bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semiparametrically Efficient Estimation in Quantile Regression of Secondary Analysis
Authors: Liang Liang , Ma Yanyuan , Wei Ying , Carroll Raymond J. 
Published: April 2018

SummaryAnalysing secondary outcomes is a common practice for case–control studies. Traditional secondary analysis employs either completely parametric models or conditional mean regression models to link the secondary outcome to covariates. In many situations, quantile regression models complement mean-based analyses and provide alternative new insights on the associations of interest. For example, biomedical outcomes are often highly asymmetric, and median regression is more useful in describing the ‘central’ behaviour than mean regressions. There are also cases where the research interest is to study the high or low quantiles of a population, as they are more likely to be at risk. We approach the secondary quantile regression problem from a semiparametric perspective, allowing the covariate distribution to be completely unspecified. We derive a class of consistent semiparametric estimators and identify the efficient member. The asymptotic properties of the resulting estimators are established. Simulation results and a real data analysis are provided to demonstrate the superior performance of our approach with a comparison with the only existing approach so far in the literature.
A depositional model for deep‐lacustrine, partially confined, turbidite fans: Early Cretaceous, North Falkland Basin
Authors: Dodd Thomas J. H. , McCarthy Dave J. , Richards Philip C. 
Published: April 2018

AbstractThis paper presents a model of facies distribution within a set of early Cretaceous, deep‐lacustrine, partially confined turbidite fans (Sea Lion Fan, Sea Lion North Fan and Otter Fan) in the North Falkland Basin, South Atlantic. As a whole, ancient deep‐lacustrine turbidite systems are under‐represented in the literature when compared with those documented in marine basins. Lacustrine turbidite systems can form extensive, good quality hydrocarbon reservoirs, making the understanding of such systems crucial to exploration within lacustrine basins. An integrated analysis of seismic cross‐sections, seismic amplitude extraction maps and 455 m of core has enabled the identification of a series of turbidite fans. The deposits of these fans have been separated into lobe axis, lobe fringe and lobe distal fringe settings. Seismic architectures, observed in the seismic amplitude extraction maps, are interpreted to represent geologically associated heterogeneities, including: feeder systems, terminal mouth lobes, flow deflection, sinuous lobe axis deposits, flow constriction and stranded lobe fringe areas. When found in combination, these architectures suggest ‘partial confinement’ of a system, something that appears to be a key feature in the lacustrine turbidite setting of the North Falkland Basin. Partial confinement of a system occurs when depositionally generated topography controls the flow‐pathway and deposition of subsequent turbidite fan deposits. The term ‘partial confinement’ provides an expression for categorising a system whose depositional boundaries are unconfined by the margins of the basin, yet exhibit evidence of internal confinement, primarily controlled by depositional topography. Understanding the controls that dictate partial confinement; and the resultant distribution of sand‐prone facies within deep‐lacustrine turbidite fans, is important, particularly considering their recent rise as hydrocarbon reservoirs in rift and failed‐rift settings.
Pleistocene sea‐floor fibrous crusts and spherulites in the Danakil Depression (Afar, Ethiopia)
Authors: Jaramillo‐Vogel David , Foubert Anneleen , Braga Juan Carlos , Schaegis Jean‐Charles , Atnafu Balemwal , Grobety Bernard , Kidane Tesfaye 
Published: April 2018

AbstractPleistocene fibrous aragonite fabrics, including crusts and spherules, occur in the Danakil Depression (Afar, Ethiopia) following the deposition of two distinctive Middle and Late Pleistocene coralgal reef units and pre‐dating the precipitation of evaporites. Crusts on top of the oldest reef unit (Marine Isotope Stage 7) cover and fill cavities within a red algal framework. The younger aragonite crusts directly cover coralgal bioherms (Marine Isotope Stage 5) and associated deposits. Their stratigraphic position between marine and evaporitic deposits, and their association to euryhaline molluscs, suggest that the crusts and spherules formed in restricted semi‐enclosed conditions. The availability of hard substrate controls crust formation with crusts more often found on steep palaeo‐slopes, from sea level up to at least 80 m depth, while spherules mainly occur associated with mobile substrate. Crusts reach up to 30 cm in thickness and can be microdigitate, columnar (branching and non‐branching) or non‐columnar, with laminated and non‐laminated fabrics. Two different lamination types are found within the crystalline fabrics: (i) isopachous lamination; and (ii) irregular lamination. These two types of lamination can be distinguished by the organization of the aragonite fibres, as well as the lateral continuity of the laminae. Scanning electron microscopy with energy dispersive X‐ray spectroscopy analyses on well‐preserved samples revealed the presence of Mg‐silicate laminae intercalated with fibrous aragonite, as well as Mg‐silicate aggregates closely associated with the fibrous aragonite crusts and spherules. The variety of observed fabrics results from a continuum of abiotic and microbial processes and, thus, reflects the tight interaction between microbially mediated and abiotic mineralization mechanisms. These are the youngest known isopachously laminated, digitate and columnar branching fibrous crusts associated with a transition from marine to evaporitic conditions. Understanding the context of formation of these deposits in Afar can help to better interpret the depositional environment of the widespread Precambrian sea‐floor precipitates.
Transcription profiling of peripheral B cells in antibody‐positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature
Authors: Imgenberg‐Kreuz J. , Sandling J. K. , Björk A. , Nordlund J. , Kvarnström M. , Eloranta M.‐L. , Rönnblom L. , Wahren‐Herlenius M. , Syvänen A.‐C. , Nordmark G. 
Published: April 2018

AbstractB cells play a key role in the pathogenesis of primary Sjögren's syndrome (pSS). The aim of this study was to analyse the transcriptome of CD19+ B cells from patients with pSS and healthy controls to decipher the B cell–specific contribution to pSS. RNA from purified CD19+ B cells from 12 anti‐SSA antibody‐positive untreated female patients with pSS and 20 healthy blood donors was subjected to whole transcriptome sequencing. A false discovery rate corrected significance threshold of α < 0.05 was applied to define differential gene expression. As validation, gene expression in B cells from 17 patients with pSS and 16 healthy controls was analysed using a targeted gene panel. RNA‐sequencing identified 4047 differentially expressed autosomal genes in pSS B cells. Upregulated expression of type I and type II interferon (IFN)‐induced genes was observed, establishing an IFN signature in pSS B cells. Among the top upregulated and validated genes were CX3CR1, encoding the fractalkine receptor involved in regulation of B‐cell malignancies, CCL5/RANTES and CCR1. Increased expression of several members of the TNF superfamily was also identified; TNFSF4/Ox40L, TNFSF10/TRAIL, TNFSF13B/BAFF, TNFRSF17/BCMA as well as S100A8 and −A9/calprotectin, TLR7, STAT1 and STAT2. Among genes with downregulated expression in pSS B cells were SOCS1 and SOCS3, CD70 and TNFAIP3/A20. We conclude that B cells from patients with anti‐SSA antibody‐positive pSS display immune activation with upregulated expression of chemokines, chemokine receptors and a prominent type I and type II IFN signature, while suppressors of cytokine signalling are downregulated. This adds insight into the autoimmune process and suggests potential targets for future functional studies.
Cretohisteridae, a new beetle family from the Early Cretaceous of China, and its implications for the early evolution of the basal group of Histeroidea (Coleoptera)
Authors: Zhou Yu‐Lingzi , Caterino Michael S. , Ślipiński Adam , Cai Chen‐Yang 
Published: April 2018

AbstractA new beetle family Cretohisteridaefam.n.is described from the Lower Cretaceous Yixian Formation (∼125 Ma) at Huangbanjigou of Beipiao City, Liaoning Province, Northeastern China based on a well preserved fossil beetle,Cretohister sinensisgen.,sp.n.This discovery has established the oldest fossil record for the superfamily Histeroidea, backdating the minimum age of the group by 25 Ma from the earliest Cenomanian (∼99 Ma) to the Barremian of the Cretaceous Period. Based on cladistic analyses of a comprehensive morphological dataset, Cretohisteridae is unambiguously recovered as the sister group of Histeridae, exhibiting several character states that bridge the span between Sphaeritidae, Synteliidae and Histeridae. The discovery of the new fossil family sheds new light on the early evolution and diversity of the Histeroidea in the Early Cretaceous, and provides new clues to solving the long‐ambiguous phylogenetic relationships among the modern families of Histeroidea.This published work has been registered in ZooBank,http://zoobank.org/urn:lsid:zoobank.org:pub:C3F85BBB‐D60E‐44BC‐87C8‐B6D54374EE00.
Photoinducible DRONPA‐s: a new tool for investigating cell–cell connectivity
Authors: Gerlitz Nadja , Gerum Richard , Sauer Norbert , Stadler Ruth 
Published: April 2018

SummaryThe development of multicellular plants relies on the ability of their cells to exchange solutes, proteins and signalling compounds through plasmodesmata, symplasmic pores in the plant cell wall. The aperture of plasmodesmata is regulated in response to developmental cues or external factors such as pathogen attack. This regulation enables tight control of symplasmic cell‐to‐cell transport. Here we report on an elegant non‐invasive method to quantify the passive movement of protein between selected cells even in deeper tissue layers. The system is based on the fluorescent protein DRONPA‐s, which can be switched on and off repeatedly by illumination with different light qualities. Using transgenic 35S::DRONPA‐s Arabidopsis thaliana and a confocal microscope it was possible to activate DRONPA‐s fluorescence in selected cells of the root meristem. This enabled us to compare movement of DRONPA‐s from the activated cells into the respective neighbouring cells. Our analyses showed that pericycle cells display the highest efflux capacity with a good lateral connectivity. In contrast, root cap cells showed the lowest efflux of DRONPA‐s. Plasmodesmata of quiescent centre cells mediated a stronger efflux into columella cells than into stele initials. To simplify measurements of fluorescence intensity in a complex tissue we developed software that allows simultaneous analyses of fluorescence intensities of several neighbouring cells. Our DRONPA‐s system generates reproducible data and is a valuable tool for studying symplasmic connectivity.
Analysis of RDR1/RDR2/RDR6‐independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci
Authors: Polydore Seth , Axtell Michael J. 
Published: April 2018

SummaryPlant small RNAs (sRNAs) modulate key physiological mechanisms through post‐transcriptional and transcriptional silencing of gene expression. Small RNAs fall into two major categories: those are reliant on RNA‐dependent RNA polymerases (RDRs) for biogenesis and those that are not. Known RDR1/2/6‐dependent sRNAs include phased and repeat‐associated short interfering RNAs, while known RDR1/2/6‐independent sRNAs are primarily microRNAs (miRNA) and other hairpin‐derived sRNAs. In this study we produced and analyzed sRNA‐seq libraries from rdr1/rdr2/rdr6 triple mutant plants. We found 58 previously annotated miRNA loci that were reliant on RDR1, ‐2, or ‐6 function, casting doubt on their classification. We also found 38 RDR1/2/6‐independent sRNA loci that are not MIRNAs or otherwise hairpin‐derived, and did not fit into other known paradigms for sRNA biogenesis. These 38 sRNA‐producing loci have as‐yet‐undescribed biogenesis mechanisms, and are frequently located in the vicinity of protein‐coding genes. Altogether, our analysis suggests that these 38 loci represent one or more undescribed types of sRNA in Arabidopsis thaliana.
Efficacy and dermal tolerance of a novel alcohol‐based skin antiseptic in horses
Authors: Tannahill Victoria J. , Cogan Tristan , Allen Kate , Acutt Elizabeth , Busschers Evita 
Published: April 2018

AbstractObjectiveTo determine the efficacy and dermal tolerance of a novel alcohol‐based skin antiseptic (ABSA) in horses.Study DesignExperimental study.Animal PopulationSystemically healthy horses (n = 25) with no history or clinical signs of skin disease.MethodsFour clipped sites on the abdomen were randomly assigned to a skin preparation protocol: saline (negative control; NC), chlorhexidine gluconate followed by isopropyl alcohol (positive control; PC), saline followed by the ABSA (ABSA A), or a commercially available horse shampoo followed by the ABSA (ABSA B). Microbiological swabs were obtained from each site and cultured on MacConkey and mannitol salt agar plates. Colony‐forming units were counted 18‐24 hours later. All sites were scored for signs of skin reaction before, immediately after, 1 hour after, and 24 hours after skin preparation.ResultsThe PC, ABSA A, and ABSA B methods reduced skin microbial burden compared with the NC method (P < .001), but no difference was detected between antiseptic products. Preparation time did not differ between ABSA A and ABSA B methods (P = 0.108); both were faster than the PC method (P < 0.001 for both). Skin reactions were most abundant 24 hours after skin preparation (30.5%), but there was no significant association with antiseptic used, and no horses required veterinary treatment.ConclusionThe ABSA preparations tested in this study were as effective and well tolerated as a chlorhexidine gluconate‐based method, but required less time in healthy horses.Clinical significanceThe ABSA tested here provides an efficacious, fast‐acting, and well‐tolerated alternative to achieve skin antisepsis in healthy horses. These results justify further investigation in clinical cases.
Effects of low‐level laser therapy on the healing of surgically closed incisions and surgically created open wounds in dogs
Authors: Gammel Jessie E. , Biskup Jeffery J. , Drum Marti G. , Newkirk Kim , Lux Cassie N. 
Published: April 2018

AbstractObjectiveTo determine the effects of low‐level laser therapy (LLLT) on primarily closed incisions and full thickness open wounds in dogs.Study designProspective, masked, placebo‐controlled design.Animal populationHealthy intact female dogs (n = 10).MethodsDogs underwent bilateral flank ovariectomy procedures, and open wounds were created bilaterally with a punch biopsy. Each side of the dog (incision and open wound) was randomly assigned to the treatment (TX) group or the control (CN) group. The TX group received LLLT once daily for 5 days with a 980‐nm laser and a total energy density of 5 J/cm2. The CN group received a sham treatment (laser turned off) for an identical amount of time each day. The wounds were assessed visually; measured; photographed at postoperative days 3, 7, 11, and 14; and biopsied on postoperative days 7 and 14. A 2‐way repeated measures multivariate analysis of variance was used to analyze differences between groups.ResultsThere was no difference between groups for subjective assessment of healing time and wound measurements (P = .7). There was no difference in histopathologic assessment except that the CN group had more necrosis and perivascular lymphocytes and macrophages at day 7 (P = .03). The TX group had more perivascular lymphocytes and macrophages at day 14 (P = .01).ConclusionLLLT did not appear to influence the healing of surgically created incisions and small wounds with the methodology reported here.Clinical significance: Results of this study do not support recommending LLLT to stimulate healing of uncomplicated, small wounds and incisions.
An investigation into precipitate behaviour for effective operation of settling tanks through selective precipitation
Authors: Oh Chamteut , Bok Songmin , Yim Giljae , Cheong Youngwook , Ji Sangwoo 
Published: April 2018

AbstractSelective precipitation (SP) is a promising remediation technique for mine drainage, minimising generation of waste sludge. The efficiency of SP is heavily dependent on how effectively precipitates fall out in a settling tank. In this research, the behaviour of iron precipitate was examined using a one dimensional column, with mine drainage pumped upwards through the settling tank. The behaviour was determined by a balance of precipitate settling and floating velocities. The experimental parameters affecting the vertical velocity of precipitates included mine drainage vertical velocity, column height and flocculant addition. The upper sediment accelerated precipitate flocculation in the input mine drainage, reducing turbidity of mine drainage discharge – a self‐filtering effect. For effective operation, discharge turbidity must be minimised and the top upper sediment edge maintained near the upper outlet. This was achieved by continuously removing precipitate from the lower outlet of the settling tank at the rate it was generated.
Is sensitization to pig antigens detrimental to subsequent allotransplantation?
Authors: Li Qi , Hara Hidetaka , Zhang Zhongqiang , Breimer Michael E. , Wang Yi , Cooper David K. C. 
Published: April 2018

AbstractAn important question in xenotransplantation is whether an allotransplant can safely be carried out in a patient who has become sensitized to a pig xenograft. To answer this question, we have searched the literature. We primarily limited our review to the clinically relevant pig‐to‐non‐human primate (NHP) model and found five studies that explored this topic. No NHP that had received a pig graft developed antibodies to alloantigens, and in vitro studies indicated no increased humoral and/or cellular alloreactivity. We carried out a small in vitro study ourselves that confirmed this conclusion. There have been three experiments in which patients undergoing dialysis were exposed to wild‐type pig kidneys and three clinical studies related to bridging a patient in hepatic failure to liver allotransplantation. Despite the development of anti‐pig antibodies, all subsequent organ (kidney or liver) allografts were successful (except possibly in one case). In addition, pig fetal islets were transplanted into patients with kidney allografts; there was no increase in panel‐reactive alloantibodies and the kidney grafts continued to function satisfactorily. In conclusion, the limited data suggest that, after sensitization to pig antigens, there is no evidence of antibody‐mediated or accelerated cellular rejection of a subsequent allograft.
Giardia duodenalisin primates: Classification and host specificity based on phylogenetic analysis of sequence data
Authors: Brynildsrud O. , Tysnes K. R. , Robertson L. J. , Debenham J. J. 
Published: April 2018

SummaryGiardia duodenaliscolonizes the gastrointestinal tract of a wide range of hosts, including humans and other primates. It is grouped into eight different Assemblages and, beyond that, into a number of sub‐Assemblages, definedad hocon the basis of genetic differences; these various groups are often considered to be associated with a specific restricted host range. The aim of this study was to use publicly available genotyping data to investigate the relatedness of human and non‐human primate (NHP)Giardiaisolates in order to evaluate the usefulness of current taxonomic classification and to assess whether there is potential for zoonotic transmission between humans andNHP. Our final data set consisted of sequence data from 165 isolates, 111 fromNHPand 54 from humans. Assemblages were well defined, but sub‐Assemblages across Assemblage B were not resolved. Although sub‐AssemblagesAIandAIIwere resolved, the terms were not found to capture any useful molecular or host/deme properties. In the phylogenetic tree,NHPisolates were scattered among human isolates across Assemblages A and B, and were even found in Assemblage E. We conclude that there does not appear to be significant molecular distinction between human andNHPGiardiaisolates across these four molecular markers. Thus, on the basis of these markers, we cannot exclude a risk for zoonotic and anthropozoonotic transmission of Assemblages A and B isolates, irrespective of sub‐Assemblage classification. We further evaluated the relative merit of the four genes used in genotyping studies. Thetpi,gdhandbggenes gave relatively congruent tree topologies, but theSSUgene did not resolve Assemblages according to the current classification. Future genotyping efforts should aim for multilocus or whole‐genome approaches and, in particular, use of theSSUgene as the sole marker should be avoided when possible.
Anxiety, Depression, and Adverse Clinical Outcomes in Patients With Atrial Fibrillation Starting Warfarin: Cardiovascular Research Network WAVE Study
Authors: Baumgartner Christine , Fan Dongjie , Fang Margaret C. , Singer Daniel E. , Witt Daniel M. , Schmelzer John R. , Williams Marc S. , Gurwitz Jerry H. , Sung Sue Hee , Go Alan S. 
Published: April 2018

Background

Anxiety and depression are associated with worse outcomes in several cardiovascular conditions, but it is unclear whether they affect outcomes in atrial fibrillation (
AF
). In a large diverse population of adults with
AF
, we evaluated the association of diagnosed anxiety and/or depression with stroke and bleeding outcomes.

Methods and Results

The Cardiovascular Research Network WAVE (Community‐Based Control and Persistence of Warfarin Therapy and Associated Rates and Predictors of Adverse Clinical Events in Atrial Fibrillation and Venous Thromboembolism) Study included adults with
AF
newly starting warfarin between 2004 and 2007 within 5 health delivery systems in the United States. Diagnosed anxiety and depression and other patient characteristics were identified from electronic health records. We identified stroke and bleeding outcomes from hospitalization databases using validated
International Classification of Diseases, Ninth Revision
(
ICD‐9
), codes. We used multivariable Cox regression to assess the relation between anxiety and/or depression with outcomes after adjustment for stroke and bleeding risk factors. In 25 570 adults with
AF
initiating warfarin, 490 had an ischemic stroke or intracranial hemorrhage (1.52 events per 100 person‐years). In multivariable analyses, diagnosed anxiety was associated with a higher adjusted rate of combined ischemic stroke and intracranial hemorrhage (hazard ratio, 1.52; 95% confidence interval, 1.01–2.28). Results were not materially changed after additional adjustment for patient‐level percentage of time in therapeutic anticoagulation range on warfarin (hazard ratio, 1.56; 95% confidence interval, 1.03–2.36). In contrast, neither isolated depression nor combined depression and anxiety were significantly associated with outcomes.

Conclusions

Diagnosed anxiety was independently associated with increased risk of combined ischemic stroke and intracranial hemorrhage in adults with
AF
initiating warfarin that was not explained by differences in risk factors or achieved anticoagulation quality.