bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-Based County Level Crop Estimates Incorporating Auxiliary Sources of Information
Authors: Erciulescu Andreea L. , Cruze Nathan B. , Nandram Balgobin 
Published: July 2018

SummaryIn 2011, the US Department of Agriculture's National Agricultural Statistics Service started the complete implementation of the County Agricultural Production Survey (CAPS). The CAPS is an annual survey to provide accurate county level acreage and production estimates of approved federal and state crop commodities. The current top down method of producing official county level estimates that satisfy the county–district–state benchmarking constraint is an expert assessment incorporating multiple sources of information. We propose a model-based method that combines the CAPS acreage data with auxiliary data and improves county level survey estimation, while providing measures of uncertainty for the county level acreage estimates. Auxiliary sources of information include remote sensing data, weather data and planted acreage administrative data from other US agencies. A hierarchical Bayesian subarea level model is proposed and implemented, with an additional hierarchical level for the sampling variances. County level, model-based acreage estimates have lower coefficients of variation than the corresponding county level survey acreage estimates. Top down benchmarking methods are investigated and the final acreage estimates satisfy the county–district–state benchmarking constraint.
Giant sawflies and their kin: morphological phylogeny of Cimbicidae (Hymenoptera)
Authors: Vilhelmsen Lars 
Published: July 2018

AbstractThe Cimbicidae is a small family including the largest extant true sawflies (Tenthredinoidea). It comprises four subfamilies, three of which have a northern hemisphere distribution (Abiinae, Cimbicinae – Holarctic/Oriental; Corynidinae – Palaearctic), whereas the Pachylostictinae are restricted to South America. No previous attempts have been made to evaluate the subfamily classification in a cladistic context. In the present paper, 144 morphological characters from the adult anatomy for a total of 95 species of Cimbicidae and 26 outgroup taxa are scored. All subfamilies and all genera of Cimbicidae except one are represented; all families of Tenthredinoidea are represented in the outgroup. Equal weights (EW) and implied weights (IW) analyses are conducted in tnt. The results largely corroborate the existing subfamily classification, except for Pachylostictinae which are paraphyletic in IW analyses with low K‐values. Abiinae + Cimbicinae is always retrieved and strongly supported; Corynidinae + Pachylostictinae is retrieved in most analyses but weakly supported. Revised diagnoses of the subfamilies are provided. Several genera are retrieved as monophyletic, notable exceptions being Praia and Trichiosoma, which are polyphyletic. The evolution of large body size in Cimbicidae is briefly discussed; possible related phenomena are intrasexual competition and mimicry, i.e. resemblance to large apids or vespids.
Ollo de Sapo Cambro‐Ordovician volcanics from the Central Iberian basement—A multiphase evolution
Authors: von Raumer Jürgen F. , Stampfli Gérard M. 
Published: July 2018

AbstractThe Cambro‐Ordovician rhyodacitic to dacitic volcanics from the Central Iberian basement, currently known as Ollo de Sapo (toads eye), have been reported as a specific group of felsic porphyritic rocks with blue quartz and large phenocrysts of K‐feldspar, in a partly vitreous or fine‐grained matrix. Interpreted to form Cambro‐Ordovician volcanic domes, they are accompanied by tuffs, ignimbrites and products of reworking in a near‐surface environment. The coarse‐ to fine‐grained rocks exhibit rather large K‐feldspar phenocrysts, plagioclase and rounded blue quartz, representing former corroded phenocrysts. Their colouration indicates unmixing of TiO2 at around 900°C during cooling from relatively high crystallisation temperatures, indicating their origin at hot lower crustal conditions. We propose at least a two‐step evolution (1) starting around 495 Ma in the lower crust of a collapsing cordillera, generating a phenocryst‐rich mush and adiabatic melting of the lower crustal protolith to produce the spectacular Ollo de Sapo porphyrites, before (2) magma ascent and crustal extension leading to a different thermal regime around 483 Ma.
Sporotrichosis in Southern Brazil, towards an epidemic?
Authors: Poester Vanice Rodrigues , Mattei Antonella Souza , Madrid Isabel Martins , Pereira Juliana Tavora Bertazo , Klafke Gabriel Baracy , Sanchotene Karine Ortiz , Brandolt Tchana Martinez , Xavier Melissa Orzechowski 
Published: July 2018

AbstractRio Grande do Sul (RS) is the second highest state with respect to sporotrichosis incidence in Brazil, with most cases occurring in the southern region. Given the importance of epidemiologic monitoring in hyperendemic areas, this study evaluated the spatial, geographical and annual sporotrichosis incidence over a period of 7 years in the southern region of RS, as well as the disease evolution over the last two decades. Data were collected from the Mycology Laboratory of the Federal University of Rio Grande (FAMED‐FURG) and from the Centre for Zoonosis Control (CZC) of the Prefeitura Municipal of Pelotas city. All feline cases of sporotrichosis diagnosed between 2010 and 2016 were included and analysed. In addition, cases of human and canine sporotrichosis were accounted for. Over the 7‐year period (2010–2016), 372 feline, 34 canine and 83 human cases of sporotrichosis were diagnosed, being the mean number of cases/year 18.33 in the first 3 years of the study and 116.33 in the last 3 years. Cases were distributed among 34 and 28 neighbourhoods in Rio Grande and Pelotas city, respectively. Socioeconomic features reinforced the result that the disease is already spreading across a major part of the southern region. In addition, the study demonstrated the intensification and expansion of the high endemicity areas. Therefore, given that the number of feline sporotrichosis cases in southern RS reached alarming proportions, we suggested that this region will promptly face an epidemic of sporotrichosis if no preventive or control measures are undertaken.
Titi monkey biogeography: Parallel Pleistocene spread byPlecturocebusandCheracebusinto a post‐Pebas Western Amazon
Authors: Byrne Hazel , Lynch Alfaro Jessica W. , Sampaio Iracilda , Farias Izeni , Schneider Horacio , Hrbek Tomas , Boubli Jean P. 
Published: July 2018

AbstractTiti monkeys, subfamily Callicebinae, are a diverse, species‐rich group of Neotropical primates with an extensive range across South America. Their distribution in space and time makes them an interesting primate model for addressing questions of Neotropical historical biogeography. Our aim was to reconstruct the biogeographic history of Callicebinae to better understand their diversification patterns and the history of their colonisation of South America since the late Miocene. We reconstructed a time‐calibrated phylogeny of 19 titi species under Bayesian inference using two mitochondrial and 11 nuclear loci. Species were assigned across eight Neotropical areas of endemism, and statistical biogeographic methods implemented in BioGeoBEARSwere employed to estimate ancestral areas using 12 biogeographic models. Our results indicate that the most recent common ancestor to extant titi monkeys was widespread from the present‐day Andean foothills in the Colombian Amazon, through the wet and dry savannas of Bolivia and Brazil, to the southern Atlantic forest of eastern Brazil. Genus‐level divergences were characterised by vicariance of ancestral range in the late Miocene. Species‐level diversification inCheracebusand thePlecturocebus molochgroup occurred as they spread across the Amazon in the Pleistocene and were largely characterised by a sequential, long‐distance “island‐hopping” dispersal model of speciation from a narrow area of origin through jump dispersal across rivers. This study comprises the first large‐scale investigation of the evolutionary history of titi monkeys in the context of Amazonian and South American historical biogeography and sheds light on the processes that generated the great diversity found among Callicebinae.
Endocrine Effects of Relative Energy Deficiency in Sport
Authors: Elliott-Sale Kirsty J. , Tenforde Adam S. , Parziale Allyson L. , Holtzman Bryan , Ackerman Kathryn E. 
Published: July 2018

The term Relative Energy Deficiency in Sport was introduced by the International Olympic Committee in 2014. It refers to the potential health and performance consequences of inadequate energy for sport, emphasizing that there are consequences of low energy availability (EA; typically defined as <30 kcal·kg−1 fat-free mass·day−1) beyond the important and well-established female athlete triad, and that low EA affects populations other than women. As the prevalence and consequences of Relative Energy Deficiency in Sport become more apparent, it is important to understand the current knowledge of the hormonal changes that occur with decreased EA. This paper highlights endocrine changes that have been observed in female and male athletes with low EA. Where studies are not available in athletes, results of studies in low EA states, such as anorexia nervosa, are included. Dietary intake/appetite-regulating hormones, insulin and other glucose-regulating hormones, growth hormone and insulin-like growth factor 1, thyroid hormones, cortisol, and gonadal hormones are all discussed. The effects of low EA on body composition, metabolic rate, and bone in female and male athletes are presented, and we identify future directions to address knowledge gaps specific to athletes.
A Xenobiotic Detoxification Pathway through Transcriptional Regulation in Filamentous Fungi
Authors: Sang Hyunkyu , Hulvey Jonathan P. , Green Robert , Xu Hao , Im Jeongdae , Chang Taehyun , Jung Geunhwa 
Published: July 2018

ABSTRACT

Fungi are known to utilize transcriptional regulation of genes that encode efflux transporters to detoxify xenobiotics; however, to date it is unknown how fungi transcriptionally regulate and coordinate different phases of detoxification system (phase I, modification; phase II, conjugation; and phase III, secretion). Here we present evidence of an evolutionary convergence between the fungal and mammalian lineages, whereby xenobiotic detoxification genes (phase I coding for cytochrome P450 monooxygenases [CYP450s] and phase III coding for ATP-binding cassette [ABC] efflux transporters) are transcriptionally regulated by structurally unrelated proteins. Following next-generation RNA sequencing (RNA-seq) analyses of a filamentous fungus,
Sclerotinia homoeocarpa
, the causal agent of dollar spot on turfgrasses, a multidrug resistant (MDR) field strain was found to overexpress phase I and III genes, coding for CYP450s and ABC transporters for xenobiotic detoxification. Furthermore, there was confirmation of a gain-of-function mutation of the fungus-specific transcription factor
S. homoeocarpa
XDR1 (ShXDR1), which is responsible for constitutive and induced overexpression of the phase I and III genes, resulting in resistance to multiple classes of fungicidal chemicals. This fungal pathogen detoxifies xenobiotics through coordinated transcriptional control of CYP450s, biotransforming xenobiotics with different substrate specificities and ABC transporters, excreting a broad spectrum of xenobiotics or biotransformed metabolites. A
Botrytis cinerea
strain harboring the mutated ShXDR1 showed increased expression of phase I (
BcCYP65
) and III (
BcatrD
) genes, resulting in resistance to fungicides. This indicates the regulatory system is conserved in filamentous fungi. This molecular genetic mechanism for xenobiotic detoxification in fungi holds potential for facilitating discovery of new antifungal drugs and further studies of convergent and divergent evolution of xenobiotic detoxification in eukaryote lineages.

IMPORTANCE
Emerging multidrug resistance (MDR) in pathogenic filamentous fungi is a significant threat to human health and agricultural production. Understanding mechanisms of MDR is essential to combating fungal pathogens; however, there is still limited information on MDR mechanisms conferred by xenobiotic detoxification. Here, we report for the first time that overexpression of phase I drug-metabolizing monooxygenases (cytochrome P450s) and phase III ATP-binding cassette efflux transporters is regulated by a gain-of-function mutation in the fungus-specific transcription factor in the MDR strains of the filamentous plant-pathogenic fungus
Sclerotinia homoeocarpa
. This study establishes a novel molecular mechanism of MDR through the xenobiotic detoxification pathway in filamentous fungi, which may facilitate the discovery of new antifungal drugs to control pathogenic fungi.
Phagocytes from Mice Lacking the Sts Phosphatases Have an Enhanced Antifungal Response to Candida albicans
Authors: Frank David , Naseem Shamoon , Russo Gian Luigi , Li Cindy , Parashar Kaustubh , Konopka James B. , Carpino Nick 
Published: July 2018

ABSTRACTMice lacking expression of the homologous phosphatases Sts-1 and Sts-2 (Sts−/−mice) are resistant to disseminated candidiasis caused by the fungal pathogenCandida albicans. To better understand the immunological mechanisms underlying the enhanced resistance of Sts−/−mice, we examined the kinetics of fungal clearance at early time points. In contrast to the rapidC. albicansgrowth seen in normal kidneys during the first 24 h postinfection, we observed a reduction in kidney fungal CFU within Sts−/−mice beginning at 12 to 18 h postinfection. This corresponds to the time period when large numbers of innate leukocytes enter the renal environment to counter the infection. Because phagocytes of the innate immune system are important for host protection against pathogenic fungi, we evaluated responses of bone marrow leukocytes. Relative to wild-type cells, Sts−/−marrow monocytes and bone marrow-derived dendritic cells (BMDCs) displayed a heightened ability to inhibitC. albicansgrowthex vivo. This correlated with significantly enhanced production of reactive oxygen species (ROS) by Sts−/−BMDCs downstream of Dectin-1, a C-type lectin receptor that plays a critical role in stimulating host responses to fungi. We observed no visible differences in the responses of other antifungal effector pathways, including cytokine production and inflammasome activation, despite enhanced activation of the Syk tyrosine kinase downstream of Dectin-1 in Sts−/−cells. Our results highlight a novel mechanism regulating the immune response to fungal infections. Further understanding of this regulatory pathway could aid the development of therapeutic approaches to enhance protection against invasive candidiasis.IMPORTANCESystemic candidiasis caused by fungalCandidaspecies is becoming an increasingly serious medical problem for which current treatment is inadequate. Recently, the Sts phosphatases were established as key regulators of the host antifungal immune response. In particular, genetic inactivation of Sts significantly enhanced survival of mice infected intravenously withCandida albicans. The Sts−/−in vivoresistance phenotype is associated with reduced fungal burden and an absence of inflammatory lesions. To understand the underlying mechanisms, we studied phagocyte responses. Here, we demonstrate that Sts−/−phagocytes have heightened responsiveness toC. albicanschallenge relative to wild-type cells. Our data indicate the Sts proteins negatively regulate phagocyte activation via regulating selective elements of the Dectin-1–Syk tyrosine kinase signaling axis. These results suggest that phagocytes lacking Sts respond to fungal challenge more effectively and that this enhanced responsiveness partially underlies the profound resistance of Sts−/−mice to systemic fungal challenge.
Cross-Regulation between Bacteria and Phages at a Posttranscriptional Level
Authors: Altuvia Shoshy , Storz Gisela , Papenfort Kai 
Published: July 2018

ABSTRACT
The study of bacteriophages (phages) and prophages has provided key insights into almost every cellular process as well as led to the discovery of unexpected new mechanisms and the development of valuable tools. This is exemplified for RNA-based regulation. For instance, the characterization and exploitation of the antiphage CRISPR (clustered regularly interspaced short palindromic repeat) systems is revolutionizing molecular biology. Phage-encoded proteins such as the RNA-binding MS2 protein, which is broadly used to isolate tagged RNAs, also have been developed as valuable tools. Hfq, the RNA chaperone protein central to the function of many base-pairing small RNAs (sRNAs), was first characterized as a bacterial host factor required for Qβ phage replication. The ongoing studies of RNAs are continuing to reveal regulatory connections between infecting phages, prophages, and bacteria and to provide novel insights. There are bacterial and prophage sRNAs that regulate prophage genes, which impact bacterial virulence as well as bacterial cell killing. Conversely, phage- and prophage-encoded sRNAs modulate the expression of bacterial genes modifying metabolism. An interesting subcategory of the prophage-encoded sRNAs are sponge RNAs that inhibit the activities of bacterial-encoded sRNAs. Phages also affect posttranscriptional regulation in bacteria through proteins that inhibit or alter the activities of key bacterial proteins involved in posttranscriptional regulation. However, what is most exciting about phage and prophage research, given the millions of phage-encoded genes that have not yet been characterized, is the vast potential for discovering new RNA regulators and novel mechanisms and for gaining insight into the evolution of regulatory RNAs.
Avoidable mortality from respiratory tract infection and sudden unexplained death in children with chronic conditions: a data linkage study
Authors: Verfürden Maximiliane L , Gilbert Ruth , Sebire Neil , Hardelid Pia 
Published: July 2018

ObjectiveTo determine the risk of death from two potentially avoidable causes with different aetiologies: respiratory tract infection (RTI) and sudden unexplained death (SUD) in children with and without chronic conditions.DesignWhole-country, birth cohort study using linked administrative health databases from Scotland.Setting and participantsChildren aged 2 months to less than 5 years in Scotland between 2000 and 2014.Main outcome measuresRelative risk of death (expressed as the HR) related to RTIs or SUD, in children with and without chronic conditions. We separately analysed deaths at ages 2–11 months and at 1–4 years and adjusted for birth characteristics, socioeconomic status and vaccination uptake using Cox regression.ResultsThe cohort comprised 761 172 children. Chronic conditions were recorded in 9.6% (n=72 901) of live births, 82.4% (n=173) of RTI-related deaths and 17.4% (n=49) of SUDs. Chronic conditions were very strongly associated with RTI mortality (2–11 months: HR 68.48, 95% CI (40.57 to 115.60), 1–4 years: HR 38.32, 95% CI (23.26 to 63.14)) and strongly associated with SUD (2–11 months: HR 2.42, 95% CI (1.67 to 3.63), 1–4 years: HR 2.53, 95% CI (1.36 to 4.71)).ConclusionsThe very strong association with chronic conditions suggests that RTI-related mortality may sometimes be a consequence of a terminal decline and not possible to defer or prevent in all cases. Recording whether death was expected on death certificates could indicate which RTI-related deaths might be avoidable through healthcare and public health measures.
Risk factors for refractory anastomotic strictures after oesophageal atresia repair: a multicentre study
Authors: Vergouwe Floor W T , Vlot John , IJsselstijn Hanneke , Spaander Manon C W , van Rosmalen Joost , Oomen Matthijs W N , Hulscher Jan B F , Dirix Marc , Bruno Marco J , Schurink Maarten , Wijnen René M H 
Published: July 2018

ObjectiveTo determine the incidence of refractory anastomotic strictures after oesophageal atresia (OA) repair and to identify risk factors associated with refractory strictures.MethodsRetrospective national multicentre study in patients with OA born between 1999 and 2013. Exclusion criteria were isolated fistula, inability to obtain oesophageal continuity, death prior to discharge and follow-up <6 months. A refractory oesophageal stricture was defined as an anastomotic stricture requiring ≥5 dilations at maximally 4-week intervals. Risk factors for development of refractory anastomotic strictures after OA repair were identified with multivariable logistic regression analysis.ResultsWe included 454 children (61% male, 7% isolated OA (Gross type A)). End-to-end anastomosis was performed in 436 (96%) children. Anastomotic leakage occurred in 13%. Fifty-eight per cent of children with an end-to-end anastomosis developed an anastomotic stricture, requiring a median of 3 (range 1–34) dilations. Refractory strictures were found in 32/436 (7%) children and required a median of 10 (range 5–34) dilations. Isolated OA (OR 5.7; p=0.012), anastomotic leakage (OR 5.0; p=0.001) and the need for oesophageal dilation ≤28 days after anastomosis (OR 15.9; p<0.001) were risk factors for development of a refractory stricture.ConclusionsThe incidence of refractory strictures of the end-to-end anastomosis in children treated for OA was 7%. Risk factors were isolated OA, anastomotic leakage and the need for oesophageal dilation less than 1 month after OA repair.
Two-thumb-encircling advantageous for lay responder infant CPR: a randomised manikin study
Authors: Pellegrino Jeffrey L , Bogumil David , Epstein Jonathan L , Burke Rita V 
Published: July 2018

ObjectivePaediatric health providers and educators influence infant mortality through advocacy and training within families and communities. This research sought to establish the efficacy and training of two-finger versus two-thumb-encircling techniques for lone responder infant chest compressions with ventilations in initially trained infant caregivers.DesignThis is a randomised, cross-over educational intervention assessed on instrumented manikins using the 2015 guideline measures of quality infant cardiopulmonary resuscitation (CPR). Additional subjective data on the experience were collected through self-reporting.SettingNon-healthcare community organisations and secondary school classrooms.ParticipantsFourteen years or older, fluent in English and had not taken infant CPR in the last 5 years.InterventionsGroups of eight participants were randomised to learn one technique, practised and then tested for 8 min. After a 30 min rest, the group repeated the process using the other technique.Main outcome measuresMean chest compression depth and rate, compression fraction, and correct hand position; tiredness and pain as reported by the caregiver.ResultsThe two-thumb-encircling technique achieved a deeper mean compression depth over the 8 min period (2.0 mm, p<0.01), closer to the minimum recommendation of 40 mm; the two-finger technique achieved higher percentages of compression fraction and complete recoil. Caregivers preferred the two-thumb technique (64%), and of these 70% had long fingernails.ConclusionsThe two-thumb-encircling technique improved compression depth, over an 8 min scenario, and was preferred by caregivers. This adds to the existing literature on the advantages of two-thumb-encircling as a technique for lone and team infant CPR, which counters current guidelines.