bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paleocene-Eocene volcanic segmentation of the Norwegian-Greenland seaway reorganized high-latitude ocean circulation
Authors: Hovikoski Jussi , Fyhn Michael B. W. , Nøhr-Hansen Henrik , Hopper John R. , Andrews Steven , Barham Milo , Nielsen Lars H. , Bjerager Morten , Bojesen-Koefoed Jørgen , Lode Stefanie , Sheldon Emma , Uchman Alfred , Skorstengaard Pia R. , Alsen Peter 
Published: August 2021

AbstractThe paleoenvironmental and paleogeographic development of the Norwegian–Greenland seaway remains poorly understood, despite its importance for the oceanographic and climatic conditions of the Paleocene–Eocene greenhouse world. Here we present analyses of the sedimentological and paleontological characteristics of Paleocene–Eocene deposits (between 63 and 47 million years old) in northeast Greenland, and investigate key unconformities and volcanic facies observed through seismic reflection imaging in offshore basins. We identify Paleocene–Eocene uplift that culminated in widespread regression, volcanism, and subaerial exposure during the Ypresian. We reconstruct the paleogeography of the northeast Atlantic–Arctic region and propose that this uplift led to fragmentation of the Norwegian–Greenland seaway during this period. We suggest that the seaway became severely restricted between about 56 and 53 million years ago, effectively isolating the Arctic from the Atlantic ocean during the Paleocene–Eocene thermal maximum and the early Eocene.
Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning
Authors: Beugnon Rémy , Du Jianqing , Cesarz Simone , Jurburg Stephanie D , Pang Zhe , Singavarapu Bala , Wubet Tesfaye , Xue Kai , Wang Yanfen , Eisenhauer Nico 
Published: August 2021

Abstract
Microbial respiration is critical for soil carbon balance and ecosystem functioning. Previous studies suggest that plant diversity influences soil microbial communities and their respiration. Yet, the linkages between tree diversity, microbial biomass, microbial diversity, and microbial functioning have rarely been explored. In this study, we measured two microbial functions (microbial physiological potential, and microbial respiration), together with microbial biomass, microbial taxonomic and functional profiles, and soil chemical properties in a tree diversity experiment in South China, to disentangle how tree diversity affects microbial respiration through the modifications of the microbial community. Our analyses show a significant positive effect of tree diversity on microbial biomass (+25% from monocultures to 24-species plots), bacterial diversity (+12%), and physiological potential (+12%). In addition, microbial biomass and physiological potential, but not microbial diversity, were identified as the key drivers of microbial respiration. Although soil chemical properties strongly modulated soil microbial community, tree diversity increased soil microbial respiration by increasing microbial biomass rather than changing microbial taxonomic or functional diversity. Overall, our findings suggest a prevalence of microbial biomass over diversity in controlling soil carbon dynamics.
Characterization of SARS-CoV-2 and host entry factors distribution in a COVID-19 autopsy series
Authors: Wang Xiao-Ming , Mannan Rahul , Xiao Lanbo , Abdulfatah Eman , Qiao Yuanyuan , Farver Carol , Myers Jeffrey L. , Zelenka-Wang Sylvia , McMurry Lisa , Su Fengyun , Wang Rui , Pantanowitz Liron , Jentzen Jeffrey , Wilson Allecia , Zhang Yuping , Cao Xuhong , Chinnaiyan Arul M. , Mehra Rohit 
Published: August 2021

Abstract
Background
SARS-CoV-2 is a highly contagious virus that causes the disease COVID-19. We have recently reported that androgens regulate the expression of SARS-CoV-2 host entry factors ACE2 and TMPRSS2, and androgen receptor (AR) in lung epithelial cells. We also demonstrated that the transcriptional repression of the AR enhanceosome inhibited SARS-CoV-2 infection in vitro.

Methods
To better understand the various sites of SARS-CoV-2 infection, and presence of host entry factors, we extensively characterized the tissue distribution and localization of SARS-CoV-2 virus, viral replication, and host entry factors in various anatomical sites sampled via autopsy. We applied RNA in-situ-hybridization (RNA-ISH), immunohistochemistry (IHC) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) approaches. We also assessed histopathological changes in SARS-CoV-2 infected tissues.

Results
We detect SARS-CoV-2 virus and viral replication in pulmonary tissues by RNA-ISH and IHC and a variety of non-pulmonary tissues including kidney, heart, liver, spleen, thyroid, lymph node, prostate, uterus, and colon by qRT-PCR. We observe heterogeneity in viral load and viral cytopathic effects among various organ systems, between individuals and within the same patient. In a patient with a history of kidney transplant and under immunosuppressant therapy, we observe an unusually high viral load in lung tissue by RNA-ISH, IHC and qRT-PCR. SARS-CoV-2 virus is also detected in this patent’s kidney, liver and uterus. We find ACE2, TMPRSS2 and AR expression to overlap with the infection sites.

Conclusions
This study portrays the impact of dispersed SARS-CoV-2 infection in diverse organ systems, thereby facilitating avenues for systematic therapeutic approaches.
Transient mixed lubrication model of the human knee implant
Authors: Butt Hamza , Nissim Lee , Gao Leiming , Myant Connor , de Boer Greg , Hewson Robert 
Published: August 2021

AbstractThe human knee implant is computationally modelled in the mixed lubrication regime to investigate the tribological performance of the implant. This model includes the complex geometry of the implant components, unlike elliptical contact models that approximate this geometry. Film thickness and pressure results are presented for an ISO gait cycle to determine the lubrication regime present within the implant during its operation. It was found that it was possible for the lubrication regime to span between elastohydrodynamic, mixed and boundary lubrication depending on the operating conditions of the implant. It was observed that the tribological conditions present in one condyle were not necessarily representative of the other. Multiple points of contact were found within the same condyle, which cannot be computed by the elliptical contact solvers. This model can be used to balance forces in all directions, instead of only the normal loads, as often done in elliptical contact models. This work is an initial step towards understanding the role of the complex geometry in the tribological characteristics of the human knee implant when operating in physiological conditions.
Adaptive second‐order terminal PID sliding mode control design for integer‐order approximation of wind turbine system for maximum power extraction
Authors: Abolvafaei Mahnaz , Ganjefar Soheil 
Published: August 2021

AbstractThe main purpose of this paper is to extract the maximum power from the variable speed wind turbine (VSWT), which is modelled using fractional calculus. The use of the fractional‐order operator can harden the practical implementation and numerical simulation of the fractional‐order systems. To apply the fractional calculus theory, we assume that the orders of all fractional derivatives of the system have a small deviation from the nearest integers. By defining this small deviation as a perturbation parameter, an integer‐order approximation method is presented for approximating the fractional‐order system into a perturbed integer‐order system in the time domain. Then, a new adaptive second‐order sliding mode control (SOSMC) method is proposed using the terminal proportional integral derivative (TPID) sliding surface to achieve maximum power extraction and reduce mechanical loads and chattering. A TPID sliding surface is employed to ensure better tracking, have a zero steady‐state error, decrease the mechanical stresses, and eliminate the chattering phenomenon. The stability of the adaptive SOSMC based on the obtained integer‐order approximation is analyzed using the Lyapunov stability criterion. The simulation results of the proposed method are presented and compared with some designed controllers for wind turbines (WTs) modelled with fractional and integer derivatives. The obtained results show the effectiveness of the proposed strategy.
Enabling interoperable data and application services in a federated ScienceMesh
Authors: Arora Ishank , Alfageme Sainz Samuel , Ferreira Pedro , Gonzalez Labrador Hugo , Moscicki Jakub 
Published: August 2021

In recent years, cloud sync & share storage services, provided by academic and research institutions, have become a daily workplace environment for many local user groups in the High Energy Physics (HEP) community. These, however, are primarily disconnected and deployed in isolation from one another, even though new technologies have been developed and integrated to further increase the value of data. The EU-funded CS3MESH4EOSC project is connecting locally and individually provided sync and share services, and scaling them up to the European level and beyond. It aims to deliver the ScienceMesh service, an interoperable platform to easily sync and share data across institutions and extend functionalities by connecting to other research services using streamlined sets of interoperable protocols, APIs and deployment methodologies. This supports multiple distributed application workflows: data science environments, collaborative editing and data transfer services.
In this paper, we present the architecture of ScienceMesh and the technical design of its reference implementation, a platform that allows organizations to join the federated service infrastructure easily and to access application services outof-the-box. We discuss the challenges faced during the process, which include diversity of sync & share platforms (Nextcloud, Owncloud, Seafile and others), absence of global user identities and user discovery, lack of interoperable protocols and APIs, and access control and protection of data endpoints. We present the rationale for the design decisions adopted to tackle these challenges and describe our deployment architecture based on Kubernetes, which enabled us to utilize monitoring and tracing functionalities. We conclude by reporting on the early user experience with ScienceMesh.
ESCAPE Data Lake
Authors: Di Maria Riccardo , Dona Rizart ,   on behalf of the ESCAPE project
Published: August 2021

The European-funded ESCAPE project (Horizon 2020) aims to address computing challenges in the context of the European Open Science Cloud. The project targets Particle Physics and Astronomy facilities and research infrastructures, focusing on the development of solutions to handle Exabyte-scale datasets. The science projects in ESCAPE are in different phases of evolution and count a variety of specific use cases and challenges to be addressed.
This contribution describes the shared-ecosystem architecture of services, the Data Lake, fulfilling the needs in terms of data organisation, management, and access of the ESCAPE community. The Pilot Data Lake consists of several storage services operated by the partner institutes and connected through reliable networks, and it adopts Rucio to orchestrate data management and organisation. The results of a 24-hour Full Dress Rehearsal are also presented, highlighting the achievements of the Data Lake model and of the ESCAPE sciences.
The use of Boosted Decision Trees for Energy Reconstruction in JUNO experiment
Authors: Gavrikov Arsenii , Ratnikov Fedor ,   on behalf of the JUNO Collaboration
Published: August 2021

The Jiangmen Underground Neutrino Observatory (JUNO) is a neutrino experiment with a broad physical program. The main goals of JUNO are the determination of the neutrino mass ordering and high precision investigation of neutrino oscillation properties. The precise reconstruction of the event energy is crucial for the success of the experiment.
JUNO is equiped with 17 612 + 25 600 PMT channels of two kind which provide both charge and hit time information. In this work we present a fast Boosted Decision Trees model using small set of aggregated features. The model predicts event energy deposition. We describe the motivation and the details of our feature engineering and feature selection procedures. We demonstrate that the proposed aggregated approach can achieve a reconstruction quality that is competitive with the quality of much more complex models like Convolution Neural Networks (ResNet, VGG and GNN).
ALICE Central Trigger System for LHC Run 3
Authors: Kvapil Jakub , Bhasin Anju , Bombara Marek , Evans David , Jusko Anton , Kluge Alexander , Krivda Marian , Kralik Ivan , Lietava Roman , Nayak Sanket Kumar , Ragoni Simone , Villalobos Baillie Orlando 
Published: August 2021

A major upgrade of the ALICE experiment is in progress and will result in high-rate data taking during LHC Run 3 (2022-2024). The LHC interaction rate at Point 2 where the ALICE experiment is located will be increased to 50 kHz in Pb–Pb collisions and 1 MHz in pp collisions. The ALICE experiment will be able to read out data at these interaction rates leading to an increase of the collected luminosity by a factor of up to about 100 with respect to LHC Runs 1 and 2. To satisfy these requirements, a new readout system has been developed for most of the ALICE detectors, allowing the full readout of the data at the required interaction rates without the need for a hardware trigger selection. A novel trigger and timing distribution system will be implemented, based on Passive Optical Network (PON) and GigaBit Transceiver (GBT) technology. To assure backward compatibility a triggered mode based on RD12 Trigger- Timing-Control (TTC) technology, as used in the previous LHC runs, will be maintained and re-implemented under the new Central Trigger System (CTS). A new universal ALICE Trigger Board (ATB) based on the Xilinx Kintex Ultrascale FPGA has been designed to function as a Central Trigger Processor (CTP), Local Trigger Unit (LTU), and monitoring interfaces.
In this paper, this new hybrid multilevel system with continuous readout will be described, together with the triggering mechanism and algorithms. An overview of the CTS, the design of the ATB and the different communication protocols will be presented.
Risk of bleeding following double balloon enteroscopy in patients on continued antiplatelet and/or anticoagulation therapy
Authors: Zaver Himesh B. , Ghoz Hassan , Stancampiano Fernando , Alnahhal Khaled I. , Malviya Balkishan , Patel Krupa , Rodriguez Andrea C. , Oberoi Mansi , Koralewski Andrea , Crawford Matthew J. , Choudhry Aruj , Mareth Karl , Werlang Monia E. , Kroner Paul T. , Simons-Linares C. Roberto , Lukens Frank , Bartel Michael J. , Stark Mark , Brahmbhatt Bhaumik 
Published: August 2021

Abstract
Background and study aims Anticoagulation (AC) and antiplatelet (AP) therapy may increase the risk of gastrointestinal bleeding after double balloon enteroscopy (DBE); however, limited data are currently available regarding the incidence. The aim of this study was to assess the incidence and clinical characteristics of post-DBE bleeding in patients on AC and AP therapy.
Patients and methods The medical records of patients who underwent DBE between 2009 and 2013 at Mayo Clinic, Florida, were retrospectively reviewed. Patients were divided into three groups: 1) continued AP therapy; 2) AC therapy; and 3) neither AP nor AC at the time of DBE. Follow-up data were collected at 60 days and 1 year.
Results A total of 683 patients were identified; 43 on AC, 183 on AP and 457 not on AP or AC therapy. The most common indication for DBE was obscure gastrointestinal bleeding in the groups on and not on AP (85.3 % vs 70.9 %, P < 0.0001). There was no statistical difference in post-DBE bleeding rates in patients on AP vs not on AP at 60 days (11.5 % vs 7.5 %, P = 0.12) or 1 year (19.9 % vs 15.7 %, P = 0.23). Rates of bleeding in patients on AC were 11.6 % within 60 days and 22.5 % within 1 year. Multivariate analysis reflected American Society of Anesthesiologist > 3 and indication for DBE of GI bleeding were independent risk factors for post-DBE bleeding within 1 year.
Conclusions Continued antiplatelet use at the time of DBE was not an independent risk factor for bleeding post-DBE at 60 days or 1 year of follow up.
Thyroid Nodules in Patients with Acromegaly: Frequency According to the ACR TI-RADS Classification and its Relationship with Disease Activity
Authors: Can Mustafa , Kocabaş Muhammet , Karakose Melia , Burgucu Hatice Caliskan , Yarar Zeliha , Kulaksizoglu Mustafa , Karakurt Feridun 
Published: August 2021

Abstract
Purpose: In our study, we aimed to determine the frequency of thyroid nodules in patients with acromegaly according to the American College of Radiology (ACR) Thyroid Imaging, Reporting and Data System (TI-RADS) classification and its relationship with acromegaly disease activity.
Methods: A total of 56 patients with acromegaly and age, sex, and body mass index matched with 56 healthy control subjects were included in our study. Thyroid-stimulating hormone, free thyroxine, and anti-thyroperoxidase antibody levels of patients and control subjects were measured. In addition, patients and healthy controls were evaluated by ultrasonography to determine thyroid structure, thyroid volume, and thyroid nodules and to make ACR TI-RADS classification.
Results: Thyroid nodules were present in 31 (55.4%) of 56 patients in the acromegaly group and 20 (35.7%) of 56 subjects in the control group, and the frequency of thyroid nodules was significantly higher in the acromegaly group (p=0.038). The mean number of nodules in the acromegaly group and control group was 1.27±1.43 and 0.48±0.73, respectively, and the mean number of nodules was significantly higher in the acromegaly group (p=0.003). The number of patients with TI-RADS 1, TI-RADS 2, and TI-RADS 4 nodules in the acromegaly group was higher than the control group (p=0.026, p=0.049, p=0.007, respectively). No difference was found in terms of cytological findings between those who have undergone FNAB in the acromegaly group and control group.
Conclusion: In our study, we found that the frequency of thyroid nodules, the number of thyroid nodules, and the number of TI-RADS 1, TI-RADS 2, and TI-RADS 4 nodules increased in patients with acromegaly. There was no significant difference between acromegaly disease activity and thyroid nodule frequency, number of thyroid nodules, and TI-RADS classifications.
Safety, efficacy, and maneuverability of a self-propelled capsule endoscope for observation of the human gastrointestinal tract
Authors: Ota Kazuhiro , Kojima Yuichi , Kakimoto Kazuki , Nouda Sadaharu , Takeuchi Toshihisa , Shindo Yasunori , Ohtsuka Yoshitake , Ohtsuka Naotake , Higuchi Kazuhide 
Published: August 2021

Abstract
Background and study aims We developed a self-propelled capsule endoscope that can be controlled from outside the body with real-time observation. To improve the device, we conducted a clinical trial of total gastrointestinal capsule endoscopy in healthy subjects to ascertain whether our first-generation, self-propelled capsule endoscope was safe and effective for observing the entire human gastrointestinal tract.
Patients and methods After adequate gastrointestinal pretreatment, five healthy subjects were instructed to swallow a self-propelling capsule endoscope and the safety of a complete gastrointestinal capsule endoscopy with this device was assessed. We also investigated basic problems associated with complete gastrointestinal capsule endoscopy.
Results No adverse effects of the magnetic field were identified in any of the subjects. No mucosal damage was noted in any of the subjects with the use of our first-generation, self-propelling capsule endoscope. We found that it took longer than expected to observe the stomach; the view was compromised by the swallowed saliva. The pylorus was extremely difficult to navigate, and the endoscope’s fin sometimes got caught in the folds of the small intestine and colon.
Conclusions To resolve the problems associated with the existing self-propelling capsule endoscope, it may be necessary to not only improve the capsule endoscopes, but also to control the environment within the gastrointestinal tract with medications and other means. Our results could guide other researchers in developing capsule endoscopes controllable from outside the body, thus allowing real-time observation.
Quantitative Assessment of Ataxia in Multiple Sclerosis Patients using Spatiotemporal Parameters: A Relief-Based Machine Learning Analysis
Authors: Bilek Furkan , Balgetir Ferhat , Demir Caner Feyzi , Alkan Gökhan , Arslan-Tuncer Seda 
Published: August 2021

Abstract
Background and Objective Multiple sclerosis (MS) is a chronic, progressive, and autoimmune disease of the central nervous system (CNS) characterized by inflammation, demyelination, and axonal injury. In patients with newly diagnosed MS (ndMS), ataxia can present either as mild or severe and can be difficult to diagnose in the absence of clinical disability. Such difficulties can be eliminated by using decision support systems supported by machine learning methods. The present study aimed to achieve early diagnosis of ataxia in ndMS patients by using machine learning methods with spatiotemporal parameters.
Materials and Methods The prospective study included 32 ndMS patients with an Expanded Disability Status Scale (EDSS) score of≤2.0 and 32 healthy volunteers. A total of 14 parameters were elicited by using a Win-Track platform. The ndMS patients were differentiated from healthy individuals using multiple classifiers including Artificial Neural Network (ANN), Support Vector Machine (SVM), the k-nearest neighbors (K-NN) algorithm, and Decision Tree Learning (DTL). To improve the performance of the classification, a Relief-based feature selection algorithm was applied to select the subset that best represented the whole dataset. Performance evaluation was achieved based on several criteria such as Accuracy (ACC), Sensitivity (SN), Specificity (SP), and Precision (PREC).
Results ANN had a higher classification performance compared to other classifiers, whereby it provided an accuracy, sensitivity, and specificity of 89, 87.8, 90.3% with the use of all parameters and provided the values of 93.7, 96.6%, and 91.1% with the use of parameters selected by the Relief algorithm, respectively.
Significance To our knowledge, this is the first study of its kind in the literature to investigate the diagnosis of ataxia in ndMS patients by using machine learning methods with spatiotemporal parameters. The proposed method, i. e. Relief-based ANN method, successfully diagnosed ataxia by using a lower number of parameters compared to the numbers of parameters reported in clinical studies, thereby reducing the costs and increasing the performance of the diagnosis. The method also provided higher rates of accuracy, sensitivity, and specificity in the diagnosis of ataxia in ndMS patients compared to other methods. Taken together, these findings indicate that the proposed method could be helpful in the diagnosis of ataxia in minimally impaired ndMS patients and could be a pathfinder for future studies.