethylene (PTFE) membrane and collagen membrane.

Methods:
Sixteen white Vienna rabbits were used for experiments. Initially 1 defect was created on the parietal bone of all animals and cement was placed inside the defects. After 8 weeks, the bone cements were removed, without damaging the induced membrane formed in the defect cavity. And then 2 more defects were created. All defects were filled with xsenogenic graft materials and were covered with newly formed induced membrane, d-PTFE membrane and collagen membrane. Eight animals were sacrificed at 4th week and other 8 animals were sacrificed at 8th week and all bone specimens were histologically evaluated.

Results:
New bone formation and bone marrow ratios were significantly higher in induced membrane and d-PTFE membrane group compared to collagen membrane group (P < 0.05) at 4th week. Mature bone ratios were significantly higher in induced membrane and d-PTFE membrane group compared to collagen membrane group (P < 0.05) at 8th week. The best CD31 value was detected with d-PTFE membrane group at 4th week and with induced membrane at 8th week.

Conclusion:
Induced membrane can act as a strong barrier membrane and stimulate bone regeneration. Induced membrane technique can be accepted as a good alternative for the reconstruction of critical size defects in maxillofacial region.
Improving Deconvolution Methods in Biology through Open Innovation Competitions: An Application to the Connectivity Map
Authors: Blasco Andrea , Natoli Ted , Endres Michael G. , Sergeev Rinat A. , Randazzo Steven , Paik Jin H. , Maximilian Macaluso N. J. , Narayan Rajiv , Lu Xiaodong , Peck David , Lakhani Karim R. , Subramanian Aravind 
Published: January 2020

AbstractDo machine learning methods improve standard deconvolution techniques for gene expression data? This paper uses a unique new dataset combined with an open innovation competition to evaluate a wide range of gene-expression deconvolution approaches developed by 294 competitors from 20 countries. The objective of the competition was to separate the expression of individual genes from composite measures of gene pairs. Outcomes were evaluated using direct measurements of single genes from the same samples. Results indicate that the winning algorithm based on random forest regression outperformed the other methods in terms of accuracy and reproducibility. More traditional gaussian-mixture methods performed well and tended to be faster. The best deep learning approach yielded outcomes slightly inferior to the above methods. We anticipate researchers in the field will find the dataset and algorithms developed in this study to be a powerful research tool for benchmarking their deconvolution methods and a useful resource for multiple applications.
Impact of trait exaggeration on sex-biased gene expression and genome architecture in a water strider
Authors: Toubiana William , Armisén David , Dechaud Corentin , Arbore Roberto , Khila Abderrahman 
Published: January 2020

AbstractExaggerated secondary sexual traits are widespread in nature and often evolve under strong directional sexual selection. Although heavily studied from both theoretical and empirical viewpoints, we have little understanding of how sexual selection influences sex-biased gene regulation during the development of sex-specific phenotypes, and how these changes are reflected in genomic architecture. This is primarily due to the lack of a representative genome and transcriptomes to study the development of secondary sexual traits. Here we present the genome and developmental transcriptomes, focused on the legs of the water striderMicrovelia longipes, a species where males exhibit strikingly long third legs used as weapons. The quality of the genome assembly is such that over 90% of the sequence is captured in 13 scaffolds. The most exaggerated legs in males were particularly enriched in sex-biased genes, indicating a specific signature of gene expression in association with sex-specific trait exaggeration. We also found that male-biased genes showed patterns of fast evolution compared to non-biased and female-biased genes, indicative of directional or relaxed purifying selection. Interestingly, we found that female-biased genes that are expressed in the third legs only, but not male-biased genes, were over-represented in the X chromosome compared to the autosomes. An enrichment analysis for sex-biased genes along the chromosomes revealed that they can arrange in large genomic regions or in small clusters of two to four consecutive genes. The number and expression of these enriched regions were often associated with the exaggerated legs of males, suggesting a pattern of common regulation through genomic proximity in association with trait exaggeration. Our findings shed light on how directional sexual selection drives sex-biased gene expression and genome architecture along the path to trait exaggeration and sexual dimorphism.
Short-term exposure to high-water temperature causes a shift in the microbiome of the common aquarium spongeLendenfeldia chondrodes
Authors: Vargas Sergio , Leiva Laura , Wörheide Gert 
Published: January 2020

AbstractMarine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of culturedLendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria.Lendenfeldia chondrodesexhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome ofL. chondrodesto short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience ofL. chondrodesand the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
Behavioral evidence for memory replay of video episodes in macaque monkeys
Authors: Zuo Shuzhen , Wang Lei , Shin Junghan , Cai Yudian , Lee Sang Wan , Appiah Kofi , Zhou Yong-di , Kwok Sze Chai 
Published: January 2020

ABSTRACTHumans recall the past by replaying fragments of events temporally. Here, we demonstrate a similar effect in macaques. We trained six rhesus monkeys with a temporal-order judgement (TOJ) task and collected 5000 TOJ trials. In each trial, they watched a naturalistic video of about 10 s comprising two across-context clips, and after a 2-s delay, performed TOJ between two frames from the video. The monkeys apply a non-linear forward, time-compressed replay mechanism during the temporal-order judgement. In contrast with humans, such compression of replay is however not sophisticated enough to allow them to skip over irrelevant information by compressing the encoded video globally. We also reveal that the monkeys detect event contextual boundaries and such detection facilitates recall by an increased rate of information accumulation. Demonstration of a time-compressed, forward replay like pattern in the macaque monkeys provides insights into the evolution of episodic memory in our lineage.Impact StatementMacaque monkeys temporally compress past experiences and use a forward-replay mechanism during judgment of temporal-order between episodes.
A New Model of Genetic Variation and Evolution Evaluates Relative Impacts of Background Selections and Selective Sweeps
Authors: Gu Xun 
Published: January 2020

AbstractIntra-population genetic variation and interspecies divergence in chromosome regions can be considerably affected by different local recombination rates. There are two models: (i) the selective sweeps that reduces the genetic diversity at linked sites and elevates the divergence rate; and (ii) the background selection that reduces the genetic diversity at linked sites and divergence rate. An intriguing question, yet highly controversial, is which one is dominant. In this paper, I develop a framework of generalize background selection, formulated by a diffusion model with two killing functions: the one associated with (negative) background selection is the rate to stop a fixation process of a mutation randomly, and the other associated with positive background selection (selective sweep) is the rate to stop a loss process of a mutation randomly. A simple relationship between the level of reduced diversity and the rate of divergence is derived, depending on the strength of generalized background selection (G) and the proportion of positive background selection (β). We analyzed the interspecies divergence and intra-population diversity in low-recombination regions of three organisms (fruitfly, soybean and human). Strikingly, all datasets demonstrated the dominance of (negative) background selection, and the positive background selection (selective sweeps) only has a small contribution (β∼10%). However, our analysis rejects the notion ofβ=0, namely, a complete negative background selection is unlikely. These findings may shed some lights on the long-term debates around Neutral Theory.