bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel tool for time‐locking study plans to results
Authors: Mazor Matan , Mazor Noam , Mukamel Roy 
Published: November 2018

AbstractOften researchers wish to mark an objective line between study plans that were specified before data acquisition and decisions that were made following data exploration. Contrary to common perception, registering study plans to an online platform prior to data collection does not by itself provide such an objective distinction, even when the registration is time‐stamped. Here, we adapt a method from the field of cryptography to allow encoding of study plans and predictions within random aspects of the data acquisition process. Doing so introduces a causal link between the preregistered content and objective attributes of the acquired data, such as the timing and location of brain activations. This guarantees that the preregistered plans and predictions are indeed specified prior to data collection. Our time‐locking system does not depend on any external party and can be performed entirely in‐lab. We provide code for easy implementation and a detailed example from the field of functional Magnetic Resonance Imaging (fMRI).
Synchronization and maintenance of circadian timing in the mammalian clockwork
Authors: Maywood Elizabeth S. 
Published: November 2018

AbstractThe hypothalamic suprachiasmatic nucleus (SCN) is the principal circadian pacemaker in mammals. Cells in the SCN contain cell‐autonomous transcriptional‐translational feedback loops, which are synchronised to each other and thereby provide a coherent output to direct synchrony of peripheral clocks located in the brain and body. A major difference between these peripheral clocks and the SCN is the requirement for intercellular coupling mechanisms, which confer robustness, stability and amplitude to the system. There has been remarkable progress to our understanding of the intra‐ and inter‐cellular mechanisms of the SCN circuitry over the last ~20 years, which has come hand‐in‐hand with the development of new technologies to measure and manipulate the clock.
Interaction between interferon regulatory factor 6 and glycine receptor beta shows a protective effect on developing nonsyndromic cleft lip with or without cleft palate in the Han Chinese population
Authors: Wu Di , Wang Mei , Wang Xingang , Zhang Yong‐Biao , Song Tao , Yin Ningbei , Zhao Zhenmin 
Published: November 2018

Single‐nucleotide polymorphisms (SNPs) in protein‐coding regions of genes which were previously reported to be associated with nonsyndromic cleft lip, with or without palate involvement (NSCL/P), were investigated. Twelve candidate loci [platelet‐derived growth factor C (PDGFC), platelet‐derived growth factor subunit A (PDGFA), platelet‐derived growth factor receptor alpha (PDGFRA), glycine receptor alpha 2 (GLRA2), glycine receptor beta (GLRB), ATP binding cassette subfamily A member 4 (ABCA4), MAF bZIP transcription factor B (MAFB), interferon regulatory factor 6 (IRF6), CCDC26 long non‐coding RNA (CCDC26), paired box 7 (PAX7), ventral anterior homeobox 1 (VAX1), and netrin 1 (NTN1)] covering 1.5 Mbp were sequenced in 136 NSCL/P patients and 54 healthy controls. Twenty‐five genomic variants identified were further validated in another 400 NSCL/P and 200 controls. Two SNPs in IRF6 showed a protective effect against the development of NSCL/P (rs12405750, OR = 0.54, 95% CI: 0.41–0.69; and rs2235371, OR = 0.55, 95% CI: 0.43–0.71). The missense variant, rs2235371, alters the conserved amino acid valine to isoleucine at codon 274 (V274I). We observed that SNPs at IRF6 (rs2235371 and rs12405750) and GLRB (rs73856838 and rs72685584) show consistent interaction effects. The association between the missense SNP rs2235371 in gene IRF6 and NSCL/P suggests that this SNP may play an important role as a risk factor for NSCL/P in the Han Chinese populations. The marginal signal near 4q31 detected in previous genome‐wide association studies might be caused by an interaction between the IRF6 and GLRB genes. This interaction needs to be further validated by experimentation in follow‐up studies.
Using mixed stock analysis to assess source populations for at‐sea bycaught juvenile and adult loggerhead turtles (Caretta caretta) in the north‐west Atlantic
Authors: Stewart Kelly R. , LaCasella Erin L. , Jensen Michael P. , Epperly Sheryan P. , Haas Heather L. , Stokes Lesley W. , Dutton Peter H. 
Published: November 2018

AbstractAssessments of fisheries by‐catch on marine megafauna are important for developing effective management strategies. For sea turtles, impacts may be evident in nesting population trends, but generally only after a lag, as turtles are slow to mature. We examined 850 loggerhead turtle (Caretta caretta) by‐catch samples collected over 14 years throughout the western North Atlantic to identify source nesting populations. We identified proportions of turtles from 19 distinct management units (MUs), using mitochondrial DNA and mixed stock analysis, considering population size. We found a significant split in the distribution of small versus large loggerheads to the north and south of Cape Hatteras, North Carolina (latitude 35°N). North of Cape Hatteras, large turtles came from south‐east Florida (SEFL; 44% ± 15%) and the northern United States (33% ± 16%) MUs, while south of Cape Hatteras, the major contributors were Central East Florida (52% ± 20%) and south‐east Florida (SEFL; 41% ± 20%). Small turtles in the north came from Central East Florida (64% ± 14%), and in the south, south‐east Florida had the highest representation (56% ± 25%). There was little contribution from Mediterranean and Cape Verde populations, indicating low risk from western North Atlantic by‐catch to MUs in the Mediterranean. Understanding where threats may impact source populations is important, particularly for larger size turtles, as these individuals have the highest reproductive value. These findings allow more informed threat assessments to be conducted for loggerhead turtles considering spatial and demographic structure.
Benthivorous fish bioturbation reduces methane emissions, but increases total greenhouse gas emissions
Authors: Oliveira Junior Ernandes S. , Temmink Ralph J. M. , Buhler Beatriz F. , Souza Renata M. , Resende Nathália , Spanings Tom , Muniz Claumir C. , Lamers Leon P. M. , Kosten Sarian 
Published: November 2018

Abstract

Globally, aquatic systems face increasing challenges with respect to increased greenhouse gas (GHG) emissions, eutrophication and strongly altered fish community composition. Although it is known that benthivorous fish can influence sediment and water column biogeochemistry, studies showing causal relationships are largely lacking.

Here, we used a mesocosm approach with Common carp (Cyprinus carpio) to unravel the effects of bioturbation on GHG and nutrient dynamics. We hypothesised that fish bioturbation decreases methane (CH4) emissions and increases carbon dioxide (CO2) emissions by increased sediment oxygenation. Additionally, lower phosphorus (P) mobilisation was expected due to increased binding to ferric iron (Fe3+).

We found that benthivorous fish increased water turbidity, and reduced CH4 diffusion to the atmosphere by 33%, and ebullition by 67%, probably because of sediment oxygenation. Simultaneously, however, CO2 emissions increased due to higher aerobic decomposition, leading to higher overall GHG emissions. In contrast to our hypothesis, we did not find indications of bioturbation affecting P mobilisation from the sediment, probably because P binding was already high in the control treatment as a result of high porewater Fe:P ratios.

We conclude that bioturbation by fish has strong effects on GHG emissions as a result of higher overall decomposition rates offsetting reduced CH4 emissions. Depending on porewater Fe:P ratios, benthivorous fish may additionally reduce P mobilisation.
The role of phytoplankton in the diet of the bladderwort Utricularia australis R.Br. (Lentibulariaceae)
Authors: Ellwood Neil T. W. , Congestri Roberta , Ceschin Simona 
Published: November 2018

Abstract

It is becoming more apparent that the aquatic carnivorous plants Utricularia (Lentibulariaceae) can capture and utilise a wide range of small aquatic organisms. Although they can take up nutrients directly from the water by rootless shoots, much of their overall nutrition comes from prey caught in their traps. Most of the early literature was focused mainly on animal prey, hence the term carnivorous to describe Utricularia spp., but more recently the contribution of other microorganisms and detritus to their diet is being realised. Specifically, the importance of the phytoplankton in traps as prey is proving interesting. However, most investigations have focused on the trap communities with few comparisons to phytoplankton as potential prey, which could reveal the occurrence of feeding selectivity.

The eurytopic species Utricularia australis was surveyed across 12 sites in central Italy in lentic waterbodies ranging from oligotrophic to eutrophic. Phytoplankton communities outside the traps were composed of 135 taxa from 21 orders belonging to eight phyla and the algal community in the traps comprised 124 taxa from 17 orders belonging to eight phyla, recorded from all sampling sites. Among the 12 sites phytoplankton communities were highly diverse; however, communities inside and outside the traps at each site were very similar. This similarity indicated that feeding was not selective.

Algal movements are not able to elicit a trap response, yet around 70% of the traps contained phytoplankton only (no animal prey). Therefore, regular spontaneous trap firing, known to occur in U. australis, is thought to be responsible for the similarities in trap and plankton algal communities.

At two sites, a Euglenophyte (Lepocinclis sp.) and a Cryptophyte (Chilomonas sp.) proliferated, which were otherwise very rare in the phytoplankton community. This is indicative of favourable growth conditions in the traps and possibly of commensal relationships. It seems that the diet requirements of U. australis are met by having a highly varied prey spectrum.
Beyond the Last Glacial Maximum: Island endemism is best explained by long‐lasting archipelago configurations
Authors: Norder Sietze J. , Proios Konstantinos , Whittaker Robert J. , Alonso María R. , Borges Paulo A. V. , Borregaard Michael K. , Cowie Robert H. , Florens F. B. Vincent , de Frias Martins António M. , Ibáñez Miguel , Kissling W. Daniel , de Nascimento Lea , Otto Rüdiger , Parent Christine E. , Rigal François , Warren Ben H. , Fernández‐Palacios José María , van Loon E. Emiel , Triantis Kostas A. , Rijsdijk Kenneth F. 
Published: November 2018

AbstractAimTo quantify the influence of past archipelago configuration on present‐day insular biodiversity patterns, and to compare the role of long‐lasting archipelago configurations over the Pleistocene to configurations of short duration such as at the Last Glacial Maximum (LGM) and the present‐day.Location53 volcanic oceanic islands from 12 archipelagos worldwide—Azores, Canary Islands, Cook Islands, Galápagos, Gulf of Guinea, Hawaii, Madeira, Mascarenes, Pitcairn, Revillagigedo, Samoan Islands and Tristan da Cunha.Time periodThe last 800 kyr, representing the nine most recent glacial–interglacial cycles.Major taxa studiedLand snails and angiosperms.MethodsSpecies richness data for land snails and angiosperms were compiled from existing literature and species checklists. We reconstructed archipelago configurations at the following sea levels: the present‐day high interglacial sea level, the intermediate sea levels that are representative of the Pleistocene and the low sea levels of the LGM. We fitted two alternative linear mixed models for each archipelago configuration using the number of single‐island endemic, multiple‐island endemic and (non‐endemic) native species as a response. Model performance was assessed based on the goodness‐of‐fit of the full model, the variance explained by archipelago configuration and model parsimony.ResultsSingle‐island endemic richness in both taxonomic groups was best explained by intermediate palaeo‐configuration (positively by area change, and negatively by palaeo‐connectedness), whereas non‐endemic native species richness was poorly explained by palaeo‐configuration. Single‐island endemic richness was better explained by intermediate archipelago configurations than by the archipelago configurations of the LGM or present‐day.Main conclusionsArchipelago configurations at intermediate sea levels—which are representative of the Pleistocene—have left a stronger imprint on single‐island endemic richness patterns on volcanic oceanic islands than extreme archipelago configurations that persisted for only a few thousand years (such as the LGM). In understanding ecological and evolutionary dynamics of insular biota it is essential to consider longer‐lasting environmental conditions, rather than extreme situations alone.
Climate seasonality as an essential predictor of global fire activity
Authors: Saha Michael V. , Scanlon Todd M. , D'Odorico Paolo 
Published: November 2018

AbstractAimFire is a globally important disturbance that affects nearly all vegetated biomes. Previous regional studies have suggested that the predictable seasonal pattern of a climatic time series, or seasonality, might aid in the prediction of average fire activity, but it is not known whether these findings are applicable globally. Here, we investigate how seasonality can be used to explain variations in fire activity on a global scale.LocationGlobal, 60° S–60° N.Time periodData averaged over the period 1999–2015.MethodsWe describe a method to partition a periodic seasonal cycle into two seasons and define conceptually simple temporal metrics that describe spatial variability in seasonality. We explore the usefulness of these metrics in explaining global fire activity using the average monthly time series of precipitation and temperature and a flexible machine learning procedure (random forests).ResultsA simple model that uses only precipitation and temperature amplitude and synchrony between wet and warm seasons correctly predicts 66% of the variability in global fire activity, substantially more than a model with mean annual temperature and precipitation. A more complex model that includes all nine metrics predicts 87% of variability in global fire activity.Main conclusionsThis study shows that seasonality of temperature and precipitation can be used to predict multi‐year average fire activity in a globally relevant way. The mechanisms highlighted in our work could be used to improve global fire models and enhance their ability to represent the spatial patterns of fire activity. Our method might also be useful in hindcasting historical fire using reanalysis or predicting future fire regimes using coarse output from climate models.
High frequency of getting out of bed in patients with Alzheimer's disease monitored by non‐wearable actigraphy
Authors: Higami Yoko , Yamakawa Miyae , Shigenobu Kazue , Kamide Kei , Makimoto Kiyoko 
Published: November 2018

AimSleep disturbances in patients with Alzheimer's disease have not been systematically evaluated, because sleep monitoring has proved difficult. Our goal was to quantitatively characterize sleep disturbances in patients with Alzheimer's disease.MethodsThe present study was a cross‐sectional descriptive study, carried out in dementia care units in Japan. Participants were 63 patients with Alzheimer's disease (mean age 77.6 ± 8.0 years) with severe behavioral and psychological symptoms of dementia. A non‐wearable actigraphy device placed under patient mattresses was used to measure sleep parameters: sleep time, time in bed, number of wakings and number of times they left the bed. Cut‐off points for sleep parameters were based on the interquartile range of the data.ResultsMedian nocturnal sleep time was 6.2 h (interquartile range 2.7 h). Median frequency of waking was eight times (5)/night. Median frequency of leaving the bed was five times (6), with a maximum of 31/night. We identified three types of sleep disturbance: frequent bed leaving, short sleep time and excessive sleep time. Multiple linear regression showed that duration of dementia was a significant predictor of frequent bed leaving at night (P = 0.042).ConclusionsFrequent bed leaving at night reflects severe sleep deprivation in patients with mild‐to‐severe Alzheimer's disease. Safety measures are required to prevent accidents related to sleep disturbances, regardless of dementia severity. Geriatr Gerontol Int 2019; 19: 130–134.
Utility valuation of health states for haemophilia and related complications in Europe and in the United States
Authors: Hoxer Christina S. , Zak Marek , Benmedjahed Khadra , Lambert Jérémy 
Published: November 2018

IntroductionThere is currently a paucity of health utility data describing the consequences of haemophilia and related complications.AimTo quantify the impact of distinct stages of severity of haemophilia and disease‐related complications on health‐related quality of life, expressed as health utilities in Europe and the United States.MethodsNine health state descriptions were developed based on literature review and interviews with haematologists and haemophilia patients. Three descriptions characterized the impact of mild, moderate and severe haemophilia without inhibitors. Six descriptions characterized disease‐related complications added to the moderate haemophilia description (arthroscopic synovectomy, prosthetic joint replacement, chronic pain, spontaneous bleed, traumatic bleed and end‐stage joint disease). Time trade‐off (TTO) interviews were conducted with 100 adults from the general public in the UK, France, Germany, Italy, Sweden and the United States. Mean TTO‐derived utility values were expressed on a scale from 0 (death) to 1 (full health).ResultsUtility values obtained for the health states corresponding to mild (0.73‐0.86), moderate (0.68‐0.76) and severe (0.64‐0.71) haemophilia followed the increase in severity. The addition of a complication to the “moderate” state leads to a decrease in the associated utility value. The most severe disutility (0.23‐0.36) across all countries was associated with the burden of end‐stage joint disease.ConclusionsThis study underlines the value that the French, Italian, German, Swedish, United States and UK populations ascribe to the avoidance of disease progression in haemophilia without inhibitors. Improved treatment options hold a potential for important benefits to haemophilia patients.
Helicobacter pylori antimicrobial resistance during a 5‐year period (2013‐2017) in northern Spain and its relationship with the eradication therapies
Authors: Cosme Angel , Torrente Iranzo Silvia , Montes Ros Milagrosa , Fernández‐Reyes Silvestre María , Alonso Galán Horacio , Lizasoain Jacobo , Bujanda Luis 
Published: November 2018

AbstractBackgroundAntibiotic resistance is the main cause for Helicobacter pylori therapy failure. Frequently, empirical regimens have been recommended in patients with various H. pylori eradication failures. In patients with H. pylori‐resistant to various families of antibiotics, the treatment guided by antimicrobial susceptibility testing allows the achievement of good eradication rates.AimTo evaluate the effectiveness of susceptibility‐guided antimicrobial treatment for H. pylori infection in patients with resistance to one or various families of antibiotics.MethodsA total of 3170 consecutive patients infected by H. pylori during 2013‐2017 were tested for antimicrobial susceptibility. 66.6% patients showed resistance to one antimicrobial, 18.9% to two, and 2.4% to three families of antibiotics. A cohort of 162 H. pylori‐positive patients were enrolled in this study. Forty‐three with single H. pylori resistance to clarithromycin (CLR) were treated with omeprazole (PPI), amoxicillin (AMX), and levofloxacin (LVX)—OAL (31 subjects) or omeprazole, AMX, and metronidazole (MTZ)—OAM (12 patients) and 77 patients with dual H. pylori resistance (51 to CLR and MTZ, 12 to CLR plus LVX, and 14 to MTZ plus LVX) received OAL or OBTM (PPI, bismuth subcitrate, tetracycline, and MTZ), OAM, and OAC, respectively. Other 42 patients with triple H. pylori resistance (CLR, LVX, and MTZ) were treated with PPI, AMX, and rifabutin—OAR (18 subjects), PPI, AMX, and doxycycline—OAD (8), OADB (7), OBTM (6), and ODBR (3). All subjects received standard doses for 10 days. Eradication rate was confirmed by 13C‐UBT. Adverse events were assessed by a questionnaire.ResultsIntention‐to‐treat analysis demonstrates that eradication rates using triple therapies in patients with H. pylori resistance to one and to two families of antibiotics were 93% and 94.8%, respectively. In subjects with H. pylori‐resistant to three families of antibiotics, cure rate was higher in naïve patients treated with OAR‐10 days compared to those treated with bismuth‐containing quadruple therapies (90% vs 75%). Adverse events were limited (18 of 162, 11.1%), all of them mild‐moderate.ConclusionsThe implementation of susceptibility‐guided triple therapy for 10 days leads to eradication rate ≥95% in naïve patients with H. pylori resistance to one or two families of antimicrobials. In naïve patients with H. pylori resistance to three families, OAR treatment achieved a 90% of eradication.
Evolution of major non‐HIV‐related comorbidities in HIV‐infected patients in the Italian Cohort of Individuals, Naïve for Antiretrovirals (ICONA) Foundation Study cohort in the period 2004–2014
Authors: d'Arminio Monforte A , Diaz‐Cuervo H , De Luca A , Maggiolo F , Cingolani A , Bonora S , Castagna A , Girardi E , Antinori A , Lo Caputo S , Guaraldi G , Cozzi‐Lepri A ,   the ICONA Foundation Study Group
Published: November 2018

ObjectivesThe management of HIV disease is complicated by the incidence of a new spectrum of comorbid noncommunicable diseases (NCDs). It is important to document changes in the prevalence of NCDs over time. The aim of the study was to describe the impact of ageing on HIV markers and on the prevalence of NCDs in people living with HIV (PLWHIV) in the Italian Cohort of Individuals, Naïve for Antiretrovirals (ICONA) seen for care in 2004–2014.MethodsAnalyses were conducted separately for a closed cohort (same people seen at both times) and an open cohort (all people under follow‐up). We used the χ2 test for categorical factors and the Wilcoxon test for quantitative factors to compare profiles over time.ResultsThe closed cohort included 1517 participants and the open cohort 3668 under follow‐up in 2004 and 6679 in 2014. The median age of the open cohort was 41 [interquartile range (IQR) 37–46] years in 2004 and 44 (IQR 36–52) years in 2014. Analysis of the closed cohort showed an increase in the prevalence of some NCDs [the prevalence of dyslipidaemia increased from 75% in 2004 to 91% in 2014, that of hypertension from 67 to 84%, and that of cardiovascular disease (CVD) from 18 to 32%] and a decrease in renal function (5% with eGFR < 60 mL/min per 1.73 m2 in 2004 versus 30% in 2014); the percentage of people in the high‐risk group for the Framingham CHD score more than tripled (from 13 to 45%). Results in the open cohort were similar.ConclusionsThe burden of NCDs in our PLWHIV population markedly worsened over a 10‐year time‐span, which is likely to be a result of the effects of both ageing and HIV infection as well as their interaction. Special attention must be given to the management and prevention of NCDs.