bluuebunny/crossref_metadata_2025 huggingface dataset:
GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey – I. A low-frequency extragalactic catalogue
Authors: Hurley-Walker N , Callingham J R , Hancock P J , Franzen T M O , Hindson L , Kapińska A D , Morgan J , Offringa A R , Wayth R B , Wu C , Zheng Q , Murphy T , Bell M E , Dwarakanath K S , For B , Gaensler B M , Johnston-Hollitt M , Lenc E , Procopio P , Staveley-Smith L , Ekers R , Bowman J D , Briggs F , Cappallo R J , Deshpande A A , Greenhill L , Hazelton B J , Kaplan D L , Lonsdale C J , McWhirter S R , Mitchell D A , Morales M F , Morgan E , Oberoi D , Ord S M , Prabu T , Shankar N Udaya , Srivani K S , Subrahmanyan R , Tingay S J , Webster R L , Williams A , Williams C L
Published: September 2016

Using the Murchison Widefield Array (MWA), the low-frequency Square Kilometre Array precursor located in Western Australia, we have completed the GaLactic and Extragalactic All-sky MWA (GLEAM) survey, and present the resulting extragalactic catalogue, utilizing the first year of observations. The catalogue covers 24 831 square degrees, over declinations south of +30° and Galactic latitudes outside 10° of the Galactic plane, excluding some areas such as the Magellanic Clouds. It contains 307 455 radio sources with 20 separate flux density measurements across 72–231 MHz, selected from a time- and frequency-integrated image centred at 200 MHz, with a resolution of ≈2 arcmin. Over the catalogued region, we estimate that the catalogue is 90 per cent complete at 170 mJy, and 50 per cent complete at 55 mJy, and large areas are complete at even lower flux density levels. Its reliability is 99.97 per cent above the detection threshold of 5σ, which itself is typically 50 mJy. These observations constitute the widest fractional bandwidth and largest sky area survey at radio frequencies to date, and calibrate the low-frequency flux density scale of the southern sky to better than 10 per cent. This paper presents details of the flagging, imaging, mosaicking and source extraction/characterization, as well as estimates of the completeness and reliability. All source measurements and images are available online.1 This is the first in a series of publications describing the GLEAM survey results.
Sex Differences and Drug Dose Influence the Role of the α7 Nicotinic Acetylcholine Receptor in the Mouse Dextran Sodium Sulfate-Induced Colitis Model
Authors: AlSharari Shakir D. , Bagdas Deniz , Akbarali Hamid I. , Lichtman Patraic A. , Raborn Erinn S. , Cabral Guy A. , Carroll F. Ivy , McGee Elizabeth A. , Damaj M. Imad
Published: September 2016

Introduction:

α7 nicotinic acetylcholine receptors (nAChRs) play an important role in vagus nerve-based cholinergic anti-inflammatory effects. This study was designed to assess the role of α7 nAChRs in dextran sodium sulfate (DSS)-induced colitis in male and female mouse. We first compared disease activity and pathogenesis of colitis in α7 knockout and wild-type mice. We then evaluated the effect of several α7 direct and indirect agonists on the severity of disease in the DSS-induced colitis.

Methods:

Male and female adult mice were administered 2.5% DSS solution freely in the drinking water for 7 consecutive days and the colitis severity (disease activity index) was evaluated as well as colon length, colon histology, and levels of tumor necrosis factor-alpha colonic levels.

Results:

Male, but not female, α7 knockout mice displayed a significantly increased colitis severity and higher tumor necrosis factor-alpha levels as compared with their littermate wild-type mice. Moreover, pretreatment with selective α7 ligands PHA-543613, choline, and PNU-120596 decreased colitis severity in male but not female mice. The anti-colitis effects of these α7 compounds dissipated when administered at higher doses.

Conclusions:

Our results suggest the presence of a α7-dependent anti-colitis endogenous tone in male mice. Finally, our results show for the first time that female mice are less sensitive to the anti-colitis activity of α7 agonists. Ovarian hormones may play a key role in the sex difference effect of α7 nAChRs modulation of colitis in the mouse.

Implications:

Our collective results suggest that targeting α7 nAChRs could represent a viable therapeutic approach for intestinal inflammation diseases such as ulcerative colitis with the consideration of sex differences.
Adam Smith, Watch Prices, and the Industrial Revolution *
Authors: Kelly Morgan , Ó Gráda Cormac
Published: September 2016

Although largely absent from modern accounts of the Industrial Revolution, watches were the first mass-produced consumer durable and were Adam Smith’s preeminent example of technological progress. In fact, Smith makes the notable claim that watch prices may have fallen by up to 95% over the preceding century, a claim that this article attempts to evaluate. We look at changes in the reported value of over 3,200 stolen watches from criminal trials in the Old Bailey in London from 1685 to 1810. Before allowing for quality improvements, we find that the real price of watches in nearly all categories falls steadily by 1.3% a year, equivalent to a fall of 75% over a century, showing that sustained innovation in the production of a highly complex artifact had already appeared in one important sector of the British economy by the early eighteenth century.
Exposed to an Accumulation of Burdensome Feelings
Authors: Vatne Solfrid
Published: September 2016

Seriously mentally ill patients' unusual behavior is considered challenging in caring relationships, but we know little about how this affects mental health nurses' vulnerability. This article uses a phenomenological design inspired by Heidegger's philosophy with the results of fieldwork and reflection groups with 11 nurses on an acute ward. The nurses were exposed to an accumulation of negative emotions, caused by potentially or actually harmful scenarios that were more extreme than those in other nursing contexts. They protected themselves through limit-setting approaches, which conflicted with their standards of building trusting relationships with patients. The feeling of guilt might function as an appeal for authentic practice, but a change in practice requires the use of acknowledgment approaches and the systematic debriefing of accumulated burdensome feelings.
Simultaneous bilateral avulsion fracture of the anterior–superior iliac spine in a teenager: a case report with a literature review
Authors: Yin Hao , Huang Zhang , Pan Zhengjun
Published: September 2016

An anterior–superior iliac spine avulsion fracture is an uncommon injury in adolescent athletes and simultaneous bilateral avulsion fracture is fairly rare. The authors report cases of traumatic avulsion fractures of anterior–superior iliac spine after sports activity in teenagers. Open reduction and cannulate screws fixation resulted in an excellent functional outcome for this relatively uncommon fracture. The authors also stress the importance of careful clinical examination and recommend open reduction and internal fixation for patients requiring rapid rehabilitation.
Advancing the Measurement of Care Coordination in Pediatric Behavioral Health
Authors: Jorina Maria , Cammaerts Ayesha , Singer Janice , Ozonoff Al , Chan Eugenia , Antonelli Richard , Gurvitz Michelle , Jenkins Kathy
Published: September 2016

Objective:

To describe the measure review and evaluation process used to identify new measures of care coordination for children with behavioral health needs conducted as part of Massachusetts' Children's Health Insurance Program Reauthorization Act Quality Demonstration Grant.

Method:

The Massachusetts Child Health Quality Coalition identified a shortage of pediatric measures of care coordination in behavioral health. After an extensive literature review, the Measure Development Committee applied the Care Coordination Key Elements Framework (Framework), which was designed as part of the grant work, and used a modified RAND Delphi method to conduct feasibility and validity evaluation and propose the new candidate measures for further rigorous testing.

Results:

Thirty-two measures were evaluated. One existing Healthcare Effectiveness Data and Information Set and 8 newly proposed measures met the criteria for feasibility and reliability. These measures represented each of the key elements contained in the Framework. The measures need further testing to ensure scientific acceptability and wide usability.

Conclusion:

A multipronged methodology was used to propose measures of care coordination in the space of pediatric behavioral health to fill the identified gaps in existing measures.
A Model for Staffing and Scheduling at Emergency Center Pharmacies
Authors: Ait Aiss Mohamed , Burke Laura , Dozier Dawn
Published: September 2016

Optimization of staffing and scheduling is critical for maximizing efficiency and providing safe patient care. The Emergency Center (EC) at The University of Texas MD Anderson Cancer Center treats 60 to 80 patients per day. The EC pharmacy processes and fills medication orders for EC patients 24 hours a day and fills medication orders for other clinics as needed after other pharmacies close. To identify ways to improve staffing and scheduling, we assessed needs for pharmacists and technicians in the pharmacy at different times of day and on different days of the week. All work activities done in the pharmacy were tabulated and then evaluated using time-motion analysis to determine standard times for each activity. Data were then analyzed from multiple institutional sources to determine the frequency of each activity by hour of day for weekdays and weekends. We developed Microsoft Excel macros to calculate recommended staffing for each position under baseline conditions and with changes in patient volume and work distribution. A scheduling tool was programmed to allow comparison of current staff schedules with staffing needs. Shift start times and shift lengths can be modified in the tool to change the number of staff at each hour of the day. These changes automatically update graphs that display recommended staffing and proposed staffing. This tool allows leadership to experiment with new staffing schedules in order to determine optimal coverage. The staffing model and scheduling tool can be used by the EC pharmacy to ensure appropriate staffing, create a safer environment in the EC, and provide the best care for patients.
Laser and Other Light-Emitting Medical Devices Used in Healthcare Settings—Considerations Regarding Device Safety
Authors: Erchul Daniel , Kaushiva Anchal , Ogden Neil
Published: September 2016

Light-emitting medical devices are used for a variety of purposes in healthcare facilities, and these devices can differ widely in output characteristics, indications for use, and in safety precautions. This article is intended to provide some technical background, applications, and common safety considerations for these devices. It also touches on the mechanisms for reporting serious adverse effects and medical device malfunctions involving these devices to the US Food and Drug Administration.
Design and Testing of a Novel Slot Retractor for Neonatal Frenotomy
Authors: Rahman Tariq , Tran Nghia N. , Jani Gita , Udenze-Utah Chinedum N. , Siddiqui Shehla S. , Golub Leonard M. , Restrepo-Ormsby Adriana , Shaffer Thomas H.
Published: September 2016

A new slot retractor for frenotomy has been developed that offers a unique design that will lead to fewer complications and allow primary care physicians (neonatologists, pediatricians, family physicians) to perform frenotomy in the nursery or office. The novel 3-dimensional printed retractor has side walls for better tissue protection, a built-in slot, and an ergonomic handle. An efficacy and safety study was conducted with 43 infants with the newly designed slot retractor. Results showed that there were no partial divisions at discharge; all babies were able to breastfeed almost immediately after frenotomy and continued to breastfeed until hospital discharge, and there were no adverse events.
Primary Mediastinal Yolk Sac Tumors: An Immunohistochemical Analysis of 14 Cases
Authors: Weissferdt Annikka , Kalhor Neda , Rodriguez Canales Jaime , Fujimoto Junya , Wistuba Ignacio I. , Moran Cesar A.
Published: September 2016

Primary mediastinal germ cell tumors are uncommon tumors that can pose diagnostic difficulties due to their morphologic spectrum and unusual site. Immunohistochemistry plays an increasing role in the diagnosis of these tumors. Whereas the immunophenotype of testicular yolk sac tumors (YST) is rather well known, the opposite is true for primary mediastinal YST leading us to investigate the immunohistochemical features of 14 such neoplasms. Fourteen cases of primary mediastinal YST were reviewed and representative whole tissue sections were selected for immunohistochemical analysis using antibodies directed against CAM5.2, SALL4, OCT3/4, glypican-3, CD30, α-fetoprotein (AFP), CD117, placental alkaline phosphatase (PLAP), GATA-3, and CDX2. The percentage of positive tumor cells and the intensity of staining were evaluated and scored. All cases (100%) showed strong and diffuse expression of CAM5.2 and SALL4, 10 cases (71%) reacted with glypican-3 and AFP in a patchy manner, 5 cases (36%) showed focal positivity with PLAP and GATA-3, 4 cases (29%) showed staining for CDX2, 3 (21%) showed expression of CD117, and a single case was positive for CD30 (7%). None of the cases showed any staining for OCT3/4. Primary mediastinal YST appear to have a similar immunohistochemical phenotype as their testicular counterparts. Coexpression of CAM5.2, SALL4, glypican-3, and AFP provides the best support for YST differentiation; however, it has to be noted that none of these markers is specific for these tumors and immunohistochemical results will always have to be interpreted in the context of morphologic, clinical, and radiologic information.
Managing Incidental Lung Nodules in Patients With a History of Oncologic Disease
Authors: Occhipinti Mariaelena , Heidinger Benedikt H. , Pfannenberg Christina , Munden Reginald F. , Eisenberg Ronald L. , Bankier Alexander A.
Published: September 2016

Purpose:

The aim of this study was to analyze the impact that a clinical history of an oncologic disease may have on the management decisions for incidentally detected lung nodules on chest computed tomographic (CT) examinations.

Materials and Methods:

An electronic survey was sent to all 796 members of the Society of Thoracic Radiology regarding criteria for the management of incidentally detected lung nodules in oncologic patients, as well as recommendations for nodule follow-up. Nodule characteristics and clinical parameters used by respondents were analyzed. Differences between variables were examined using the χ2 test.

Results:

Of the 796 Society of Thoracic Radiology members, 178 (22.36%) replied. Most respondents were subspecialized in cardiothoracic imaging (92.70%) and practiced in an “academic or teaching hospital setting” (75.28%) with a “dedicated oncology center” (94.03%). “History of oncologic disease” was the most important factor (98.87%) for management decisions. In patients with such a history, respondents most commonly used “experience and common sense” (56.74%) and reported “all incidentally found lung nodules” (65.73%, P<0.0001). “Size” and “shape” were the 2 most important nodule characteristics (33.61% and 27.05%, respectively) used to consider a nodule “clinically relevant,” and “size” (44.07%) was also the most important nodule characteristic prompting recommendation for short-term CT follow-up. Follow-up CT examinations in oncologic patients were recommended by 75.84% of respondents.

Conclusions:

In patients with a history of oncologic disease, radiologists tend to report every detected nodule and to routinely recommend follow-up CT examinations. Although most radiologists rely on “experience and common sense” in managing these nodules, greater standardization of lung nodule management in oncologic patients is needed, ideally through guidelines tailored to this patient population.
Application of the stochastic labeling methods with random-sequence barcodes for simultaneous quantification and sequencing of environmental 16S rRNA genes
Authors: Hoshino Tatsuhiko , Inagaki Fumio
Published: September 2016

Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5’ end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103to 5.0 × 104copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.
Identification of outcome-related driver mutations in cancer using conditional co-occurrence distributions
Authors: Treviño Victor , Martínez-Ledesma Emmanuel , Tamez-Peña José
Published: September 2016

The methods proposed for the detection of cancer driver mutations are based on the estimation of background mutation rate, impact on protein function, or network influence. Instead, we focus on those influencing patient survival. For this, an approximation of the log-rank test has been systematically applied even though it assumes a large and similar number of patients in both risk groups, which is violated in cancer genomics. Here, we propose VALORATE, a novel algorithm for the estimation of the null distribution for the log-rank test independently of the number of mutations. VALORATE is based on conditional distributions of the co-occurrences between events and mutations. The results using simulations, comparisons with other methods, TCGA and ICGC cancer datasets, and validations, suggests that VALORATE is accurate, fast, and can identify known and novel gene mutations. Our proposal and results may have important implications in cancer biology, in bioinformatics analyses, and ultimately in precision medicine.
kWIP: Thek-mer Weighted Inner Product, ade novoEstimator of Genetic Similarity
Authors: Murray Kevin D. , Webers Christfried , Ong Cheng Soon , Borevitz Justin , Warthmann Norman
Published: September 2016

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals or samples in an unbiased manner, preferablyde novo. The rapid and unbiased estimation of genetic relatedness has the potential to overcome reference genome bias, to detect mix-ups early, and to verify that biological replicates belong to the same genetic lineage before conclusions are drawn using mislabelled, or misidentified samples.

We present thek-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity.kWIPcombines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from theirk-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include detecting sample identity and mix-up, non-obvious genomic variation, and population structure.

We show thatkWIPcan reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses.kWIPis written in C++, licensed under the GNU GPL, and is available fromhttps://github.com/kdmurray91/kwip.

Author Summary

Current analysis of the genetic similarity of samples is overly dependent on alignment to reference genomes, which are often unavailable and in any case can introduce bias. We address this limitation by implementing an efficient alignment free sequence comparison algorithm (kWIP). The fast, unbiased analysiskWIPperforms should be conducted in preliminary stages of any analysis to verify experimental designs and sample metadata, catching catastrophic errors earlier.

kWIPextends alignment-free sequence comparison methods by operating directly on sequencing reads.kWIPuses an entropy-weighted inner product overk-mers as a estimator of genetic relatedness. We validatekWIPusing rigorous simulation experiments. We also demonstrate high sensitivity and accuracy even where there is modest divergence between genomes, and/or when sequencing coverage is low. We show high sensitivity in replicate detection, and faithfully reproduce published reports of population structure and stratification of microbiomes. We provide a reproducible workflow for replicating our validation experiments.

kWIPis an efficient, open source software package. Our software is well documented and cross platform, and tutorial-style workflows are provided for new users.
Antibiotic susceptibility of bacterial colonies: An assay and experiments withStaphylococcus aureus
Authors: Shao Xinxian , Kim Justin , Jeong Ha Jun , Levin Bruce
Published: September 2016

A method is presented to evaluatein vitrothe efficacy of antibiotics to treat bacteria growing as discrete colonies on surfaces and the contribution of the colony structure to the antibiotic susceptibility of bacteria. Using this method, we explored the relative efficacy of six bactericidal and three bacteriostatic antibiotics to inhibit the growth and killStaphylococcus aureuscolonies of different sizes, densities and ages. As measured by the reduction in viable cell density relative to untreated controls, of the bactericidal drugs tested ciprofloxacin and gentamicin were most effective. By this criteria, ampicillin was more effective than oxacillin. Daptomycin and vancomycin were virtually ineffective for treatingS. aureusgrowing as colonies. The bacteriostatic antibiotic tested, tetracycline, linezolid and erythromycin were all able to prevent the growth ofS. aureuscolonies and did so even more effectively than daptomycin, which is highly bactericidal in liquid culture. The results of these experiments and other observations suggest that relative inefficacy of oxacillin, vancomycin and daptomycin to killS. aureusin colonies is due to the density and physiological state of the bacteria rather than the inability of these drugs to penetrate the colonies. The methods developed here are general and can be used to explore the efficacy of antibiotics to treat bacteria growing in biofilms as well as discrete colonies.
Aerobic H2respiration enhances metabolic flexibility of methanotrophic bacteria
Authors: Carere Carlo R. , Hards Kiel , Houghton Karen M. , Power Jean F. , McDonald Ben , Collet Christophe , Gapes Daniel J. , Sparling Richard , Cook Gregory M. , Greening Chris , Stott Matthew B.
Published: September 2016

Methanotrophic bacteria are important soil biofilters for the climate-active gas methane. The prevailing opinion is that these bacteria exclusively metabolise single-carbon, and in limited instances, short-chain hydrocarbons for growth. This specialist lifestyle juxtaposes metabolic flexibility, a key strategy for environmental adaptation of microorganisms. Here we show that a methanotrophic bacterium from the phylum Verrucomicrobia oxidises hydrogen gas (H2) during growth and persistence.Methylacidiphilumsp. RTK17.1 expresses a membrane-bound hydrogenase to aerobically respire molecular H2at environmentally significant concentrations. While H2oxidation did not support growth as the sole electron source, it significantly enhanced mixotrophic growth yields under both oxygen-replete and oxygen-limiting conditions and was sustained in non-growing cultures starved for methane. We propose that H2is consumed by this bacterium for mixotrophic growth and persistence in a manner similar to other non-methanotrophic soil microorganisms. We have identified genes encoding oxygen-tolerant uptake hydrogenases in all publicly-available methanotroph genomes, suggesting that H2oxidation serves a general strategy for methanotrophs to remain energised in chemically-limited environments.
Lipid metabolic perturbation is an early-onset phenotype in adultspinmutants: aDrosophilamodel for lysosomal storage disorders
Authors: Hebbar Sarita , Khandelwal Avinash , Jayashree R , Hindle Samantha J. , Chiang Yin Ning , Yew Joanne Y. , Sweeney Sean T. , Schwudke Dominik
Published: September 2016

Intracellular accumulation of lipids and swollen dysfunctional lysosomes are linked to several neurodegenerative diseases including lysosomal storage disorders (LSD). A detailed characterization of lipid metabolic changes in relation to the onset and progression of neurodegeneration is currently missing. In this study, we systematically analyzed lipid perturbations inspinster (spin)mutants, aDrosophilamodel of neurodegeneration associated with LSD. Our results highlight an imbalance in brain ceramide and sphingosine as a crucial phenotype in the early stages of neurodegeneration. This perturbation in ceramide metabolism precedes the accumulation of endomembranous structures, manifestation of altered behavior and buildup of lipofuscin (the ageing pigment). Manipulating levels ofceramidase, and, consequently further altering these lipids inspinmutants have allowed us to conclude that ceramide/sphingosine homeostasis is the driving force in disease progression and is integral tospinfunction in the adult nervous system. Furthermore, we have identified 29 novel and direct interaction partners of Spin. We specifically focused on the lipid carrier protein, Lipophorin (Lpp), and demonstrate its localization with Spin in the adult nervous system and in organs specialized for lipid metabolism including fat bodies and oenocytes. Our observations inspinmutants of altered Lpp immunostaining, and of increased levels of lipid metabolites produced by oenocytes, allude to a functional relevance of the Spin-Lpp interaction.

Overall, these results detailing the kinetics of ceramide perturbations in the context of lipofuscin accumulation, as well as the proteomics experiment, represent a valuable resource to further unravel the mechanistic link between systemic changes in lipid metabolism and lysosomal storage disorders.

Summary Statement

Elevations in specific brain lipids and connections to relevant metabolic genes are identified in a fly model for lysosomal storage disorders. This enables a better understanding of disease progression.
The species problem from the modeler’s point of view
Authors: Manceau Marc , Lambert Amaury
Published: September 2016

How to define a partition of individuals into species is a long-standing question called thespecies problemin systematics. Here, we focus on this problem in the thought experiment where individuals reproduce clonally and both the differentiation process and the population genealogies are explicitly known. We point out three desirable properties of species partitions: (A) Heterotypy between species, (B) Homotypy within species and (M) Monophyly of each species. We then ask: How and when is it possible to delineate species in a way satisfying these properties?

We point out that the three desirable properties cannot in general be satisfied simultaneously, but that any two of them can. We mathematically prove the existence of the finest partition satisfying (A) and (M) and the coarsest partition satisfying (B) and (M). For each of them, we propose a simple algorithm to build the associated phylogeny out of the genealogy.

The ways we propose to phrase the species problem shed new light on the interaction between the genealogical and phylogenetic scales in modeling work. The two definitions centered on the monophyly property can readily be used at a higher taxonomic level as well, e.g. to cluster species into monophyletic genera.
Evapotranspiration is resilient in the face of land cover and climate change in a humid temperate catchment
Authors: Hamilton S. K. , Hussain M. Z. , Lowrie C. , Basso B. , Robertson G. P.
Published: September 2016

In temperate humid catchments, evapotranspiration returns more than half of the annual precipitation to the atmosphere, thereby determining the balance available to recharge groundwaters and support stream flow and lake levels. Changes in evapotranspiration rates and therefore catchment hydrology could be driven by changes in land use or climate. Here we examine the catchment water balance over the past 50 y for a catchment in southwest Michigan covered by cropland, grassland, forest, and wetlands. Over the study period about 27% of the catchment has been abandoned from row-crop agriculture to perennial vegetation and about 20% of the catchment has reverted to deciduous forest, and the climate has warmed by 1.14°C. Despite these changes in land use, precipitation and stream discharge, and by inference catchment-scale evapotranspiration, have been stable over the study period. The remarkably stable rates of evapotranspirative water loss from the catchment across a period of significant land cover change suggest that rainfed annual crops and perennial vegetation do not differ greatly in evapotranspiration rates, and this is supported by measurements of evapotranspiration from various vegetation types based on soil water monitoring in the same catchment. Compensating changes in the other meteorological drivers of evaporative water demand besides air temperature—wind speed, atmospheric humidity, and net radiation—are also possible, but cannot be evaluated due to insufficient local data across the 50-y period. Regardless of the explanation, this study shows that the water balance of this landscape has been resilient in the face of both land cover and climate change over the past 50 y.
Better together: a transboundary approach to brown bear monitoring in the Pyrenees
Authors: Piédallu Blaise , Quenette Pierre-Yves , Jordana Ivan Afonso , Bombillon Nicolas , Gastineau Adrienne , Jato Ramón , Miquel Christian , Muñoz Pablo , Palazón Santiago , Solà de la Torre Jordi , Gimenez Olivier
Published: September 2016

Human administrative borders have no effect on wild animals, and the vast home ranges of large carnivores often cause them to live simultaneously on the territory of two or more countries or jurisdictions with different management policies. Here, we investigate the importance of transboundary population monitoring using as a case study the Pyrenean brown bear population (Ursus arctos) that lives in France, Andorra and Spain. Using capture-recapture models and the Pollock’s robust design, we estimated abundance and demographic parameters using data collected separately in France and Spain and a dataset gathered from joint monitoring on both sides of the border. As expected, the abundance estimates from French (from 11 bears in 2008 to 13 in 2014) or Spanish (from 4 bears in 2008 to 9 in 2014) data only were lower than abundance obtained from both sides of the border (from 11 in 2008 to 18 in 2014). The joint monitoring dataset also highlighted the importance of individual detection heterogeneity that, if ignored, would lead to underestimation. Our results reinforce the importance of transboundary cooperation when dealing with animal populations with territory spanning two or more administrative jurisdictions for collecting reliable scientific data and providing relevant abundance estimation to take sound management decisions.
Insertional mutagenesis in PLNR9Ctransgenic mouse: a case report and a review of the literature on cardiac-specific transgenic expression
Authors: Kraev Alexander
Published: September 2016

A mouse line with heterozygous transgenic expression of phospholamban carrying a substitution of cysteine for arginine 9 (PLNR9C) under the control of α-myosin heavy chain (αMHC) promoter features dilated cardiomyopathy, heart failure and premature death. In this line the transgenic array of 13 PLNR9Cexpression cassettes, arranged in a head-to-tail tandem orientation, has integrated into the homologous genomic site, the bi-directional promoter of the αMHC (Myh6) gene and the gene for the regulatory non-coding RNA Myheart (Mhrt), both of which are involved in the execution of the α/β MHC switch during cardiac development and pathology. PLNR9Coverexpression is evident at the age of 1 month but declines dramatically along with a less pronounced concomitant decline of the resident PLN expression, until the animals die. Expression of the non-coding RNA Mhrt in PLNR9Cmice also exhibits a profound deregulation, despite the presence of the second, intact allele. Hence the mouse strain does not faithfully model a human PLNR9Cheterozygote, wherein both the mutant and the wildtype PLN alleles have, in all likelihood, the same temporal expression profile. The intricate regulatory circuit of the α/β MHC switch, involving the non-coding RNA Mhrt, was described in detail only recently, and since publications about αMHC-driven transgenes rarely contain the definition of the transgene integration site or temporal expression profile, it is suggested that some of the pathological phenomena attributed to expression of αMHC-driven transgenes may have an alternative explanation.
RNA–DNA sequence differences in Saccharomyces cerevisiae
Authors: Wang Isabel X. , Grunseich Christopher , Chung Youree G. , Kwak Hojoong , Ramrattan Girish , Zhu Zhengwei , Cheung Vivian G.
Published: September 2016

Alterations of RNA sequences and structures, such as those from editing and alternative splicing, result in two or more RNA transcripts from a DNA template. It was thought that in yeast, RNA editing only occurs in tRNAs. Here, we found that Saccharomyces cerevisiae have all 12 types of RNA–DNA sequence differences (RDDs) in the mRNA. We showed these sequence differences are propagated to proteins, as we identified peptides encoded by the RNA sequences in addition to those by the DNA sequences at RDD sites. RDDs are significantly enriched at regions with R-loops. A screen of yeast mutants showed that RDD formation is affected by mutations in genes regulating R-loops. Loss-of-function mutations in ribonuclease H, senataxin, and topoisomerase I that resolve RNA–DNA hybrids lead to increases in RDD frequency. Our results demonstrate that RDD is a conserved process that diversifies transcriptomes and proteomes and provide a mechanistic link between R-loops and RDDs.
Thermographic measurements of the commercial laser powder bed fusion process at NIST
Authors: Lane Brandon , Moylan Shawn , Whitenton Eric P. , Ma Li
Published: September 2016

Purpose

Quantitative understanding of the temperatures, gradients and heating/cooling rates in and around the melt pool in laser powder bed fusion (L-PBF) is essential for simulation, monitoring and controls development. The research presented here aims to detail experiment design and preliminary results of high speed, high magnification, in-situ thermographic monitoring setup on a commercial L-PBF system designed to capture temperatures and dynamic process phenomena.

Design/methodology/approach

A custom door with angled viewport was designed for a commercial L-PBF system which allows close access of an infrared camera. Preliminary finite element simulations provided size, speed and scale requirements to design camera and optics setup to capture melt pool region temperatures at high magnification and frame rate speed. A custom thermal calibration allowed maximum measurable temperature range of 500°C to 1,025°C. Raw thermographic image data were converted to temperature assuming an emissivity of 0.5. Quantitative temperature results are provided with qualitative observations with discussion regarding the inherent challenges to future thermographic measurements and process monitoring.

Findings

Isotherms around the melt pool change in size depending on the relative location of the laser spot with respect to the stripe edges. Locations near the edges of a stripe are cooled to lower temperatures than the center of a stripe. Temperature gradients are highly localized because of rough or powdery surface. At a specific location, temperatures rise from below the measurable temperature range to above (<550°C to >1100°C) within two frames (<1.11 m/s). Particle ejection is a notable phenomenon with measured ejection speeds >11.7 m/s.

Originality/value

Several works are detailed in the Introduction of this paper that detail high-speed visible imaging (not thermal imaging) of custom or commercial LBPF processes, and lower-speed thermographic measurements for defect detection. However, no work could be found that provides calibrated, high-speed temperature data from a melt-pool monitoring configuration on a commercial L-PBF system. In addition, the paper elucidates several sources of measurement uncertainty (e.g. calibration, emissivity and time and spatial resolution), describes inherent measurement challenges based on observations of the thermal images and discusses on the implications to model validation and process monitoring and control.
Constructions, reconstructions and deconstructions of ‘family’ amongst people who live apart together (LATs)
Authors: Stoilova Mariya , Roseneil Sasha , Carter Julia , Duncan Simon , Phillips Miranda
Published: September 2016

This article explores how people who live apart from their partners in Britain describe and understand ‘family’. It investigates whether, and how far, non‐cohabiting partners, friends, ‘blood’ and legal ties are seen as ‘family’, and how practices of care and support, and feelings of closeness are related to these constructions. It suggests that people in LAT relationships creatively draw and re‐draw the boundaries of family belonging in ways that involve emotionally subjective understandings of family life, and that also refer to normative constructions of what ‘family’ ought to be, as well as to practical recognitions of lived family ‘realities’. This often involves handling uncertainties about what constitutes ‘family’.
The Predictive Value of Preendoscopic Risk Scores to Predict Adverse Outcomes in Emergency Department Patients With Upper Gastrointestinal Bleeding: A Systematic Review
Authors: Ramaekers Rosa , Mukarram Muhammad , Smith Christine A. M. , Thiruganasambandamoorthy Venkatesh
Published: September 2016

Objectives

Risk stratification of emergency department (ED) patients with upper gastrointestinal bleeding (UGIB) using preendoscopic risk scores can aid ED physicians in disposition decision‐making. We conducted a systematic review to assess the predictive value of preendoscopic risk scores for 30‐day serious adverse events.

Methods

We searched MEDLINE, PubMed, Embase, and the Cochrane Database of Systematic Reviews from inception to March 2015. We included studies involving adult ED UGIB patients evaluating preendoscopic risk scores and excluded reviews, case reports, and animal studies. The composite outcome included 30‐day mortality, recurrent bleeding, and need for intervention. In two phases (screening and full review), two reviewers independently screened articles for inclusion and extracted patient‐level data. The consensus data were used for analysis. We reported sensitivity, specificity, positive and negative predictive value, and positive and negative likelihood ratios with 95% confidence intervals.

Results

We identified 3,173 articles, of which 16 were included: three studied Glasgow Blatchford score (GBS); one studied clinical Rockall score (cRockall); two studied AIMS65; six compared GBS and cRockall; three compared GBS, a modification of the GBS, and cRockall; and one compared the GBS and AIMS65. Overall, the sensitivity and specificity of the GBS were 0.98 and 0.16, respectively; for the cRockall they were 0.93 and 0.24, respectively; and for the AIMS65 they were 0.79 and 0.61, respectively. The GBS with a cutoff point of 0 had a sensitivity of 0.99 and a specificity of 0.08.

Conclusion

The GBS with a cutoff point of 0 was superior over other cutoff points and risk scores for identifying low‐risk patients but had a very low specificity. None of the risk scores identified by our systematic review were robust and, hence, cannot be recommended for use in clinical practice. Future prospective studies are needed to develop robust new scores for use in ED patients with UGIB.
The perfect storm: Weed invasion and intense storms in tropical forests
Authors: Murphy Helen T. , Metcalfe Daniel J.
Published: September 2016

Climate change scientists predict an increased intensity of storms (cyclones, hurricanes and typhoons) in the future. Intense storms facilitate plant invasion by increasing resource availability, reducing competition and increasing opportunities for propagule dispersal. We document here the state of current understanding about the response of invasive plant species to intense storms and suggest that the structure and function of forests in storm‐prone regions may be much altered in the future as a result of weed invasion. Intense storms provide a large spatial and temporal window of opportunity for invasion and empirical research demonstrates growth and recruitment rates of invasive species increase following such events, and they spread readily. In particular, lianas and woody invasive species that are shade tolerant and recruit from the seedling layer may constitute the greatest threat to tropical forests following storm events. Forests persisting in fragmented landscapes will be exposed to some of the most severe consequences of intense storms and subsequent weed invasion. In storm‐prone regions, forests of the future are likely to experience a decrease in diversity of native species and homogenization of communities at landscape and regional scales, slower rates of forest succession, increasing degradation of forest fragments and ultimately a decrease in ecosystem function.
Medical and social egg freezing: internet‐based survey of knowledge and attitudes among women in Denmark and the UK
Authors: Lallemant Camille , Vassard Ditte , Nyboe Andersen Anders , Schmidt Lone , Macklon Nick
Published: September 2016

Introduction

Until recently, limited options for preserving fertility in order to delay childbearing were available. Although egg freezing and successful thawing is now possible, it remains unclear to what extent women are aware of the availability of this technique, their attitudes towards its use, or the circumstances under which this technique may be considered.

Material and methods

An online cross‐sectional survey was designed to investigate knowledge and attitudes of women in Denmark and the UK on egg freezing and their potential intentions regarding the procedure.

Results

Data was collected from September 2012 to September 2013 and the responses of 973 women were analyzed. In total, 83% of women reported having heard of egg freezing, and nearly all considered it acceptable for medical indications, whilst 89% considered it acceptable for social reasons. Overall, 19% expressed active interest in the procedure, and 27% expressed possible interest. Key factors found to positively influence attitudes to accepting the procedure were reassurance that it would not affect future fertility and greater than 50% chance of achieving a live birth. Characteristics significantly associated with intention to freeze eggs were being single, age under 35 years, childlessness, and a history of infertility. In this group, risk and cost were less important considerations.

Conclusions

This study indicates that there is widespread awareness and support of the availability of eggs freezing for reproductive planning. Reassurance regarding its efficacy appears more important than its potential adverse effects on their health or that of future children, or the costs of the procedure.
Serum fatty acids in infants, reflecting family fish consumption, were inversely associated with allergy development but not related to farm residence
Authors: Jonsson Karin , Barman Malin , Moberg Sara , Sjöberg Agneta , Brekke Hilde K. , Hesselmar Bill , Sandberg Ann‐Sofie , Wold Agnes E.
Published: September 2016

Aim

In this study, differences in serum fatty acid patterns between farm and nonfarm infants were investigated and related to subsequent allergy development. We also related allergy‐related serum fatty acids to maternal diet and breast milk fatty acids.

Methods

The FARMFLORA birth cohort included 28 farm and 37 nonfarm infants. Serum was obtained from 21 farm infants and 29 controls at four months post‐partum and analysed for phospholipid fatty acids. Allergy was diagnosed by paediatricians at three years of age.

Results

Serum fatty acid patterns were similar in farm and control infants, although farm infants had lower 18:1 omega‐7 proportions. Serum proportions of eicosapentaenoic acid (EPA) were unrelated to farming status, but lower in children who subsequently developed allergy, with an odds ratio of 0.47 and 95% confidence interval of 0.27–0.83 (p = 0.01) for every 0.1% EPA increase. The infants’ serum EPA proportions correlated with breast milk EPA proportions, which, in turn, correlated with maternal oily fish intake during lactation.

Conclusion

The allergy‐protective effect of farming was not linked to infant serum fatty acid composition. However, healthy infants had higher proportions of EPA in their sera, probably reflecting a family diet rich in fish, compared to subsequently allergic children.