bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geology along the Bedretto tunnel: kinematic and geochronological constraints on the evolution of the Gotthard Massif (Central Alps)
Authors: Rast Markus , Galli Andrea , Ruh Jonas B. , Guillong Marcel , Madonna Claudio 
Published: March 2022

AbstractThe unlined Bedretto tunnel crosses large parts of the pre-Triassic basement of the Gotthard massif (Central Alps), giving the possibility to study late-Variscan plutonic rocks (Rotondo granite) and their Caledonian (poly-)metamorphic host rocks (Tremola and Prato series). The Rotondo granite consists mostly of an equigranular, fine-grained granite and to a lesser extent of a porphyritic granite. Commonly, the Rotondo granite is massive or only slightly foliated. Ductile deformation is localized along discrete shear zones composed of granitic or quartz-biotite-rich lithologies. This paper reviews the geology of the Bedretto tunnel with emphasis on the Rotondo granite and presents constraints based on kinematic, microstructural, and U–Pb geochronological evidence, which can be summarized as follows: (1) Both granitic and quartz-biotite-rich shear zones (QB-SZ) in the Rotondo granite generally dip moderately to steeply towards north and are related to top-to-south reverse shearing, indicating south-verging backthrusting during the exhumation of the Gotthard massif. (2) Zircons from both the equigranular and porphyritic Rotondo granite show overlapping $${}^{206}\hbox {Pb}/{}^{238}\hbox {U}$$

206

Pb
/

238

U

-age ranges of 285–319 Ma and 280–335 Ma, respectively, which indicate that both are part of the same late-Variscan magmatic episode. Almost no older inherited cores are reported. (3) In zircons from a QB-SZ, $$30\%$$

30
%

of the concordant age spots scatter between 339 and 589 Ma. This suggests that the parent material of the QB-SZ is unrelated to the magmatic episode that formed the Rotondo granite, but rather that the QB-SZ represent sheared xenoliths within the granite.
Minor cutting edge force contribution in wood bandsawing
Authors: Meulenberg Vanessa , Ekevad Mats , Svensson Mikael , Broman Olof 
Published: March 2022

AbstractAs the sawmill industry is moving towards thinner bandsaws for higher yields, it is important to study the cutting force in more detail. The cutting force can be split into two zones. Zone I concerns the force on the major cutting edge as well as the friction force on the major first flank. Zone II considers the forces on the minor cutting edges as well as the friction forces on the minor first flanks. Zone II cutting can significantly affect the cutting force and has not been studied in great detail. Frozen, non-frozen and dry heartwood of Norway spruce and Scots pine were cut using different tooth geometries and the cutting force was measured. The major cutting edge, clearance, band thickness, minor cutting edge angle and minor cutting edge clearance angle were investigated. The y-intercept of the cutting force–width graph was used as the Zone II force (at this point the Zone I forces are assumed to be zero). The Zone II force contribution to the cutting force was studied. The results show that frozen wood has less elastic spring-back and therefore less Zone II cutting. Dried wood showed a significantly higher degree of Zone II cutting (55−75% contribution to the cutting force). Changing the major cutting edge from 2.87 mm to 1.6 mm resulted in 10–15% higher Zone II force contributions.
Comparing the relative and absolute effect of erenumab: is a 50% response enough? Results from the ESTEEMen study
Authors: Ornello Raffaele , Baraldi Carlo , Guerzoni Simona , Lambru Giorgio , Andreou Anna P. , Raffaelli Bianca , Gendolla Astrid , Barbanti Piero , Aurilia Cinzia , Egeo Gabriella , Cevoli Sabina , Favoni Valentina , Vernieri Fabrizio , Altamura Claudia , Russo Antonio , Silvestro Marcello , Valle Elisabetta Dalla , Mancioli Andrea , Ranieri Angelo , Alfieri Gennaro , Latysheva Nina , Filatova Elena , Talbot Jamie , Cheng Shuli , Holle Dagny , Scheffler Armin , Nežádal Tomáš , Čtrnáctá Dana , Šípková Jitka , Matoušová Zuzana , Casalena Alfonsina , Maddestra Maurizio , Viola Stefano , Affaitati Giannapia , Giamberardino Maria Adele , Pistoia Francesca , Reuter Uwe , Sacco Simona 
Published: March 2022

Abstract
Background
Monoclonal antibodies acting on the calcitonin gene-related peptide (CGRP) or its receptor have changed migraine preventive treatment. Those treatments have led to reconsidering the outcomes of migraine prevention. Available data mostly considered benefits in terms of relative efficacy (percent or absolute decrease in monthly migraine days [MMDs] or headache days compared with baseline). However, not enough attention has been paid to residual MMDs and/or migraine-related disability in treated patients. In the present study, we aimed at comparing the relative and absolute efficacy of erenumab.

Methods
ESTEEMen was a collaborative project among 16 European headache centers which already performed real-life data collections on patients treated with erenumab for at least 12 weeks. For the present study, we performed a subgroup analysis on patients with complete data on MMDs at baseline and at weeks 9-12 of treatment. Starting from efficacy thresholds proposed by previous literature, we classified patients into 0-29%, 30-49%, 50-74%, and ≥75% responders according to MMD decrease from baseline to weeks 9-12 of treatment. For each response category, we reported the median MMDs and Headache Impact test-6 (HIT-6) scores at baseline and at weeks 9-12. We categorized the number of residual MMDs at weeks 9-12 as follows: 0-3, 4-7, 8-14, ≥15. We classified HIT-6 score into four categories: ≤49, 50-55, 56-59, and ≥60. To keep in line with the original scope of the ESTEEMen study, calculations were performed in men and women.

Results
Out of 1215 patients, at weeks 9-12, 381 (31.4%) had a 0-29% response, 186 (15.3%) a 30-49% response, 396 (32.6%) a 50-74% response, and 252 (20.7%) a ≥75% response; 246 patients (20.2%) had 0-3 residual MMDs, 443 (36.5%) had 4-7 MMDs, 299 (24.6%) had 8-14 MMDs, and 227 (18.7%) had ≥15 MMDs. Among patients with 50-74% response, 246 (62.1%) had 4-7 and 94 (23.7%) 8-14 residual MMDs, while among patients with ≥75% response 187 (74.2%) had 0-3 and 65 (25.8%) had 4-7 residual MMDs.

Conclusions
The present study shows that even patients with good relative response to erenumab may have a clinically non-negligible residual migraine burden. Relative measures of efficacy cannot be enough to thoroughly consider the efficacy of migraine prevention.
RETRACTED ARTICLE:Parecoxib inhibits esophageal squamous cell carcinoma progression via the PDK1–AKT pathway
Authors: Huang Han-Ming , Huang Xiao-Yu , Wu Shao-Ping , Chen Can-Keng , He Xin-Hua , Zhang Yong-Fa 
Published: March 2022

Abstract
Background
Parecoxib plays an important role in inhibition of human cancer. However, the effect of parecoxib on esophageal squamous cell carcinoma (ESCC) is still not well known. The purpose of this study was to investigate the effect of parecoxib on ESCC and its underlying mechanism.

Methods
RNA-sequence analysis was performed to identify functional alterations and mechanisms. Cell cycle, proliferation, invasion, and migration were assessed using flow cytometry, CCK-8 assay, colony formation, transwell, and wound healing assays. Extracellular matrix (ECM) degradation was detected by substrate gel zymography and 3D cell culture assay. Western blotting was used to detect parecoxib-dependent mechanisms involving cell cycle, proliferation, invasion, and migration. Tumor formation in vivo was detected by mouse assay.

Results
Functional experiments indicated that parecoxib induced ESCC cell cycle arrest in G2 phase, and inhibited cell proliferation, invasion, and migration in vitro. Western blotting revealed that parecoxib downregulated the phosphorylation levels of AKT and PDK1, as well as the expression of the mutant p53, cyclin B1, and CDK1, while upregulating p21waf1. Parecoxib inhibited matrix metalloproteinase-2 (MMP2) secretion and invadopodia formation, which were related to ECM degradation. Furthermore, we found that parecoxib suppressed ESCC growth in heterotopic tumor models.

Conclusion
Parecoxib inhibits ESCC progression, including cell cycle, proliferation, invasion, and migration, via the PDK1–AKT signaling pathway.
Environmental quality standards for diclofenac derived under the European water framework directive: 2. Avian secondary poisoning
Authors: Peters A. , Crane M. , Merrington G. , Ryan Jim 
Published: March 2022

AbstractDiclofenac is a nonsteroidal anti-inflammatory human and veterinary medicine widely detected in European surface waters, especially downstream from Wastewater Treatment Plants. With some notable exceptions, veterinary uses of diclofenac in Europe are greatly restricted, so wastewater is the key Europe-wide exposure route for wildlife that may be exposed via the aquatic environment. Proposed Environmental Quality Standards (EQS) which include an assessment of avian exposure from secondary poisoning are under consideration by the European Commission (EC) to support the aims of the Water Framework Directive (WFD). In this paper we summarise information on avian toxicity plus laboratory and field evidence on diclofenac bioaccumulation and bioconcentration in avian food items. A safe diclofenac threshold value for birds of 3 μg kg−1 wet weight in food was previously derived by the European Medicines Agency and should be adopted as an EQS under the WFD to maintain consistency across European regulations. This value is also consistent with values of 1.16–3.99 µg kg−1diet proposed by the EC under the WFD. Water-based EQS of 5.4 or 230 ng L−1 in freshwater are derived from these dietary standards, respectively, by the EC and by us, with the large difference caused primarily by use of different values for bioaccumulation. A simple assessment of potential water-based EQS compliance is performed for both of these latter values against reported diclofenac concentrations in samples collected from European freshwaters. This shows that exceedances of the EC-derived EQS would be very widespread across Europe while exceedances of the EQS derived by us are confined to a relatively small number of sites in only some Member States. Since there is no evidence for any declines in European waterbird populations associated with diclofenac exposure we recommend use of conservative EQS of 3 µg kg−1diet or 230 ng L−1 in water to protect birds from diclofenac secondary poisoning through the food chain.
Spatiotemporal distribution patterns and risk characteristics of heavy metal pollutants in the soil of lead–zinc mines
Authors: Cao Jie , Xie Cheng-yu , Hou Zhi-ru 
Published: March 2022

Abstract
Background
The current soil environmental assessment system is inadequate in terms of the spatiotemporal distribution of heavy metal pollutants. This study employed the numerical simulation technique to predict spatiotemporal distribution patterns of heavy metals within 50 days and to assess the soil risk characteristics of heavy metal pollution near a lead–zinc mine in Hunan Province, China.

Results
The spatiotemporal distribution results indicate that the soil in the sewage plant and mining areas served as the pollution center, exhibiting a ladder-shaped pollution diffusion trend outward. When the pollution migration time reached 20 days, pollutant migration and changes tended to remain stable, high-pollution areas exhibited no drastic changes within 10 m, and low-pollution and medium-pollution areas revealed obvious changes. Moreover, the low-pollution area width approached 2 m, the depth reached 2 m, the medium-pollution area width was close to 2.5 m, and the depth approached 4 m. The percentage of areas containing lead–zinc mine soil with high to extremely high risks reached 82.88%, and extremely high-risk farmland, mining and residential areas accounted for up to 100%, 95% and 90%, respectively, of the total area. Among the pollution sources, high-risk and extremely high-risk areas in regard to heavy metal Cd accounted for 13.51 and 49.55%, respectively, of the total area.

Conclusion
This study provides new insights into the migration patterns and risk characteristics of pollutants to address soil environmental assessment system problems.
High miRNA-378 expression has high diagnostic values for pulmonary tuberculosis and predicts adverse outcomes
Authors: Sun Xiaolu , Liu Kai , Zhao Yan , Zhang Tianhua 
Published: March 2022

Abstract
Background
Pulmonary tuberculosis (TB) is a chronic infectious disease. microRNA (miR)-378 is involved in TB diagnosis. This study explored the effects of miR-378 on TB patients.

Methods
A total of 126 TB patients were selected, including 63 active TB and 63 latent TB, with 62 healthy subjects as controls. Serum miR-378 expression was detected. The diagnostic value of miR-378 in TB was analyzed using the ROC curve. Immune inflammatory factor levels were detected and their correlations with miR-378 expression were analyzed. The drug resistance of active TB patients was recorded after standard treatment. miR-378 expression in drug-resistant TB patients was detected. The effects of miR-378 on adverse outcome incidence were analyzed.

Results
miR-378 expression was highly expressed in TB and the expression was higher in the active group than the latent group. Serum miR-378 expression > 1.490 had high sensitivity and specificity in TB diagnosis. miR-378 expression was correlated with TB clinical indexes. IL-4, IL-6, and IL-1β levels were highly expressed, while IFN-γ, TNF-α, and IL-12 levels were lowly expressed in TB patients. Serum miR-378 level in the active group was positively correlated with serum IL-4, IL-6, and IL-1β, and negatively correlated with serum IFN-γ, TNF-α, and IL-12 concentrations. miR-378 expression was downregulated in the TB treated, single (SDR TB) and multi-drug resistance (MDR TB) groups, the miR-378 expression in SDR TB and MDR TB groups was higher than the TB treated group and lower in the SDR TB group than the MDR TB group. High miR-378 expression predicted higher adverse outcome incidence.

Conclusions
High miR-378 expression assisted TB diagnosis and predicted adverse outcomes.
Growth hormone receptor gene influences mitochondrial function and chicken lipid metabolism by AMPK-PGC1α-PPAR signaling pathway
Authors: Yang Minmin , Hu Bowen , Sun Donglei , Zhao Changbin , Wei Haohui , Li Dajian , Liao Zhiying , Zhao Yongxia , Liang Jinping , Shi Meiqing , Luo Qingbin , Nie Qinghua , Zhang Xiquan , Zhang Dexiang , Li Hongmei 
Published: March 2022

Abstract
Background
Adipose tissue is an important endocrine and energy-storage organ in organisms, and it plays a crucial role in the energy-metabolism balance. Previous studies have found that sex-linked dwarf (SLD) chickens generally have excessively high abdominal fat deposition during the growing period, which increases feeding costs. However, the underlying mechanism of this fat deposition during the growth of SLD chickens remains unknown.

Results
The Oil Red O staining showed that the lipid-droplet area of SLD chickens was larger than that of normal chickens in E15 and 14d. Consistently, TG content in the livers of SLD chickens was higher than that of normal chickens in E15 and 14d. Further, lower ΔΨm and lower ATP levels and higher MDA levels were observed in SLD chickens than normal chickens in both E15 and 14d. We also found that overexpression of GHR reduced the expression of genes related to lipid metabolism (AMPK, PGC1α, PPARγ, FAS, C/EBP) and oxidative phosphorylation (CYTB, CYTC, COX1, ATP), as well as reducing ΔΨm and ATP levels and increasing MDA levels. In addition, overexpression of GHR inhibited fat deposition in CPPAs, as measured by Oil Red O staining. On the contrary, knockdown of GHR had the opposite effects in vitro.

Conclusions
In summary, we demonstrate that GHR promotes mitochondrial function and inhibits lipid peroxidation as well as fat deposition in vivo and in vitro. Therefore, GHR is essential for maintaining the stability of lipid metabolism and regulating mitochondrial function in chicken.
Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks
Authors: Cherchame Emeline , Guillier Laurent , Lailler Renaud , Vignaud Marie-Leone , Jourdan-Da Silva Nathalie , Le Hello Simon , Weill François-Xavier , Cadel-Six Sabrina 
Published: March 2022

Abstract
Background
Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirmed human cases. Clustering studies by single nucleotide polymorphism (SNP) core-genome phylogenetic analysis of outbreaks due to these major serovars are simplified by the availability of many complete genomes in the free access databases. This is not the case for outbreaks due to less common serovars, such as Welikade, for which no reference genomes are available. In this study, we propose a method to solve this problem. We propose to perform a core genome MLST (cgMLST) analysis based on hierarchical clustering using the free-access EnteroBase to select the most suitable genome to use as a reference for SNP phylogenetic analysis. In this study, we applied this protocol to a retrospective analysis of a Salmonella enterica serovar Welikade (S. Welikade) foodborne outbreak that occurred in France in 2016. Finally, we compared the cgMLST and SNP analyses. SNP phylogenetic reconstruction was carried out considering the effect of recombination events identified by the ClonalFrameML tool. The accessory genome was also explored by phage content and virulome analyses.

Results
Our findings revealed high clustering concordance using cgMLST and SNP analyses. Nevertheless, SNP analysis allowed for better assessment of the genetic distance among strains. The results revealed epidemic clones of S. Welikade circulating within the poultry and dairy sectors in France, responsible for sporadic and non-sporadic human cases between 2012 and 2019.

Conclusions
This study increases knowledge on this poorly described serovar and enriches public genome databases with 42 genomes from human and non-human S. Welikade strains, including the isolate collected in 1956 in Sri Lanka, which gave the name to this serovar. This is the first genomic analysis of an outbreak due to S. Welikade described to date.
DNA methylation changes in cord blood and the developmental origins of health and disease – a systematic review and replication study
Authors: Akhabir Loubna , Stringer Randa , Desai Dipika , Mandhane Piush J , Azad Meghan B , Moraes Theo J , Subbarao Padmaja , Turvey Stuart E , Paré Guillaume , Anand Sonia S. ,   for the NutriGen Alliance, Anand Sonia S. , Atkinson Stephanie A. , Azad Meghan B. , Becker Allan B. , Brook Jeffrey , Denburg Judah A. , Desai Dipika , de Souza Russell J. , Gupta Milan , Kobor Michael , Lefebvre Diana L. , Lou Wendy , Mandhane Piushkumar J. , McDonald Sarah , Mente Andrew , Meyre David , Moraes Theo J. , Morrison Katherine , Paré Guillaume , Sears Malcolm R. , Subbarao Padmaja , Teo Koon K. , Turvey Stuart E. , Wilson Julie , Yusuf Salim , Atkinson Stephanie , Wahi Gita , Zulyniak Michael A. 
Published: March 2022

AbstractBackgroundEnvironmental exposuresin uterowhich modify DNA methylation may have a long-lasting impact on health and disease in offspring. We aimed to identify and replicate previously published genomic loci where DNA methylation changes are attributable toin uteroexposures in the NutriGen birth cohort studies Alliance.MethodsWe reviewed the literature to identify differentially methylated sites of newborn DNA which are associated with the following five traits of interest maternal diabetes, pre-pregnancy body mass index (BMI), diet during pregnancy, smoking, and gestational age. We then attempted to replicate these published associations in the Canadian Healthy Infant Longitudinal Development (CHILD) and the South Asian birth cohort (START) cord blood epigenome-wide data.ResultsWe screened 68 full-text articles and identified a total of 17 cord blood epigenome-wide association studies (EWAS) of the traits of interest. Out of the 290 CpG sites reported, 19 were identified in more than one study; all of them associated with maternal smoking. In CHILD and START EWAS, thousands of sites associated with gestational age were identified and maintained significance after correction for multiple testing. In CHILD, there was differential methylation observed for 8 of the published maternal smoking sites. No other traits tested (i.e., folate levels, gestational diabetes, birthweight) replicated in the CHILD or START cohorts.ConclusionsMaternal smoking during pregnancy and gestational age are strongly associated with differential methylation in offspring cord blood, as assessed in the EWAS literature and our birth cohorts. There are a limited number of reported methylation sites associated in more than two independent studies related to pregnancy. Additional large studies of diverse populations with fine phenotyping are needed to produce robust epigenome-wide data in order to further elucidate the effect of intrauterine exposures on the infants’ methylome.
Automatic identification and annotation of MYB gene family members in plants
Authors: Pucker Boas 
Published: March 2022

Abstract
Background
MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies.

Results
A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator.

Conclusions
This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.