bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Global Adaptation Mapping Initiative (GAMI): Part 1 – Introduction and overview of methods
Authors: Berrang-Ford Lea , Lesnikowski Alexandra , Fischer A. Paige , Siders A.R. , Mach Katharine J. , Thomas Adelle , Callaghan Max , Haddaway Neal , Kerr Rachel Bezner , Biesbroek Robbert , Bowen Kathryn , Deryng Delphine , Elliott Susan , Ford James D. , Garschagen Matthias , Gilmore Elisabeth , Harper Sherliee , Hassnoot Marjolijn , Lissner Tabea , Lwasa Shuaib , Magnan Alexandre K. , Minx Jan , Morecroft Mike , New Mark , Perez Erin Coughlan de , Reckien Diana , Simpson Nick , Singh Chandni , Stringer Lindsay , Totin Edmond , Trisos Chris , Aalst Maarten Van 
Published: February 2021

Abstract
Context: It is now widely accepted that the climate is changing, and that societal responses will need to be rapid and comprehensive to prevent the most severe impacts. A key milestone in global climate governance is to assess progress on adaptation. To-date, however, there has been negligible robust, systematic synthesis of progress on adaptation or adaptation-relevant responses globally. Aim: The purpose of this review protocol is to outline the methods used by the Global Adaptation Mapping Initiative (GAMI) to systematically review human adaptation responses to climate-related changes that have been documented globally since 2013 in the scientific literature. The broad question underpinning this review is: Are we adapting to climate change? More specifically, we ask ‘what is the evidence relating to human adaptation-related responses that can (or are) directly reducing risk, exposure, and/or vulnerability to climate change?’ This work responds to the recognition of the need for high-level syntheses of adaptation research to inform global and regional climate assessments.Methods: We review scientific literature 2013-2019 to identify documents empirically reporting on observed adaptation-related responses to climate change in human systems that can directly reduce risk. We exclude non-empirical (theoretical & conceptual) literature and adaptation in natural systems that occurs without human intervention. Included documents were coded across a set of questions focused on: Who is responding? What responses are documented? What is the extent of the adaptation-related response? What is the evidence that adaptation-related responses reduce risk, exposure and/or vulnerability? Once articles are coded, we conduct a quality appraisal of the coding and develop ‘evidence packages’ for regions and sectors. We supplement this systematic mapping with an expert elicitation exercise, undertaken to assess bias and validity of insights from included/coded literature vis a vis perceptions of real-world adaptation for global regions and sectors, with associated confidence assessments. Related protocols: This protocol represents Part 1 of a 5-part series outlining the phases of methods for this initiative. Part 1 provides an introduction to the Global Adaptation Mapping Initiative (GAMI) and an overview of methods.
The Global Adaptation Mapping Initiative (GAMI): Part 3 – Coding protocol
Authors: Lesnikowski Alexandra , Berrang-Ford Lea , Siders A.R. , Haddaway Neal , Biesbroek Robbert , Harper Sherilee , Minx Jan , Perez Erin Coughlan de , Reckien Diana , New Mark , Singh Chandni , Thomas Adelle , Totin Edmond , Trisos Chris , Bavel Bianca Van 
Published: February 2021

Abstract
Context: It is now widely accepted that the climate is changing, and that societal response will need to be rapid and comprehensive to prevent the most severe impacts. A key milestone in global climate governance is to assess progress on adaptation. To-date, however, there has been negligible robust, systematic synthesis of progress on adaptation or adaptation-relevant responses globally. Aim: The purpose of this review protocol is to outline the methods used by the Global Adaptation Mapping Initiative (GAMI) to systematically review human adaptation responses to climate-related changes that have been documented globally since 2013 in the scientific literature. The broad question underpinning this review is: Are we adapting to climate change? More specifically, we ask ‘what is the evidence relating to human adaptation-related responses that can (or are) directly reducing risk, exposure, and/or vulnerability to climate change?’ Methods: We review scientific literature 2013-2019 to identify documents empirically reporting on observed adaptation-related responses to climate change in human systems that can directly reduce risk. We exclude non-empirical (theoretical & conceptual) literature and adaptation in natural systems that occurs without human intervention. Included documents were coded across a set of questions focused on: Who is responding? What responses are documented? What is the extent of the adaptation-related response? What is the evidence that adaptation-related responses reduce risk, exposure and/or vulnerability? Once articles are coded, we conduct a quality appraisal of the coding and develop ‘evidence packages’ for regions and sectors. We supplement this systematic mapping with an expert elicitation exercise, undertaken to assess bias and validity of insights from included/coded literature vis a vis perceptions of real-world adaptation for global regions and sectors, with associated confidence assessments. Related protocols: This protocol represents Part 3 of a 5-part series outlining the phases of this initiative. Part 3 outlines the methods used to extract data on adaptation from documents (coding), as well as procedures for data quality assurance. See Figure 1.
COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance
Authors: Simonetti Michele , Zhang Ning , Harbers Luuk , Milia Maria Grazia , Nguyen Thi Thu Huong , Brossa Silvia , Bienko Magda , Sapino Anna , Sottile Antonino , Ghisetti Valeria , Crosetto Nicola 
Published: February 2021

Abstract
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the spread and evolution of the virus across different populations, geographical regions and species. Here, we present a streamlined workflow—COVseq—based on the CUTseq method that we previously described, which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms, from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We validated COVseq on RNA extracted from the supernatant of a SARS-CoV-2 culture as well as from 85 left-over samples from nasopharyngeal swabs, demonstrating the ability of COVseq to achieve almost complete genome coverage, including the S region encoding the spike protein. A cost analysis showed that COVseq could be used to sequence thousands of samples per week at less than 20 USD per sample. COVseq is a versatile and scalable method that can be readily applied for genomic surveillance of the ongoing pandemic and easily adapted to other pathogens such as influenza viruses.
Driving After Total Knee and Hip Arthroplasty - an Observational Study From the Perspective of Rehabilitative Orthopaedic Therapy
Authors: Lazar Tiberiu-Adrian , Edelmann Martin , Lohmann Christoph , Awiszus Friedemann 
Published: February 2021

Abstract
Objective: Considering the legal stipulations in Germany regarding fitness to drive a motor vehicle, the aim of this study is to find out when patients with a total knee arthroplasty (TKA) or total hip arthroplasty (THA) actually take up driving again after surgery; how the replaced joint, side, gender, place of residence and physician’s recommendations, influences the patient in making the decision to start driving again.Background: For a large proportion of the population, especially those residing in the countryside, the use of a car for daily activities is indispensable. Following a TKA or THA procedure, the overseeing physician will usually recommend refraining from driving, sometimes up to 12 weeks after surgery with a major social and economical impact on patient’s life. Methods: 92 eligible participants, contained within the frame of a prospective experimental observational study, were contacted via telephone 12 weeks after surgery and interviewed using a structured questionnaire. The answers were statistically analysed using SPSS®.Discussion: There were statistically significant differences regarding operated side, gender and place of residence. Male patients drove in the 6th and 7th postoperative week, while female patients drove in the 8th and 9th postoperative week. For 58.6% of patients the reasoning for the first post-operative drive was medical: the journey to physiotherapy or to a doctor’s appointment. TKA impaired patients the most. Patients recovering from a TKA drive considerably later. Patients recovering from a right sided TKA have an increased risk by a factor of nine, not to become an “early driver”. Female patients who underwent TKA had an increased risk by a factor of 21, of becoming a “late driver”. Conclusions: The rehabilitation following a right sided TKA proved a challenge with regard to the reuptake of driving. This should be taken into account when planning the course of therapy for patients who are driving regulary. Female patients could benefit from special training. Trial registration: DRKS00018693. Registered 20 September 2019 https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00018693
Geographically Masking Addresses to Study COVID-19 Clusters
Authors: Houfaf-Khoufaf Walid , Touya Guillaume 
Published: February 2021

Abstract
The spatial analysis of health data usually raises geoprivacy issues. But with the virulence of COVID-19, scientists and crisis managers do need to analyse the spatio-temporal distribution and spreading of the disease with spatially precise data. In particular, it is useful to locate each case on a map to identify clusters of cases in space and time. To allow such analyses with breach of geoprivacy, geomasking techniques are necessary. This paper experiments the geomasking techniques from the literature to solve this problem: masking the real address of positive cases while preserving the local cluster patterns. In particular, two diﬀerent approaches based on aggregation and perturbation are adapted to the geomasking of addresses in areas with diﬀerent densities of population. A new simulated crowding method is also proposed to preserve clusters as much as possible. The results show that geomasking techniques can spatially anonymize addresses while preserving clusters, and the best geomasking method depends on the use of the anonymized data.
Central metabolic responses of microorganisms to years and decades of soil warming
Authors: Söllinger Andrea , Dahl Mathilde Borg , Séneca Joana , Prommer Judith , Verbruggen Erik , Sigurdsson Bjarni , Janssens Ivan , Penuelas Josep , Urich Tim , Richter Andreas , Tveit Alexander 
Published: February 2021

Abstract
Microbial physiological responses to long-term warming are poorly understood. Here we applied metatranscriptomics to investigate how microorganisms react to medium-term (8 years) and long-term (>5 decades) subarctic grassland soil warming of +6 °C.
Decades, but not years, of warming induced changes in relative abundances of eukaryotic, prokaryotic, and viral transcripts and reduced functional richness. However, irrespective of the duration of warming, we observed a community-wide upregulation of central (carbon) metabolisms and cell replication in the warmed soils, whereas essential energy metabolism and protein biosynthesis complexes and pathways were downregulated. This coincided with a decrease of microbial biomass and lower soil substrate concentrations (e.g. dissolved organic carbon and phosphorus).
We conclude that permanently accelerated reaction rates at higher temperatures facilitate a downregulation of energy metabolism and protein biosynthesis, potentially freeing energy and matter for substrate acquisition and growth. This resource allocation seems to be a common response in microorganisms and allows sustaining high metabolic activities and replication rates even after decades of soil warming.
Discovery of Novel Class of Histone Deacetylase Inhibitors as Anticancer Agents
Authors: El-Awady Raafat , Salah Ekram , Hamoudi Rifat , Mazitschek Ralph , Ramadan Wafaa , Nael Manal , Elokely Khaled , Abou-Gharbia Magid , Childers Wayne , Srinivas Vunnam , Aloum Lujain , Menon Varsha , Al-Tel Taleb 
Published: February 2021

Abstract
Selective inhibition of histone deacetylases (HDACs) is a paramount strategy in the field of anticancer lead drug development. However, the lack of selectivity among these isozymes and the adverse side effects that arise from the inhibition of certain HDACs limits their clinical applications. Phenotypic screening of an in-house pilot library of about 70 small molecules against various HDAC isozymes led to the discovery of five compounds which displayed varying degrees of HDAC isozyme selectivity. The anticancer activities of these molecules were validated using various biological assays including transcriptomic studies. Compounds 15, 14, and 19 possessed selective inhibitory activity against HDAC5, while 28 displayed selective inhibition of HDAC1 and HDAC2. Compound 22 was found to be a selective inhibitor for HDAC3 and HDAC9. In the MCF7 breast cancer cell line the new compounds showed potent anti-proliferative activity, increased acetylation of histones and induced cells apoptosis. The new compounds’ apoptotic effects were validated through the upregulation of caspases3 and 7 and downregulation of C-MYC, BCL2, BCL3 and NFĸB genes. Furthermore, the new compounds arrested cell cycle at different phases, which was confirmed through downregulation of the CDK1, 2, 4, 6, E2F1 and RB1 proteins. Together our findings provide the foundation for the development of new chemical probes as potential lead drug candidates for the treatment of cancer.
Evaluation of Two Highly Effective Lipid-Lowering Therapies in Subjects With Acute Myocardial Infarction: A Lipidomic Analysis
Authors: Klassen Aline , Sussulini Alessandra , Derogis Priscilla , Ferreira Carlos , Lopes Aline , Cruz Elisa , Faccio Andre , Bastos Rafaela , Fontoura Stefanie , Neto Antonio , Tavares Marina , Izar Maria , Fonseca Francisco 
Published: February 2021

Abstract
Introduction For cardiovascular disease prevention, statins alone or combined with ezetimibe have been recommended to achieve low density lipoprotein - cholesterol targets, but their effects on other lipids are less reported. Objective To examine lipid changes in subjects with ST-segment elevation myocardial infarction (STEMI) after two highly effective lipid-lowering therapies. Methods Twenty patients with STEMI were randomized to be treated with rosuvastatin 20 mg qd or simvastatin 40 mg combined with ezetimibe 10 mg qd during 30 days. Fasting blood samples were collected in the first day (D1) and after 30 days (D30). Lipidomic analysis was performed using the Lipidyzer platform. Selected reaction monitoring (SRM) was used in positive and negative ionization modes with and without differential mobility spectrometry (DMS). Univariate and multivariate analyses were performed. Results Comparable classic lipid profile was observed in both groups of lipid-lowering therapies at D1 and after treatments. However, differences in other lipids were observed between groups at these time points. After treatments, main differences between groups were for lysophosphatidylcholine and triacylglycerides. Conclusion Despite similar changes in the classic lipid profile, differences in lipidomic analysis were found before and after exposure to highly effective lipid-lowering therapies in subjects after STEMI. Trial registration: ClinicalTrials.gov, NCT02428374, registered on 28/09/2014.
HDAC6/FOXP3/HNF4α axis promotes bile acids induced gastric intestinal metaplasia
Authors: Wang Na , Wu Siran , Zhang Luyao , Chen Min , Zeng Jiaoxia , Lu Guofang , Zhou Fenli , Wu Qiong , Liu Junye , Shi Yongquan 
Published: February 2021

Abstract
Background: Gastric intestinal metaplasia (IM) is an important precancerous lesion. Our previous study has shown that ectopic expression of HDAC6 promotes the activation of intestinal markers in bile acids (BA) induced gastric IM cells; however, the mechanism underlying how HDAC6-mediated epigenetic modifications regulate intestinal markers is not clear.Methods: RNA-sequencing (RNA-seq) was used to detect the molecular changes in GES-1 cells after HDAC6 overexpression. The potential binding sites of FOXP3 with the promoter region of HNF4α were verified by ChIP and luciferase reporter gene assays. The ChIP assay was also used to detect the histone deacetylation. The levels of mucin in gastric or intestinal mucosa were detected by AB-PAS staining. Transgenic mice were used to explore the pro-metaplastic function of DCA and HNF4α in vivo.Results: Deoxycholic acid (DCA) upregulated HDAC6 in gastric cells, which further inhibited the transcription of FOXP3. Then, FOXP3 transcriptionally inhibited HNF4α, which further inhibits the expression of downstream intestinal markers. These molecules have been shown to be clinically relevant, as FOXP3 levels were negatively correlated with HDAC6 and HNF4α in IM tissues. Transgenic mice experiments confirmed that HNF4α overexpression combined with DCA induced gastric mucosa to secrete intestinal mucus and caused an abnormal mucosal structure. Conclusions: Our findings suggest that HDAC6 reduces FOXP3 through epigenetic modification, thus forming HDAC6/FOXP3/HNF4α axis to promote gastric IM. Inhibition of HDAC6 may be a potential approach to prevent gastric IM in patients with bile reflux.
ggtreeExtra: Compact visualization of richly annotated phylogenetic data
Authors: Xu Shuangbin , Dai Zehan , Guo Pingfan , Fu Xiaocong , Liu Shanshan , Zhou Lang , Tang Wenli , Feng Tingze , Chen Meijun , Zhan Li , Wu Tianzhi , Hu Erqiang , Yu Guangchuang 
Published: February 2021

Abstract
We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree (https://www.bioconductor.org/packages/ggtreeExtra). It supports more data types and visualization methods than other tools and has many features that are not available elsewhere. The ggtreeExtra package is a universal tool for tree data visualization. It extends the applications of phylogenetic tree in different disciplines by making more domain specific data to be available to visualize and interpret on the evolutionary context.
Asymmetric Patterns of Visual Field Loss in Primary Angle Closure Glaucoma, High Tension Glaucoma, and Normal Tension Glaucoma
Authors: Jiang Junhong , Ye Cong , Zhang Cong , Ye Wenqing , Wang Xiaoyan , Shang Xiao , Xu Xiang , Zhang Hongte , Zhang Shaodan , Zheng Jingwei , Zuo Jingjing , Hu Jingjing , Congdon Nathan , Lu Fan , Liang Yuanbo 
Published: February 2021

Abstract
The data directly comparing the spatial pattern of VF defects between primary angle-closure glaucoma (PACG), high-tension glaucoma (HTG) and normal-tension glaucoma (NTG) is not available. We aim to compare the asymmetric patterns of VF defects in patients with PACG, NTG and HTG across different severity levels. A total of 162 eyes of 114 patients with PACG, 111 eyes of 74 patients with HTG and 148 eyes of 102 patients with NTG were included. VF examinations were performed with standard automated perimetry (HFA, SITA-standard strategy, 24-2), and defects were categorized into 3 stages (early, moderate, and advanced) and each hemifield was divided into 5 regions according to Glaucoma Hemifield Test (GHT). The mean total deviation (TD) of each GHT region was calculated. The relationship between the values of pattern standard deviation (PSD) and mean TD was assessed. In the early stage, nasal region of PACG, central region of HTG and all five regions of NTG in the superior hemifield had significantly worse mean TD than their counterparts in the inferior hemifield. In the moderate stage, three regions of NTG in the superior hemifield had significantly worse mean TD than their inferior counterparts. In the advanced stage, central region of PACG, and central and paracentral regions of HTG in the superior hemifield had significantly worse mean TD than their inferior counterparts. When participants were matched by age, sex and mean deviation, in PACG and HTG eyes, all 5 GHT regions in the superior hemifield had worse mean TD than that that of their inferior-hemifield counterparts; however, the differences were not statistically significant. In NTG eyes, the paracentral, nasal, arcuate 1 and arcuate 2 regions in the superior hemifield had significantly worse mean TDs than their inferior counterparts. The superior hemifield is affected more severely than the inferior hemifield in all 3 subtypes of primary glaucoma. This asymmetric tendency was more pronounced in NTG compared to PACG and HTG.
Financial toxicity of cancer care in low and middle-income countries: a systematic review and meta-analysis
Authors: Donkor Andrew , Atuwo-Ampoh Vivian Della , Yakanu Frederick , Torgbenu Eric , Ameyaw Edward Kwabena , Kitson-Mills Doris , Vanderpuye Verna , Kyei Kofi Adesi , Anim-Sampong Samuel , Khader Omar , Khader Jamal 
Published: February 2021

Abstract
Introduction: The costs associated with cancer diagnosis, treatment and care present enormous financial toxicity. However, evidence of financial toxicity associated with cancer in low and middle-income countries (LMICs) is scarce.Aim: To identify the extent of cancer-related financial toxicity and how it has been measured in LMICs.Methods: Four electronic databases were searched to identify studies of any design that reported financial toxicity among cancer patients in LMICs. Random-effects meta-analysis was used to derive the pooled prevalence of financial toxicity. Sub-group analyses were performed according to: costs; and determinants of financial toxicity.Results: A total of 31 studies were included in this systematic review and meta-analysis. The pooled prevalence of financial toxicity was 56.96% [95% CI, 30.51, 106.32]. In sub-group meta-analyses, the financial toxicity was higher among cancer patients with household size of more than four (1.17% [95% CI, 1.03, 1.32]; p = 0.02; I2 = 0%), multiple cycles of chemotherapy (1.94% [95% CI, 1.00, 3.75]; p = 0.05; I2 = 43%) and private health facilities (2.87% [95% CI, 1.89, 4.35]; p < 0.00001; I2 = 26%). Mean medical costs per cancer patients were $2,740.18 [95% CI, $1,953.62, $3,526.74]. The ratio of cost of care to gross domestic product (GDP) per capita varied considerably across the LMICs included in this review, which ranged from 0.06 in Vietnam to 327.65 in Ethiopia.Conclusions: This study indicates that cancer diagnosis, treatment and care impose high financial toxicity on cancer patients in LMICs. Further rigorous research on cancer-related financial toxicity is needed.