bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining breakthrough invasive fungal infection–Position paper of the mycoses study group education and research consortium and the European Confederation of Medical Mycology
Authors: Cornely Oliver A. , Hoenigl Martin , Lass‐Flörl Cornelia , Chen Sharon C. ‐A. , Kontoyiannis Dimitrios P. , Morrissey C. Orla , Thompson George R. ,   for the Mycoses Study Group Education and Research Consortium (MSG‐ERC) and the European Confederation of Medical Mycology (ECMM)
Published: June 2019

SummaryBreakthrough invasive fungal infections (IFIs) have emerged as a significant problem in patients receiving systemic antifungals; however, consensus criteria for defining breakthrough IFI are missing. This position paper establishes broadly applicable definitions of breakthrough IFI for clinical research. Representatives of the Mycoses Study Group Education and Research Consortium (MSG‐ERC) and the European Confederation of Medical Mycology (ECMM) reviewed the relevant English literature for definitions applied and published through 2018. A draft proposal for definitions was developed and circulated to all members of the two organisations for comment and suggestions. The authors addressed comments received and circulated the updated document for approval. Breakthrough IFI was defined as any IFI occurring during exposure to an antifungal drug, including fungi outside the spectrum of activity of an antifungal. The time of breakthrough IFI was defined as the first attributable clinical sign or symptom, mycological finding or radiological feature. The period defining breakthrough IFI depends on pharmacokinetic properties and extends at least until one dosing interval after drug discontinuation. Persistent IFI describes IFI that is unchanged/stable since treatment initiation with ongoing need for antifungal therapy. It is distinct from refractory IFI, defined as progression of disease and therefore similar to non‐response to treatment. Relapsed IFI occurs after treatment and is caused by the same pathogen at the same site, although dissemination can occur. These proposed definitions are intended to support the design of future clinical trials and epidemiological research in clinical mycology, with the ultimate goal of increasing the comparability of clinical trial results.
Handedness in plant cell expansion: a mutant perspective on helical growth
Authors: Buschmann Henrik , Borchers Agnes 
Published: June 2019

SummaryMany plant mutants are known that exhibit some degree of helical growth. This ‘twisted’ phenotype has arisen frequently in mutant screens of model organisms, but it is also found in cultivars of ornamental plants, including trees. The phenomenon, in many cases, is based on defects in cell expansion symmetry. Any complete model which explains the anisotropy of plant cell growth must ultimately explain how helical cell expansion comes into existence – and how it is normally avoided. While the mutations observed in model plants mainly point to the microtubule system, additional affected components involve cell wall functions, auxin transport and more. Evaluation of published data suggests a two‐way mechanism underlying the helical growth phenomenon: there is, apparently, a microtubular component that determines handedness, but there is also an influence arising in the cell wall that feeds back into the cytoplasm and affects cellular handedness. This idea is supported by recent reports demonstrating the involvement of the cell wall integrity pathway. In addition, there is mounting evidence that calcium is an important relayer of signals relating to the symmetry of cell expansion. These concepts suggest experimental approaches to untangle the phenomenon of helical cell expansion in plant mutants.
A high‐throughput BAC end analysis protocol (BAC‐anchor) for profiling genome assembly and physical mapping
Authors: Yang Xiaohui , Yang Yu , Ling Jian , Guan Jiantao , Guo Xiao , Dong Daofeng , Jin Liping , Huang Sanwen , Liu Jun , Li Guangcun 
Published: June 2019

SummaryTraditional approaches for sequencing insertion ends of bacterial artificial chromosome (BAC) libraries are laborious and expensive, which are currently some of the bottlenecks limiting a better understanding of the genomic features of auto‐ or allopolyploid species. Here, we developed a highly efficient and low‐cost BAC end analysis protocol, named BAC‐anchor, to identify paired‐end reads containing large internal gaps. Our approach mainly focused on the identification of high‐throughput sequencing reads carrying restriction enzyme cutting sites and searching for large internal gaps based on the mapping locations of both ends of the reads. We sequenced and analysed eight libraries containing over 3 200 000 BAC end clones derived from the BAC library of the tetraploid potato cultivar C88 digested with two restriction enzymes, Cla I and Mlu I. About 25% of the BAC end reads carrying cutting sites generated a 60–100 kb internal gap in the potato DM reference genome, which was consistent with the mapping results of Sanger sequencing of the BAC end clones and indicated large differences between autotetraploid and haploid genotypes in potato. A total of 5341 Cla I‐ and 165 Mlu I‐derived unique reads were distributed on different chromosomes of the DM reference genome and could be used to establish a physical map of target regions and assemble the C88 genome. The reads that matched different chromosomes are especially significant for the further assembly of complex polyploid genomes. Our study provides an example of analysing high‐coverage BAC end libraries with low sequencing cost and is a resource for further genome sequencing studies.
Differential responses by two closely related native fishes to restoration actions
Authors: Raymond Scott , Koehn John , Tonkin Zeb , Todd Charles , Stoessel Daniel , Hackett Graeme , O'Mahony Justin , Berry Kelvin , Lyon Jarod , Sharley Joanne , Moloney Paul 
Published: June 2019

Globally, river degradation has decimated freshwater fish populations. To help reverse this trend in a southeastern Australia river, we used multiple restoration actions, including reintroduction of instream woody habitat, riparian revegetation, removal of a weir hindering fish movement, fencing out livestock, and controlling riparian weeds. We monitored the responses of native fish at the segment scale (20 km) and reach scale (0.3 km) over 7 years to assess the effectiveness of the different restoration strategies. Two closely related species, Murray cod Maccullochella peeli and trout cod Maccullochella macquariensis, increased at the restored segment compared with the control segment. However, inherent differences between river segments and low sample size hampered assessment of the mechanisms responsible for segment‐scale changes in fish abundance. In contrast, at the reach scale, only M. peeli abundance significantly increased in reaches supplemented with wood. These differential responses by 2 closely related fish species likely reflect species‐specific responses to increased habitat availability and enhanced longitudinal connectivity when the weir improved passage around a fishway. Changes in M. peeli abundance in segments supplemented with and without wood suggest an increase in carrying capacity and not simply a redistribution of individuals within the segment, facilitated the observed expansion. Our findings confirm the need to consider individual fish species' habitat preferences carefully when designing restoration interventions. Further, species‐specific responses to restoration actions provide waterway managers with precise strategies to target fish species for recovery and the potential to predict fish outcomes based on ecological preferences.
Upper Pleistocene tectonics in western Sardinia (Italy): Insights from the Sinis peninsula structural high
Authors: Cocco Fabrizio , Andreucci Stefano , Sechi Daniele , Cossu Giulia , Funedda Antonio 
Published: June 2019

AbstractThe Corsica‐Sardinia block is a lithospheric fragment whose recent role in the geodynamics of the central‐Western Mediterranean basin is still enigmatic. The most recent regional structure in Sardinia is the Plio‐Pleistocene Campidano Basin, which is considered in a ‘post‐rift’ stage since the Middle Pleistocene. New structural and stratigraphic geological surveys along with luminescence ages provide evidence to support an ongoing tectonic activity since the Marine Isotopic Stage 7 (MIS7; ca. 220 ka) on the Sinis peninsula, the structural high that bounds the north‐western side of the Campidano Basin. In particular, this paper reveals for the first time the presence of N–S striking normal faults system offsetting late Pleistocene aeolianites (130 ± 12 ka; 82 ± 9 ka).
Outcome and failure patterns of localized sinonasal lymphoma in cats treated with first‐line single‐modality radiation therapy: A retrospective study
Authors: Meier Valeria S. , Beatrice Laura , Turek Michelle , Poirier Valerie J. , Cancedda Simona , Stiborova Katerina , Körner Maximilian , Marconato Laura , Weyland Mathias S. , Rohrer Bley Carla 
Published: June 2019

AbstractFailure rate and site are not well defined in localized sinonasal lymphoma in cats treated with radiotherapy. In this study, we describe (a) failure pattern, (b) outcome, (c) influence of previously reported prognostic variables on the outcome in cats with suspected localized sinonasal lymphoma. In this multi‐institutional retrospective study, we included 51 cats treated with single‐modality radiotherapy. Cats were irradiated using 10x4.2Gy (n = 32), 12x3Gy (n = 11) or 5x6Gy (n = 8). Regional lymph nodes were prophylactically irradiated in 24/51 cats (47.1%). Twenty‐five cats (49.0%) developed progressive disease: progression was local (nasal) in five (9.8%), locoregional (nodal) in two (3.9%), local and locoregional in three (5.9%), systemic in nine (17.6%) and both local and systemic in six cats (11.8%). No cat receiving prophylactic nodal irradiation had progression in the locoregional lymph nodes. The median time to progression was 974 days (95%CI: 283;1666), with 58% and 53% of cats free of progression at 1 and 2 years, respectively. Median overall survival was 922 days (95%CI: 66;1779) with 61% and 49% alive at 1 and 2 years, respectively. Half of the cats that died of relapse/progression (13/26) died within 6 months of treatment, suggesting possible shortcomings of staging, rapid dissemination of disease or sequential lymphomagenesis. None of the prognostic factors evaluated were predictive of outcome (prednisolone use, anaemia, nasopharyngeal involvement, modified canine Adams tumour stage, protocol, total dose). Radiotherapy is an effective treatment for localized sinonasal lymphoma with a long time to progression. However, in one‐third of the cats, systemic disease progression occurs soon after radiotherapy.
Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers, continuous characters and geometric morphometric data
Authors: Solis‐Zurita Carolina , De Luna Efraín , González Dolores 
Published: June 2019

AbstractThe monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.
Mapping Together Kinetic and Kinematic Abilities of the Hand
Authors: Drost Joshua P. , Hong Hyokyoung G. , Bush Tamara Reid 
Published: June 2019

Abstract
Millions of people have reduced hand function; this loss of function can be due to injury, disease, or aging. Loss of hand function is identified as reduced motion abilities in the fingers or a decrease in the ability of the fingers to generate force. Unfortunately, there are limited data available regarding each finger's ability to produce force and how those force characteristics vary with changes in finger posture. To relate motion and force abilities of the fingers, first, an approach to measure and map them together is needed. The goal of this work was to develop and demonstrate a method to quantify the force abilities of the fingers and map these forces to the kinematic space associated with each finger. Using motion capture and multiaxis load cells, finger forces were quantified at different positions over their ranges of motion. These two sets of data were then converted to the same coordinate space and mapped together. Further, the data were normalized for the index finger and mapped as a population space model. The ability to quantify motion and force data for each finger and map them together will provide an improved understanding of the effects of treatments and rehabilitation, identifying functional loss due to injury or disease, and device design.
Seismic Fragility Curves of an Arch Dam With Special Regard to Ultimate Limit State
Authors: Gasser Christian , Goldgruber Markus , Bucher Christian 
Published: June 2019

AbstractThe seismic safety of an arch dam is analyzed by calculating fragility curves for different damage and failure mechanisms. The model includes fluid–structure–foundation interaction and considers contact and material type nonlinearities. The ultimate limit state (failure) is studied by means of a plastic-damage concrete model, especially developed for cyclic loadings. The time histories of the ground motions are generated randomly by means of Kanai–Tajimi filter. Moreover, ten parameters of the model are considered as random variables, including the water level. To the best knowledge of the authors, for the first time, water-level variability is accounted for in a probabilistic seismic analysis of a dam. It is studied if it is admissible to increase the efficiency of the Monte Carlo simulation (MCS) by assuming lognormal distributions for the fragility curves. In general, the aim of this work is to show the possibilities and difficulties of probabilistic seismic analysis tools when applied to a sophisticated mechanical model of a real structure.
Optimization Approaches for the Numerical Design of Structures Under Consideration of Polymorphic Uncertain Data
Authors: Edler Philipp , Freitag Steffen , Kremer Katharina , Meschke Günther 
Published: June 2019

Abstract
In this paper, optimization approaches for the numerical design of structures are presented. The uncertainty of structural parameters is considered by means of random variables and interval design parameters within the optimization. A new space subdividing technique is introduced to substitute time-consuming failure probability constraint evaluations. In order to solve optimization problems with polymorphic uncertain parameters, surrogate objectives are formulated and solved by means of a particle swarm optimization (PSO) approach in combination with Monte Carlo simulation and interval analysis. Two computational schemes are presented and verified by a benchmark example. Finally, an application is shown, where the reinforcement layout of a reinforced concrete bridge structure is optimized by minimizing the crack widths at the reinforcement layers in order to improve the durability of the structure. A nonlinear finite element (FE) model is used to compute the uncertain crack patterns and the load bearing capacity. The stochastic objective function and the failure probability constraint are approximated by neural network based surrogate models.
Tidal volumes at birth as predictor for adverse outcome in congenital diaphragmatic hernia
Authors: Mank Arenda , Carrasco Carrasco Cristina , Thio Marta , Clotet Jordi , Pauws Steffen C , DeKoninck Philip , te Pas Arjan B 
Published: June 2019

ObjectiveTo assess the predictive value of tidal volume (Vt) of spontaneous breaths at birth in infants with congenital diaphragmatic hernia (CDH).DesignProspective study.SettingTertiary neonatal intensive care unit.PatientsThirty infants with antenatally diagnosed CDH born at Hospital Sant Joan de Déu in Barcelona from September 2013 to September 2015.InterventionsSpontaneous breaths and inflations given in the first 10 min after intubation at birth were recorded using respiratory function monitor. Only expired Vt of uninterrupted spontaneous breaths was included for analysis. Receiver operating characteristics (ROC) analysis was performed and the area under the curve (AUC) was estimated to assess the predictive accuracy of Vt.Main outcome measuresMortality before hospital discharge and chronic lung disease (CLD) at day 28 of life.ResultsThere were 1.233 uninterrupted spontaneous breaths measured, and the overall mean Vt was 2.8±2.1 mL/kg. A lower Vt was found in infants who died (n=14) compared with survivors (n=16) (1.7±1.6 vs 3.7±2.1 mL/kg; p=0.008). Vt was lower in infants who died during admission or had CLD (n=20) compared with survivors without CLD (n=10) (2.0±1.7 vs 4.3±2.2 mL/kg; p=0.004). ROC analysis showed that Vt ≤2.2 mL/kg predicted mortality with 79% sensitivity and 81% specificity (AUC=0.77, p=0.013). Vt ≤3.4 mL/kg was a good predictor of death or CLD (AUC=0.80, p=0.008) with 85% sensitivity and 70% specificity.ConclusionVt of spontaneous breaths measured immediately after birth is associated with mortality and CLD. Vt seems to be a reliable predictor but is not an independent predictor after adjustment for observed/expected lung to head ratio and liver position.
Development of a peer-led, network mapping intervention to improve the health of individuals with severe mental illnesses: protocol for a pilot study
Authors: Collom Jennifer Rose Deborah , Davidson Jonathan , Sweet Daryl , Gillard Steve , Pinfold Vanessa , Henderson Claire 
Published: June 2019

IntroductionAdults with severe mental illness (SMI) have reduced life expectancy and many have comorbid physical health conditions. Primary care providers are experiencing increased demands for care for people with SMI. Barriers to accessing physical healthcare have been identified which negatively affect quality of care. We propose that peer support workers (PSWs) could deliver an intervention to service users to promote their physical health by drawing on existing social support. The aim of this research was to pilot a novel PSW-led intervention, including personal well-being network mapping, to improve access to primary care for physical health needs.Methods and analysisTwenty-four participants will be recruited from community-based mental health teams in two boroughs of London. Each participant will be offered a six-session intervention. Quantitative data will be collected before and after intervention (at 4-month follow-up). Qualitative interviews will be conducted with PSWs after completion of the intervention and with participants at a 4-month follow-up. Some intervention sessions will be observed by a member of the research team. This is a pilot study with a small sample aiming to assess acceptability and feasibility of an intervention. We aim to use the results to refine the existing theory of change and to optimise the intervention and its evaluation in a future randomised controlled trial. This study is strengthened by its potential clinical importance and origin in previous research where service users engaged with well-being network mapping.Ethics and disseminationThis study has been approved by the London-Chelsea Regional Ethics Committee (ref: 17/LO/0585). The findings will be disseminated to participants, the National Health Service trusts that we recruited from, primary care mental health leads, commissioners and in peer-reviewed journals and academic conferences.
Patterns and co-occurrence of risk factors for hepatocellular carcinoma in four Asian American communities: a cross-sectional study
Authors: Stewart Susan L , Dang Julie HT , Török Natalie J , Chen Moon S 
Published: June 2019

ObjectivesTo investigate risk factor patterns and the simultaneous occurrence of multiple risk factors in the viral, metabolic and lifestyle domains among Asian Americans, who have had the highest mortality rates from hepatocellular carcinoma (HCC).SettingSacramento County, California, USA.ParticipantsEligible participants were county residents ages 18 and older who had not been screened for chronic hepatitis B virus (HBV) and were born in a CDC-defined endemic area or whose parent was born in that area. Of 1004 enrolled, 917 were foreign-born Chinese (130 women, 94 men), Hmong (133 women, 75 men), Korean (178 women, 90 men) or Vietnamese (136 women, 81 men) with complete risk factor data.Primary and secondary outcome measuresWe tested participants for HBV and chronic hepatitis C virus (HCV); measured haemoglobin A1c and waist circumference; and recorded self-reported history of diabetes, hypertension, alcohol use and smoking status. We identified risk factor patterns using cluster analysis and estimated gender-specific age-standardised prevalence rates.ResultsWe identified four patterns: (1) viral (chronic HBV or HCV); (2) lifestyle (current smoker or alcohol user, no viral); (3) metabolic (≥2 metabolic, no lifestyle or viral); and (4) lower risk (≤1 metabolic, no lifestyle or viral). Vietnamese men (16.3%, 95% CI 7.4% to 25.3%) and Hmong women (15.1%, 95% CI 7.8% to 22.5%) had the highest viral pattern prevalence. Hmong women had the highest metabolic (37.8%, 95% CI 29.8% to 45.9%), and Vietnamese men the highest lifestyle (70.4%, 95% CI 59.1% to 81.7%) pattern prevalence. In multiple domains, Hmong men and women were most likely to have viral+metabolic risk factors (men: 14.4%, 95% CI 6.0% to 22.7%; women: 11.9%, 95% CI 5.6% to 18.3%); Vietnamese men were most likely to have lifestyle+viral (10.7%, 95% CI 2.7% to 18.8%), and lifestyle+metabolic but not viral (46.4%, 95% CI 34.4% to 58.5%) risk factors.ConclusionsEfforts to reduce HCC must comprehensively address multiple risk factors.Trial registration numberNCT02596438.