bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging with pre-stack migration based on Sp scattering kernels
Authors: Hua Junlin , Fischer Karen M , Mancinelli Nicholas J , Bao Tiezhao 
Published: October 2019

SUMMARYSp receiver functions have been widely used to detect the lithosphere–asthenosphere boundary (LAB) and other mantle discontinuities. However, traditional common conversion point (CCP) stacking can be biased by the assumption of horizontal layers and this method typically underestimates scattering amplitudes from velocity boundaries with significant dips. A new pre-stack migration method based on recently developed Sp scattering kernels offers an alternative that more accurately captures the timing and amplitude of scattering. When calculating kernels, Sp-S times are estimated with the fast-marching method, and scattering amplitude versus direction, geometrical spreading and phase shifts are accounted for. To minimize imaging artefacts with larger station spacing, Sp receiver functions are interpolated to more closely spaced pseudo-stations using either compressive sampling or spatial averaging algorithms. To test the kernel-based stacking method, synthetic Sp phases were predicted using SPECFEM2D for velocity models with a flat Moho and a negative mantle velocity gradient with a ramp structure. The kernel-based stacking method resolves horizontal interfaces equally well as CCP stacking and outperforms CCP stacking when imaging boundaries with dips of more than 8°, although dip resolution is still limited. Use of more vertically incident phases such as SKSp improves retrieval of dipping discontinuity segments. A second approach is to down-weight the portions of the kernels that have the greatest positive interference among neighbouring stations, thus enhancing scattering from dipping structures where positive interference is lower. With this downweighting, the kernel-based stacking method applied to Sp data is able to continuously resolve LAB discontinuities with dips up to 15° and to partially resolve continuous LAB discontinuities with dips of ∼20°. The intrinsic properties of teleseismic Sp phase kernels limit their ability to resolve LAB structures with dips of ∼20–35°, but still larger dips of ∼40–50° are resolvable with dense and appropriately placed stations. Analysis of Sp scattering kernels also explains the effectiveness of CCP stacking for quasi-horizontal interfaces.
Associations with metabolites in Chinese suggest new metabolic roles in Alzheimer’s and Parkinson’s diseases
Authors: Chai Jin-Fang , Raichur Suryaprakash , Khor Ing Wei , Torta Federico , Chew Wee Siong , Herr Deron Raymond , Ching Jian-Hong , Kovalik Jean Paul , Khoo Chin Meng , Wenk Markus R , Tai E Shyong , Sim Xueling 
Published: October 2019

Abstract
Metabolites are small intermediate products of cellular metabolism perturbed in a variety of complex disorders. Identifying genetic markers associated with metabolite concentrations could delineate disease-related metabolic pathways in humans. We tested genetic variants for associations with 136 metabolites in 1,954 Chinese from Singapore. At a conservative genome-wide threshold (3.7 x 10-10), we detected 1,899 variant-metabolite associations at 16 genetic loci. Three loci (ABCA7, A4GALT, GSTM2) represented novel associations with metabolites, with the strongest association observed between ABCA7 and d18:1/24:1 dihexosylceramide. Among 13 replicated loci, we identified six new variants independent of previously reported metabolite or lipid signals. We observed variant-metabolite associations at two loci (ABCA7, CHCHD2) that have been linked to neurodegenerative diseases. At SGPP1 and SPTLC3 loci, genetic variants showed preferential selectivity for sphingolipids with d16 (rather than d18) sphingosine backbone, including sphingosine-1-phosphate (S1P). Our results provide new genetic associations for metabolites and highlight the role of metabolites as intermediate modulators in disease metabolic pathways.
Breast development and satisfaction in women with disorders/differences of sex development
Authors: van de Grift Tim C , Kreukels Baudewijntje P C ,   dsd-LIFE
Published: October 2019

Abstract

STUDY QUESTION
What are the levels of breast development and satisfaction in women with a Disorder/Difference of Sex Development (DSD)?

SUMMARY ANSWER
Compared with normative data, women with DSD reached lower Tanner stages and reported less breast satisfaction.

WHAT IS KNOWN ALREADY
Women with DSD may have chromosomal and hormonal variations that can impact typical breast development. While much emphasis is placed on genital development in this group, little is known about breast development, satisfaction and their association.

STUDY DESIGN, SIZE, DURATION
Data collection was part of the cross-sectional European multicenter dsd-LIFE study. Fourteen recruiting sites included 1040 participants between February 2014 and September 2015.

PARTICIPANTS/MATERIALS, SETTING, METHODS
A total of 695 female-identifying participants were included (Turner n = 332, 46,XY DSD n = 141 and congenital adrenal hyperplasia n = 222), with a median age of 28 years. Clinical (i.e. history of hormone and surgical treatments, Tanner breast examination) and patient-reported (i.e. breast satisfaction, relationship status, sexual satisfaction and experienced femininity) data was collected by independent trained research staff. The relationship between breast development, satisfaction and femininity was assessed. Control data on breast development and satisfaction in women without DSD was retrieved from the literature.

MAIN RESULTS AND THE ROLE OF CHANCE
Of the 695 participants, 61% had received estrogen replacement and 51% puberty induction therapy, whereas 2% had received breast augmentation surgery. Approximately 65% of participants had reached Tanner breast stage 5, which is substantially less than the general population (90%). Breast satisfaction was lower than normative data as well (P &lt; 0.001, Cohen’s d = 0.45). Breast size and breast satisfaction were associated with feelings of femininity.

LIMITATIONS, REASONS FOR CAUTION
Limitations include the sample representativeness (e.g. regarding the clinical heterogeneity) and the limited in-depth knowledge on (prior) hormonal regimens. Furthermore, no (matched) control data was collected as part of this study.

WIDER IMPLICATIONS OF THE FINDINGS
In order to support the psychosexual well-being of women with DSD, enhancing breast development by sufficient hormone replacement and possible augmentation surgery is advocated. The scope of DSD management should be beyond genital development only and consider breasts as well.

STUDY FUNDING/COMPETING INTEREST(S)
The study was funded by the European Union Seventh Framework Program (FP7/2007–2013) under grant agreement no. 305 373. There are no competing interests.

TRIAL REGISTRATION NUMBER
German Clinical Trials Register: Registration identification number: DRKS00006072.
Attracted to the outside: a meso-scale response pattern of lesser black-backed gulls at an offshore wind farm revealed by GPS telemetry
Authors: Vanermen Nicolas , Courtens Wouter , Daelemans Robin , Lens Luc , Müller Wendt , Van de walle Marc , Verstraete Hilbran , Stienen Eric W M 
Published: October 2019

Abstract
Among seabirds, lesser black-backed gulls (Larus fuscus) are considered to be at high risk of colliding with offshore wind turbines. In this respect, we used GPS tracking data of lesser black-backed gulls caught and tagged in two colonies along the Belgian North Sea coast (Ostend and Zeebrugge) to study spatial patterns in the species’ presence and behaviour in and around the Thornton Bank offshore wind farm (OWF). We found a significant decrease in the number of GPS fixes of flying birds from up to a distance of at least 2000 m towards the middle of the wind farm. Non-flying birds showed a similar avoidance of the wind farm interior, yet presence strongly peaked right at the wind farm’s edge, demonstrated to represent gulls perching on the outer turbine jacket foundations. The findings of this study reveal a strong within-wind farm variability in bird density, a most crucial parameter in collision risk modelling. The method presented here is straightforward and similar studies conducted at other wind farm sites on a range of large gull species (Larus sp.) would allow to assess the potential and species-specific variation in meso-scale response patterns and to gain insight in the underlying ecological incentives, which in turn would provide widely applicable and much-needed input for (cumulative) collision impact assessments.
Comparison of Microneutralization and Histo-Blood Group Antigen–Blocking Assays for Functional Norovirus Antibody Detection
Authors: Atmar Robert L , Ettayebi Khalil , Ayyar B Vijayalakshmi , Neill Frederick H , Braun Ralph P , Ramani Sasirekha , Estes Mary K 
Published: October 2019

Abstract

Background
The development of an in vitro cultivation system for human noroviruses allows the measurement of neutralizing antibody levels.

Methods
Serum neutralizing antibody levels were determined using a GII.4/Sydney/2012-like virus in human intestinal enteroids in samples collected before and 4 weeks after administration of an investigational norovirus vaccine and were compared with those measured in histo-blood group antigen (HBGA)–blocking assays.

Results
Neutralizing antibody seroresponses were observed in 71% of 24 vaccinated adults, and antibody levels were highly correlated (r = 0.82, P < .001) with those measured by HBGA blocking.

Conclusions
HBGA-blocking antibodies are a surrogate for neutralization in human noroviruses.

Clinical Trials Registration
NCT02475278.
Use of electronic medical records to conduct surveillance of malaria among Peace Corps volunteers
Authors: Davlantes Elizabeth , Henderson Susan , Ferguson Rennie W , Lewis Lauren , Tan Kathrine R 
Published: October 2019

Abstract

Objective
The Peace Corps’ disease surveillance for Peace Corps Volunteers (PCVs) was incorporated into an electronic medical records (EMR) system in 2015. We evaluated this EMR-based surveillance system, focusing particularly on malaria as it is deadly but preventable.

Materials and Methods
In 2016, we administered a survey to Peace Corps Medical Officers (PCMOs), who manage PCVs’ medical care, and semistructured phone interviews to headquarters staff. We assessed the structure of the surveillance system and its utility to stakeholders, evaluated surveillance case definitions for malaria, and compared clinical information in the EMR for malaria cases captured by surveillance during the first half of 2016.

Results
Of 131 PCMOs, 77 (59%) completed the survey. Of 53 respondents in malaria-endemic nations, 98% believed most PCVs contact them about possible malaria. Of 134 cases with a malaria clinical diagnosis in the EMR between January and August 2016, 58 (43% sensitivity) were reported to the surveillance system by PCMOs. The remaining cases in the surveillance system were added during data cleaning, which is time-intensive. Among the 48 malaria cases identified by surveillance between January and June 2016, positive predictive value was 67%.

Discussion
Areas for improvement include streamlining PCMO documentation, refining case definitions, and improving data quality. With such improvements, surveillance data can be used to inform epidemiological analysis, clinical care, health education, and policy.

Conclusion
The EMR is an important tool for malaria surveillance among PCVs and, with the refinements mentioned, could serve as a framework for other multinational organizations to monitor their staff.
Selection of Reference Genes for Normalization of Real-Time PCR Data in Calliptamus italicus (Orthoptera: Acrididae) Under Different Temperature Conditions
Authors: Hu Hongxia , Ye Xiaofang , Wang Han , Ji Rong 
Published: October 2019

Abstract
Global warming has dominated worldwide climate change trends, and adaptability to high temperatures is the main factor underlying the spread of the pest Calliptamus italicus in Xinjiang Province, China. However, knowledge about the molecular mechanisms responsible for this adaptability and other related biological properties of C. italicus remain relatively unclear. Real-time quantitative polymerase chain reaction (RT-qPCR) is a key tool for gene expression analysis associated with various biological processes. Reference genes are necessary for normalizing gene expression levels across samples taken from specific experimental conditions. In this study, transcript level of five genes (GAPDH, 18S, TUB, ACT, and EF1α), commonly used as reference genes, were evaluated under nine different temperatures (27, 30, 33, 36, 39, 42, 45, 48, and 51°C) to assess their expression stability and further select the most suitable to be used on normalization of target gene expression data. Gene expression profiles were analyzed using geNorm, NormFinder, and BestKeeper software packages. The combined results demonstrated that the best-ranked reference genes for C. italicus are EF1α, GAPDH, and ACT under different thermal stress conditions. This is the first study that assesses gene expression analysis across a range of temperatures to select the most appropriate reference genes for RT-qPCR data normalization in C. italicus. These results should assist target gene expression analysis associated with heat stress in C. italicus.
Distinct Expression Patterns of Carbonic Anhydrase IX in Clear Cell, Microcystic, and Angiomatous Meningiomas
Authors: Chkheidze Rati , Cimino Patrick J , Hatanpaa Kimmo J , White Charles L , Ferreira Manuel , Piccirillo Sara G M , Li Li , Rajaram Satwik , Nyagilo James O , Burns Dennis K , Raisanen Jack M , Cai Chunyu 
Published: October 2019

Abstract
Clear cell, microcytic, and angiomatous meningiomas are 3 vasculature-rich variants with overlapping morphological features but different prognostic and treatment implications. Distinction between them is not always straightforward. We compared the expression patterns of the hypoxia marker carbonic anhydrase IX (CA-IX) in meningiomas with predominant clear cell (n = 15), microcystic (n = 9), or angiomatous (n = 11) morphologies, as well as 117 cases of other World Health Organization recognized histological meningioma variants. Immunostaining for SMARCE1 protein, whose loss-of-function has been associated with clear cell meningiomas, was performed on all clear cell meningiomas, and selected variants of meningiomas as controls. All clear cell meningiomas showed absence of CA-IX expression and loss of nuclear SMARCE1 expression. All microcystic and angiomatous meningiomas showed diffuse CA-IX immunoreactivity and retained nuclear SMARCE1 expression. In other meningioma variants, CA-IX was expressed in a hypoxia-restricted pattern and was highly associated with atypical features such as necrosis, small cell change, and focal clear cell change. In conclusion, CA-IX may serve as a useful diagnostic marker in differentiating clear cell, microcystic, and angiomatous meningiomas.
Adequacy of Timber Trespass Civil Awards: A Louisiana Case Study
Authors: Mcconnell T Eric , Vanderschaaf Curtis L , Holderieath Jason J , Crosby Michael K 
Published: October 2019

Abstract
Timber trespass in Louisiana is a civil offense punishable by restitution of three times the timber’s current market value, yet whether this compensation level alone is adequate at present is unclear. We modeled a loblolly pine plantation across a range of site qualities in Louisiana. First, we estimated financial returns from a traditional sawtimber rotation using historical state timber prices that included three harvests: two thinnings and a final cut; harvest times differed by site quality. We then assumed all timber was taken at the first thinning. Net present value (NPV) determined appropriateness of compensation at 1×, 2×, and 3× stumpage revenues and was compared to the traditional rotation’s NPV. The NPVs were calculated with and without additional settlement for reforestation costs. We concluded that reforestation costs in addition to 3× stumpage value reimbursement were required to negate the effect of timber prices and better the traditional rotation’s NPV.
Author identification of short texts using dependency treebanks without vocabulary
Authors: Gorman Robert 
Published: October 2019

Abstract
How to classify short texts effectively remains an important question in computational stylometry. This study presents the results of an experiment involving authorship attribution of ancient Greek texts. These texts were chosen to explore the effectiveness of digital methods as a supplement to the author’s work on text classification based on traditional stylometry. Here it is crucial to avoid confounding effects of shared topic, etc. Therefore, this study attempts to identify authorship using only morpho-syntactic data without regard to specific vocabulary items. The data are taken from the dependency annotations published in the Ancient Greek and Latin Dependency Treebank. The independent variables for classification are combinations generated from the dependency label and the morphology of each word in the corpus and its dependency parent. To avoid the effects of the combinatorial explosion, only the most frequent combinations are retained as input features. The authorship classification (with thirteen classes) is done with standard algorithms—logistic regression and support vector classification. During classification, the corpus is partitioned into increasingly smaller ‘texts’. To explore and control for the possible confounding effects of, e.g. different genre and annotator, three corpora were tested: a mixed corpus of several genres of both prose and verse, a corpus of prose including oratory, history, and essay, and a corpus restricted to narrative history. Results are surprisingly good as compared to those previously published. Accuracy for fifty-word inputs is 84.2–89.6%. Thus, this approach may prove an important addition to the prevailing methods for small text classification.
Modifying a covarying protein–DNA interaction changes substrate preference of a site-specific endonuclease
Authors: Laforet Marc , McMurrough Thomas A , Vu Michael , Brown Christopher M , Zhang Kun , Junop Murray S , Gloor Gregory B , Edgell David R 
Published: October 2019

Abstract
Identifying and validating intermolecular covariation between proteins and their DNA-binding sites can provide insights into mechanisms that regulate selectivity and starting points for engineering new specificity. LAGLIDADG homing endonucleases (meganucleases) can be engineered to bind non-native target sites for gene-editing applications, but not all redesigns successfully reprogram specificity. To gain a global overview of residues that influence meganuclease specificity, we used information theory to identify protein–DNA covariation. Directed evolution experiments of one predicted pair, 227/+3, revealed variants with surprising shifts in I-OnuI substrate preference at the central 4 bases where cleavage occurs. Structural studies showed significant remodeling distant from the covarying position, including restructuring of an inter-hairpin loop, DNA distortions near the scissile phosphates, and new base-specific contacts. Our findings are consistent with a model whereby the functional impacts of covariation can be indirectly propagated to neighboring residues outside of direct contact range, allowing meganucleases to adapt to target site variation and indirectly expand the sequence space accessible for cleavage. We suggest that some engineered meganucleases may have unexpected cleavage profiles that were not rationally incorporated during the design process.
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments
Authors: Chèneby Jeanne , Ménétrier Zacharie , Mestdagh Martin , Rosnet Thomas , Douida Allyssa , Rhalloussi Wassim , Bergon Aurélie , Lopez Fabrice , Ballester Benoit 
Published: October 2019

AbstractReMap (http://remap.univ-amu.fr) aims to provide the largest catalogs of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and regulators from DNA-binding experiments in Human and Arabidopsis (Arabidopsis thaliana). In this 2020 update of ReMap we have collected, analyzed and retained after quality control 2764 new human ChIP-seq and 208 ChIP-exo datasets available from public sources. The updated human atlas totalize 5798 datasets covering a total of 1135 transcriptional regulators (TRs) with a catalog of 165 million (M) peaks. This ReMap update comes with two unique Arabidopsis regulatory catalogs. First, a catalog of 372 Arabidopsis TRs across 2.6M peaks as a result of the integration of 509 ChIP-seq and DAP-seq datasets. Second, a catalog of 33 histone modifications and variants across 4.5M peaks from the integration of 286 ChIP-seq datasets. All catalogs are made available through track hubs at Ensembl and UCSC Genome Browsers. Additionally, this update comes with a new web framework providing an interactive user-interface, including improved search features. Finally, full programmatically access to the underlying data is available using a RESTful API together with a new R Shiny interface for a TRs binding enrichment analysis tool.
Discussions of lifestyle habits as an integral part of care management: a cross-sectional cohort study in patients with established rheumatoid arthritis in Sweden
Authors: Malm Karina , Bergman Stefan , Bremander Ann , Larsson Ingrid , Andersson Maria L E ,   BARFOT study group
Published: October 2019

Abstract

Objectives
The primary aim was to determine whether patients with RA recalled having discussions concerning lifestyle habits during their health-care visits. The secondary aim was to study the association between patients' reported lifestyle and their wish to discuss it.

Methods
A postal questionnaire sent to 1542 eligible patients from the Better Anti-Rheumatic Pharmacotherapy (BARFOT) study included questions on lifestyle habits (physical activity, diet, smoking and alcohol), on whether these were discussed during health-care visits and on whether there was an interest in such discussions.

Results
A total of 1061 patients (68%) responded [mean age 67 (s.d. 13) years, 73% women]. Half of the patients (49%) recalled discussions on physical activity, and 23% recalled discussions about diet. Those who reported health-enhancing levels of physical activity were more likely to discuss physical activity with their health professionals. Likewise, patients who reported having a non-traditional mixed diet were more likely to discuss diet. Smoking was discussed with 25% of the patients, more often with current smokers than with non-smokers (32 vs 17%; P < 0.001). Alcohol was discussed with 17% of the patients. Of those patients who reported having hazardous drinking habits, 77% had not discussed alcohol use with any health professional.

Conclusion
Discussions about lifestyle were recalled by half of the patients with established RA. There is a need for improvement, because lifestyle habits may affect the long-term outcome in a chronic disease, such as RA. Patient education concerning lifestyle habits should be an integral part of care management and an interactive process.