bluuebunny/crossref_metadata_2025_split huggingface dataset:
One planet: one health. A call to support the initiative on a global science–policy body on chemicals and waste
Authors: Brack Werner , Barcelo Culleres Damia , Boxall Alistair B. A. , Budzinski Hélène , Castiglioni Sara , Covaci Adrian , Dulio Valeria , Escher Beate I. , Fantke Peter , Kandie Faith , Fatta-Kassinos Despo , Hernández Félix J. , Hilscherová Klara , Hollender Juliane , Hollert Henner , Jahnke Annika , Kasprzyk-Hordern Barbara , Khan Stuart J. , Kortenkamp Andreas , Kümmerer Klaus , Lalonde Brice , Lamoree Marja H. , Levi Yves , Lara Martín Pablo Antonio , Montagner Cassiana C. , Mougin Christian , Msagati Titus , Oehlmann Jörg , Posthuma Leo , Reid Malcolm , Reinhard Martin , Richardson Susan D. , Rostkowski Pawel , Schymanski Emma , Schneider Flurina , Slobodnik Jaroslav , Shibata Yasuyuki , Snyder Shane Allen , Fabriz Sodré Fernando , Teodorovic Ivana , Thomas Kevin V. , Umbuzeiro Gisela A. , Viet Pham Hung , Yew-Hoong Karina Gin , Zhang Xiaowei , Zuccato Ettore 
Published: March 2022

AbstractThe chemical pollution crisis severely threatens human and environmental health globally. To tackle this challenge the establishment of an overarching international science–policy body has recently been suggested. We strongly support this initiative based on the awareness that humanity has already likely left the safe operating space within planetary boundaries for novel entities including chemical pollution. Immediate action is essential and needs to be informed by sound scientific knowledge and data compiled and critically evaluated by an overarching science–policy interface body. Major challenges for such a body are (i) to foster global knowledge production on exposure, impacts and governance going beyond data-rich regions (e.g., Europe and North America), (ii) to cover the entirety of hazardous chemicals, mixtures and wastes, (iii) to follow a one-health perspective considering the risks posed by chemicals and waste on ecosystem and human health, and (iv) to strive for solution-oriented assessments based on systems thinking. Based on multiple evidence on urgent action on a global scale, we call scientists and practitioners to mobilize their scientific networks and to intensify science–policy interaction with national governments to support the negotiations on the establishment of an intergovernmental body based on scientific knowledge explaining the anticipated benefit for human and environmental health.
Ultra-low dose external beam radiotherapy for presumed choroidal lymphoma: a case report
Authors: Flanagan Jeremy P. M. , Ng Michael , Kibrom Awet Z. , Filshie Robin J. A. , Stawell Richard J. , O’Day Roderick F. 
Published: March 2022

AbstractPrimary choroidal lymphoma is a rare, slowly progressive intraocular malignancy. Most are low grade B cell lymphomas, often involving tissues adjacent to the choroid such as the subconjunctival space, lacrimal gland or orbit. Ideally, these lesions are biopsied to establish histopathological diagnosis. The most accessible ocular structure is biopsied. Obtaining tissue by transvitreal choroidal biopsy imparts a small but significant risk of ocular morbidity, including the need for multiple surgeries, retinal detachment and vision loss.External beam radiotherapy (EBRT) is a common and effective treatment of low-grade lymphomas. EBRT has been found to very successfully treat primary marginal zone lymphomas of the ocular adnexa, which are typically of the same cell type as most primary choroid lymphomas. Ultra-low dose EBRT, most commonly using a total dose of 4 Gy, has been shown to be as effective as higher doses of radiotherapy for follicular or marginal zone lymphomas. The use of this low dose regimen for conjunctival lymphomas has been recently explored. The role of EBRT, and especially ultra-low dose EBRT, for treatment of primary choroidal lymphoma has been confined to case reports.We describe a case of presumed primary choroidal lymphoma diagnosed on clinical findings alone as the risks of ocular biopsy were deemed too high, and report outcome following treatment with ultra-low dose EBRT.
DrGA: cancer driver gene analysis in a simpler manner
Authors: Nguyen Quang-Huy , Nguyen Tin , Le Duc-Hau 
Published: March 2022

AbstractBackgroundTo date, cancer still is one of the leading causes of death worldwide, in which the cumulative of genes carrying mutations was said to be held accountable for the establishment and development of this disease mainly. From that, identification and analysis of driver genes were vital. Our previous study indicated disagreement on a unifying pipeline for these tasks and then introduced a complete one. However, this pipeline gradually manifested its weaknesses as being unfamiliar to non-technical users, time-consuming, and inconvenient.ResultsThis study presented an R package named DrGA, developed based on our previous pipeline, to tackle the mentioned problems above. It wholly automated four widely used downstream analyses for predicted driver genes and offered additional improvements. We described the usage of the DrGA on driver genes of human breast cancer. Besides, we also gave the users another potential application of DrGA in analyzing genomic biomarkers of a complex disease in another organism.ConclusionsDrGA facilitated the users with limited IT backgrounds and rapidly created consistent and reproducible results. DrGA and its applications, along with example data, were freely provided athttps://github.com/huynguyen250896/DrGA.
Genome-wide recombination map construction from single sperm sequencing in cattle
Authors: Yang Liu , Gao Yahui , Li Mingxun , Park Ki-Eun , Liu Shuli , Kang Xiaolong , Liu Mei , Oswalt Adam , Fang Lingzhao , Telugu Bhanu P. , Sattler Charles G. , Li Cong-jun , Cole John B. , Seroussi Eyal , Xu Lingyang , Yang Lv , Zhou Yang , Li Li , Zhang Hongping , Rosen Benjamin D. , Van Tassell Curtis P. , Ma Li , Liu George E. 
Published: March 2022

Abstract
Background
Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, it is not well studied in livestock, including cattle.

Results
To investigate their distributions in the cattle sperm genome, we sequenced 143 single sperms from two Holstein bulls. We mapped meiotic recombination events at high resolution based on phased heterozygous single nucleotide polymorphism (SNP). In the absence of evolutionary selection pressure in fertilization and survival, recombination events in sperm are enriched near distal chromosomal ends, revealing that such a pattern is intrinsic to the molecular mechanism of meiosis. Furthermore, we further validated these findings in single sperms with results derived from sequencing its family trio of diploid genomes and our previous studies of recombination in cattle.

Conclusions
To our knowledge, this is the first large-scale single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of recombination, genome instability, and male infertility.
Plastome phylogenomics and historical biogeography of aquatic plant genus Hydrocharis (Hydrocharitaceae)
Authors: Li Zhi-Zhong , Lehtonen Samuli , Gichira Andrew W. , Martins Karina , Efremov Andrey , Wang Qing-Feng , Chen Jin-Ming 
Published: March 2022

AbstractBackgroundHydrocharisL. andLimnobiumRich. are small aquatic genera, including three and two species, respectively. The taxonomic status, phylogenetic relationships and biogeographical history of these genera have remained unclear, owing to the lack of Central African endemicH. chevalierifrom all previous studies. We sequenced and assembled plastomes of all threeHydrocharisspecies andLimnobium laevigatumto explore the phylogenetic and biogeographical history of these aquatic plants.ResultsAll four newly generated plastomes were conserved in genome structure, gene content, and gene order. However, they differed in size, the number of repeat sequences, and inverted repeat borders. Our phylogenomic analyses recovered non-monophyleticHydrocharis. The African speciesH. chevalieriwas fully supported as sister to the rest of the species, andL. laevigatumwas nested inHydrocharisas a sister toH.dubia.Hydrocharis-Limnobiuminitially diverged from the remaining genera at ca. 53.3 Ma, then began to diversify at ca. 30.9 Ma. The biogeographic analysis suggested thatHydrocharisprobably originated in Europe and Central Africa.ConclusionBased on the phylogenetic results, morphological similarity and small size of the genera, the most reasonable taxonomic solution to the non-monophyly ofHydrocharisis to treatLimnobiumas its synonym. The African endemicH. chevalieriis fully supported as a sister to the remaining species.Hydrocharismainly diversified in the Miocene, during which rapid climate change may have contributed to the speciation and extinctions. The American species of formerLimnobiumprobably dispersed to America through the Bering Land Bridge during the Miocene.
A nationwide registry study on heart failure in Norway from 2008 to 2018: variations in lookback period affect incidence estimates
Authors: Ødegaard Kristina Malene , Lirhus Sandre Svatun , Melberg Hans Olav , Hallén Jonas , Halvorsen Sigrun 
Published: March 2022

Abstract
Background
The incidence of heart failure (HF) has declined in Europe during the past two decades. However, incidence estimates from registry-based studies may vary, partly because they depend on retrospective searches to exclude previous events. The aim of this study was to assess to what extent different lookback periods (LPs) affect temporal trends in incidence, and to identify the minimal acceptable LP. Further, we wanted to estimate temporal trends in incidence and prevalence of HF in a nationwide population, using the minimal acceptable LP.

Methods
We identified all in- and out-patient contacts for HF in Norway during 2008 to 2018 from the Norwegian Patient Registry. To calculate the influence of varying LP on incident cases, we defined 2018 with 10 years of LP as a reference and calculated the relative difference by using one through 9 years of lookback. Temporal trends in incidence rates were estimated with sensitivity analyses applying varying LPs and different case definitions. Standardised incidence rates and prevalence were calculated by applying direct age- and sex-standardization to the 2013 European Standard Population.

Results
The overestimation of incident cases declined with increasing number of years included in the LP. Compared to a 10-year LP, application of 4, 6, and 8 years resulted in an overestimation of incident cases by 13.5%, 6.2% and 2.3%, respectively. Temporal trends in incidence were affected by the number of years in the LP and whether the LP was fixed or varied. Including all available data mislead to conclusions of declining incidence rates over time due to increasing LPs.

Conclusions
When taking the number of years with available data and HF mortality and morbidity into consideration, we propose that 6 years of fixed lookback is sufficient for identification of incident HF cases. HF incidence rates and prevalence increased from 2014 to 2018.

Trial registration

Retrospectively registered.
The association between skinfold thicknesses and estimated glomerular filtration rate in adolescents: a cross-sectional study
Authors: Yang Yongchang , Wu Yubin 
Published: March 2022

Abstract
Background
Obesity is one of the causes of glomerular hyperfiltration. Studies on the relationship between body fat content and glomerular hyperfiltration have been limited to special children. Therefore, we aimed to evaluate the correlation between skinfold thickness, which represents body fat content, and estimated glomerular filtration rate (eGFR).

Methods
The cross-sectional study included 6655 participants (3532 boys and 3123 girls; age: 12 − 17.99 years); data was obtained from the National Health and Nutrition Examination Survey (NHANES; 2001–2010). The independent variables were subscapular skinfold thickness and triceps skinfold thickness. The dependent variable was eGFR. We used multivariate linear regression models to evaluate their associations and also performed subgroup analyses.

Results
After adjusting for age, standing height, race, family income, blood urea nitrogen and uric acid variables, multivariate regression analysis identified that triceps skinfold thickness and subscapular skinfold thickness were positively correlated with eGFR and glomerular hyperfiltration in boys. In subgroup analyses stratified by age and body mass index, triceps skinfold thickness was also associated with glomerular hyperfiltration in boys. There was a linear relationship between triceps skinfold thickness and eGFR in boys (β = 0.389, P < 0.001) and girls (β = 0.159, P = 0.0003).

Conclusions
Triceps skinfold thickness and subscapular skinfold thickness are positively correlated with eGFR and glomerular hyperfiltration in US male adolescents. In all adolescents, there is a linear relationship between triceps skinfold thickness and eGFR.
Association of triglyceride-glucose index and stroke recurrence among nondiabetic patients with acute ischemic stroke
Authors: Yang Xiaomeng , Wang Guangyao , Jing Jing , Wang Anxin , Zhang Xiaoli , Jia Qian , Meng Xia , Zhao Xingquan , Liu Liping , Li Hao , Wang Yongjun , Wang Yilong 
Published: March 2022

AbstractBackgroud and purposeTriglyceride-glucose (TyG) index has been considered a surrogate marker of insulin resistance. We investigated the association between TyG index and stroke recurrence and compared the effectiveness of TyG index with homeostasis model assessment of insulin resistance (HOMA-IR) in predicting stroke recurrence and death in nondiabetic acute ischemic stroke patients.MethodsNondiabetic acute ischemic stroke patients from the ACROSS-China (Abnormal Glucose Regulation in Patients with Acute Stroke across China) registry were included. TyG index was performed and classified into four groups by quartiles. The outcomes were stroke recurrence and death within 1 year. The association between TyG index and the risk of stroke recurrence and death were analyzed by Cox regression models. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the prediction of TyG index and HOMA-IR for stroke recurrence and death. Delong test was used for comparing the differences between area under the curve (AUC) of TyG index and HOMA-IR.ResultsAmong the 1226 patients included, the median (interquartile range) of TyG index was 5.8 (5.5–6.2). Both the third and fourth quartiles of TyG index were associated with an increased risk of stroke recurrence (adjusted hazard ratio 2.04, 95% confidence interval 1.26–3.31; adjusted hazard ratio 1.86, 95% confidence interval 1.13–3.06). Patients with fourth quartiles of TyG index were associated with a higher mortality risk (adjusted hazard ratio, 2.91; 95% confidence interval, 1.62–2.53). Regarding stroke recurrence within 1 year, the AUC (95% confidence interval) of the ROC curve for the TyG index was similar to that of the HOMA-IR[0.56 (0.52–0.61) vs 0.57 (0.52–0.61);P = 0.93]. Regarding death within 1 year, the AUCs (95% confidence interval) of the ROC curve for the TyG index and HOMA-IR were 0.55 (0.50–0.61) and 0.59 (0.53–0.64), respectively (P = 0.32).ConclusionsElevated TyG index was associated with an increased risk of stroke recurrence and death. However, neither of TyG nor HOMA-IR can be a qualified predictor of stroke recurrence and death in nondiabetic acute ischemic stroke patients.
Different inflammatory blood markers correlate with specific outcomes in incident HPV-negative head and neck squamous cell carcinoma: a retrospective cohort study
Authors: Boscolo-Rizzo Paolo , D’Alessandro Andrea , Polesel Jerry , Borsetto Daniele , Tofanelli Margherita , Deganello Alberto , Tomasoni Michele , Nicolai Piero , Bossi Paolo , Spinato Giacomo , Menegaldo Anna , Ciorba Andrea , Pelucchi Stefano , Bianchini Chiara , Cazzador Diego , Ramaciotti Giulia , Lupato Valentina , Giacomarra Vittorio , Molteni Gabriele , Marchioni Daniele , Fabbris Cristoforo , Occhini Antonio , Bertino Giulia , Fussey Jonathan , Tirelli Giancarlo 
Published: March 2022

Abstract
Background
Inflammatory blood markers have been associated with oncological outcomes in several cancers, but evidence for head and neck squamous cell carcinoma (HNSCC) is scanty. Therefore, this study aims at investigating the association between five different inflammatory blood markers and several oncological outcomes.

Methods
This multi-centre retrospective analysis included 925 consecutive patients with primary HPV-negative HNSCC (median age: 68 years) diagnosed between April 2004 and June 2018, whose pre-treatment blood parameters were available. Neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), lymphocyte to monocyte ratio (LMR), systemic inflammatory marker (SIM), and systemic immune-inflammation index (SII) were calculated; their associations with local, regional, and distant failure, disease-free survival (DFS), and overall survival (OS) was calculated.

Results
The median follow-up was 53 months. All five indexes were significantly associated with OS; the highest accuracy in predicting patients’ survival was found for SIM (10-year OS = 53.2% for SIM < 1.40 and 40.9% for SIM ≥ 2.46; c-index = 0.569) and LMR (10-year OS = 60.4% for LMR ≥ 3.76 and 40.5% for LMR < 2.92; c-index = 0.568). While LMR showed the strongest association with local failure (HR = 2.16; 95% CI:1.22–3.84), PLR showed the strongest association with regional (HR = 1.98; 95% CI:1.24–3.15) and distant failure (HR = 1.67; 95% CI:1.08–2.58).

Conclusion
Different inflammatory blood markers may be useful to identify patients at risk of local, regional, or distant recurrences who may benefit from treatment intensification or intensive surveillance programs.
High Intensity Aerobic exercise training and Immune cell Mobilization in patients with lung cancer (HI AIM)—a randomized controlled trial
Authors: Holmen Olofsson Gitte , Mikkelsen Marta Kramer , Ragle Anne-Mette , Christiansen Anne Birgitte , Olsen Anne Pries , Heide-Ottosen Lise , Horsted Cecilia Bech , Pedersen Cia Moon Scharbau , Engell-Noerregaard Lotte , Lorentzen Torben , Persson Gitte Fredberg , Vinther Anders , Nielsen Dorte Lisbet , thor Straten Per 
Published: March 2022

Abstract
Background
The increasing role of exercise training in cancer care is built on evidence that exercise can reduce side effects of treatment, improve physical functioning and quality of life. We and others have shown in mouse tumor models, that exercise leads to an adrenalin-mediated increased influx of T and NK cells into the tumor, altering the tumor microenvironment (TME) and leading to reduced tumor growth. These data suggest that exercise could improve immune responses against cancer cells by increase immune cell infiltration to the tumor and potentially having an impact on disease progression. Additionally, there are data to suggest that infiltration of T and NK cells into the TME is correlates with response to immune checkpoint inhibitors in patients. We have therefore initiated the clinical trial HI AIM, to investigate if high intensity exercise can mobilize and increase infiltration of immune cells in the TME in patients with lung cancer.

Methods
HI AIM (NCT04263467) is a randomized controlled trial (70 patients, 1:1) for patients with non-small cell lung cancer. Patients in the treatment arm, receive an exercise-intervention consisting of supervised and group-based exercise training, comprising primarily intermediate to high intensity interval training three times per week over 6 weeks. All patients will also receive standard oncological treatments; checkpoint inhibitors, checkpoint inhibitors combined with chemotherapy or oncological surveillance. Blood samples and biopsies (ultrasound guided), harvested before, during and after the 6-week training program, will form basis for immunological measurements of an array of immune cells and markers. Primary outcome is circulating NK cells. Secondary outcome is other circulating immune cells, infiltration of immune cells in tumor, inflammatory markers, aerobic capacity measured by VO2 max test, physical activity levels and quality of life measured by questionnaires, and clinical outcomes.

Discussion
To our knowledge, HI AIM is the first project to combine supervised and monitored exercise in patients with lung cancer, with rigorous analyses of immune and cancer cell markers over the course of the trial. Data from the trial can potentially support exercise as a tool to mobilize cells of the immune system, which in turn could potentiate the effect of immunotherapy.

Trial registration
The study was prospectively registered at ClinicalTrials.gov on February 10th 2020, ID: NCT04263467. https://clinicaltrials.gov/ct2/show/NCT04263467
Comparison of tumors with HER2 overexpression versus HER2 amplification in HER2-positive breast cancer patients
Authors: Horimoto Yoshiya , Ishizuka Yumiko , Ueki Yuko , Higuchi Toru , Arakawa Atsushi , Saito Mitsue 
Published: March 2022

Abstract
Background
Human epidermal growth factor receptor 2 (HER2)-positive tumors are defined by protein overexpression (3+) or gene amplification using immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH), respectively. HER2-positive tumors have historically included both IHC(3+) and IHC(2+, equivocal)/FISH(+) tumors and received the same treatment. Differences in biology between these two tumor types, however, are poorly understood. Considering anti-HER2 drugs bind directly to HER2 protein on the cell surface, we hypothesized anti-HER2 therapies would be less effective in IHC(2+)/FISH(+) tumors than in IHC(3+) tumors, leading to differences in patient outcomes.

Methods
A total of 447 patients with HER2-positive invasive carcinoma who underwent curative surgery were retrospectively investigated. HER2 status was assessed in surgical specimens, except in patients who received neo-adjuvant chemotherapy, where biopsy specimens were employed.

Results
Age, tumor size, lymph node status and ER status were independent factors relating to disease-free-survival, but no difference was observed between IHC(3+) and IHC(2+)/FISH(+) tumors. Kaplan-Meier analysis found patient outcomes did not differ, even after stratifying into those that did (n = 314), or did not (n = 129), receive chemotherapy with anti-HER2 drugs. In 134 patients who received NAC, pathological complete response rates in IHC(3+) and IHC(2+)/FISH(+) tumors were 45% and 21%, respectively. Survival after developing metastasis was significantly shorter in the IHC(2+)/FISH(+) group.

Conclusions
The prognosis of patients with IHC(2+)/FISH(+) tumors did not differ from IHC(3+) tumors. However, the significance of HER2 protein overexpression in relation to treatment response remains unclear and warrants further investigations.