bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-Cell Multi-omics Sequencing of Human Early Embryos
Authors: Li Lin , Guo Fan , Gao Yun , Ren Yixin , Yuan Peng , Yan Liying , Li Rong , Lian Ying , Li Jingyun , Hu Boqiang , Gao Junpeng , Wen Lu , Tang Fuchou , Qiao Jie 
Published: January 2019

(Abstracted from Nat Cell Biol 2018;20:847–858)
DNA methylation and chromatin states are critical epigenetic indicators in embryogenesis that have been extensively studied during mouse preimplantation development. DNA methylation dynamics and parental allele-specific DNA methylation in human preimplantation embryos have been analyzed thoroughly; however, chromatin remodeling, parental allele-specific chromatin accessibility, and interrelationships between these omics are not well understood.
Speech Outcomes After LeFort I Advancement Among Cleft Lip and Palate Patients
Authors: Schultz Kelly P. , Braun Tara L. , Hernandez Cristina , Wilson Kristina D. , Moore Ellen E. , Wirthlin John O. , Dempsey Robert F. , Buchanan Edward P. , Monson Laura A. 
Published: January 2019

Background
Velopharyngeal insufficiency (VPI) results from incomplete closure of the velopharyngeal (VP) sphincter with oral pressure consonants during speech. Maxillary hypoplasia is common among cleft children and often requires LeFort I advancement. This results in anterior movement of the soft palate with the bony maxillary segment. Consequently, the size of the VP sphincter is increased and may result postoperative VPI or worsening of prior VPI. To better counsel our patients and their families of the risk of VPI after LeFort I advancement, we chose to evaluate our own cohort.

Methods
We conducted an institutional review board–approved prospective review of all cleft children presenting to Texas Children's Hospital who underwent LeFort I advancement after previous palatoplasty between 2013 and 2016 in a three-surgeon, consecutive patient series. Data collected included age, sex, ethnicity, cleft type, prior secondary speech surgery, presence of preoperative fistula, planned distance of advancement, orthognathic surgery performed, and any concurrent procedures performed. Primary outcomes measured included preoperative and postoperative VP function and hypernasality as measured by a certified speech pathologist.

Results
Velopharyngeal function was unchanged in 67% of our cohort after LeFort I advancement. Of those patients, 83% had evidence of VPI preoperatively, and 17% had normal speech preoperatively. Twenty-two percent of the patients displayed worsening VP function after surgery, and 6% displayed evidence of improvement. Velopharyngeal function was unable to be assessed in 6% of patients. Nasality ratings worsened in 39% of patients, were unchanged in 39%, and improved in 22%. Of the patients with incompetent VP function after surgery, 50% already received or are currently scheduled for secondary speech surgery, 25% declined secondary surgery, and 25% are pending scheduling.

Conclusions
Although VP function remains unchanged in a majority of patients after LeFort I advancement, VPI should be carefully screened for after surgery. If detected, secondary operations to correct speech should be strongly considered.
Quantitative Assessment of Blood Flow in the Gastric Conduit With Thermal Imaging for Esophageal Reconstruction
Authors: Nishikawa Katsunori , Fujita Tetsuji , Yuda Masami , Tanaka Yujiro , Matsumoto Akira , Tanishima Yuichiro , Hanyu Nobuyoshi , Yanaga Katsuhiko 
Published: January 2019

Objective:
The study's primary aim was to evaluate the effectiveness of thermal imaging (TI) and its secondary aim was to compare TI and indocyanine green (ICG) fluorescence angiography, with respect to the evaluation of the viability of the gastric conduit.

Summary Background Data:
The optimal method for evaluating perfusion in the gastric conduit for esophageal reconstruction has not been established.

Methods:
We reviewed the prospectively collected data of 263 patients who had undergone esophagectomy with gastric conduit reconstruction. TI was used in all patients. ICG fluorescence was concomitantly used in 24 patients to aid comparison with TI. A cut-off value of the anastomotic viability index (AVI) was calculated using the receiver operating characteristic curve in TI.

Results:
Anastomotic leak was significantly less common in patients with AVI > 0.61 compared with those with AVI ≤ 0.61 (2% vs 28%, P
< 0.001). Microvascular augmentation was performed in 20 patients with a low AVI score and/or preoperative chemoradiotherapy. Overall ability was comparable between TI and ICG fluorescence regarding the qualitative evaluation of the gastric conduit. However, TI was superior in the quantitative assessment of viability.

Conclusions:
TI could delineate the area of good perfusion in the gastric conduit for esophageal reconstruction, which can help identify patients at high risk of anastomotic leak.
Optical clearing of living brains with MAGICAL to extendin vivoimaging
Authors: Iijima Kouichirou , Oshima Takuto , Kawakami Ryosuke , Nemoto Tomomi 
Published: January 2019

AbstractTo understand brain functions, it is important to observe directly how multiple neural circuits are performing in living brains. However, due to tissue opaqueness, observable depth and spatiotemporal resolution are severely degradedin vivo. Here, we propose an optical brain clearing method forin vivofluorescence microscopy, termed MAGICAL (Magical Additive Glycerol Improves Clear Alive Luminance). MAGICAL enabled two-photon microscopy to capture vivid images with fast speed, at cortical layer V and hippocampal CA1in vivo. Moreover, MAGICAL promoted conventional confocal microscopy to visualize finer neuronal structures including synaptic boutons and spines in unprecedented deep regions, without intensive illumination leading to phototoxic effects. Fluorescence Emission Spectrum Transmissive Analysis (FESTA) showed that MAGICAL improvedin vivotransmittance of shorter wavelength light, which is vulnerable to optical scattering thus unsuited forin vivomicroscopy. These results suggest that MAGICAL would transparentize living brains via scattering reduction.
TaxonKit: a cross-platform and efficient NCBI taxonomy toolkit
Authors: Shen Wei , Xiong Jie 
Published: January 2019

AbstractSummaryTaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. TaxonKit demonstrates competitive performance in execution time compared to similar tools. The efficiency, scalability, and usability of TaxonKit enable researchers to rapidly investigate taxonomy data.AvailabilityTaxonkit is implemented in Go programming language. It is open-source and freely available for download and use from https://github.com/shenwei356/taxonkit.
Circulating metabolites and the risk of type 2 diabetes: a prospective study of 11,896 young adults from four Finnish cohorts
Authors: Ahola-Olli Ari V. , Mustelin Linda , Kalimeri Maria , Kettunen Johannes , Jokelainen Jari , Auvinen Juha , Puukka Katri , Havulinna Aki S. , Lehtimäki Terho , Kähönen Mika , Juonala Markus , Keinänen-Kiukaanniemi Sirkka , Salomaa Veikko , Perola Markus , Järvelin Marjo-Riitta , Ala-Korpela Mika , Raitakari Olli , Würtz Peter 
Published: January 2019

ABSTRACTObjectiveAdvances in metabolomics now allow high-throughput biomarker profiling of large population studies. We aimed to identify circulating metabolic biomarkers predictive of type 2 diabetes in young adults.MethodsNuclear magnetic resonance metabolomics was used to quantify 229 metabolic measures in 11,896 individuals from four Finnish cohorts (mean age 33 years, range 24–45). Associations between baseline metabolites and risk of type 2 diabetes onset during 8–15 years of follow-up (392 incident cases) were assessed by logistic regression adjusted for sex, age, body mass index, and fasting glucose.ResultsOut of 229 metabolic measures, 113 were associated with incident diabetes in meta-analysis of the four cohorts (P<0.0009; odds ratios per 1-SD: 0.59–1.50). Among the strongest predictors of diabetes risk were branched-chained and aromatic amino acids (odds ratios 1.31–1.33), triglyceride fractions within the largest very-low-density lipoprotein particles (VLDL; odds ratios 1.33–1.50)), as well as linoleic omega-6 fatty acids (odds ratio 0.75) and free cholesterol in large high-density lipoprotein particles (HDL; odds ratio 0.59). A biomarker score comprised of phenylalanine, free cholesterol in large HDL, and the ratio of cholesteryl esters to total lipids in large VLDL was predictive of the risk for future diabetes in an independent validation cohort (odds ratio 10.1 [95% confidence intervals 4.2-24.1] comparing individuals in upper vs lower fifth of biomarker score). Adjustment for routine lipids and insulin attenuated the odds ratio to 5.8 [2.2-15.1].ConclusionsMetabolic aberrations across multiple molecular pathways are predictive of the long-term risk of type 2 diabetes in young adults. Comprehensive metabolic profiling may potentially help targeting preventive interventions for young asymptomatic individuals at increased risk for type 2 diabetes.
MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1
Authors: Cairns Junmei , Ingle James N. , Kalari Krishna R. , Shepherd Lois E. , Kubo Michiaki , Goetz Matthew P. , Weinshilboum Richard M. , Wang Liewei 
Published: January 2019

AbstractOur previous GWAS using the MA.27 aromatase inhibitors (AIs) adjuvant trial identified SNPs in the lncRNA MIR2052HG associated with breast cancer free interval. Here we report that MIR2052HG depletion in breast cancer cells results in a decrease in LMTK3 expression and cell growth. Mechanistically, MIR2052HG interacts with EGR1 and facilitates its recruitment to the LMTK3 promoter. LMTK3 sustains ERα levels by reducing PKC activity, resulting in increased ESR1 transcription mediated through AKT/FOXO3 and reduced ERα degradation mediated by the PKC/MEK/ERK/RSK1 pathway. MIR2052HG regulated LMTK3 in a SNP- and aromatase inhibitor - dependent fashion: the variant SNP increased EGR1 binding to LMTK3 promoter in response to androstenedione, relative to wild-type genotype, a pattern that can be reversed by aromatase inhibitor treatment. Finally, LMTK3 overexpression abolished the effect of MIR2052HG on PKC activity and ERα levels. These results reveal a direct role of MIR2052HG in LMTK3 regulation and raise the possibility of targeting MIR2052HG or LMTK3 in ERα-positive breast cancer.
Direct medical and non-medical costs of a one-year care pathway for early breast cancer: results of a French multicenter prospective study
Authors: Héquet Delphine , Huchon Cyrille , Soilly Anne-Laure , Asselain Bernard , Berseneff Hélène , Trichot Caroline , Combes Alix , Alves Karine , Nguyen Thuy , Rouzier Roman , Baffert Sandrine 
Published: January 2019

ABSTRACTIntroductionThe organization of health care for breast (BC) constitutes a public health challenge to ensure quality of care, while also controlling expenditure. Few studies have assessed the global care pathway of early BC patients, including a description of direct medical costs and their determinants.MethodsOPTISOINS01 was a multicenter, prospective, observational study including early BC patients from diagnosis to one-year follow-up. Direct medical costs (in-hospital and out-ofhospital costs, supportive care costs) and direct non-medical costs (transportation and sick leave costs) were calculated by using a cost-of-illness analysis based on a bottom-up approach. Resources consumed were recorded in situ for each patient, using a prospective direct observation method.ResultsData from 604 patients were analyzed. Median direct medical costs of 1 year of management after diagnosis in operable BC patients were €12,250. Factors independently associated with higher direct medical costs were: diagnosis on the basis of clinical signs, invasive cancer, lymph node involvement and conventional hospitalization for surgery. Median sick leave costs were €8,841 per patient and per year. Chemotherapy was an independent determinant of sick leave costs (€3,687/patient/year without chemotherapy versus €10,706 with chemotherapy). Forty percent (n=242) of patients declared additional personal expenditure of €614/patient/year. No drivers of these costs were identified.ConclusionInitial stage of disease and the treatments administered were the main drivers of direct medical costs. Direct non-medical costs essentially consisted of sick leave costs, accounting for one-half of direct medical costs for working patients. Out-of-pocket expenditure had a limited impact on the household.
Absenteeism and indirect costs during the year following the diagnosis of an operable breast cancer
Authors: Ferrier Clement , Thebaut Clémence , Levy Pierre , Baffert Sandrine , Asselain Bernard , Rouzier Roman , Hequet Delphine 
Published: January 2019

AbstractIntroductionThe consequences of disease on work for individual patients as well as the consequences of absenteeism from work are subjects of interest for decision-makers.MethodsWe analyzed duration of absenteeism and related indirect costs for patients with a paid job during the year following diagnosis of early-stage breast cancer in the prospective OPTISOINS01 cohort. A human capital and friction costs approaches were considered for evaluation of lost working days. For this analysis, the friction period was estimated from recent French data. Statistical analysis included simple and multiple linear regression to identify determinants of absenteeism and indirect costs.Results93% of patients had at least one period of sick leave, with an average of 2 periods of sick leave and a mean total duration of 186 days. 24% of patients returned to work part-time after an average sick leave of 114 days (i.e. 41 LWD). Estimated indirect costs were €22,722.00 and €7,724.00 per patient, for the human capital and friction cost approaches, respectively. In the multiple linear regression model, factors associated with absenteeism were: invasive tumor (p=.043), mastectomy (p=.038), redo surgery (p=.002), chemotherapy (p=.027), being a manager (p=.025) or a craftsman (p=.005).ConclusionBreast cancer is associated with long periods of absenteeism during the year following diagnosis, but almost all patients were able to return to work. Major differences in the results were observed between the friction cost and human capital approaches, highlighting the importance of considering both approaches in such studies.
NanoR: a user-friendly R package to analyze and compare nanopore sequencing data
Authors: Bolognini Davide , Bartalucci Niccolò , Mingrino Alessandra , Vannucchi Alessandro Maria , Magi Alberto 
Published: January 2019

AbstractMinION and GridION X5 from Oxford Nanopore Technologies are devices for real-time DNA and RNA sequencing. On the one hand, MinION is the only real-time, low cost and portable sequencing device and, thanks to its unique properties, is becoming more and more popular among biologists; on the other, GridION X5, mainly for its costs, is less widespread but highly suitable for researchers with large sequencing projects. Despite the fact that Oxford Nanopore Technologies’ devices have been increasingly used in the last few years, there is a lack of high-performing and user-friendly tools to handle the data outputted by both MinION and GridION X5 platforms. Here we present NanoR, a cross-platform R package designed with the purpose to simplify and improve nanopore data visualization. Indeed, NanoR is built on few functions but overcomes the capabilities of existing tools to extract meaningful informations from MinION sequencing data; in addition, as exclusive features, NanoR can deal with GridION X5 sequencing outputs and allows comparison of both MinION and GridION X5 sequencing data in one command. NanoR is released as free package for R at https://github.com/davidebolo1993/NanoR.
Dynamic Predictive Accuracy of Electrocardiographic Biomarkers of Sudden Cardiac Death within a Survival Framework: The Atherosclerosis Risk in Communities (ARIC) study
Authors: Perez-Alday Erick A. , Bender Aron , Li-Pershing Yin , German David , Mai Tuan , Mukundan Srini V. , Hamilton Christopher , Thomas Jason , Tereshchenko Larisa G. 
Published: January 2019

AbstractBackgroundThe risk of sudden cardiac death (SCD) is known to be dynamic. However, an accuracy of a dynamic SCD prediction, and “expiration date” of ECG biomarkers is unknown. Our goal was to measure dynamic predictive accuracy of ECG biomarkers of SCD and competing outcomes.MethodsAtherosclerosis Risk In Community study participants with analyzable digital ECGs were included (n=15,768; 55% female, 73% white, age 54.2±5.8 y). ECGs of 5 follow-up visits were analyzed. Global electrical heterogeneity (GEH) and traditional ECG metrics were measured. Adjudicated SCD served as the primary outcome; non-sudden cardiac death served as competing outcome. Time-dependent area under the (receiver operating characteristic) curve (AUC) analysis was performed to assess prediction accuracy of a continuous biomarker in a period of 3,6,9 months, and 1,2,3,5,10, and 15 years, using survival analysis framework.ResultsOver a median 24.4 y follow-up, there were 581 SCDs (incidence 1.77 (95%CI 1.63-1.92)/1,000 person-years), and 838 nonSCDs [2.55 (95%CI 2.39-2.73)]. Resting heart rate was the strongest (AUC 0.930) short-term (3-month) non-specific SCD predictor, whereas spatial peak QRS-T angle predicted specifically SCD 15 years after ECG recording (AUC 0.719). QRS duration (AUC 0.885) and QTc (AUC 0.711) short-term predicted advanced structural heart disease better than SCD. “Expiration date” for most ECG biomarkers was two years after ECG recording. GEH significantly improved reclassification of SCD risk beyond age, sex, race, diabetes, hypertension, coronary heart disease and stroke.ConclusionShort-term predictors of SCD, nonSCD, and biomarkers of long-term SCD risk differed, reflecting differences in transient vs. persistent SCD substrates.
Afferent connections of the primary somatosensory cortex of the mouse for contextual and multisensory processing
Authors: Massé Ian Omer , Blanchet-Godbout Sohen , Bronchti Gilles , Boire Denis 
Published: January 2019

AbstractSensory information is conveyed from peripheral receptors through specific thalamic relays to primary areas of the cerebral cortex. Information is then routed to specialized areas for the treatment of specific aspects of the sensory signals and to multisensory associative areas. Information processing in primary sensory cortices is influenced by contextual information from top-down projections of multiple cortical motor and associative areas as well as areas of other sensory modalities and higher order thalamic nuclei. The primary sensory cortices are thus located at the interface of the ascending and descending pathways. The theory of predictive coding implies that the primary areas are the site of comparison between the sensory information expected as a function of the context and the sensory information that comes from the environment. To better understand the anatomical basis of this model of sensory systems we have charted the cortical and subcortical afferent inputs in the ipsilateral and contralateral hemispheres of the primary somatosensory cortex of adult C57Bl/6 mice. Iontophoretic injections of the b-fragment of cholera toxin were performed inside the mystacial caudal barrel field, more rostral barrel field and somatosensory cortex outside the barrel field to test the hypothesis that differences exist between these three parts and to compare their projections to the subnetworks built from the Mouse Connectome Project data. The laminar distribution of retrogradely labeled cell bodies was used to classify the projections as feedback, feedforward or lateral. Layer indices range between −1 and 1, indicating feedback and feedforward connections respectively. The primary somatosensory cortex and the barrel field have afferent connections with somatosensory areas, non-somatosensory primary sensory areas, multisensory, motor, associative, and neuromodulatory areas. The caudal part of the barrel field displays different and more abundant cortical and subcortical connections compared to the rest of the primary somatosensory cortex. Layer indices of cortical projections to the primary somatosensory cortex and the barrel field were mainly negative and very similar for ipsilateral and contralateral projections. These data demonstrate that the primary somatosensory cortex receives sensory and non-sensory information from cortical and subcortical sources.
EvolvingSTEM: A microbial evolution-in-action curriculum that enhances learning of evolutionary biology and biotechnology
Authors: Cooper Vaughn S. , Warren Taylor M. , Matela Abigail M. , Handwork Michael , Scarponi Shani 
Published: January 2019

AbstractEvolution is a central, unifying theory for all of life science, yet the subject is poorly represented in most secondary-school biology courses, especially in the United States. One challenge to learning evolution is that it is taught as a conceptual, retrospective subject with few tangible outcomes for students. These typical passive learning strategies lead to student disengagement with the material and misunderstanding of evolutionary concepts. To promote greater investment and comprehension, we developed EvolvingSTEM, an inquiry-based laboratory curriculum that demonstrates concepts of natural selection, heredity, and ecological diversity through experimental evolution of a benign bacterium. Students transfer populations ofPseudomonas fluorescensgrowing on plastic beads, which selects for biofilm formation and mutants with new, conspicuous phenotypes. We introduced our curriculum to four introductory high school biology classes alongside their standard curriculum materials and found that students who learned evolution through EvolvingSTEM scored significantly better on a common assessment targeted to Next Generation Science Standards than students taught only the standard curriculum. This latter group subsequently achieved similar scores once they too completed our curriculum. Our work demonstrates that inquiry-based, hands-on experiences with evolving bacterial populations can greatly enhance student learning of evolutionary concepts.