bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meditating on rights and responsibility: remarks on ‘the limits and burdens of rights’
Authors: Sikkink Kathryn 
Published: December 2020

AbstractKratochwil's critique of rights as a dominant moral theory that cannot avoid ‘hegemonic’ politics appears to be too crude. This article suggests that more theoretical and practical attention to the responsibilities necessary to implement rights could address some of Kratochwil's concerns. The language of political and ethical responsibilities is often missing from the practical action discourse of human rights. The article emphasizes the multitude of potential ‘agents of justice’ and how they can discharge forward-looking responsibilities in open and discretionary ways.
Global Wet‐Reduced Nitrogen Deposition Derived From Combining Satellite Measurements With Output From a Chemistry Transport Model
Authors: Liu Lei , Yang Yuyu , Xi Ruipeng , Zhang Xiuying , Xu Wen , Liu Xuejun , Li Yi , Liu Pu , Wang Zhen 
Published: December 2020

AbstractWet‐reduced nitrogen (NH4+) is the main component of atmospheric nitrogen (N) deposition. Due to the poor coverage of ground‐based measurements, it is still challenging to characterize the global wet‐reduced NH4+ deposition. Here we utilize NH3 measurements from satellite retrievals (Infrared Atmospheric Sounding Interferometer) to estimate global wet NH4+ deposition at 0.1° grids for nine years (2008–2016). We achieve this by developing a novel approach by calculating the feedback ratio between wet NH4+ concentration in precipitation and atmospheric NH3 columns using a global chemistry transport model (GEOS‐Chem). Satellite‐based wet NH4+ concentration and deposition is relatively highly correlated with the ground‐based measurements (r = 0.88 and bias = 12% for wet deposition). The largest increase in the satellite‐derived wet NH4+ deposition occurs in southern China (>0.5 kg N ha−1 yr−1), followed by northeastern India, North America, and Western Europe. The proposed method is simple, fast, and effective in estimating wet NH4+ deposition using the satellite observations without depending on the ground‐based measurements for constructing the models. It is particularly helpful in estimating wet NH4+ deposition over regions with few monitoring sites. Our unique satellite‐derived wet NH4+ deposition can be applied for evaluating its impacts on ecosystems in the future.
Reconstructing Paleo‐oxygenation for the Last 54,000 Years in the Gulf of Alaska Using Cross‐validated Benthic Foraminiferal and Geochemical Records
Authors: Sharon  , Belanger Christina , Du Jianghui , Mix Alan 
Published: December 2020

AbstractHolocene and Pleistocene marine sediment records in the North Pacific record multiple dysoxic events proximal to continental margins and oxygen minimum zones (OMZs). High‐resolution paleoenvironmental studies in the Gulf of Alaska (GoA) were previously restricted to the last ∼17,000 years, limiting our knowledge of oxygenation in the high latitude North Pacific. Here we develop a ∼54,000‐year‐long record of co‐registered benthic foraminiferal assemblages and redox sensitive metal concentrations (Mo/Al and U/Al) at Site U1419 in the upper OMZ of GoA to reconstruct the history of OMZ extent and intensity at multi‐centennial resolution. Using multivariate analyses of total benthic foraminiferal assemblages, we develop quantitative dissolved oxygen estimates that are robust to differences in the benthic foraminiferal size fraction analyzed, replicate modern oxygenation patterns in the GoA, and are cross‐validated by redox sensitive metal concentrations. We identify dysoxic events in the early Holocene and in the Bølling‐Allerød (B/A), consistent with previous studies, as well as two dysoxic events during MIS 3 that are comparable in severity to the B/A event and lower in oxygen than the modern GoA OMZ. We further record short‐duration (<300 years) dysoxic events during glacial times similar to those recorded at more southern latitudes. Rates of oxygenation change can be abrupt with transitions exceeding 1 ml/L O2 in 100 years. Quantitative estimates of paleo‐oxygenation, such as those possible with benthic foraminiferal assemblages, are important for forecasting future oxygenation changes in OMZs and their potential impacts on the marine ecosystems.
Modeling Nitrate Export From a Mesoscale Catchment Using StorAge Selection Functions
Authors: Nguyen Tam V. , Kumar Rohini , Lutz Stefanie R. , Musolff Andreas , Yang Jie , Fleckenstein Jan H. 
Published: December 2020

AbstractStorAge Selection (SAS) functions describe how catchments selectively remove water of different ages in storage via discharge, thus controlling the transit time distribution (TTD) and solute composition of discharge. SAS‐based models have been emerging as promising tools for quantifying catchment‐scale solute export, providing a coherent framework for describing both velocity‐driven and celerity‐driven transport. Due to their application in headwaters only, the spatial heterogeneity of catchment physiographic characteristics, land use management practices, and large‐scale validation have not been adequately addressed with SAS‐based models. Here, we integrated SAS functions into the grid‐based mHM‐Nitrate model (mesoscale Hydrological Model) at both grid scale (distributed model) and catchment scale (lumped model). The proposed model provides a spatially distributed representation of nitrogen dynamics within the soil zone and a unified approach for representing both velocity‐driven and celerity‐driven subsurface transport below the soil zone. The model was tested in a heterogeneous mesoscale catchment. Simulated results show a strong spatial heterogeneity in nitrogen dynamics within the soil zone, highlighting the necessity of a spatially explicit approach for describing near‐surface nitrogen processing. The lumped model could well capture instream nitrate concentration dynamics and the concentration–discharge relationship at the catchment outlet. In addition, the model could provide insights into the relations between subsurface storage, mixing scheme, solute export, and the TTDs of discharge. The distributed model shows results that are comparable to the lumped model. Overall, the results reveal the potential for large‐scale applications of SAS‐based transport models, contributing to the understanding of water quality‐related issues in agricultural landscapes.
Superspreading in early transmissions of COVID-19 in Indonesia
Authors: Hasan Agus , Susanto Hadi , Kasim Muhammad Firmansyah , Nuraini Nuning , Lestari Bony , Triany Dessy , Widyastuti Widyastuti 
Published: December 2020

AbstractThis paper presents a study of early epidemiological assessment of COVID-19 transmission dynamics in Indonesia. The aim is to quantify heterogeneity in the numbers of secondary infections. To this end, we estimate the basic reproduction number$$\mathscr {R}_0$$R0and the overdispersion parameter$$\mathscr {K}$$Kat two regions in Indonesia: Jakarta–Depok and Batam. The method to estimate$$\mathscr {R}_0$$R0is based on a sequential Bayesian method, while the parameter$$\mathscr {K}$$Kis estimated by fitting the secondary case data with a negative binomial distribution. Based on the first 1288 confirmed cases collected from both regions, we find a high degree of individual-level variation in the transmission. The basic reproduction number$$\mathscr {R}_0$$R0is estimated at 6.79 and 2.47, while the overdispersion parameter$$\mathscr {K}$$Kof a negative-binomial distribution is estimated at 0.06 and 0.2 for Jakarta–Depok and Batam, respectively. This suggests that superspreading events played a key role in the early stage of the outbreak, i.e., a small number of infected individuals are responsible for large numbers of COVID-19 transmission. This finding can be used to determine effective public measures, such as rapid isolation and identification, which are critical since delay of diagnosis is the most common cause of superspreading events.
Neonatal hyperoxia enhances age-dependent expression of SARS-CoV-2 receptors in mice
Authors: Yee Min , David Cohen E. , Haak Jeannie , Dylag Andrew M. , O’Reilly Michael A. 
Published: December 2020

AbstractThe severity of COVID-19 lung disease is higher in the elderly and people with pre-existing co-morbidities. People who were born preterm may be at greater risk for COVID-19 because their early exposure to oxygen (hyperoxia) at birth increases the severity of respiratory viral infections. Hyperoxia at birth increases the severity of influenza A virus infections in adult mice by reducing the number of alveolar epithelial type 2 (AT2) cells. Since AT2 cells express the SARS-CoV-2 receptors angiotensin converting enzyme (ACE2) and transmembrane protease/serine subfamily member 2 (TMPRSS2), their expression should decline as AT2 cells are depleted by hyperoxia. Instead, ACE2 was detected in airway Club cells and endothelial cells at birth, and then AT2 cells at one year of age. Neonatal hyperoxia stimulated expression of ACE2 in Club cells and in AT2 cells by 2 months of age. It also stimulated expression of TMPRSS2 in the lung. Increased expression of SARS-CoV-2 receptors was blocked by mitoTEMPO, a mitochondrial superoxide scavenger that reduced oxidative stress and DNA damage seen in oxygen-exposed mice. Our finding that hyperoxia enhances the age-dependent expression of SARS-CoV-2 receptors in mice helps explain why COVID-19 lung disease is greater in the elderly and people with pre-existing co-morbidities.
Inclusive groups can avoid the tragedy of the commons
Authors: Hintze Arend , Staudacher Jochen , Gelhar Katja , Pothmann Alexander , Rasch Juliana , Wildegger Daniel 
Published: December 2020

AbstractThe public goods game is a famous example illustrating the tragedy of the commons (Hardin in Science 162:1243–1248, 1968). In this game cooperating individuals contribute to a pool, which in turn is distributed to all members of the group, including defectors who reap the same rewards as cooperators without having made a contribution before. The question is now, how to incentivize group members to all cooperate as it maximizes the common good. While costly punishment (Helbing et al. in New J Phys 12:083005, 2010) presents one such method, the cost of punishment still reduces the common good. The selfishness of the group members favors defectors. Here we show that including other members of the groups and sharing rewards with them can be another incentive for cooperation, avoiding the cost required for punishment. Further, we show how punishment and this form of inclusiveness interact. This work suggests that a redistribution similar to a basic income that is coupled to the economic success of the entire group could overcome the tragedy of the commons.
Cognitive impairment without altered levels of cerebrospinal fluid biomarkers in patients with encephalitis caused by varicella-zoster virus: a pilot study
Authors: Eckerström Marie , Nilsson Staffan , Zetterberg Henrik , Blennow Kaj , Grahn Anna 
Published: December 2020

AbstractVaricella-zoster virus (VZV) is one of the most common agents causing viral infections of the central nervous system (CNS). VZV encephalitis is associated with severe neurological sequelae, despite antiviral treatment. Cognitive impairment has been reported and VZV has been associated with dementia. Our aim was to investigate the cognitive impairment and cerebrospinal fluid biomarkers in a follow-up study of patients with VZV encephalitis. Thirteen patients with VZV encephalitis, diagnosed by detection of VZV DNA in cerebrospinal fluid (CSF) by PCR and concomitant symptoms of encephalitis, were included. Neuropsychological assessment in parallel with a lumbar puncture to obtain CSF was performed 1.5–7 years after acute disease. The CSF biomarkers neurofilament light chain (NFL), S100B, glial fibrillary acidic protein (GFAP), amyloid-β (Aβ) 40 and Aβ42, total tau (t-tau) and phosphorylated tau (p-tau) were analysed and compared to controls (n = 24). Cognitive impairment was shown in the domains of executive functions and speed/attention and to a minor degree in the domains of learning/memory and language, indicated by a significantly poorer performance on seven neuropsychological test variables. No convincing evidence of alterations in concentrations of biomarkers in the CSF were shown. Our results indicate that patients with VZV encephalitis suffer from cognitive impairment long time after acute disease. Importantly, these impairments do not seem to be accompanied by biomarker evidence of ongoing neuronal or astrocytic injury/activation or induction of dementia-related brain pathologies by the infection.
A meta-analysis of accuracy and sensitivity of chest CT and RT-PCR in COVID-19 diagnosis
Authors: Khatami Fatemeh , Saatchi Mohammad , Zadeh Seyed Saeed Tamehri , Aghamir Zahra Sadat , Shabestari Alireza Namazi , Reis Leonardo Oliveira , Aghamir Seyed Mohammad Kazem 
Published: December 2020

AbstractNowadays there is an ongoing acute respiratory outbreak caused by the novel highly contagious coronavirus (COVID-19). The diagnostic protocol is based on quantitative reverse-transcription polymerase chain reaction (RT-PCR) and chests CT scan, with uncertain accuracy. This meta-analysis study determines the diagnostic value of an initial chest CT scan in patients with COVID-19 infection in comparison with RT-PCR. Three main databases; PubMed (MEDLINE), Scopus, and EMBASE were systematically searched for all published literature from January 1st, 2019, to the 21st May 2020 with the keywords "COVID19 virus", "2019 novel coronavirus", "Wuhan coronavirus", "2019-nCoV", "X-Ray Computed Tomography", "Polymerase Chain Reaction", "Reverse Transcriptase PCR", and "PCR Reverse Transcriptase". All relevant case-series, cross-sectional, and cohort studies were selected. Data extraction and analysis were performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5. Among 1022 articles, 60 studies were eligible for totalizing 5744 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan compared to RT-PCR were 87% (95% CI 85–90%), 46% (95% CI 29–63%), 69% (95% CI 56–72%), and 89% (95% CI 82–96%), respectively. It is important to rely on the repeated RT-PCR three times to give 99% accuracy, especially in negative samples. Regarding the overall diagnostic sensitivity of 87% for chest CT, the RT-PCR testing is essential and should be repeated to escape misdiagnosis.
Ultra-low temperature water–gas shift reaction catalyzed by homogeneous Ru-complexes in a membrane reactor – membrane development and proof of concept
Authors: Logemann Morten , Wolf Patrick , Loipersböck Jürgen , Schrade Alexander , Wessling Matthias , Haumann Marco 
Published: December 2020

Supported ionic liquid-phase (SILP) catalyzed water–gas shift reaction with in situ product removal is presented. A facilitated transport membrane coated onto the smooth outside of the SiC monolith allowed preferential removal of CO2 compared to H2.
Successful Endoscopic Removal of a Transmural Internally Migrating Gossypiboma
Authors: Agarwal Ashish , Chauhan Ashish , Sharma Sanchit , Madhusudhan Kumble Seetharama , Panwar Rajesh 
Published: December 2020

AbstractAn accidentally retained sponge inside the body of a patient (gossypiboma) is a rare and serious adverse event after a surgical procedure with serious medicolegal implications and complications. It is commonly associated with abdominal surgeries with cholecystectomy most commonly implicated. Whorl-like appearance or mottled translucencies and radiopaque marker on imaging is diagnostic. Transmural migration into a hollow viscous has been infrequently reported. The preferred approach for the removal of gossypiboma is surgery. However, in cases of complete transmural migration, endoscopic removal remains a viable option.
A Novel Method to Prevent Migration of Gastric Stent
Authors: Singla Vikas , Khare Shivam , Arora Anil , Anikhindi Shrihari Anil 
Published: December 2020

AbstractSelf expandable metal stent (SEMS) are widely used in patients with gastric outlet obstruction. Stent migration can occur in these patients, and is an important issue, which needs to be addressed. We used a novel technique for prevention of migration of gastric stent in an 80 year old female. Patient presented with recurrent vomiting due to gastric outlet obstruction by a growth in the antrum. SEMS was placed for palliation of symptoms. A nylon thread multiloop and through the scope clips were used to fix the SEMS with the gastric wall. The technique was used successfully to prevent the migration of SEMS.
Successful Treatment of an Early Barrett's Adenocarcinoma in a High-Risk Patient with Portal Hypertension: The “Band and Leave” Strategy
Authors: Fraile-López Miguel , Ortiz-Fernández-Sordo Jacobo , James Martin , Kaye Philip , Ragunath Krish 
Published: December 2020

Abstract“Band and leave” strategy has been described for the resection of submucosal tumors of the digestive tract to reduce the complications related to deep submucosal resection such as bleeding and perforation. We present the case of a patient with multiple comorbidities, chronic liver disease, and portal hypertension diagnosed to have T1 adenocarcinoma in Barrett's esophagus overlying a column of varix. This was successfully treated by band ligation and allowing the neoplastic mucosa to slough. We propose this technique as an alternative therapeutic option for the management of early Barrett's neoplasia in such high-risk patients with portal hypertension.
Brillouin light scattering investigations of films and magnetic tunnel junctions with perpendicular magnetic anisotropy at the CoFeB–MgO interface
Authors: Tacchi S , Casoli F , Pini M G , Rettori A , Madami M , Åkerman J , Le T T , Pham Q N , Pham H L , Anh Nguyen T N 
Published: December 2020

Abstract
Alternating gradient force magnetometry and Brillouin light scattering (BLS) experiments were exploited to investigate the perpendicular magnetic anisotropy (PMA) localized at the CoFeB–MgO interface, both in Ta/CoFeB/MgO heterostructures (bottom samples) and in the inverted ones MgO/CoFeB/Ta (top samples). Thermal treatment was found to induce a marked increase of the PMA with respect to the as grown state. Using linear spin wave theory, an analysis of the spin wave frequencies was performed which allowed to estimate the thickness dependence of the PMA in the single CoFeB film. Magnetic tunnel junctions with the Ta/CoFeB/MgO/CoFeB/Ta structure were also studied by BLS. The analysis of the experimental results, performed via the linear spin wave theory, revealed that there is an antiferromagnetic interlayer exchange coupling between the free and the fixed CoFeB layers which increases after the annealing procedure.
Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints
Authors: Han Renmin , Li Guojun , Gao Xin 
Published: December 2020

Abstract

Motivation
Electron tomography (ET) has become an indispensable tool for structural biology studies. In ET, the tilt series alignment and the projection parameter calibration are the key steps toward high-resolution ultrastructure analysis. Usually, fiducial markers are embedded in the sample to aid the alignment. Despite the advances in developing algorithms to find correspondence of fiducial markers from different tilted micrographs, the error rate of the existing methods is still high such that manual correction has to be conducted. In addition, existing algorithms do not work well when the number of fiducial markers is high.

Results
In this article, we try to completely solve the fiducial marker correspondence problem. We propose to divide the workflow of fiducial marker correspondence into two stages: (i) initial transformation determination, and (ii) local correspondence refinement. In the first stage, we model the transform estimation as a correspondence pair inquiry and verification problem. The local geometric constraints and invariant features are used to reduce the complexity of the problem. In the second stage, we encode the geometric distribution of the fiducial markers by a weighted Gaussian mixture model and introduce drift parameters to correct the effects of beam-induced motion and sample deformation. Comprehensive experiments on real-world datasets demonstrate the robustness, efficiency and effectiveness of the proposed algorithm. Especially, the proposed two-stage algorithm is able to produce an accurate tracking within an average of  ⩽ 100 ms per image, even for micrographs with hundreds of fiducial markers, which makes the real-time ET data processing possible.

Availability and implementation
The code is available at https://github.com/icthrm/auto-tilt-pair. Additionally, the detailed original figures demonstrated in the experiments can be accessed at https://rb.gy/6adtk4.

Supplementary information
Supplementary data are available at Bioinformatics online.
A network-based deep learning methodology for stratification of tumor mutations
Authors: Liu Chuang , Han Zhen , Zhang Zi-Ke , Nussinov Ruth , Cheng Feixiong 
Published: December 2020

Abstract

Motivation
Tumor stratification has a wide range of biomedical and clinical applications, including diagnosis, prognosis and personalized treatment. However, cancer is always driven by the combination of mutated genes, which are highly heterogeneous across patients. Accurately subdividing the tumors into subtypes is challenging.

Results
We developed a network-embedding based stratification (NES) methodology to identify clinically relevant patient subtypes from large-scale patients’ somatic mutation profiles. The central hypothesis of NES is that two tumors would be classified into the same subtypes if their somatic mutated genes located in the similar network regions of the human interactome. We encoded the genes on the human protein–protein interactome with a network embedding approach and constructed the patients’ vectors by integrating the somatic mutation profiles of 7344 tumor exomes across 15 cancer types. We firstly adopted the lightGBM classification algorithm to train the patients’ vectors. The AUC value is around 0.89 in the prediction of the patient’s cancer type and around 0.78 in the prediction of the tumor stage within a specific cancer type. The high classification accuracy suggests that network embedding-based patients’ features are reliable for dividing the patients. We conclude that we can cluster patients with a specific cancer type into several subtypes by using an unsupervised clustering algorithm to learn the patients’ vectors. Among the 15 cancer types, the new patient clusters (subtypes) identified by the NES are significantly correlated with patient survival across 12 cancer types. In summary, this study offers a powerful network-based deep learning methodology for personalized cancer medicine.

Availability and implementation
Source code and data can be downloaded from https://github.com/ChengF-Lab/NES.

Supplementary information
Supplementary data are available at Bioinformatics online.