bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted versus untargeted omics — the CAFSA story
Authors: del Mar Amador Maria , Colsch Benoit , Lamari Foudil , Jardel Claude , Ichou Farid , Rastetter Agnès , Sedel Frédéric , Jourdan Fabien , Frainay Clément , Wevers Ronald A. , Roze Emmanuel , Depienne Christel , Junot Christophe , Mochel Fanny 
Published: February 2018

AbstractBackgroundIn 2009, untargeted metabolomics led to the delineation of a new clinico‐biological entity called cerebellar ataxia with elevated cerebrospinal free sialic acid, or CAFSA. In order to elucidate CAFSA, we applied sequentially targeted and untargeted omic approaches.Methods and resultsFirst, we studied five of the six CAFSA patients initially described. Besides increased CSF free sialic acid concentrations, three patients presented with markedly decreased 5‐methyltetrahydrofolate (5‐MTHF) CSF concentrations. Exome sequencing identified a homozygous POLG mutation in two affected sisters, but failed to identify a causative gene in the three sporadic patients with high sialic acid but low 5‐MTHF. Using targeted mass spectrometry, we confirmed that free sialic acid was increased in the CSF of a third known POLG‐mutated patient. We then pursued pathophysiological analyses of CAFSA using mass spectrometry‐based metabolomics on CSF from two sporadic CAFSA patients as well as 95 patients with an unexplained encephalopathy and 39 controls. This led to the identification of a common metabotype between the two initial CAFSA patients and three additional patients, including one patient with Kearns‐Sayre syndrome. Metabolites of the CSF metabotype were positioned in a reconstruction of the human metabolic network, which highlighted the proximity of the metabotype with acetyl‐CoA and carnitine, two key metabolites regulating mitochondrial energy homeostasis.ConclusionOur genetic and metabolomics analyses suggest that CAFSA is a heterogeneous entity related to mitochondrial DNA alterations either through POLG mutations or a mechanism similar to what is observed in Kearns‐Sayre syndrome.
Hepatocellular carcinoma in Gaucher disease: an international case series
Authors: Regenboog Martine , van Dussen Laura , Verheij Joanne , Weinreb Neal J. , Santosa David , vom Dahl Stephan , Häussinger Dieter , Müller Meike N. , Canbay Ali , Rigoldi Miriam , Piperno Alberto , Dinur Tama , Zimran Ari , Mistry Pramod K. , Salah Karima Yousfi , Belmatoug Nadia , Kuter David J. , Hollak Carla E. M. 
Published: February 2018

AbstractGaucher disease (GD) is associated with an increased risk for malignancies. Next to hematological malignancies, the development of solid tumors in several organs has been described. The liver is one of the major storage sites involved in GD pathogenesis, and is also affected by liver‐specific complications. In this case series, we describe 16 GD type 1 (GD1) patients from eight different referral centers around the world who developed hepatocellular carcinoma (HCC). Potential factors contributing to the increased HCC risk in GD patients are studied. Eleven patients had undergone a splenectomy in the past. Liver cirrhosis, one of the main risk factors for the development of HCC, was present in nine out of 14 patients for whom data was available. Three out of seven examined patients showed a transferrin saturation > 45%. In these three patients the presence of iron overload after histopathological examination of the liver was shown. Chronic hepatitis C infection was present in three of 14 examined cases. We summarized all findings and made a comparison to the literature. We recommend that GD patients, especially those with prior splenectomy or iron overload, be evaluated for signs of liver fibrosis and if found to be monitored for HCC development.
Time Costs for Genetic Counseling in Preconception Carrier Screening with Genome Sequencing
Authors: Lynch Frances L. , Himes Patricia , Gilmore Marian J. , Morris Elissa M. , Schneider Jennifer L. , Kauffman Tia L. , Shuster Elizabeth , Reiss Jacob A. , Dickerson John F. , Leo Michael C. , Davis James V. , McMullen Carmit K. , Wilfond Benjamin S. , Goddard Katrina A.B. 
Published: February 2018

AbstractAdvances in technology and the promise of personalized health care are driving greater use of genome sequencing (GS) for a variety of clinical scenarios. As health systems consider adopting GS, they need to understand the impact of GS on the organization and cost of care. While research has documented a dramatic decrease in the cost of sequencing and interpreting GS, few studies have examined how GS impacts genetic counseling workloads. This study examined the time needed to provide genetic counseling for GS in the context of preconception carrier screening. Genetic counselors prospectively reported on the time spent in the results disclosure process with 107 study participants who were part of the NextGen study. We found that the median time for results disclosure was 64 min (ranged from 5 to 229 min). Preparation work was the most time‐consuming activity. Qualitative data from journal entries, debrief interviews with genetic counselors, and detailed case conference notes provided information on factors influencing time for results disclosure and implications for practice. Results suggest that expanded carrier screening could require significant increases in genetic counseling time, unless we are able to generate new resources to reduce preparation work or develop other strategies such as the creation of new models to deliver this type of service.
Marital Status and Mothers’ Time Use: Childcare, Housework, Leisure, and Sleep
Authors: Pepin Joanna R. , Sayer Liana C. , Casper Lynne M. 
Published: February 2018

AbstractAssumptions that single mothers are “time poor” compared with married mothers are ubiquitous. We tested theorized associations derived from the time poverty thesis and the gender perspective using the 2003–2012 American Time Use Surveys (ATUS). We found marital status differentiated housework, leisure, and sleep time, but did not influence the amount of time that mothers provided childcare. Net of the number of employment hours, married mothers did more housework and slept less than never-married and divorced mothers, counter to expectations of the time poverty thesis. Never-married and cohabiting mothers reported more total and more sedentary leisure time than married mothers. We assessed the influence of demographic differences among mothers to account for variation in their time use by marital status. Compositional differences explained more than two-thirds of the variance in sedentary leisure time between married and never-married mothers, but only one-third of the variance between married and cohabiting mothers. The larger unexplained gap in leisure quality between cohabiting and married mothers is consistent with the gender perspective.
Fever and systemic inflammatory response syndrome after retrograde intrarenal surgery: Risk factors and predictive model
Authors: Li Tian , Sun Xiang‐Zhou , Lai De‐Hui , Li Xun , He Yong‐Zhong 
Published: February 2018

AbstractThis paper investigates the characteristics of patients who underwent retrograde intrarenal surgery (RIRS) to determine the predictive factors for post‐operative fever and systemic inflammatory response syndrome (SIRS) and to construct a predictive nomogram to help with risk‐stratification. A retrospective study of 337 patients who underwent RIRS was performed. Fever and SIRS were defined according to a previous consensus. Multivariate logistic regression coefficients were used to generate nomograms. Post‐operative fever was found in 59 patients (17.5%), and SIRS was found in 22 patients (6.5%). Septic shock developed in 2 patients (0.6%). Three patients (0.9%) suffered from obstructive hydronephrosis. By multivariate analysis, concomitant diabetes mellitus (p = 0.015), high pre‐operative C‐reactive protein (CRP) (p = 0.015), long surgical times (p = 0.007), high stone burden (p = 0.004) and positive stone culture (p = 0.003) were independent risk factors for fever. Only high pre‐operative CRP (p = 0.001), long surgical times (p = 0.001) and high stone burden (p = 0.001) were found to significantly affect the occurrence of SIRS. Predictive nomograms were built for fever and SIRS and the c‐statistics for the two predictive models were 0.766 and 0.887, respectively. All patients recovered well after proper treatment, which included antipyretics, antibiotics, and inotropic support and nephrostomy when needed. In conclusion, high stone burden, long surgical time, positive stone culture, high pre‐operative CRP and the presence of diabetes mellitus was could increase the risk of fever or SIRS after RIRS for kidney stone. The constructed nomograms could help clinicians in evaluating the risk for post‐operative infectious complications.
Humans Should Not Colonize Mars
Authors: STONER IAN 
Published: February 2018

ABSTRACT:This article offers two arguments for the conclusion that we should refuse on moral grounds to establish a human presence on the surface of Mars. The first argument appeals to a principle constraining the use of invasive or destructive techniques of scientific investigation. The second appeals to a principle governing appropriate human behavior in wilderness. These arguments are prefaced by two preliminary sections. The first preliminary section argues that authors working in space ethics have good reason to shift their focus away from theory-based arguments in favor of arguments that develop in terms of pretheoretic beliefs. The second argues that of the popular justifications for sending humans to Mars only appeals to scientific curiosity can survive reflective scrutiny.
A Bundle of Measures to Control an Outbreak of Pseudomonas aeruginosa Associated With P-Trap Contamination
Authors: Gbaguidi-Haore Houssein , Varin Amélie , Cholley Pascal , Thouverez Michelle , Hocquet Didier , Bertrand Xavier 
Published: February 2018

OBJECTIVETo describe an outbreak of multidrug-resistant Pseudomonas aeruginosa in which the hospital waste-pipe system was the likely source of contamination and to report the bundle of measures that facilitated the long-term control of the outbreak.DESIGNOutbreak investigation.SETTINGThe hematology unit of a tertiary-care referral center.PATIENTSPatients who were colonized or infected with P. aeruginosa belonging to the clonal outbreak.METHODSPatients admitted to our 15-bed stem-cell transplantation hematology unit were screened for P. aeruginosa carriage. Pseudomonas aeruginosa isolates were also obtained from diagnostic samples. We assessed the microbiological contamination of P-traps, water and toilets for 42 months. Extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) were screened and identified by polymerase chain reaction (PCR) and sequencing. Molecular typing of ESBL- or MBL-producing isolates was carried out using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).RESULTSFrom 2009 to 2013, a biclonal outbreak of IMP-19–producing ST235 (11 cases) and IMP-29–producing ST111 (10 cases) of P. aeruginosa occurred. The environmental investigation strongly suggested that P-traps were the reservoirs for the outbreak strains. A bundle of infection control measures, including engineering interventions on water outlets and disinfection of P-traps, controlled the outbreak.CONCLUSIONSWe report a prolonged outbreak of IMP-producing high-risk clones of P. aeruginosa, for which P-traps seems to play a major role in cross-transmission. It appears essential to implement proactive measures to limit the bacterial load in water fittings of high-risk units.Infect Control Hosp Epidemiol 2018;39:164–169
BOUNDED POLYNOMIALS AND HOLOMORPHIC MAPPINGS BETWEEN CONVEX SUBRINGS OF *
Authors: KHALFALLAH ADEL , KOSAREW SIEGMUND 
Published: February 2018

AbstractUsing convex subrings of *$\mathbb{C}$, a nonstandard extension of $\mathbb{C}$, we define several kinds of complex bounded polynomials and we provide their associated analytic functions obtained by taking the quasistandard part.
Emmental squares are tasty
Authors: Crilly Tony , Dolan Stan , Fletcher Colin R. 
Published: February 2018

A shape is called equable if its area and perimeter are numerically equal relative to some given system of units. For example, if a square is equable, then its side, a, must satisfy 4a = a2. So there is only one equable square, and it has side 4.It is easy to investigate this idea for other shapes. Though not connected with this problem, the work of Imre Lakatos suggested a generalisation to us. Lakatos showed that Euler's classical formula V + F = E − 2 for polyhedra could be extended when the notion of tunnels was introduced [1].
Axes for symmetric convex curves
Authors: Farnsworth David L. 
Published: February 2018

Curves are given in polar coordinates (r, θ)by equations of the form r = f (θ), where for f (θ) > 0 all θ. Consider curves which are symmetric about the origin O, so that, f(θ + π) = f (θ) for all θ. For such a curve, its interior is the set {(r, θ) : 0 ≤ r ≤ f (θ)}. Further, assume that the curve is convex. Recall that a closed curve is convex if a line segment between any two of its points has no points exterior to the curve [1], [2, pp. 198-203]. We call these curves M-curves, because the curves are fundamental objects in Minkowski geometry, where they are called Minkowski circles or simply circles [3, 4]. That application is briefly discussed in the Section 4 but is not required for our purposes.Examples of M-curves are displayed in Figures 1 to 6. In order to express these curves as functions in rectangular coordinates, we need axes.
The potential ofDicyphus hesperusas a biological control agent of potato psyllid and sweetpotato whitefly in tomato
Authors: Calvo F.J. , Torres A. , González E.J. , Velázquez M.B. 
Published: February 2018

AbstractThe potential of the mirid predatorDicyphus hesperusKnight (Heteroptera: Miridae) as a biological control agent of the sweetpotato whitefly,Bemisia tabaciGennadius (Hemiptera: Aleyrodidae) and the potato psyllid,Bactericera cockerelliSulcer (Hemiptera: Psyllidae) in tomato was investigated in two experiments. The first experiment focused on the study of the life history traits ofD. hesperuswhen fed on nymphs of the potato psyllid compared with the factitious preyEphestia kuehniellaZeller (Lepidoptera: Pyrallidae) eggs. Although reproductive and development rates were higher onE. kuehniellaeggs, the predator exhibited a good intrinsic rate of natural increase (rm) when feeding onB. cockerellinymphs (rm:B. cockerelli0.069 ± 0.0001;E. kuehniella0.078 ± 0.0001), thus reflecting good potential as a biocontrol agent of this pest. The second experiment focused on the efficacy ofD. hesperusas a biocontrol agent of the potato psyllid and the sweetpotato whitefly in a tomato greenhouse. Prey species were offered individually or together in a series of five treatments in greenhouse cages. Results showed that the predator was able to establish and suppress populations of both pests inhabiting tomato plants when pests occurred alone or together. Thus,D. hesperuswas demonstrated to be a suitable biocontrol agent of these two important pests that could be used in tomato greenhouses.
Primary care practitioner perceptions and attitudes of complementary medicine: a content analysis of free-text responses from a survey of non-metropolitan Australian general practitioners
Authors: Wardle Jon L. , Sibbritt David W. , Adams Jon 
Published: February 2018

AimThis study examines GP perceptions, attitudes and knowledge of complementary medicine (CM), and to understand contextual factors that influence these perceptions, attitudes and knowledge.BackgroundCM use is increasing, and its influence on primary care becoming increasingly significant. Although general practitioners (GPs) often have central primary care gate-keeper roles within health systems, few studies have looked specifically at GPs’ perceptions, attitudes and knowledge of CM.MethodsA questionnaire was mailed to all 1486 GPs registered as practicing in non-metropolitan areas of New South Wales. The survey included one free-text qualitative question, where respondents were invited to highlight issues associated with CM in their own words. Free-text responses were analyzed qualitatively using thematic analysis.FindingsIn total, 585 GPs responded to the survey (adjusted response rate 40.1%), with 152 (26.0%) filling in the free-text question. Central themes which emerged were risk as a primary concern; opposition to, resistance to and the inappropriateness of complementary therapies; struggles with complexity and ambivalent tolerance.ConclusionGPs in Australia have a wide variety of perceptions toward CM. A minority of GPs have absolute views on CM, with most GPs having numerous caveats and qualifications of individual CM. Efficacy is only one aspect of CM critically evaluated by GPs when gauging support for individual therapies – risk, alignment with medical principles and an openness to exploring new avenues of treatment where others have failed, all appear to be equally important considerations when GPs form their views around CM.
Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane
Authors: Teikari Jonna E , Fewer David P , Shrestha Rashmi , Hou Shengwei , Leikoski Niina , Mäkelä Minna , Simojoki Asko , Hess Wolfgang R , Sivonen Kaarina 
Published: February 2018

Abstract
Nodularia spumigena is a nitrogen-fixing cyanobacterium that forms toxic blooms in the Baltic Sea each summer and the availability of phosphorous is an important factor limiting the formation of these blooms. Bioinformatic analysis identified a phosphonate degrading (phn) gene cluster in the genome of N. spumigena suggesting that this bacterium may use phosphonates as a phosphorus source. Our results show that strains of N. spumigena could grow in medium containing methylphosphonic acid (MPn) as the sole source of phosphorous and released methane when growing in medium containing MPn. We analyzed the total transcriptomes of N. spumigena UHCC 0039 grown using MPn and compared them with cultures growing in Pi-replete medium. The phnJ, phosphonate lyase gene, was upregulated when MPn was the sole source of phosphorus, suggesting that the expression of this gene could be used to indicate the presence of bioavailable phosphonates. Otherwise, growth on MPn resulted in only a minor reconstruction of the transcriptome and enabled good growth. However, N. spumigena strains were not able to utilize any of the anthropogenic phosphonates tested. The phosphonate utilizing pathway may offer N. spumigena a competitive advantage in the Pi-limited cyanobacterial blooms of the Baltic Sea.
Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota
Authors: Liu Yang , Zhou Zhichao , Pan Jie , Baker Brett J , Gu Ji-Dong , Li Meng 
Published: February 2018

Abstract
Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood–Ljungdahl (WL) pathways for CO2 reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin–Benson–Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.
Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma
Authors: Yang Biwei , Li Meiyi , Tang Wenqing , Liu Weixin , Zhang Si , Chen Luonan , Xia Jinglin 
Published: February 2018

AbstractDeveloping predictive biomarkers that can detect the tipping point before metastasis of hepatocellular carcinoma (HCC), is critical to prevent further irreversible deterioration. To discover such early-warning signals or biomarkers of pulmonary metastasis in HCC, we analyse time-series gene expression data in spontaneous pulmonary metastasis mice HCCLM3-RFP model with our dynamic network biomarker (DNB) method, and identify CALML3 as a core DNB member. All experimental results of gain-of-function and loss-of-function studies show that CALML3 could indicate metastasis initiation and act as a suppressor of metastasis. We also reveal the biological role of CALML3 in metastasis initiation at a network level, including proximal regulation and cascading influences in dysfunctional pathways. Our further experiments and clinical samples show that DNB with CALML3 reduced pulmonary metastasis in liver cancer. Actually, loss of CALML3 predicts shorter overall and relapse-free survival in postoperative HCC patients, thus providing a prognostic biomarker and therapy target in HCC.
MiR-27a-5p Increases Steer Fat Deposition Partly by Targeting Calcium-sensing Receptor (CASR)
Authors: Yang Wucai , Tang Keqiong , Wang Yaning , Zan Linsen 
Published: February 2018

AbstractCastration increases fat deposition, improving beef quality in cattle. Here, the steer group exhibited a significantly higher intramuscular fat (IMF) content than the bull group. To determine the potential roles of microRNAs (miRNAs) in castration-induced fat deposition, differential expression patterns of miRNA in liver tissue were investigated in bulls and steers. A total of 7,827,294 clean reads were obtained from the bull liver library, and 8,312,483 were obtained from the steer liver library; 452 conserved bovine miRNAs and 20 novel miRNAs were identified. The results showed that the expression profiles of miRNA in liver tissue were changed by castration, and 12 miRNAs that were differentially expressed between bulls and steers were identified. Their target genes were majorly involved in the metabolic, PI3K-Akt, and MAPK signaling pathways. Furthermore, six differentially expressed miRNAs were validated by quantitative real-time PCR, and luciferase reporter assays verified that calcium-sensing receptor (CASR) was the direct target of miR-27a-5p. Meantime, we found that the expression level of CASR was significantly higher in steers than in bulls, and revealed that CASR gene silencing in bovine hepatocytes significantly inhibited triacylglycerol (TAG) accumulation and reduced secretion of very low density lipoprotein (VLDL). These results obtained in the liver indicate that miR-27a-5p may increase fat deposition partly by targeting CASR in steers.