bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex systems for the most vulnerable
Authors: Omodei Elisa , Garcia-Herranz Manuel , Paolotti Daniela , Tizzoni Michele 
Published: March 2022

Abstract
In a rapidly changing world, facing an increasing number of socioeconomic, health and environmental crises, complexity science can help us to assess and quantify vulnerabilities, and to monitor and achieve the UN sustainable development goals. In this perspective, we provide three exemplary use cases where complexity science has shown its potential: poverty and socioeconomic inequalities, collective action for representative democracy, and computational epidemic modeling. We then review the challenges and limitations related to data, methods, capacity building, and, as a result, research operationalization. We finally conclude with some suggestions for future directions, urging the complex systems community to engage in applied and methodological research addressing the needs of the most vulnerable.
The need for agricultural productive uses in the national electrification plan of sub-Saharan African countries—a call to action for Ethiopia
Authors: Van-Hein Sackey Charles , Nock Destenie 
Published: March 2022

Abstract
Access to electricity is a crucial aspect of sub-Saharan Africa’s path towards development. In light of the potential for electricity access to improve quality of life, the United Nations aims to achieve universal access to ‘clean, reliable, affordable and modern’ electricity as Goal 7 of its Sustainable Development Goals (SDG 7). As such, governments of sub-Saharan African (SSA) countries, such as Ethiopia, have developed national electrification plans to outline their pathway to universal access to electricity. In this paper, we identify why it is essential for the national electrification plans of SSA countries to prioritize electricity access for productive uses in its agricultural sector, using Ethiopia as a case study. Reviewing existing literature and using the authors’ research, we point out that there is 3.04 terawatt-hours of latent demand for small-scale pressurized cereal-crop irrigation alone in Ethiopia. Supplying this electricity demand for small-scale irrigation could lead to a reduction in the levelized cost of electricity of up to 95%. We conclude our paper by recommending the creation of a cross-sector national productive use commission that would be tasked with collecting and sharing relevant data from each sector and collaboratively creating a national productive use program that would ensure that Ethiopia reaps the full benefits and potential for wealth creation from access to electricity.
Exploring the impacts of tourism and weather on water consumption at different spatiotemporal scales: evidence from a coastal area on the Adriatic Sea (northern Italy)
Authors: Mazzoni Filippo , Marsili Valentina , Alvisi Stefano , Franchini Marco 
Published: March 2022

Abstract
The growth of tourism in the last decades has left behind a significant footprint on water resources, which is particularly evident in the regions affected by water scarcity or consistent seasonal population fluctuations. However, only limited efforts were spent in evaluating the effects of tourism on water consumption with regard to specific non-residential users such as bathing facilities. The current work aimed at providing an insight into the effects of seaside tourism on water consumption in a case study coastal area in northern Italy that is typically subjected to high tourist fluctuations throughout the year. Analyses were carried out at multiple spatiotemporal scales—from urban to user level, and from yearly to daily scale—by exploiting hourly flow data collected at the inflow points of the area and at some touristic users (i.e. nine bathing facilities and a holiday home). In addition, the impact of weather—temperature and rainfall—on water use was explored. The study revealed consistent inflow fluctuations in the area concerned based on tourism (with a ratio between the maximum and minimum monthly average inflow of about 15.7) and demonstrated that the touristic component of water inflow was considerably higher than the residential component at the height of tourist season (i.e., 176 L/s against 42 L/s). Moreover, significant variations in the water inflow due to tourism and weather were also observed on a daily scale, along with considerable water consumption fluctuations in bathing facilities.
Assessment of chimeric antigen receptor T cytotoxicity by droplet microfluidics in vitro
Authors: Wong Kuan Un , Shi Jingxuan , Li Peng , Wang Haitao , Jia Yanwei , Deng Chuxia , Jiang Lianmei , Wong Ada Hang-Heng 
Published: March 2022

Abstract
Chimeric antigen receptor T (CAR-T) cells are cytotoxic T cells engineered to specifically kill cancer cells expressing specific target receptor(s). Prior CAR-T efficacy tests include CAR expression analysis by qPCR or ELISA, in vitro measurement of interferon-γ (IFNγ) or interleukin-2 (IL-2), and xenograft models. However, the in vitro measurements did not reflect CAR-T cytotoxicity, whereas xenograft models are low throughput and costly. Here, we presented a robust in vitro droplet microfluidic assay for CAR-T cytotoxicity assessment. This method not only enabled assessment of CAR-T cytotoxic activity under different fluid viscosity conditions, but also facilitated measurement of CAR-T expansion and dissection of mechanism of action via phenotype analysis in vitro. Furthermore, our data suggested that label-free cytotoxicity analysis is feasible by acquiring data before and after treatment. Hence, this study presented a novel in vitro method for assessment of cellular cytotoxicity that could potentially be applied to any cytotoxicity experiment with varying solvent composition.
Identifying preeclampsia-associated genes using a control theory method
Authors: Li Xiaomei , Liu Lin , Whitehead Clare , Li Jiuyong , Thierry Benjamin , Le Thuc D , Winter Marnie 
Published: March 2022

AbstractPreeclampsia is a pregnancy-specific disease that can have serious effects on the health of both mothers and their offspring. Predicting which women will develop preeclampsia in early pregnancy with high accuracy will allow for improved management. The clinical symptoms of preeclampsia are well recognized, however, the precise molecular mechanisms leading to the disorder are poorly understood. This is compounded by the heterogeneous nature of preeclampsia onset, timing and severity. Indeed a multitude of poorly defined causes including genetic components implicates etiologic factors, such as immune maladaptation, placental ischemia and increased oxidative stress. Large datasets generated by microarray and next-generation sequencing have enabled the comprehensive study of preeclampsia at the molecular level. However, computational approaches to simultaneously analyze the preeclampsia transcriptomic and network data and identify clinically relevant information are currently limited. In this paper, we proposed a control theory method to identify potential preeclampsia-associated genes based on both transcriptomic and network data. First, we built a preeclampsia gene regulatory network and analyzed its controllability. We then defined two types of critical preeclampsia-associated genes that play important roles in the constructed preeclampsia-specific network. Benchmarking against differential expression, betweenness centrality and hub analysis we demonstrated that the proposed method may offer novel insights compared with other standard approaches. Next, we investigated subtype specific genes for early and late onset preeclampsia. This control theory approach could contribute to a further understanding of the molecular mechanisms contributing to preeclampsia.
kc-hits: a tool to aid in the evaluation and classification of chemical carcinogens
Authors: Reisfeld Brad , de Conti Aline , El Ghissassi Fatiha , Benbrahim-Tallaa Lamia , Gwinn William , Grosse Yann , Schubauer-Berigan Mary 
Published: March 2022

Abstract

Motivation
The evaluation of chemicals for their carcinogenic hazard requires the analysis of a wide range of data and the characterization of these results relative to the key characteristics of carcinogens. The workflow used historically requires many manual steps that are labor-intensive and can introduce errors, bias and inconsistencies.

Results
The automation of parts of the evaluation workflow using the kc-hits software has led to significant improvements in process efficiency, as well as more consistent and comprehensive results.

Availability and implementation
https://gitlab.com/i1650/kc-hits.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Magnetization transfer ratio for assessing remyelination after transcranial ultrasound stimulation in the lysolecithin rat model of multiple sclerosis
Authors: Huang Li-Hsin , Pan Zih-Yun , Pan Yi-Ju , Yang Feng-Yi 
Published: March 2022

AbstractIt has been shown that transcranial ultrasound stimulation (TUS) is capable of attenuating myelin loss and providing neuroprotection in animal models of brain disorders. In this study, we investigated the ability of TUS to promote remyelination in the lysolecithin (LPC)-induced local demyelination in the hippocampus. Demyelination was induced by the micro-injection of 1.5 μL LPC (1%) into the rat hippocampus and the treated group received daily TUS for 5 or 12 days. Magnetic resonance imaging techniques, including magnetization transfer ratio (MTR) and T2-weighted imaging, were used to longitudinally characterize the demyelination model. Furthermore, the therapeutic effects of TUS on LPC-induced demyelination were assessed by Luxol fast blue (LFB) staining. Our data revealed that reductions in MTR values observed during demyelination recover almost completely upon remyelination. The MTR values in demyelinated lesions were significantly higher in TUS-treated rats than in the LPC-only group after undergoing TUS. Form histological observation, TUS significantly reduced the size of demyelinated lesion 7 days after LPC administration. This study demonstrated that MTR was a sensitive and reproducible quantitative marker to assess remyelination process in vivo during TUS treatment. These findings might open new promising treatment strategies for demyelinating diseases such as multiple sclerosis.
Polydopamine Coating Doped with Graphene Oxide Enhances Enantioseparation of Capillary Column
Authors: Zhao Shiyuan , Miao Panden , Zhang Jian , Gan Jie , Du Yingxiang , Chen Cheng , Sun Xiaodong , Feng Zijie , Ma Xiaofei , Ma Mingxuan , Xi Ying , Ding Wen 
Published: March 2022

AbstractHow to improve the enantiomer separation efficiency of drugs is a hot topic. In this paper, polydopamine (PDA) coating doped with graphene oxide (GO) by physical adsorption was used to modify the capillary column to enhance the enantioseparation efficiency of the drugs. In the capillary electrochromatography (CEC) system, the novel capillary column with carboxymethyl-β-cyclodextrin (CM-β-CD) as a chiral selector has completed the enantioseparation of four basic drugs (propranolol, metoprolol, amlodipine and chlorpheniramine). The optimum separation conditions were obtained by optimizing the pH of the buffer, the concentration of organic modifier, the concentration of the chiral selector and the voltage, and the resolution and peak shape were significantly improved compared with uncoated bare-fused column. The stability and reproducibility of the new capillary column were satisfactory and the relative standard deviation of intra-day and inter-day was &lt;3.2%, and of column-to-column was &lt;4.8%. The rich functional groups of GO are key factors to improve the enantioseparation efficiency, which also indicates that nanomaterials with easy modification of functional groups and large specific surface area are excellent resources for capillary modification applications.
Use of a smartphone electrocardiogram to diagnose arrhythmias during exercise in athletes: a case series
Authors: Jewson Jacob L , Orchard John W , Semsarian Chris , Fitzpatrick Jane , La Gerche Andre , Orchard Jessica J 
Published: March 2022

Abstract

Background
While athletes are generally very fit, intense exercise can increase the risk of atrial fibrillation. Moreover, other arrhythmias such as atrial flutter or supraventricular tachycardia can cause distressing, exercise-related symptoms. Given symptoms are infrequent and may occur during intense exertion, traditional monitoring devices are often impractical to use during exercise. Smartphone electrocardiograms (ECGs) such as the Alivecor Kardia device may be the portable and reliable tool required to help identify arrhythmias in this challenging population. This case series highlights the use of such devices in aiding the diagnosis of arrhythmias in the setting of exercise-related symptoms in athletes.

Case summary
The six cases in this series included one elite non-endurance athlete, two elite cricketers, one amateur middle-distance runner, and two semi-elite ultra-endurance runners, with an age range of 16–48 years. An accurate diagnosis of an arrhythmia was obtained in five cases (atrial fibrillation/flutter and supraventricular tachycardias) using the smartphone ECG, which helped guide definitive treatment. No arrhythmia was identified in the final case despite using the device during multiple symptomatic events.

Discussion
The smartphone ECG was able to accurately detect arrhythmias and provide a diagnosis in cases where traditional monitoring had not. The utility of detecting no arrhythmia during symptoms in one case was also highlighted, providing the athlete with the confidence to continue exercising. This reassurance and confidence across all cases is perhaps the most valuable aspect of this device, where clinicians and athletes can be more certain of reaching a diagnosis and undertaking appropriate management.
Systematic review ofListeria monocytogenesfrom food and clinical samples in Chinese mainland from 2010 to 2019
Authors: Cheng Ying , Dong Qingli , Liu Yangtai , Liu Hong , Zhang Hongzhi , Wang Xiang 
Published: March 2022

AbstractListeria monocytogenes (L. monocytogenes), a foodborne pathogen, can cause human listeriosis. Listeriosis is a potentially fatal gastrointestinal illness, which is closely related to the spread of food to humans. We review the literature published during 2010–2019 to better understand the prevalence of L. monocytogenes in food products, incidence of human listeriosis, and their characteristics in Chinese mainland. We found the main sequence types (STs) strains from foods are similar globally, and the prevalence of L. monocytogenes from raw meat was the highest among all food products. The most common STs in food products and clinical cases were ST9 (serogroup I.2) strains and ST87 (serogroup II.2) strains, respectively. The ST87 strains being the most common STs of clinical cases might be related to the existence of Listeria pathogenicity island 4 gene and Chinese eating habits for ready-to-eat foods, among which the prevalence of ST87 strain was the highest in ready-to-eat foods. Therefore, more research should be conducted to explore the reasons for the L. monocytogenes isolates differences in food and clinical sources.
Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
Authors: D’Amico-Willman Katherine M , Ouma Wilberforce Z , Meulia Tea , Sideli Gina M , Gradziel Thomas M , Fresnedo-Ramírez Jonathan 
Published: March 2022

Abstract
Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including ‘Nonpareil,’ which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for ‘Nonpareil’ is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment.
Mapping the sex determination region in the Salix F1 hybrid common parent population confirms a ZW system in six diverse species
Authors: Wilkerson Dustin G , Taskiran Bircan , Carlson Craig H , Smart Lawrence B 
Published: March 2022

Abstract
Within the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing 6 Salix species (Salix viminalis, Salix suchowensis, Salix integra, Salix koriyanagi, Salix udensis, and Salix alberti) to common male and female Salix purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S.suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra × S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop.
GNSS-corrected InSAR displacement time-series spanning the 2019 Ridgecrest, CA earthquakes
Authors: Guns Katherine , Xu Xiaohua , Bock Yehuda , Sandwell David 
Published: March 2022

SUMMARYInSAR displacement time-series are emerging as a valuable product to study a number of Earth processes. One challenge to current time-series processing methods, however, is that when large earthquakes occur, they can leave sharp coseismic steps in the time-series. These discontinuities can cause current atmospheric correction and noise smoothing algorithms to break down, as these algorithms commonly assume that deformation is steady through time. Here, we aim to remedy this by exploring two methods for correcting earthquake offsets in InSAR time-series: a simple difference offset estimate (SDOE) process and a multiparameter offset estimate (MPOE) parametric time-series inversion technique. We apply these methods to a 2-yr time-series of Sentinel-1 interferograms spanning the 2019 Ridgecrest, CA earthquake sequence. Descending track results indicate that the SDOE method precisely corrects for only 20 per cent of the coseismic offsets at 62 study locations included in our scene and only partially corrects or sometimes overcorrects for the rest of our study sites. On the other hand, the MPOE estimate method successfully corrects the coseismic offset for the majority of sites in our analysis. This MPOE method allows us to produce InSAR time-series and data-derived estimates of deformation during each phase of the earthquake cycle. In order to better isolate and estimate the signal of post-seismic lithospheric deformation in the InSAR time-series, we apply a GNSS-based correction to our interferograms. This correction ties the interferograms to median-filtered weekly GNSS displacements and removes additional atmospheric artefacts. We present InSAR-based estimates of post-seismic deformation for the area around the Ridgecrest rupture, as well as a 2-yr coseismic-corrected, GNSS-corrected InSAR time-series data set. This GNSS-corrected InSAR time-series will enable future modelling of post-seismic processes such as afterslip in the near field of the rupture, poroelastic deformation at intermediate distances and viscoelastic deformation at longer timescales in the far field.
Ranking earthquake forecasts using proper scoring rules: binary events in a low probability environment
Authors: Serafini Francesco , Naylor Mark , Lindgren Finn , Werner Maximilian J , Main Ian 
Published: March 2022

SUMMARYOperational earthquake forecasting for risk management and communication during seismic sequences depends on our ability to select an optimal forecasting model. To do this, we need to compare the performance of competing models in prospective experiments, and to rank their performance according to the outcome using a fair, reproducible and reliable method, usually in a low-probability environment. The Collaboratory for the Study of Earthquake Predictability conducts prospective earthquake forecasting experiments around the globe. In this framework, it is crucial that the metrics used to rank the competing forecasts are ‘proper’, meaning that, on average, they prefer the data generating model. We prove that the Parimutuel Gambling score, proposed, and in some cases applied, as a metric for comparing probabilistic seismicity forecasts, is in general ‘improper’. In the special case where it is proper, we show it can still be used improperly. We demonstrate the conclusions both analytically and graphically providing a set of simulation based techniques that can be used to assess if a score is proper or not. They only require a data generating model and, at least two forecasts to be compared. We compare the Parimutuel Gambling score’s performance with two commonly used proper scores (the Brier and logarithmic scores) using confidence intervals to account for the uncertainty around the observed score difference. We suggest that using confidence intervals enables a rigorous approach to distinguish between the predictive skills of candidate forecasts, in addition to their rankings. Our analysis shows that the Parimutuel Gambling score is biased, and the direction of the bias depends on the forecasts taking part in the experiment. Our findings suggest the Parimutuel Gambling score should not be used to distinguishing between multiple competing forecasts, and for care to be taken in the case where only two are being compared.