bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease
Authors: Sookoian Silvia , Salatino Adrian , Castaño Gustavo Osvaldo , Landa Maria Silvia , Fijalkowky Cinthia , Garaycoechea Martin , Pirola Carlos Jose 
Published: January 2020

ObjectiveWe aimed to characterise the liver tissue bacterial metataxonomic signature in two independent cohorts of patients with biopsy-proven non-alcoholic fatty liver disease (NAFLD) diagnosis, as differences in the host phenotypic features—from moderate to severe obesity—may be associated with significant changes in the microbial DNA profile.Design and methodsLiver tissue samples from 116 individuals, comprising of 47 NAFLD overweight or moderately obese patients, 50 NAFLD morbidly obese patients elected for bariatric surgery and 19 controls, were analysed using high-throughput 16S rRNA gene sequencing.ResultsLiver bacterial DNA profile significantly differs between morbidly obese and non-morbidly obese patients with NAFLD. Bacteroidetes (p=1.8e-18) and Firmicutes (p=0.0044) were over-represented in morbidly obese patients and Proteobacteria (p=5.2e-10)—specifically Gammaproteobacteria and Alphaproteobacteria, and Deinococcus-Thermus (p=0.00012)—were over-represented in the non-morbidly obese cohort. Cohort-specific analysis of liver microbial DNA signatures shows patterns linked to obesity. The imbalance in Proteobacteria (Alpha or Gamma) among non-morbidly obese patients, and Peptostreptococcaceae, Verrucomicrobia, Actinobacteria and Gamma Proteobacteria DNA among morbidly obese patients was associated with histological severity. Decreased amounts of bacterial DNA from the Lachnospiraceae family were associated with more severe histological features. Proteobacteria DNA was consistently associated with lobular and portal inflammation scores. Microbial DNA composition corresponded to predicted functional differences.ConclusionThis is the first comprehensive study showing that the liver tissue of NAFLD patients contains a diverse repertoire of bacterial DNA (up to 2.5×104read counts). The liver metataxonomic signature may explain differences in the NAFLD pathogenic mechanisms as well as physiological functions of the host.
Impairment of spermatogenesis and sperm motility by the high-fat diet-induced dysbiosis of gut microbes
Authors: Ding Ning , Zhang Xin , Zhang Xue Di , Jing Jun , Liu Shan Shan , Mu Yun Ping , Peng Li Li , Yan Yun Jing , Xiao Geng Miao , Bi Xin Yun , Chen Hao , Li Fang Hong , Yao Bing , Zhao Allan Z 
Published: January 2020

ObjectiveHigh-fat diet (HFD)-induced metabolic disorders can lead to impaired sperm production. We aim to investigate if HFD-induced gut microbiota dysbiosis can functionally influence spermatogenesis and sperm motility.DesignFaecal microbes derived from the HFD-fed or normal diet (ND)-fed male mice were transplanted to the mice maintained on ND. The gut microbes, sperm count and motility were analysed. Human faecal/semen/blood samples were collected to assess microbiota, sperm quality and endotoxin.ResultsTransplantation of the HFD gut microbes into the ND-maintained (HFD-FMT) mice resulted in a significant decrease in spermatogenesis and sperm motility, whereas similar transplantation with the microbes from the ND-fed mice failed to do so. Analysis of the microbiota showed a profound increase in genusBacteroidesandPrevotella, both of which likely contributed to the metabolic endotoxaemia in the HFD-FMT mice. Interestingly, the gut microbes from clinical subjects revealed a strong negative correlation between the abundance ofBacteroides-Prevotellaand sperm motility, and a positive correlation between blood endotoxin andBacteroidesabundance. Transplantation with HFD microbes also led to intestinal infiltration of T cells and macrophages as well as a significant increase of pro-inflammatory cytokines in the epididymis, suggesting that epididymal inflammation have likely contributed to the impairment of sperm motility. RNA-sequencing revealed significant reduction in the expression of those genes involved in gamete meiosis and testicular mitochondrial functions in the HFD-FMT mice.ConclusionWe revealed an intimate linkage between HFD-induced microbiota dysbiosis and defect in spermatogenesis with elevated endotoxin, dysregulation of testicular gene expression and localised epididymal inflammation as the potential causes.Trial registration numberNCT03634644.
Restoration of Temozolomide Sensitivity by PARP Inhibitors in Mismatch Repair Deficient Glioblastoma is Independent of Base Excision Repair
Authors: Higuchi Fumi , Nagashima Hiroaki , Ning Jianfang , Koerner Mara V.A. , Wakimoto Hiroaki , Cahill Daniel P. 
Published: January 2020

Abstract

Purpose:
Emergence of mismatch repair (MMR) deficiency is a frequent mechanism of acquired resistance to the alkylating chemotherapeutic temozolomide (TMZ) in gliomas. Poly(ADP-ribose) polymerase inhibitors (PARPi) have been shown to potentiate TMZ cytotoxicity in several cancer types, including gliomas. We tested whether PARP inhibition could re-sensitize MSH6-null MMR-deficient gliomas to TMZ, and assessed the role of the base excision repair (BER) DNA damage repair pathway in PARPi-mediated effects.

Experimental Design:
Isogenic pairs of MSH6 wild-type and MSH6-inactivated human glioblastoma (GBM) cells (including both IDH1/2 wild-type and IDH1 mutant), as well as MSH6-null cells derived from a patient with recurrent GBM were treated with TMZ, the PARPi veliparib or olaparib, and combination thereof. Efficacy of PARPi combined with TMZ was assessed in vivo. We used genetic and pharmacological approaches to dissect the contribution of BER.

Results:
While having no detectable effect in MSH6 wild-type GBMs, PARPi selectively restored TMZ sensitivity in MSH6-deficient GBM cells. This genotype-specific restoration of activity translated in vivo, where combination treatment of veliparib and TMZ showed potent suppression of tumor growth of MSH6-inactivated orthotopic xenografts, compared with TMZ monotherapy. Unlike PARPi, genetic and pharmacological blockage of BER pathway did not re-sensitize MSH6-inactivated GBM cells to TMZ. Similarly, CRISPR PARP1 knockout did not re-sensitize MSH6-inactivated GBM cells to TMZ.

Conclusions:
PARPi restoration of TMZ chemosensitivity in MSH6-inactivated glioma represents a promising strategy to overcome acquired chemoresistance caused by MMR deficiency. Mechanistically, this PARPi-mediated synthetic phenotype was independent of BER blockage and was not recapitulated by loss of PARP1.
Grãos sacralizados
Authors: Sulis Marcella , Melchior Myriam 
Published: January 2020

Em nossas pesquisas acerca de uma cultura brasileira do milho, notamos algumas dinâmicas que dizem respeito à assimilação social e aos significados simbólicos do milho no Brasil que ajudam a descortinar a sua importância como alimento de resistência associado a uma sacralidade pouco visível à historiografia oficial (ver Gastronomia, Cultura e Memória: por uma cultura brasileira do milho, organizado por Myriam Melchior, em 2017). Tal seria a difusão do milho em preparações culinárias no Brasil devida aos povos afrodescendentes que adaptaram o seu uso doméstico e ritualístico, desde o período colonial (ver A Cultura Alimentar Paulista: uma civilização do milho?, de Rafaela Basso, de 2014). Este dado parece ser um elemento-chave para compreender a sobrevivência do milho em preparações culinárias populares, tendo em vista que, durante o período colonial, o milho foi quase sempre desprezado pelo colonizador. Ademais, a utilização do milho nos rituais afro-indígenas rivalizava com os cultos cristãos onde o trigo era o alimento simbólico máximo, perfazendo o vínculo metafórico com o corpo sagrado de Cristo (ver o capítulo “Formação e dinâmica das religiões afro-brasileiras”, de Vagner Gonçalves da Silva, em Religião e Sociedade na América Latina, de 2010). Embora sejam raras as informações sobre as religiões originais dos povos nativos, sobretudo no que concerne à utilização de alimentos, é possível comparar algumas práticas ritualísticas atuais herdeiras das etnias indígenas e afrodescendentes com relatos do período colonial brasileiro. A partir desta comparação, encontramos algumas características semelhantes presentes nos rituais religiosos afro-indígenas que apontam para um traço de união importantíssimo à sobrevivência do milho na alimentação brasileira.
O estudo sobre a sacralidade do milho sinaliza para modos de transmissão de uma cultura alimentar envolta em embates vinculados às suas representações e potencialidades simbólicas e mágicas. Para tanto, utilizamos fontes bibliográficas no âmbito da história da alimentação, da antropologia cultural e da memória social. Também nos apoiamos em algumas investigações de artistas brasileiros contemporâneos que nos permitiram expandir as reflexões acerca do tema. Neste sentido, este estudo busca novas formas de se pensar e perceber as tradições alimentares cujos aspectos memoriais são difusos, rarefeitos ou, por vezes, pouco visíveis na historiografia gastronômica fundamentada por aspectos ambientais, econômicos ou meramente biológicos nos quais os alimentos e suas trajetórias são observados. Trata-se também de um estudo acerca dos significados e usos simbólicos e poéticos dos alimentos na existência humana.
A doçaria paulista no início do século XX
Authors: Scheliga Paola Biselli Ferreira 
Published: January 2020

Esta pesquisa discute a mudança de hábitos alimentares voltados ao consumo de doces no processo de urbanização da cidade de São Paulo entre o final do século XIX e o início do século XX.
Através de uma abordagem qualitativa, o estudo faz um levantamento bibliográfico teórico-reflexivo tanto dos autores basilares sobre a alimentação no Brasil, bem como acompanha historicamente a formação da doçaria nacional e seu desenvolvimento. Esse esforço culmina com um aprofundamento sobre a doçaria caipira com suas raízes já não mais comuns na cidade de São Paulo.
Por fim, através de uma abordagem quantitativa e também qualitativa, foram focalizados cinco livros de receitas publicados entre 1910 e 1930, como fontes para os estudos da alimentação com o objetivo de compreender a doçaria paulista no início do século XX. O resultado foi uma base de dados de 700 receitas para identificação dos principais ingredientes utilizados. Os livros selecionados foram: A sciencia no lar moderno (1912), Delícias das sinhás: receitas culinárias da segunda metade do século XIX e início do século XX (2007), Culinária tradicional do Vale do Paraíba (1992), A doceira paulista (1916), Guia prático da doceira (1930).
De acordo com a análise realizada é possível perceber uma forte influência da confeitaria tradicional portuguesa. A partir do levantamento de receitas realizado, foi possível perceber a predominância de ingredientes como a farinha de trigo, os ovos, a manteiga, a canela, o cravo e a amêndoa. Todos estes ingredientes são muito utilizados na doçaria tradicional portuguesa.
Poucas foram as referências encontradas nos livros que remetem aos ingredientes reconhecidos como base da alimentação caipira, como o milho, o amendoim, a mandioca, a abóbora, entre outros. Os estudos sobre o caipira são muito mais aprofundados em relação a seus hábitos culturais, sua formação étnica, peculiaridades sobre a sua linguagem do que sobre os hábitos alimentares propriamente ditos. Há uma carência de material específico sobre a doçaria caipira e isto está diretamente relacionado à perda de referências e tradições.
Mais do que definir quais as principais influências na culinária paulista do início do século XX, este trabalho traz a conclusão de que outros caminhos de pesquisa podem ser utilizados para estudos sobre cultura material e cultura alimentar brasileiras ainda pouco explorados. A busca por novas fontes de pesquisa pode trazer resultados diferentes do esperado e propiciar um novo entendimento sobre a formação cultural da sociedade paulistana.
Nurses’ experiences of informal coercion on adult psychiatric wards
Authors: Andersson Urban , Fathollahi Jafar , Gustin Lena Wiklund 
Published: January 2020

Background: Informal coercion, that is, situations where caregivers use subtle coercive measures to impose their will on patients, is common in adult psychiatric inpatient care. It has been described as ‘a necessary evil’, confronting nurses with an ethical dilemma where they need to balance between a wish to do good, and the risk of violating patients’ dignity and autonomy. Aim: To describe nurses’ experiences of being involved in informal coercion in adult psychiatric inpatient care. Research design: The study has a qualitative, inductive design. Participants and research context: Semi-structured interviews with 10 Swedish psychiatric nurses were analysed with qualitative content analysis. Ethical considerations: The study was performed in accordance with the Declaration of Helsinki. In line with the Swedish Ethical Review Act, it was also subject to ethical procedures at the university. Findings: Four domains comprise informal coercion as a process over time. These domains contain 11 categories focusing on different experiences involved in the process: Striving to connect, involving others, adjusting to the caring culture, dealing with laws, justifying coercion, waiting for the patient, persuading the patient, negotiating with the patient, using professional power, scrutinizing one’s actions and learning together. Discussion: Informal coercion is associated with moral stress as nurses might find themselves torn between a wish to do good for the patient, general practices and ‘house rules’ in the caring culture. In addition, nurses need to be aware of the asymmetry of the caring relationship, in order to avoid compliance becoming a consequence of patients subordinating to nurse power, rather than a result of mutual understanding. Reflections are thus necessary through the process to promote mutual learning and to avoid violations of patients’ dignity and autonomy. Conclusion: If there is a need for coercion, that is, if the coercion is found to be an ‘unpleasant good’, rather than ‘necessary evil’ considering the consequences for the patient, it should be subject to reflecting and learning together with the patient.
Endovascular Treatment of Long Superficial Femoral Artery–Chronic Total Occlusions Using the Gogo Catheter With IVUS Via a Popliteal Puncture Method Is Effective, Safe, and Useful
Authors: Nakamura Shinichi , Rokutanda Taku , Kurokawa Hirofumi , Onoue Yoshirou 
Published: January 2020

Objectives: We aimed to investigate the usefulness of inserting a 6Fr sheath guided by duplex ultrasonography via a popliteal artery puncture. We also aimed to demonstrate endoluminal tracking using a retrograde approach using the Gogo catheter with intravascular ultrasound (IVUS). Background: The bidirectional approach is useful for increasing the success rate of the procedure for long superficial femoral artery–chronic total occlusions (SFA-CTOs). However, this procedure becomes somewhat complicated. Since the proximal blood vessel diameter is clearly larger than the distal end of the CTO and the body surface duplex guide can also be used in the proximal part, it is easier to introduce a retrograde guidewire (GW) into the proximal end. Methods: We performed endovascular treatment for long SFA-CTOs with a Gogo catheter + IVUS guide in 31 consecutive cases (male 20/female 11; mean age, 75.6 ± 7.6) from May 2017 to November 2018. We advanced the IVUS until the true lumen could be confirmed and advanced the Gogo catheter toward the IVUS for reinforcement. We attempted to approach the long CTO by repeating this procedure. We named this procedure the GIP method (GIP: Gogo catheter with IVUS via a popliteal puncture). Hemostasis of the popliteal artery was achieved using a commercially available compression hemostatic kit (Tometa-kun, XEMEX, Japan). Results: Successful revascularization was achieved in all cases (in 2 cases, a femoral artery puncture was added, and a bidirectional approach was used, and in 1 case, a CROSSER system was used). On average, the fluoroscopy time was 42.2 ± 30.4 minutes, radiation dose 93.7 ± 78.7 mGy, and amount of contrast medium used 15.0 ± 9.6 mL. The procedure time was defined as from the start of the popliteal artery puncture to the time the GW passed through the CTO lesion, including the posture transformation time from prone to the supine position. The procedure time was 42.1 ± 40.2 minutes. There were no major adverse events or other major complications, such as a distal embolism, rupture of the CTO lesion, arteriovenous fistula, or major hematoma requiring a transfusion or surgical treatment. Only 2 small hematomas occurred at the popliteal artery puncture site. The patients were treated conservatively and were discharged as usual. Conclusions: Endovascular treatment of long SFA-CTOs via the popliteal approach was effective and safe. Using the GIP method to address long SFA-CTOs is recommended.
Update on covered endovascular reconstruction of the aortic bifurcation
Authors: Reijnen Michel MPJ 
Published: January 2020

Objective The covered endovascular reconstruction of the aortic bifurcation (CERAB) technique was introduced in 2009 in order to provide an anatomically and physiologically optimal endovascular reconstruction of the aortic bifurcation. Method In the current review, all available evidence on this technique was summarized. Results In vitro studies have shown a more favorable geometry of CERAB compared to kissing stents, leading to better local flow conditions. The results of CERAB are at least as good as those achieved with kissing stents in a more complex group of treated patients. The mid-term patency rates approach those of surgical reconstruction. Initial data show that the technique can also be used in combination with chimney grafts in order to preserve side branches. Conclusion CERAB has proven to be the most optimal endovascular treatment option for aorto-iliac occlusive disease with regard to geometry and flow and is related to promising clinical outcomes. Prospective and comparative trials are necessary to elucidate the most optimal treatment algorithm for patients with aorto-iliac occlusive disease.
Early Addition of Parathyroid Hormone–Related Peptide Regulates the Hypertrophic Differentiation of Mesenchymal Stem Cells
Authors: Rajagopal Karthikeyan , Ramesh Sowmya , Madhuri Vrisha 
Published: January 2020

Objective Chondrogenic differentiation of mesenchymal stem cells (MSCs) into hyaline cartilage is complicated by terminal hypertrophic differentiation. In growth plate, parathyroid hormone–related peptide (1-34) (PTHrP) plays a crucial role in maintaining chondrocytes in their proliferation state by counteracting the hypertrophic differentiation. This study aims to test the effect of PTHrP supplementation at different time points on chondrogenic differentiation of MSCs and assess the final quality of differentiated chondrocytes. Methods Human periosteum and bone marrow MSCs isolated from 3 patient samples (donor unmatched) were characterized by flow cytometry and multilineage differentiation. The cells were differentiated into chondrocytes in the presence of transforming growth factor-β (TGF-β) and the PTHrP (1-34) was added from 4th or 14th day of culture. The outcome was analyzed by histology, immunohistochemistry, and gene expression. Results Flow cytometry and multilineage differentiation confirmed that the cells isolated from periosteum and bone marrow exhibited the phenotype of MSCs. During chondrogenic differentiation, pellets that received PTHrP from the 4th day of culture showed a significant reduction in hypertrophic markers (COL10A1 and RUNX) than the addition of PTHrP from the 14th day and TGF-β alone treated samples. Furthermore, 4th day supplementation of PTHrP significantly improved the expression of cartilage-specific markers (COL2A1, SOX9, ACAN) in both periosteum and bone marrow-derived MSCs. Histology and immunostaining with collagen type X data corroborated the gene expression outcomes. Conclusion The outcome showed that supplementing PTHrP from the 4th day of chondrogenic differentiation produced better chondrocytes with less hypertrophic markers in both bone marrow and periosteal-derived MSCs.
Transcriptomic analyses of Pinus koraiensis under different cold stresses
Authors: Wang Fang , Chen Song , Liang Deyang , Qu Guan-Zheng , Chen Su , Zhao Xiyang 
Published: January 2020

Abstract
Background
Pinus koraiensis is an evergreen tree species with strong cold resistance. However, the transcriptomic patterns in response to cold stress are poorly understood for P. koraiensis. In this study, global transcriptome profiles were generated for P. koraiensis under cold stress (− 20 °C) over time by high-throughput sequencing.

Results
More than 763 million clean reads were produced, which assembled into a nonredundant data set of 123,445 unigenes. Among them, 38,905 unigenes had homology with known genes, 18,239 were assigned to 54 gene ontology (GO) categories and 18,909 were assigned to 25 clusters of orthologous groups (COG) categories. Comparison of transcriptomes of P. koraiensis seedlings grown at room temperature (20 °C) and low temperature (− 20 °C) revealed 9842 differential expressed genes (DEGs) in the 6 h sample, 9250 in the 24 h sample, and 9697 in the 48 h sample. The number of DEGs in the pairwise comparisons of 6 h, 24 h and 48 h was relatively small. The accuracy of the RNA-seq was validated by analyzing the expression patterns of 12 DEGs by quantitative real-time PCR (qRT-PCR). In this study, 34 DEGs (22 upregulated and 12 downregulated) were involved in the perception and transmission of cold signals, 96 DEGs (41 upregulated and 55 downregulated) encoding 8 transcription factors that regulated cold-related genes expression, and 27 DEGs (17 upregulated and 10 downregulated) were involved in antioxidant mechanisms in response to cold stress. Among them, the expression levels of c63631_g1 (annexin D1), c65620_g1 (alpha-amylase isozyme 3C), c61970_g1 (calcium-binding protein KIC), c51736_g1 (ABA), c58408_g1 (DREB3), c66599_g1 (DREB3), c67548_g2 (SOD), c55044_g1 (CAT), c71938_g2 (CAT) and c11358_g1 (GPX) first increased significantly and then decreased significantly with the extension of stress time.

Conclusions
A large number of DEGs were identified in P. koraiensis under cold stress, especially the DEGs involved in the perception and transmission of cold signals, the DEGs encoding TFs related to cold regulation and the DEGs removing ROS in antioxidation mechanisms. The transcriptome and digital expression profiling of P. koraiensis could facilitate the understanding of the molecular control mechanism related to cold responses and provide the basis for the molecular breeding of conifers.