bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new global dataset of bioclimatic indicators
Authors: Noce Sergio , Caporaso Luca , Santini Monia 
Published: November 2020

AbstractThis study presents a new global gridded dataset of bioclimatic indicators at 0.5° by 0.5° resolution for historical and future conditions. The dataset, called CMCC-BioClimInd, provides a set of 35 bioclimatic indices, expressed as mean values over each time interval, derived from post-processing both climate reanalysis for historical period (1960–1999) and an ensemble of 11 bias corrected CMIP5 simulations under two greenhouse gas concentration scenarios for future climate projections along two periods (2040–2079 and 2060–2099). This new dataset complements the availability of spatialized bioclimatic information, crucial aspect in many ecological and environmental wide scale applications and for several disciplines, including forestry, biodiversity conservation, plant and landscape ecology. The data of individual indicators are publicly available for download in the commonly used Network Common Data Form 4 (NetCDF4) format.
CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties
Authors: Arneson Douglas , Elliott Matthew , Mosenia Arman , Oskotsky Boris , Solodar Samuel , Vashisht Rohit , Zack Travis , Bleicher Paul , Butte Atul J. , Rudrapatna Vivek A. 
Published: November 2020

AbstractManagement of the COVID-19 pandemic has proven to be a significant challenge to policy makers. This is in large part due to uneven reporting and the absence of open-access visualization tools to present local trends and infer healthcare needs. Here we report the development of CovidCounties.org, an interactive web application that depicts daily disease trends at the level of US counties using time series plots and maps. This application is accompanied by a manually curated dataset that catalogs all major public policy actions made at the state-level, as well as technical validation of the primary data. Finally, the underlying code for the site is also provided as open source, enabling others to validate and learn from this work.
High resolution spatiotemporal patterns of seawater temperatures across the Belize Mesoamerican Barrier Reef
Authors: Helmuth Brian , Leichter James J. , Rotjan Randi D. , Castillo Karl D. , Fieseler Clare , Jones Scott , Choi Francis 
Published: November 2020

AbstractCoral reefs are under increasingly severe threat from climate change and other anthropogenic stressors. Anomalously high seawater temperatures in particular are known to cause coral bleaching (loss of algal symbionts in the family Symbiodiniaceae), which frequently leads to coral mortality. Remote sensing of sea surface temperature (SST) has served as an invaluable tool for monitoring physical conditions that can lead to bleaching events over relatively large scales (e.g. few kms to 100 s of kms). But, it is also well known that seawater temperatures within a site can vary significantly across depths due to the combined influence of solar heating of surface waters, water column thermal stratification, and cooling from internal waves and upwelling. We deployed small autonomous benthic temperature sensors at depths ranging from 0–40 m in fore reef, back reef, and lagoonal reef habitats on the Belize Mesoamerican Barrier Reef System from 2000–2019. These data can be used to calculate depth-specific climatologies across reef depths and sites, and emphasize the dynamic and spatially-variable nature of coral reef physical environments.
Chemotherapy-induced changes in bronchoalveolar lavage fluid CD4 + and CD8 + cells of the opposite lung to the cancer
Authors: Karpathiou Georgia , Mihailidis Vasilios , Nakou Evangelia , Anevlavis Stavros , Tzouvelekis Argyrios , Kouliatsis George , Ntolios Paschalis , Bouros Demosthenes , Kotsianidis Ioannis , Froudarakis Marios E. 
Published: November 2020

AbstractPublished articles support the effect of chemotherapy in the immune environment of tumors, including lung carcinomas. The role of CD4 + T-cells is crucial for expansion and accumulation of other antigen-specific immune cells, and the participation of CD8 + cells in tumor killing activity has been confirmed by many studies. However, little is known about the effect of chemotherapy on the healthy lung parenchyma from lung cancer patients, and whether there are differences between the different chemotherapy compounds used to treat this patient population. The aim of our study was to explore the effect of chemotherapy on CD4 + and CD8 + cells in the bronchoalveolar lavage fluid (BALF) of the healthy lung in patients treated with standard chemotherapy regimens. Fifteen patients underwent BAL, in the healthy lung before and after six chemotherapy courses. Platinum-based regimens included vinolerbine (VN) in 6 patients, gemcitabine (GEM) in 4 patients and etoposide (EP) in 5 patients. All patients but one were males and smokers (93%). The median age of patients was 56 years (42–75). No significant difference was noted in the patients’ age between the three treated groups. Furthermore, between the three groups, no significant changes in the means of CD4 + and CD8 + cells were noted. However, when we compared the mean CD4 + cells before and after chemotherapy within each group, changes were noted when comparing VN before versus after (p = 0.05), GEM before versus after (p = 0.03), and EP before versus after (p = 0.036). In our pilot study, changes were noted in BALF CD4 + cells for the three most applied regimens at the normal lung parenchyma.
Risk attitudes and human mobility during the COVID-19 pandemic
Authors: Chan Ho Fai , Skali Ahmed , Savage David A. , Stadelmann David , Torgler Benno 
Published: November 2020

AbstractBehavioural responses to pandemics are less shaped by actual mortality or hospitalisation risks than they are by risk attitudes. We explore human mobility patterns as a measure of behavioural responses during the COVID-19 pandemic. Our results indicate that risk-taking attitudes are a critical factor in predicting reductions in human mobility and social confinement around the globe. We find that the sharp decline in mobility after the WHO (World Health Organization) declared COVID-19 to be a pandemic can be attributed to risk attitudes. Our results suggest that regions with risk-averse attitudes are more likely to adjust their behavioural activity in response to the declaration of a pandemic even before official government lockdowns. Further understanding of the basis of responses to epidemics, e.g., precautionary behaviour, will help improve the containment of the spread of the virus.
Comparing effects of intraoperative fluid and vasopressor infusion on intestinal microcirculation
Authors: Fan Chia-Ning , Yang Szu-Jen , Shih Po-Yuan , Wang Ming-Jiuh , Fan Shou-Zen , Tsai Jui-Chang , Sun Wei-Zen , Liu Chih‑Min , Yeh Yu-Chang 
Published: November 2020

AbstractSeveral studies have revealed that vasopressor may be more appropriate for treating intraoperative hypotension and preventing hypervolemia. This study compared the effects of vasopressor infusion and fluid supplementation on intestinal microcirculation during treating intraoperative hypotension. Thirty-two rats were randomly divided into the following four groups: Light Anesthesia group (LA, 0.8–1% isoflurane); Deep Anesthesia group (DA, 1.5–1.8% isoflurane); Fluid DA group (1.5–1.8% isoflurane and fluid supplementation); and Norepinephrine DA group (1.5–1.8% isoflurane and norepinephrine infusion). At 240 min, perfused small vessel density (PSVD) of the mucosa did not differ significantly between the Fluid DA and Norepinephrine DA groups [26.2 (3.2) vs 28.9 (2.5) mm/mm2, P = 0.077], and tissue oxygen saturation of the mucosa was lower in the Fluid DA groups than in the Norepinephrine DA groups [ 48 (7) vs 57 (6) %, P = 0.02]. At 240 min, TSVD and PSVD of the seromuscular layer were higher in the Norepinephrine DA group than in the Fluid DA group. Fluid administration was higher in the Fluid DA group than in the Norepinephrine DA group [66 (25) vs. 9 (5) μL/g, P = 0.001]. Our results showed that norepinephrine can resuscitate intraoperative hypotension related microcirculatory alteration and avoid fluid overload.
A radiological study of bone remodeling with two different types of porous β-tricalcium phosphate in humans
Authors: Kikuchi Naoya , Yoshioka Tomokazu , Arai Norihito , Hyodo Kojiro , Kanamori Akihiro , Yamazaki Masashi 
Published: November 2020

AbstractIn this study we compared the bone remodeling of unidirectional (UDPTCP) and spherical porous β-tricalcium phosphate (SPTCP) radiologically in humans. We performed a retrospective analysis of the data of 14 patients (sex, nine men and five women; age, 37–70 years) who underwent medial opening-wedge high tibial osteotomy (MOWHTO) and were followed up for 12 months after surgery. Two wedge-shaped β-TCPs (one UDPTCP and one SPTCP) were cut and placed parallel to each other in the gap. In Group A (eight knees), UDPTCP was implanted anteriorly and SPTCP posteriorly, while in Group B (six knees), SPTCP was implanted anteriorly and UDPTCP posteriorly. Computed tomography (CT) was performed at 1 week, 6 months, and 12 months after surgery, with the CT attenuation values calculated for UDPTCP and SPTCP. In Groups A and B, the CT attenuation values for UDPTCP were significantly lower at 6 and 12 months after surgery compared to those at 1 week (P < 0.05); nevertheless, no statistical difference in the comparison with SPTCP was observed. After a short-term follow-up of 12 months following MOWHTO, UDPTCP provided earlier bone remodeling than SPTCP. This outcome was achieved regardless of the position, anterior or posterior, in the MOWHTO gap.
Co-delivery of resolvin D1 and antibiotics with nanovesicles to lungs resolves inflammation and clears bacteria in mice
Authors: Gao Jin , Wang Sihan , Dong Xinyue , Leanse Leon G. , Dai Tianhong , Wang Zhenjia 
Published: November 2020

AbstractResolution is an active process that protects the host damage from inflammation responses induced by infections. Simultaneously resolving inflammation and eliminating pathogens may be effective to treat infectious diseases, but it is required to deliver therapeutics to infectious sites. Here, we proposed a strategy to incorporate RvD1 and an antibiotic (ceftazidime) in human neutrophil-membrane derived nanovesicles that can specifically target inflamed vasculature for treatment of lung infection caused by P. aeruginosa. Using the nitrogen cavitation method, we generated liposome-like nanovesicles from human neutrophil membrane. The results showed that nanovesicles loaded with RvD1 decreased cytokine levels and neutrophil lung infiltration, thus shortening the resolution intervals of lung inflammation. When RvD1 and ceftazidime were co-loaded in nanovesicles, they alleviated both inflammation and bacterial growth in the mouse lung. The studies reveal a new strategy to treat infectious diseases by designing nanoparticles to simultanesouly target host inflammatory pathways and pathogens.
Angiotensin-converting enzyme 2 (ACE2), angiotensin-(1-7) and Mas receptor in gonadal and reproductive functions
Authors: Reis Fernando M. , Reis Adelina M. 
Published: November 2020

Abstract
Angiotensin (Ang)-(1-7) is an active peptide formed from Ang I or Ang-(1-9) by multiple proteolytic steps involving angiotensin-converting enzyme (ACE) 1 and other peptidases, or by a single cleavage of Ang II catalyzed chiefly by ACE2. The effects of Ang-(1-7) are mediated by the G protein-coupled receptor Mas (or Mas1), encoded by the protooncogene MAS. The reproductive system expresses ACE2 quite abundantly and therefore is able to generate Ang-(1-7) using precursor peptides produced locally or taken from circulation. In several mammalian species, Ang-(1-7) stimulates ovarian follicle growth, oocyte maturation and ovulation. The peptide is found in human endometrium, mostly during the secretory phase of menstrual cycle when the uterus is receptive to embryo implantation. Rat models and human observational studies suggest that Ang-(1-7) is part of the maternal adaptive response to pregnancy and its deficiency is associated with poor circulation in the placental bed. Knockout mice revealed a relevant participation of Mas-mediated stimulus to the maintenance of normal spermatogenesis, even though the animal can still reproduce without it. In addition, the vasorelaxant effect of Ang-(1-7) participates in the physiological mechanism of corpus cavernosum blood influx and penile erection. We conclude that preclinical evidence encourages the pursuit of treatments for female and male reproductive dysfunctions based on Mas agonists, starting with its natural ligand Ang-(1-7).
Factor Analysis of Spontaneous Speech in Aphasia
Authors: Gordon Jean K. 
Published: November 2020

Purpose
Spontaneous speech tasks are critically important for characterizing spoken language production deficits in aphasia and for assessing the impact of therapy. The utility of such tasks arises from the complex interaction of linguistic demands (word retrieval, sentence formulation, articulation). However, this complexity also makes spontaneous speech hugely variable and difficult to assess. The current study aimed to simplify the problem by identifying latent factors underlying performance in spontaneous speech in aphasia. The ecological validity of the factors was examined by examining how well the factor structures corresponded to traditionally defined aphasia subtypes.

Method
A factor analysis was conducted on 17 microlinguistic measures of narratives from 274 individuals with aphasia in AphasiaBank. The resulting factor scores were compared across aphasia subtypes. Supervised (linear discriminant analysis) and unsupervised (latent profile analysis) classification techniques were then conducted on the factor scores and the solutions compared to traditional aphasia subtypes.

Results
Six factors were identified. Two reflected aspects of fluency, one at the phrase level (Phrase Building) and one at the narrative level (Narrative Productivity). Two other factors reflected the accuracy of productions, one at the word level (Semantic Anomaly) and one at the utterance level (Grammatical Error). The other two factors reflected the complexity of sentence structures (Grammatical Complexity) and the use of repair behaviors (Repair), respectively. Linear discriminant analyses showed that only about two thirds of speakers were classified correctly and that misclassifications were similar to disagreements between clinical diagnoses. The most accurately diagnosed syndromes were the largest groups—Broca's and anomic aphasia. The latent profile analysis also generated profiles similar to Broca's and anomic aphasia but separated some subtypes according to severity.

Conclusions
The factor solution and the classification analyses reflected broad patterns of spontaneous speech performance in a large and representative sample of individuals with aphasia. However, such data-driven approaches present a simplified picture of aphasia patterns, much as traditional syndrome categories do. To ensure ecological validity, a hybrid approach is recommended, balancing population-level analyses with examination of performance at the level of theoretically specified subgroups or individuals.

Supplemental Material

https://doi.org/10.23641/asha.13232354
Fast simulation of electromagnetic particle showers in high granularity calorimeters
Authors: Brito Da Rocha Ricardo , Carminati Federico , Khattak Gulrukh , Vallecorsa Sofia 
Published: November 2020

The future need of simulated events by the LHC experiments and their High Luminosity upgrades, is expected to increase by one or two orders of magnitude. As a consequence, research on new fast simulation solutions, including deep Generative Models, is very active and initial results look promising.
We have previously reported on a prototype that we have developed, based on 3 dimensional convolutional Generative Adversarial Network, to simulate particle showers in high-granularity calorimeters. In this contribution we present improved results on a more realistic simulation. Detailed validation studies show very good agreement with Monte Carlo simulation. In particular, we show how increasing the network representational power, introducing physics-based constraints and using a transfer-learning approach for training improve the level of agreement over a large energy range.
Distributed data analysis with ROOT RDataFrame
Authors: Padulano Vincenzo Eduardo , Cervantes Villanueva Javier , Guiraud Enrico , Tejedor Saavedra Enric 
Published: November 2020

Widespread distributed processing of big datasets has been around for more than a decade now thanks to Hadoop, but only recently higher-level abstractions have been proposed for programmers to easily operate on those datasets, e.g. Spark. ROOT has joined that trend with its RDataFrame tool for declarative analysis, which currently supports local multi-threaded parallelisation. However, RDataFrame’s programming model is general enough to accommodate multiple implementations or backends: users could write their code once and execute it as-is locally or distributedly, just by selecting the corresponding backend.
This abstract introduces PyRDF, a new python library developed on top of RDataFrame to seamlessly switch from local to distributed environments with no changes in the application code. In addition, PyRDF has been integrated with a service for web-based analysis, SWAN, where users can dynamically plug in new resources, as well as write, execute, monitor and debug distributed applications via an intuitive interface.
The GridKa Tape Storage: various performance test results and current improvements
Authors: Musheghyan Haykuhi , Petzold Andreas , Heiss Andreas , Ressmann Doris , Beitzinger Martin 
Published: November 2020

Data growth over several years within HEP experiments requires a wider use of storage systems for WLCG Tiered Centers. It also increases the complexity of storage systems, which includes the expansion of hardware components and thereby complicates existing software products more. To cope with such systems is a non-trivial task and requires highly qualified specialists. Storing petabytes of data on tape storage is a still the most cost-effective way. Year after year, the use of a tape storage increases, consequently a detailed study of its optimal use and verification of performance is a key aspect for such a system. It includes several factors, such as performing various performance tests, identifying and eliminating bottlenecks, properly adjusting and improving the current GridKa setup, etc.
At present, GridKa uses dCache as the storage system in frontend and TSM as the tape storage backend. dCache provides a plugin interface for exchanging data between dcache and tape.
TSS is a TSM-based client developed by the GridKa team. TSS has been in production for over 10 years. The interaction between the GridKa dCache instance and TSM is accomplished using additional scripts that can be further optimized to improve the overall performance of the tape storage.
This contribution provides detailed information on the results of various performance tests performed on the GridKa tape and significant improvements of our tape storage performance.
Fast distributed compilation and testing of large C++ projects
Authors: Matev Rosen 
Published: November 2020

High energy physics experiments traditionally have large software codebases primarily written in C++ and the LHCb physics software stack is no exception. Compiling from scratch can easily take 5 hours or more for the full stack even on an 8-core VM. In a development workflow, incremental builds often do not significantly speed up compilation because even just a change of the modification time of a widely used header leads to many compiler and linker invokations. Using powerful shared servers is not practical as users have no control and maintenance is an issue. Even though support for building partial checkouts on top of published project versions exists, by far the most practical development workflow involves full project checkouts because of off-the-shelf tool support (git, intellisense, etc.)
This paper details a deployment of distcc, a distributed compilation server, on opportunistic resources such as development machines. The best performance operation mode is achieved when preprocessing remotely and profiting from the shared CernVM File System. A 10 (30) fold speedup of elapsed (real) time is achieved when compiling Gaudi, the base of the LHCb stack, when comparing local compilation on a 4 core VM to remote compilation on 80 cores, where the bottleneck becomes non-distributed work such as linking. Compilation results are cached locally using ccache, allowing for even faster rebuilding. A recent distributed memcached-based shared cache is tested as well as a more modern distributed system by Mozilla, sccache, backed by S3 storage. These allow for global sharing of compilation work, which can speed up both central CI builds and local development builds. Finally, we explore remote caching and execution services based on Bazel, and how they apply to Gaudi-based software for distributing not only compilation but also linking and even testing.
GPU Usage in ATLAS Reconstruction and Analysis
Authors: Krasznahorkay Attila , Leggett Charles , Mete Alaettin Serhan , Snyder Scott , Tsulaia Vakho 
Published: November 2020

With Graphical Processing Units (GPUs) and other kinds of accelerators becoming ever more accessible, High Performance Computing Centres all around the world using them ever more, ATLAS has to find the best way of making use of such accelerators in much of its computing.
Tests with GPUs – mainly with CUDA – have been performed in the past in the experiment. At that time the conclusion was that it was not advantageous for the ATLAS offline and trigger software to invest time and money into GPUs. However as the usage of accelerators has become cheaper and simpler in recent years, their re-evaluation in ATLAS’s offline software is warranted.
We show new results of using GPU accelerated calculations in ATLAS’s offline software environment using the ATLAS offline/analysis (xAOD) Event Data Model. We compare the performance and flexibility of a couple of the available GPU programming methods, and show how different memory management setups affect our ability to offload different types of calculations to a GPU efficiently.
Impact of different compilers and build types on Geant4 simulation execution time
Authors: Marcon Caterina , Smirnova Oxana , Muralidharan Servesh 
Published: November 2020

Experimental observations and advanced computer simulations in High Energy Physics (HEP) paved the way for the recent discoveries at the Large Hadron Collider (LHC) at CERN. Currently, Monte Carlo simulations account for a very significant amount of computational resources of the Worldwide LHC Computing Grid (WLCG). The current growth in available computing performance will not be enough to fulfill the expected demand for the forthcoming High Luminosity run (HL-LHC). More efficient simulation codes are therefore required.
This study focuses on evaluating the impact of different build methods on the simulation execution time. The Geant4 toolkit, the standard simulation code for the LHC experiments, consists of a set of libraries which can be either dynamically or statically linked to the simulation executable. Dynamic libraries are currently the preferred build method.
In this work, three versions of the GCC compiler, namely 4.8.5, 6.2.0 and 8.2.0 have been used. In addition, a comparison between four optimization levels (Os, O1, O2 and O3) has also been performed.
Static builds for all the GCC versions considered, exhibit a reduction in execution times of about 10%. Switching to newer GCC version results in an average of 30% improvement in the execution time regardless of the build type. In particular, a static build with GCC 8.2.0 leads to an improvement of about 34% with respect to the default configuration (GCC 4.8.5, dynamic, O2). The different GCC optimization flags do not affect the execution times.