bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrate supply and uptake in the Atlantic Arctic sea ice zone: seasonal cycle, mechanisms and drivers
Authors: Henley Sian F. , Porter Marie , Hobbs Laura , Braun Judith , Guillaume-Castel Robin , Venables Emily J. , Dumont Estelle , Cottier Finlo 
Published: August 2020

Nutrient supply to the surface ocean is a key factor regulating primary production in the Arctic Ocean under current conditions and with ongoing warming and sea ice losses. Here we present seasonal nitrate concentration and hydrographic data from two oceanographic moorings on the northern Barents shelf between autumn 2017 and summer 2018. The eastern mooring was sea ice-covered to varying degrees during autumn, winter and spring, and was characterized by more Arctic-like oceanographic conditions, while the western mooring was ice-free year-round and showed a greater influence of Atlantic water masses. The seasonal cycle in nitrate dynamics was similar under ice-influenced and ice-free conditions, with biological nitrate uptake beginning near-synchronously in early May, but important differences between the moorings were observed. Nitrate supply to the surface ocean preceding and during the period of rapid drawdown was greater at the ice-free more Atlantic-like western mooring, and nitrate drawdown occurred more slowly over a longer period of time. This suggests that with ongoing sea ice losses and Atlantification, the expected shift from more Arctic-like ice-influenced conditions to more Atlantic-like ice-free conditions is likely to increase nutrient availability and the duration of seasonal drawdown in this Arctic shelf region. The extent to which this increased nutrient availability and longer drawdown periods will lead to increases in total nitrate uptake, and support the projected increases in primary production, will depend on changes in upper ocean stratification and their effect on light availability to phytoplankton as changes in climate and the physical environment proceed.
This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
Climate-driven benthic invertebrate activity and biogeochemical functioning across the Barents Sea polar front
Authors: Solan Martin , Ward Ellie R. , Wood Christina L. , Reed Adam J. , Grange Laura J. , Godbold Jasmin A. 
Published: August 2020

Arctic marine ecosystems are undergoing rapid correction in response to multiple expressions of climate change, but the consequences of altered biodiversity for the sequestration, transformation and storage of nutrients are poorly constrained. Here, we determine the bioturbation activity of sediment-dwelling invertebrate communities over two consecutive summers that contrasted in sea-ice extent along a transect intersecting the polar front. We find a clear separation in community composition at the polar front that marks a transition in the type and amount of bioturbation activity, and associated nutrient concentrations, sufficient to distinguish a southern high from a northern low. While patterns in community structure reflect proximity to arctic versus boreal conditions, our observations strongly suggest that faunal activity is moderated by seasonal variations in sea ice extent that influence food supply to the benthos. Our observations help visualize how a climate-driven reorganization of the Barents Sea benthic ecosystem may be expressed, and emphasize the rapidity with which an entire region could experience a functional transformation. As strong benthic-pelagic coupling is typical across most parts of the Arctic shelf, the response of these ecosystems to a changing climate will have important ramifications for ecosystem functioning and the trophic structure of the entire food web.This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
Climate change and diminishing seasonality in Arctic benthic processes
Authors: Morata Nathalie , Michaud Emma , Poullaouec Marie-Aude , Devesa Jérémy , Le Goff Manon , Corvaisier Rudolph , Renaud Paul E. 
Published: August 2020

The iconic picture of Arctic marine ecosystems shows an intense pulse of biological productivity around the spring bloom that is sustained while fresh organic matter (OM) is available, after which ecosystem activity declines to basal levels in autumn and winter. We investigated seasonality in benthic biogeochemical cycling at three stations in a high Arctic fjord that has recently lost much of its seasonal ice-cover. Unlike observations from other Arctic locations, we find little seasonality in sediment community respiration and bioturbation rates, although different sediment reworking modes varied through the year. Nutrient fluxes did vary, suggesting that, although OM was processed at similar rates, seasonality in its quality led to spring/summer peaks in inorganic nitrogen and silicate fluxes. These patterns correspond to published information on seasonality in vertical flux at the stations. Largely ice-free Kongsfjorden has a considerable detrital pool in soft sediments which sustain benthic communities over the year. Sources of this include macroalgae and terrestrial runoff. Climate change leading to less ice cover, higher light availability and expanded benthic habitat may lead to more detrital carbon in the system, dampening the quantitative importance of seasonal pulses of phytodetritus to seafloor communities in some areas of the Arctic.
This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
Diagnosis of COVID-19 from X-rays Using Combined CNN-RNN Architecture with Transfer Learning
Authors: Al-Rakhami Mabrook S. , Islam Md. Milon , Islam Md. Zabirul , Asraf Amanullah , Sodhro Ali Hassan , Ding Weiping 
Published: August 2020

AbstractThe confrontation of COVID-19 pandemic has become one of the promising challenges of the world healthcare. Accurate and fast diagnosis of COVID-19 cases is essential for correct medical treatment to control this pandemic. Compared with the reverse-transcription polymerase chain reaction (RT-PCR) method, chest radiography imaging techniques are shown to be more effective to detect coronavirus. For the limitation of available medical images, transfer learning is better suited to classify patterns in medical images. This paper presents a combined architecture of convolutional neural network (CNN) and recurrent neural network (RNN) to diagnose COVID-19 from chest X-rays. The deep transfer techniques used in this experiment are VGG19, DenseNet121, InceptionV3, and Inception-ResNetV2. CNN is used to extract complex features from samples and classified them using RNN. The VGG19-RNN architecture achieved the best performance among all the networks in terms of accuracy in our experiments. Finally, Gradient-weighted Class Activation Mapping (Grad-CAM) was used to visualize class-specific regions of images that are responsible to make decision. The system achieved promising results compared to other existing systems and might be validated in the future when more samples would be available. The experiment demonstrated a good alternative method to diagnose COVID-19 for medical staff.
Phosphate levels and pulmonary damage in COVID-19 patients based on CO-RADS scheme: is there any link between parathyroid gland and COVID-19?
Authors: Javdani Farshid , Parsa Shima , Shakeri Heshmatollah , Hatami Naser , Kalani Navid , Haghbeen Marzieh , Raufi Rahim , Abbasi Alireza , Keshavarz Pouyan , Hashemi Seyyed Abbas , shafiee Amin 
Published: August 2020

AbstractBackgroundPreliminary studies of COVID-19 have provided some evidence that electrolyte disturbances may also be present in patients. In this study we aimed to evaluate the role of the arrival electrolytes and symptoms in prediction of Lung damage in CT scan based on the CO-RADS system.MethodsThis was a retrospective cross-sectional analytical study. We included patients with laboratory confirmed COVID-19 infection, June 15 to July 7. Patients were included in study if there were no previous history of kidney disease. Demographic, clinical characteristics, laboratory findings, and CO-RADS High-resolution computed tomography (HRCT) of lung report were collected. Univariate logistic regression was employed first to identify the effective, correlated items. All statistics were performed with SPSS version 18.0.ResultsIn the current study, 36 (20 male- 16 female) patients with mean age of the 54.7±17.5 years old were studied. Most common symptom at the arrival was the Fever (52.8%), followed by Fatigue (18%), and dyspnea (44.4%). Computed tomography assessment revealed CO-RADS 2 in 4 (11.1%) patients, CORADS 3 in 1 (2.8%), CO-RADS 4 in 20 (55.6%), and CO-RADS 5 in 11 (30.6%) patients. In the comparison with the study groups based on the HRCT status (CO-RADS II,III vs. CO-RADS IV,V), patients with severe HRCT damage had significantly lower level of Phosphorus (P < 0.01). Univariate logistic regression analysis showed that only one factors was associated with HRCT damage status (Phosphorus, P=0.040). Phosphorus upper than 4.5 was associated with better HRCT results with OR ratio of 3.71 (X2(1)=5.69; p=0.017).ConclusionOur study illustrates that higher phosphate levels may be associated with better CT scan of lung outcomes in COVID-19; while hypophosphatemia is associated with severe lung injuries. This could help clinicians to manage hospitalized patients and may link the COVID-19 and parathyroid gland.
Smoking Impairs Women’s Verbal Learning and Memory Performance More than Men’s: An International Web-Cohort Study of 70,000 Participants
Authors: Lewis C.R. , Talboom J.S. , Both M.D. De , Schmidt A.M. , Naymik M.A. , Håberg A.K. , Rundek T. , Levin B.E. , Hoscheidt S. , Bolla Y. , Brinton R.D. , Hay M. , Barnes C.A. , Glisky E. , Ryan L. , Huentelman M.J. 
Published: August 2020

ABRSTACTBackgroundVascular contributions to cognitive impairment and dementia (VCID) include structural and functional blood vessel injuries linked to poor neurocognitive outcomes. Smoking might indirectly increase the likelihood of cognitive impairment by exacerbating the risks associated with underlying vascular disease. Sex disparities in VCID have been reported, however, few studies have assessed the sex-specific impact of smoking on cognitive function and with contradictory results. This is an important topic since smoking and cardiovascular disease negatively impact health and possibly women have the greater lifetime risk of stroke and dementia than men. In this study, we sought to investigate the effect-modification of sex on the relationship between smoking, cardiovascular disease and verbal learning and memory function.MethodsUsing MindCrowd, a web-based cohort of over 70,000 people aged 18 - 85, we investigated whether sex modifies the impact of smoking and cardiovascular disease on verbal memory performance on a paired-associate learning task using both multiple regression and propensity matching approaches. Artificial error introduction and permutation testing underscored the stability of our results. To demonstrate the necessity of large sample sizes to detect an interaction of sex and smoking, we performed down sampling analyses.FindingsWe found significant interactions in that smoking impacts verbal learning performance more in women and cardiovascular disease more in men across a wide age range.InterpretationThese results suggest that smoking and cardiovascular disease impact verbal learning and memory throughout adulthood. Smoking particularly affects learning and memory in women and cardiovascular disease has a larger effect in men. Although the reasons for these sex-modification effects are not entirely understood, our findings highlight the importance of considering biological sex in VCID.FundingMueller Family Charitable Trust; Arizona Alzheimer’s Consortium; Flinn Foundation; The McKnight Brain Research Foundation; NIH-NIA grant R01-AG049465.
Dynamic deformable attention (DDANet) for semantic segmentation
Authors: Rajamani Kumar T. , Siebert Hanna , Heinrich Mattias P. 
Published: August 2020

AbstractDeep learning based medical image segmentation is an important step within diagnosis, which relies strongly on capturing sufficient spatial context without requiring too complex models that are hard to train with limited labelled data. Training data is in particular scarce for segmenting infection regions of CT images of COVID-19 patients. Attention models help gather contextual information within deep networks and benefit semantic segmentation tasks. The recent criss-cross-attention module aims to approximate global self-attention while remaining memory and time efficient by separating horizontal and vertical selfsimilarity computations. However, capturing attention from all non-local locations can adversely impact the accuracy of semantic segmentation networks. We propose a new Dynamic Deformable Attention Network (DDANet) that enables a more accurate contextual information computation in a similarly efficient way. Our novel technique is based on a deformable criss-cross attention block that learns both attention coefficients and attention offsets in a continuous way. A deep segmentation network (in our case a U-Net [1]) that employs this attention mechanism is able to capture attention from pertinent non-local locations and also improves the performance on semantic segmentation tasks compared to criss-cross attention within a U-Net on a challenging COVID-19 lesion segmentation task. Our validation experiments show that the performance gain of the recursively applied dynamic deformable attention blocks comes from their ability to capture dynamic and precise (wider) attention context. Our DDANet achieves Dice scores of 73.4% and 61.3% for Ground-Glass-Opacity and Consolidation lesions for COVID-19 segmentation and improves the accuracy by 4.9% points compared to a baseline U-Net.
ICU Outcomes and Survival in Patients with Severe COVID-19 in the Largest Health Care System in Central Florida
Authors: Oliveira Eduardo , Parikh Amay , Lopez-Ruiz Arnaldo , Carrilo Maria , Goldberg Joshua , Cearras Martin , Fernainy Khaled , Andersen Sonja , Mercado Luis , Guan Jian , Zafar Hammad , Louzon Patricia , Carr Amy , Baloch Natasha , Pratley Richard , Silverstry Scott , Hsu Vincent , Sniffen Jason , Herrera Victor , Finkler Neil 
Published: August 2020

AbstractBackgroundObservational studies have consistently described poor clinical outcomes and increased ICU mortality in patients with severe coronavirus disease 2019 (COVID-19) who require mechanical ventilation (MV). Our study describes the clinical characteristics and outcomes of patients with severe COVID-19 admitted to ICU in the largest health care system in the state of Florida, United States.MethodsRetrospective cohort study of patients admitted to ICU due to severe COVID-19 in AdventHealth health system in Orlando, Florida from March 11th until May 18th, 2020. Patients were characterized based on demographics, baseline comorbidities, severity of illness, medical management including experimental therapies, laboratory markers and ventilator parameters. Major clinical outcomes analyzed at the end of the study period were: hospital and ICU length of stay, MV-related mortality and overall hospital mortality of ICU patients.ResultsOut of total of 1283 patients with COVID-19, 131 (10.2%) met criteria for ICU admission (median age: 61 years [interquartile range {IQR}, 49.5-71.5]; 35.1% female). Common comorbidities were hypertension (84; 64.1%), and diabetes (54; 41.2%). Of the 131 ICU patients, 109 (83.2%) required MV and 9 (6.9%) received ECMO. Lower positive end expiratory pressure (PEEP) were observed in survivors [9.2 (7.7-10.4)] vs non-survivors [10 (9.1-12.9] p= 0.004]. Compared to non-survivors, survivors had a longer MV length of stay (LOS) [14 (IQR 8-22) vs 8.5 (IQR 5-10.8) p< 0.001], Hospital LOS [21 (IQR 13-31) vs 10 (7-1) p< 0.001] and ICU LOS [14 (IQR 7-24) vs 9.5 (IQR 6-11), p < 0.001]. The overall hospital mortality and MV-related mortality were 19.8% and 23.8% respectively. After exclusion of hospitalized patients, the hospital and MV-related mortality rates were 21.6% and 26.5% respectively.ConclusionsOur study demonstrates an important improvement in mortality of patients with severe COVID-19 who required ICU admission and MV in comparison to previous observational reports and emphasize the importance of standard of care measures in the management of COVID-19.
Cost-effectiveness of sleeping sickness elimination campaigns in five settings of the Democratic Republic of Congo
Authors: Antillon Marina , Huang Ching-I , Crump Ronald E. , Brown Paul E. , Snijders Rian , Miaka Erick Mwamba , Keeling Matt J. , Rock Kat S. , Tediosi Fabrizio 
Published: August 2020

AbstractGambiense human African trypanosomiasis (gHAT) is marked for elimination of transmission (EOT) by 2030, but the disease persists in several low-income countries. We coupled transmission and health outcomes models to examine the cost-effectiveness of four gHAT elimination strategies in in five settings – spanning low- to high-risk – of the Democratic Republic of Congo. Alongside passive screening (PS) in fixed health facilities, the strategies included active screening (AS) at average or intensified coverage levels, alone or with vector control (VC) with a scale-back algorithm when no cases were reported for three consecutive years. In high or moderate-risk settings, costs of gHAT strategies are primarily driven by AS and, if used, VC. Due to the cessation of AS and VC, most investments (75-80%) will be made by 2030 and VC might be cost-saving while ensuring EOT. In low-risk settings, costs are driven by PS, and minimum-cost strategies consisting of AS and PS lead to EOT by 2030 with high probability.
Using Citizen Science to build baseline data on tropical tree phenology
Authors: Ramaswami Geetha , Sidhu Swati , Quader Suhel 
Published: August 2020

AbstractLarge-scale and long-term understanding of the phenology of widespread tree species is lacking in the tropics, and particularly in the Indian subcontinent. In the absence of baseline information, the impacts of climate on tree phenology, and thus on trophic interactions downstream of tree phenology, are also poorly understood. Citizen scientists can help bridge this gap by contributing simple, technology-based information over large spatial scales and over the long term. In this study, we describe an India-wide citizen science initiative called SeasonWatch, with preliminary insights into contributor behaviour and species phenology. Over a period of 8 years, between 2011 and 2019, cumulative contributor numbers have increased every year, although consistent contribution remains constant and low. The phenological patterns in the 4 most-observed species (JackfruitArtocarpus heterophyllusLam., MangoMangifera indicaL., TamarindTamarindus indicaL., and Indian LaburnumCassia fistulaL.) are described, with discernible seasonal peaks in flowering and fruiting. Seasonal peaks are influenced by tree phenology reported in the south Indian state of Kerala, which has the maximum number of contributors and most number of observations per contributor, comprising 89% of all observations. We look in detail at the flowering phenology of one particular species,Cassia fistula, which appears to show aberrant phenology, reflecting a potential shift away from historical baselines. Latitudinal patterns in the phenology of widespread species such asMangifera indicaare also discernible from 4 seasonal bioblitz events organised during 2018-19, with trees in lower latitudes exhibiting flowering and fruiting phenology earlier than the higher latitudes. We conclude that there are signs of shifts in phenological patterns, as in the case ofC. fistula, and extend a call for action to sustain long-term interest and participation by contributors to develop a baseline for common tropical tree species that can be used to understand long-term consequences of climate change on tropical tree phenology.
Abundant proteins contribute strongly to noise in the growth rate of optimally growing bacteria
Authors: Krah L.H.J. , Hermsen R. 
Published: August 2020

AbstractIn bacterial cells, protein expression is a highly stochastic process. At the same time, physiological variables such as the cellular growth rate also fluctuate significantly. A common intuition is that, due to their relatively high noise amplitudes, proteins with a low mean expression level are the most important causes of these fluctuations on a larger, physiological scale. Noise in highly expressed proteins, whose stochastic fluctuations are relatively small, is often ignored. In this work, we challenge this intuition by developing a theory that predicts the contribution of a protein’s expression noise to the noise in the instantaneous, cellular growth rate. Using mathematical analysis, we decomposed the contribution of each protein into two factors: the noise amplitude of the protein, and the sensitivity of the growth rate to fluctuations in that protein’s concentration. Next, we incorporated evolution, which has shaped the mean abundances of growth-related proteins to optimise the growth rate, causing protein abundances, but also cellular sensitivities to be non-random. We show that in cells that grow optimally fast, the growth rate is most sensitive to fluctuations in highly abundant proteins. This causes such proteins to overall contribute strongly to the noise in the growth-rate, despite their low noise levels. The results are confirmed in a stochastic toy model of cellular growth.
How bank vole-PUUV interactions influence the eco-evolutionary processes driving nephropathia epidemica epidemiology: An experimental and genomic approach
Authors: Madrières Sarah , Tatard Caroline , Murri Séverine , Vulin Johann , Galan Maxime , Piry Sylvain , Pulido Coralie , Loiseau Anne , Artige Emmanuelle , Benoit Laure , Leménager Nicolas , Lakhdar Latifa , Charbonnel Nathalie , Marianneau Philippe , Castel Guillaume 
Published: August 2020

AbstractIn Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of haemorrhagic fever with renal syndrome (HFSR). Despite the presence of its reservoir, the bank vole, on most of French territory, the geographic distribution of NE cases is heterogeneous and NE endemic and non-endemic areas have been reported. In this study we analyzed whether bank vole-PUUV interactions could partly shape these epidemiological differences. We performed crossed-experimental infections using wild bank voles from French endemic (Ardennes) and non-endemic (Loiret) areas, and two French PUUV strains isolated from these areas. The serological response and dynamics of PUUV infection were compared between the four cross-infection combinations. We showed that the serological response and the presence of PUUV in excretory organs were more important in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs was higher than in other non-excretory organs for the NE endemic cross-infection, but not for the NE non-endemic cross-infection. Altogether, our results showed that genetically different PUUV strains, and in a lesser extent their interaction with sympatric bank voles, could affect virus replication and diversity. This could impact PUUV excretion/transmission between rodents and to humans, and in turn at least partly shape NE epidemiology in France.