bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing anin silicominimum inhibitory concentration panel test forKlebsiella pneumoniae
Authors: Nguyen Marcus , Brettin Thomas , Long S. Wesley , Olsen Randall J. , Musser James M. , Olson Robert , Shukla Maulik , Stevens Rick L. , Xia Fangfang , Yoo Hyunseung , Davis James J. 
Published: September 2017

ABSTRACTAntimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to apidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates ofKlebsiella pneumoniaeto develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics. The overall accuracy of the model, within ±1 two-fold dilution factor, is 92%. Individual accuracies are≥90% for 15/20 antibiotics. We show that the MICs predicted by the model correlate with known antimicrobial resistance genes. Importantly, the genome-wide approach described in this study offers a way to predict MICs for isolates without knowledge of the underlying gene content. This study shows that machine learning can be used to build a completein silicoMIC prediction panel forK. pneumoniaeand provides a framework for building MIC prediction models for other pathogenic bacteria.
Phototrophic microbes form endolithic biofilms in ikaite tufa columns (SW Greenland)
Authors: Trampe Erik , Castenholz Richard W. , Larsen Jens E. N. , Kühl Michael 
Published: September 2017

SummaryMarine tufa‐columns, formed by the hydrated carbonate mineral ikaite, present a unique alkaline microbial habitat only found in Ikka Fjord (SW‐Greenland). The outermost parts of the ikaite columns exhibit a multitude of physico‐chemical gradients, and the porous ikaite is colonized by endolithic phototrophic biofilms serving as a substrate for grazing epifauna, where scraping by sea urchins affects overall column‐topography. We present a detailed study of the optical microenvironment, spatial organization, and photosynthetic activity of endolithic phototrophs within the porous ikaite crystal matrix. Cyanobacteria and diatoms formed distinctly coloured zones and were closely associated with ikaite‐crystals via excretion of exopolymers. Scalar‐irradiance measurements showed strong attenuation of visible light (400–700 nm), where only ∼1% of incident irradiance remained at 20 mm depth. Transmission spectra showed in vivo absorption signatures of diatom and cyanobacterial photopigments, which were confirmed by HPLC‐analysis. Variable‐chlorophyll‐fluorescence‐imaging showed active photosynthesis with high‐light acclimation in the outer diatom layer, and low‐light acclimation in the underlying cyanobacterial part. Phototrophs in ikaite thus thrive in polymer‐bound endolithic biofilms in a complex gradient microhabitat experiencing constant slow percolation of highly alkaline phosphate‐enriched spring water mixing with cold seawater at the tufa‐column‐apex. We discuss the potential role of these biofilms in ikaite column formation.
Sexually divergent DNA methylation patterns with hippocampal aging
Authors: Masser Dustin R. , Hadad Niran , Porter Hunter L. , Mangold Colleen A. , Unnikrishnan Archana , Ford Matthew M. , Giles Cory B. , Georgescu Constantin , Dozmorov Mikhail G. , Wren Jonathan D. , Richardson Arlan , Stanford David R. , Freeman Willard M. 
Published: September 2017

SummaryDNA methylation is a central regulator of genome function, and altered methylation patterns are indicative of biological aging and mortality. Age‐related cellular, biochemical, and molecular changes in the hippocampus lead to cognitive impairments and greater vulnerability to neurodegenerative disease that varies between the sexes. The role of hippocampal epigenomic changes with aging in these processes is unknown as no genome‐wide analyses of age‐related methylation changes have considered the factor of sex in a controlled animal model. High‐depth, genome‐wide bisulfite sequencing of young (3 month) and old (24 month) male and female mouse hippocampus revealed that while total genomic methylation amounts did not change with aging, specific sites in CG and non‐CG (CH) contexts demonstrated age‐related increases or decreases in methylation that were predominantly sexually divergent. Differential methylation with age for both CG and CH sites was enriched in intergenic and intronic regions and under‐represented in promoters, CG islands, and specific enhancer regions in both sexes, suggesting that certain genomic elements are especially labile with aging, even if the exact genomic loci altered are predominantly sex‐specific. Lifelong sex differences in autosomal methylation at CG and CH sites were also observed. The lack of genome‐wide hypomethylation, sexually divergent aging response, and autosomal sex differences at CG sites was confirmed in human data. These data reveal sex as a previously unappreciated central factor of hippocampal epigenomic changes with aging. In total, these data demonstrate an intricate regulation of DNA methylation with aging by sex, cytosine context, genomic location, and methylation level.
Effects of wetland hydroperiod length on the functional structure of assemblages of Odonata
Authors: Pires Mateus M , Stenert Cristina , Maltchik Leonardo 
Published: September 2017

AbstractThe role of hydroperiod as an environmental filter in structuring wetland assemblages is usually associated with trait selection in invertebrates. However, the effects of changes in the hydroperiod of non‐permanent wetlands on invertebrate assemblages are still unclear, and few studies have assessed the functional structure of insect assemblages along the hydroperiod gradient. In this study, we investigated the effects of different hydroperiod lengths on the functional structure of Odonata assemblages in non‐permanent wetlands (posteriorly classified as ‘short‐’, ‘medium‐’ and ‘long‐hydroperiod’) in southern Brazil in 2013 and 2014. Biological traits related to life‐history strategies in temporary waters were assessed according to seasonal patterns of occurrence of nymphal and adult stages of odonates. Following the rationale of an environmental filter produced by hydroperiod, we expected to find (1) higher functional diversity in longer hydroperiods and (2) trait‐convergence patterns in odonate assemblages in shorter hydroperiods. Patterns of functional diversity were detected along the hydroperiod gradient. More specifically, higher functional dispersion was found in long‐hydroperiod wetlands and trait‐convergence patterns occurred in wetlands with shorter hydroperiods, supporting our general hypothesis. Odonate taxa with life‐history traits associated with shorter life cycles predominated in medium‐ and short‐hydroperiod wetlands. Our results thus suggest that more pronounced reductions in wetland hydroperiod length should produce odonate assemblages functionally more similar, and these results gain special importance as climate change scenarios indicate that the hydrology of wetlands will be affected by variation in rainfall regimes.
Effect of individual dietetic intervention on gestational weight gain and associated complications in obese pregnant women
Authors: Robertson Nicole , Ladlow Bridget 
Published: September 2017

BackgroundMaternal obesity and excessive gestational weight gain (GWG) are prevalent in Australia and associated with an increased risk of birth complications, gestational diabetes and caesarean delivery.AimTo assess the effect of a pilot dietetic intervention in supporting the achievement of appropriate GWG.Materials and methodsPregnant women with a pre‐pregnancy body mass index (BMI) ≥ 35 kg/m2 (n = 174, mean BMI 40.6 ± 4.3 kg/m2) were referred for individual assessment and dietary counselling conducted by a dietitian with subsequent reviews. Education was based on the Australian Guide to Healthy Eating (AGTHE), encouraged nutritional adequacy and promoted GWG in line with current Institute of Medicine (IOM) guidelines.ResultsThe intervention was associated with a significant reduction (P = 0.00) in gestational weight gain (3.57 ± 5.37 kg) when compared to previous pregnancies (14.31 ± 11.23 kg). Women who attended three or more appointments gained significantly less weight compared with those who attended the initial assessment only (P < 0.05). Rates of caesarean delivery and macrosomia were lower among participants compared to obese populations in comparable studies.ConclusionsDietetic intervention in obese pregnant women can assist in achieving and limiting gestational weight gain to within current IOM guidelines and reduced rates of gestational diabetes and caesarean section.
Nausea and vomiting of pregnancy: Effects on quality of life and day‐to‐day function
Authors: Tan Amelia , Lowe Sandra , Henry Amanda 
Published: September 2017

AimsTo investigate the effect of nausea and vomiting of pregnancy (NVP) on quality of life (QoL) and activities of daily living/socioeconomic function in a contemporary Australian setting.Materials and MethodsObservational, single centre prospective cohort study using validated survey instruments in pregnant women at 9–16 weeks gestation at a tertiary metropolitan women's hospital in Sydney, Australia. QoL measured by the Short‐Form Health Survey (SF‐12) was compared between those with and without NVP. NVP severity scores were correlated with QoL scores, work patterns and medication use.ResultsOf 116 participants, 72% had NVP, with no baseline (including mental health) differences between women with or without NVP. As classified by modified Pregnancy‐Unique‐Quantified‐Emesis (PUQE) survey, 42% had mild symptoms, 55% moderate and 1% severe. SF‐12 Physical Component Summary (PCS) scores were significantly lower for those with NVP (P < 0.001), but not Mental Component Summary (MCS) scores (P = 0.11). Decreasing QoL was associated with increasing NVP severity (P < 0.001), most markedly in the physical domain (P < 0.001). Only 39% of women used any NVP treatment and 15% pharmacotherapy. Most used treatments were vitamin B6, ginger, metoclopramide and natural remedies. Significantly more women with NVP required time off work (45% vs 16%, P = 0.003).ConclusionsNVP is a physically morbid disease, affecting most pregnancies. NVP has a significant detrimental impact on QoL, especially physical QoL and work function. Despite this, we found low treatment utilisation, even in those with moderate/severe symptoms. Women should be encouraged to seek assistance for NVP and further education is required to improve practitioner awareness and management.
Paternal age and risk of testicular germ cell tumors: a cohort study of 1,000,000 men
Authors: Levine H. , Keinan‐Boker L. , Leiba A. , Derazne E. , Rais A. , Kark J. D. 
Published: September 2017

SummaryTesticular germ cell tumors (TGCT) are the most frequent cancer among young men, with increasing incidence worldwide. Advanced paternal age has been linked to adverse health outcomes in offspring, but reports on the association of paternal age with TGCT are few and inconsistent. We aimed to examine the relationship of paternal age (PAB) at birth with the risk of TGCT and by histologic type: seminoma and non‐seminoma. A population‐based cohort of 1,056,058 males, examined at ages 16–19 between the years 1980–2011, was linked to the Israel National Cancer Registry to obtain incident TGCT through 2012. We applied multivariable Cox regression. During 16.5 million person‐years of follow‐up, 1247 incident cases (604 seminomas and 643 non‐seminomas) were detected. Increasing PAB was linearly associated with lower risk of TGCT (HRper year = 0.983, 95% CI: 0.974–0.993, p = 0.001), after adjustment for year of birth, years of education, height, cryptorchidism history and origin, and also with additional adjustment for maternal age at birth (MAB) (HRper year = 0.980: 0.965–0.995, p = 0.008). The association was stronger for seminoma (HRper year = 0.968: 0.946–0.989, p = 0.004) and persisted in a subset adjusted for sibship size (HRper year = 0.950: 0.917–0.983, p = 0.003). In the fully adjusted model, young PAB (15–24 vs. ≥30) was a risk factor for seminoma (HR = 1.41: 1.07–1.85, p = 0.014). In models adjusted for PAB, MAB was not associated with risk of TGCT. In conclusion, our findings suggest that young paternal age is a risk factor of TGCT, especially seminoma. The findings warrant further investigation into the possible impact of young paternal age on their offsprings’ testes.
Effects of testosterone supplementation therapy on lipid metabolism in hypogonadal men with T2DM: a meta‐analysis of randomized controlled trials
Authors: Zhang K.‐S. , Zhao M.‐J. , An Q. , Jia Y.‐F. , Fu L.‐L. , Xu J.‐F. , Gu Y.‐Q. 
Published: September 2017

SummaryTestosterone supplementation may be effective for the treatment of hypogonadism in men with type 2 diabetes mellitus (T2DM), but the evidence from randomized controlled trials (RCTs) is inconclusive. We aimed to systematically summarize results from intervention studies and assess the effects of testosterone supplementation therapy (TST) on lipid metabolism in RCTs of hypogonadal men with T2DM by meta‐analysis. PubMed, Embase, and Cochrane Library databases were searched for studies reporting the effect of TST on lipid metabolism in hypogonadal men with T2DM until December 31, 2016. Seven RCTs from 252 trials, enrolling a total of 612 patients in the experimental and control groups with a mean age of 58.5 years, were included in this study. The pooled results of the meta‐analysis demonstrated that TST significantly decreased TC and TG levels in hypogonadal men with T2DM compared with the control group, with mean differences (MDs) of −6.44 (95% CI: −11.82 to −1.06; I2 = 28%; p = 0.02) and −27.94 (95% CI: −52.33 to −3.54; I2 = 76%; p = 0.02). Subgroup analyses revealed that the heterogeneity (I2 = 76%) of TG originated from different economic regions, in which economic development, genetic and environmental factors, and dietary habits affect lipid metabolism of human, with a decrease (I2 = 45%) in developed countries. Additionally, subgroup analyses showed that TST increased HDL‐C level in developing countries compared with the control group (MD = 2.79; 95% CI: 0.73 to 4.86; I2 = 0%; p = 0.008), but there was no improvement in developed countries (MD = 1.02; 95% CI: −4.55 to 6.60; I2 = 91%; p = 0.72). However, LDL‐C levels were not improved consistently. Because the relationship between lipid metabolism and atherosclerosis is unequivocal, TST, which ameliorates lipid metabolism, may decrease the morbidity and mortality of cardiovascular disease in hypogonadal men with T2DM by preventing atherogenesis.
Parathyroid hormone is related to QT interval independent of serum calcium in patients with coronary artery disease
Authors: Palmeri Nicholas O. , Davidson Karina W. , Whang William , Kronish Ian M. , Edmondson Donald , Walker Marcella D. 
Published: September 2017

BackgroundElevated serum parathyroid hormone (PTH) is associated with increased risk of cardiovascular death, including sudden cardiac death, in patients with and without parathyroid disease. In small studies, PTH levels have been associated with changes in cardiac conduction and repolarization. Changes in the corrected QT interval (QTc) in particular are thought to be mediated by the effect of PTH on serum calcium. There is limited evidence to suggest PTH may affect cardiac physiology independent of its effects on serum calcium, but there is even less data linking PTH to changes in electrical conduction and repolarization independent of serum calcium.MethodsECG data were examined from the PULSE database—an observational cohort study designed to examine depression after acute coronary syndromes (ACS) at a single, urban American medical center. In all, 407 patients had PTH and ECG data for analysis.ResultsThe QTc was longer in patients with elevated PTH levels compared with those without elevated PTH levels (451 ± 38.6 ms vs. 435 ± 29.8 ms; p < .001). The difference remained statistically significant after controlling for calcium, vitamin D, and estimated glomerular filtration rate (p = .007). Inclusion of left ventricular ejection fraction in the model attenuated the association (p = .054), suggesting that this finding may be partly driven by changes in cardiac structure.ConclusionsIn one of the largest series to examine PTH, calcium, and QT changes, we found that elevated PTH is associated with longer corrected QT interval independent of serum calcium concentration in ACS survivors.
Marked exercise‐induced T‐wave heterogeneity in symptomatic diabetic patients with nonflow‐limiting coronary artery stenosis
Authors: Stocco Fernando G. , Evaristo Ederson , Shah Nishant R. , Cheezum Michael K. , Hainer Jon , Foster Courtney , Nearing Bruce D. , Gervino Ernest , Verrier Richard L. 
Published: September 2017

BackgroundT‐wave heterogeneity (TWH) independently predicted cardiovascular mortality in Health Survey 2000 based on 12‐lead ECGs recorded at rest. We investigated whether TWH is elevated during exercise tolerance testing (ETT) in symptomatic diabetic patients with nonflow‐limiting coronary artery stenosis compared to control subjects without diabetes.MethodsCases were all patients (n = 20) with analyzable ECG recordings during both rest and ETT who were enrolled in the Effects of Ranolazine on Coronary Flow Reserve (CFR) in Symptomatic Patients with Diabetes and Suspected or Known Coronary Artery Disease (RAND‐CFR) study (NCT01754259); median CFR was 1.44; 80% of cases had CFR <2. Control subjects (n = 9) were nondiabetic patients who had functional flow reserve (FFR) >0.8, a range not associated with inducible ischemia. TWH was analyzed from precordial leads V4, V5, and V6 by second central moment analysis, which assesses the interlead splay of T‐waves about a mean waveform.ResultsDuring exercise to similar rate‐pressure products (p = .31), RAND‐CFR patients exhibited a 49% increase in TWH during exercise (rest: 49 ± 5 μV; exercise: 73 ± 8 μV, p = .003). By comparison, in control subjects, TWH was not significantly altered (rest: 52 ± 11 μV; ETT: 38 ± 5 μV, p = .19). ETT‐induced ST‐segment depression >1 mm (p = .11) and Tpeak‐Tend (p = .18) and QTc intervals (p = .80) failed to differentiate cases from controls.ConclusionsTWH is capable of detecting latent repolarization abnormalities, which are present during ETT in diabetic patients with nonflow‐limiting stenosis but not in control subjects. The technique developed in this study permits TWH analysis from archived ECGs and thereby enables mining of extensive databases for retrospective studies and hypothesis testing.
A multi‐centre audit of excess steroid use in 1176 patients with inflammatory bowel disease
Authors: Selinger C. P. , Parkes G. C. , Bassi A. , Fogden E. , Hayee B. , Limdi J. K. , Ludlow H. , McLaughlin S. , Patel P. , Smith M. , Raine T. 
Published: September 2017

SummaryBackgroundCorticosteroids are central to inducing remission in inflammatory bowel disease (IBD) but are ineffective maintenance agents.AimTo benchmark steroid usage in British outpatients and assess factors associated with excess exposure.MethodsWe recorded steroid use in unselected IBD outpatients. Cases meeting criteria for steroid dependency or excess were blind peer reviewed to determine whether steroid prescriptions were avoidable. Associations between steroid use and patient/institutional factors were analysed.ResultsOf 1176 patients, 30% received steroids in the prior 12 months. 14.9% had steroid dependency or excess, which was more common in moderate/severe ulcerative colitis (UC) than Crohn's disease (CD) (42.6% vs 28.1%; P = .027). Steroid dependency or excess was deemed avoidable in 49.1%. The annual incidence of inappropriate steroid excess was 7.1%. Mixed‐effects logistic regression analysis revealed independent predictors of inappropriate steroid excess. The odds ratio (OR, 95%CI) for moderate/severe compared to mild/quiescent disease activity was 4.59 (1.53‐20.64) for UC and 4.60 (2.21‐12.00) for CD. In CD, lower rates of inappropriate steroid excess were found in centres with an IBD multi‐disciplinary team (OR 0.62 [0.46‐0.91]), whilst dedicated IBD clinics protected against inappropriate steroid excess in UC (OR 0.64, 95% CI 0.21‐0.94). The total number of GI trainees was associated with rates of inappropriate steroid excess.ConclusionsSteroid dependency or excess occurred in 14.9% of British IBD patients (in 7.1% potentially avoidable). We demonstrated positive effects of service configurations (IBD multi‐disciplinary team, dedicated IBD clinics). Routine recording of steroid dependency or excess is feasible and should be considered a quality metric.
Environment and landscape rather than planting design are the drivers of success in long‐term restoration of riparian Atlantic forest
Authors: Suganuma Marcio Seiji , Torezan José Marcelo D. , Durigan Giselda 
Published: September 2017

AbstractQuestionIdentifying the factors that lead to the success of restoration projects has been a major challenge in ecological restoration. Here we ask which factors, aside from time since restoration began, drive the recovery of tree biomass, density and richness of the understorey in riparian forests undergoing restoration.LocationSemideciduous Atlantic Forest with tropical climate and deep, fertile soils, southeast Brazil.MethodsWe sampled tree basal area (DBH ≥ 5 cm), density and richness of the understorey (DBH < 5 cm) in 26 riparian forests undergoing restoration (a chronosequence spanning 4–53 years). We assessed the following variables as possible factors, besides time, influencing community attributes: (1) planting design: density and richness of seedlings planted; (2) landscape features: proximity index measuring forest cover within a 1.5‐km radius, distance and size of the nearest forest remnant; and (3) environmental factors: invasive grasses, soil fertility, drought, average annual precipitation and proportion of fine particles in the soil. We performed correlation analyses including predictor and response variables, followed by stepwise backward regression (AIC), multiple and simple linear regressions, to investigate the relationships between those factors and the community attributes.ResultsTree basal area was primarily influenced by the proportion of small particles in the soil (+) and secondarily by rainfall (−). Understorey richness was influenced by the combination of size (+) and distance (−) of the nearest patch, rainfall (−) and soil fertility (+). Understorey density was primarily influenced by the size of the nearest forest remnant (+) and secondarily by invasive grasses (−). No influence of density or richness of the seedlings planted was observed.ConclusionEnvironmental factors and landscape configuration drive the recovery of tree biomass, density and richness in communities undergoing restoration. The most relevant ecological filters influencing restoration success are availability of soil water and nutrients and the distance and size of the nearest remnant of native vegetation. The expected influence of richness and density of seedlings planted, considered for many years as important drivers of forest restoration success, was not confirmed in this study.