bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Relationship between Serum IGF-1 and BMI by Age in the Long Life Family Study
Authors: Sherlala Rehab A. , Kammerer Candace M. , Kuipers Allison L. , Wojczynski Mary K. , Ukraintseva Svetlana V. , Feitosa Mary F. , Mengel-From Jonas , Zmuda Joseph M. , Minster Ryan L. 
Published: July 2020

AbstractBackgroundSerum levels of insulin-like growth factor 1 (IGF-1) and body mass index (BMI) are both associated with susceptibility to age-related diseases. Reports on the correlation between them have been conflicting, with both positive to negative correlations reported. However, the age ranges of the participants varied widely among these studies.MethodsUsing data on 4,241 participants (aged 24–110) from the Long Life Family Study, we investigated the relationship between IGF-1 and BMI by age groups using regression analysis.ResultsWhen stratified by age quartile, the correlation between IGF-1 and BMI varied: in the 1st quartile (Q1, 24 y–58 y) the correlation was negative (r = −0.1, P = 0.0008); in Q2 (59 y– 66 y) it was negative (r = −0.035) but non-significant; in Q3 (67 y–86 y) it was positive (r = 0.045) but non-significant; and in Q4 (87 y–110 y) the correlation was positive (r = 0.14, P < 0.0001). This pattern did not differ by sex. We observed a similar age-related pattern between IGF-1 and BMI among participants in the third National Health and Nutritional Examination Survey.ConclusionsOur results, that the relationship between IGF-1 and BMI differs by age, may explain some of the inconsistency in reports about their relationship and encourage additional studies to understand the mechanisms underlying it.
Hydroxychloroquine has no effect on SARS-CoV-2 load in nasopharynx of patients with mild form of COVID-19
Authors: Komissarov Alexey , Molodtsov Ivan , Ivanova Oxana , Maryukhnich Elena , Kudryavtseva Svetlana , Mazus Alexey , Nikonov Evgeniy , Vasilieva Elena 
Published: July 2020

AbstractDue to the constantly growing numbers of COVID-19 infections and death cases attempts were undertaken to find drugs with anti SARS-CoV-2 activity among ones already approved for other pathologies. In the framework of such attempts, in a number of in vitro, as well as in vivo, models it was shown that hydroxychloroquine (HCQ) has an effect against SARS-CoV-2. While there was not enough clinical data to support the use of HCQ, several countries including Russia have included HCQ in treatment protocols for infected patients and for prophylactic. Here, we evaluated the SARS-CoV-2 RNA in nasopharynx swabs from infected patients in mild conditions and compared the viral RNA load dynamics between patients receiving HCQ and control group without antiviral pharmacological therapy. We found statistically significant relationship between maximal RNA quantity and patients’ deteriorating medical conditions, as well as confirmed the arterial hypertension to be a risk factor for people with COVID-19. However, we showed that HCQ therapy neither shortened the viral shedding period nor reduced the virus RNA load.
Quantitative Epithermal Neutron Activation Analysis of Seven Micro Elements in Breast Milk of Lactating Mothers from the Central region of Ghana
Authors: Aboh Irene Korkoi , Vowotor Michael K. , Druye Andrews Adjei 
Published: July 2020

AbstractBackgroundEpithermal instrumental neutron activation analysis (EINAA) technique is used for the determination and estimation of the concentration levels of micronutrients such as Sodium (Na), Magnesium (Mg), Potassium (K), Calcium (Ca), Manganese (Mn), Copper (Cu) and Iodine (I) in breastmilk.AimTo examine the concentration of seven micro elements in the breastmilk of lactating mother who were exclusively breastfeeding.MethodsThis study employed quantitative experimental research where 27 lactating mothers voluntarily participated in the study from two health facilities in the Cape Coast Metropolitan area. Data was collected over a period of four weeks. A three millimetre (3mm) thick of flexible boron was used to cut off thermal neutrons in order to assess epithermal neutrons. This was done to create an activation energy which examines the amount of the 7 micro nutrients in the breastmilk. The standard reference materials used were the International Atomic Energy Agency (IAEA)-336; IAEA-407, IAEA-350 and National Institute of Standard and Technology (NIST) USA SRM 1577b. The Relative standardization method was used in the quantification of the elements.ResultsThe study achieved about 94.7% accuracy. The estimated health risk calculated showed that the concentrations of chlorine (Cl) and iodine (I) were high in the order I > Cl with all very far above the maximum Upper Limit (UL) of the daily Recommended Dietary Allowance (RDA) for all life stages except for children below 8 years.ConclusionMn is found in very high quantities in the diet consumed by the parents of babies. These children could be exposed to metabolic disorders or unexplained diseases in future without knowing their origin.
The Phase Shift Correlation function uncovers periodic Ulcerative Colitis microbiome relationships without temporal sampling
Authors: Brown Robert E. , Arlova Alena , Gillevet Patrick M. 
Published: July 2020

AbstractCorrelation analysis is a fundamental technique to determine potential relationships within biological processes. However, many biological processes have been shown to function in a periodic manner. When modeling correlations, the fluctuations that are associated with periodicity cause significant issues. We have implemented a Phase Shift Correlation (PSC) algorithm, with a corresponding value PSCrho, to address the periodicity and phase variance associated with features that vary with the same frequency -- but are phase shifted. The phase shift could well indicate causality with one feature’s quantitative change leading to the change in the other feature.We applied the PSC algorithm to Ulcerative Colitis (UC) microbiome data and compared the resulting feature relationships with the equivalent Spearman correlation function results. PSC located many instances of higher phase shifted correlations, where the corresponding Pearson correlation was low.
Profiling the intratumoral immune landscapes of primary and syngeneic Kras-driven sarcoma mouse models
Authors: Gutierrez Wade R. , Scherer Amanda , McGivney Gavin R. , Knepper-Adrian Vickie , Laverty Emily A. , Roughton Grace , Dodd Rebecca D. 
Published: July 2020

ABSTRACTThe introduction of immunotherapy has revolutionized cancer treatment and fueled interest in the immune cell composition of preclinical tumor models. Both genetically-engineered mouse models and syngeneic cell transplant approaches use immunocompetent mice to study mechanisms driving immunotherapy response and resistance. Due to their rapid and reproducible nature, there has been an expanded interest in developing new syngeneic tools from established primary tumor models. However, there are few analyses directly comparing the immune profiles of primary models with their derived syngeneic counterparts. Here we report comprehensive immunophenotyping of primary tumors from two well-established sarcoma models and four syngeneic allografts derived from these models. We observed that cell lines derived from the same type of genetically engineered primary tumor form allografts with significantly different levels of immune infiltration and intratumoral immune cell composition. Most notable are the differences in the T cell compartment of the syngeneic models, including CD4+ T cell, CD8+ T cell, and regulatory T cell populations – each of which have well-documented roles in tumor response to immunotherapy. Our findings highlight the importance of thorough characterization of syngeneic models prior to their use in preclinical studies in order to maintain scientific rigor and to increase the translatability of findings from bench to bedside.
Trantrace: a reliable, traceable, and collaborative solution to streamline the translation of emerging biomedical resources
Authors: Su Min , Wang Zhaohong , Li Mengyu , Ye Weixing , Chen Peter , Huang Mo , He Zili , Xia Chaoran , Cui Jie , Liu Rui , Wang Congmao 
Published: July 2020

AbstractBackgroundPrecision medicine is gaining popularity in routine health care, which heavily relies on the interpretation of emerging biomedical databases and professional guidelines. Translation of those biomedical materials, that is crucial to deliver research discovery to health interventions in non-native English-speaking countries, remains a large amount of work for biomedical practitioners.ResultsWe presented an application called Trantrace to facilitate the routine of large-scale long-running translation. Especially for the case that many people joined multiple translation projects, it has a rigorous task division and cooperation process: assignment, translation, review, release, and iteration. Trantrace empowers users to build own projects with different permissions, version control all the translation operation without specific skills, and further improve the translation efficiency through real-time task management tools.ConclusionsBy providing a working platform for collaborative translation and enabling long-time version correction, the Trantrace contributes towards the creation of a multilingual biomedical knowledge commons, which would be a valuable aid for personalized therapies. The source code is freely accessible athttps://github.com/sgi-drylab/trantrace.
iMDA-BN: Identification of miRNA-Disease Associations based on the Biological Network and Graph Embedding Algorithm
Authors: Zheng Kai , You Zhu-Hong , Wang Lei 
Published: July 2020

AbstractBenefiting from advances in high-throughput experimental techniques, important regulatory roles of miRNAs, lncRNAs, and proteins, as well as biological property information, are gradually being complemented. As the key data support to promote biomedical research, domain knowledge such as intermolecular relationships that are increasingly revealed by molecular genome-wide analysis is often used to guide the discovery of potential associations. However, the method of performing network representation learning from the perspective of the global biological network is scarce. These methods cover a very limited type of molecular associations and are therefore not suitable for more comprehensive analysis of molecular network representation information. In this study, we propose a computational model based on the Biological network for predicting potential associations between miRNAs and diseases called iMDA-BN. The iMDA-BN has three significant advantages: I) It uses a new method to describe disease and miRNA characteristics which analyzes node representation information for disease and miRNA from the perspective of biological networks. II) It can predict unproven associations even if miRNAs and diseases do not appear in the biological network. III) Accurate description of miRNA characteristics from biological properties based on high-throughput sequence information. The iMDA-BN predictor achieves an AUC of 0.9145 and an accuracy of 84.49% on the miRNA-disease association baseline dataset, and it can also achieve an AUC of 0.8765 and an accuracy of 80.96% when predicting unknown diseases and miRNAs in the biological network. Compared to existing miRNA-disease association prediction methods, iMDA-BN has higher accuracy and the advantage of predicting unknown associations. In addition, 45, 49, and 49 of the top 50 miRNA-disease associations with the highest predicted scores were confirmed in the case studies, respectively.
Targeting the ubiquitin-proteasome system in a pancreatic cancer subtype with hyperactive MYC
Authors: Lankes K , Hassan Z , Doffo MJ , Schneeweis C , Lier S , Öllinger R , Rad R , Krämer OH , Keller U , Saur D , Reichert M. , Schneider G , Wirth M 
Published: July 2020

AbstractPurposeThe myelocytomatosis oncogene (MYC) is an important driver in a subtype of pancreatic ductal adenocarcinoma (PDAC). However, MYC remains a challenging therapeutic target, therefore identifying druggable synthetic lethal interactions in MYC-active PDAC may lead to novel precise therapies.MethodsCluster analysis using direct MYC target genes was used to identify PDAC with active MYC. We profiled the transcriptome of established human cell lines, murine primary PDAC cell lines and also accessed public available repositories for transcriptomic profiling. Networks active in MYC hyperactive subtypes were analyzed by gene set enrichment analysis. An unbiased pharmacological drug screen with FDA-approved anti-cancer drugs was conducted to define MYC-associated vulnerabilities, which were validated by analysis of drug response repositories and genetic gain- and loss-of-function experiments.ResultsIn an unbiased pharmacological drug screen with FDA-approved anti-cancer drugs we detected that the proteasome inhibitor bortezomib triggers a MYC-associated vulnerability. By integrating publicly available data sets we found the unfolded protein response as a signature connected to MYC. Furthermore, the increased sensitivity of MYC hyperactive PDACs to bortezomib was validated in genetically modified PDAC cells.ConclusionsIn sum, we provide evidence that perturbing the ubiquitin proteasome system might be an option to target MYC hyperactive PDAC cells and our data provide the rationale to further develop precise targeting of the ubiquitin-proteasome system as a subtype-specific therapeutic approach.
HYPERGLYCEMIA-INDUCED MIR-467 DRIVES TUMOR INFLAMMATION AND GROWTH IN BREAST CANCER
Authors: Gajeton Jasmine , Krukovets Irene , Muppala Santoshi , Verbovetskiy Dmitriy , Zhang Jessica , Stenina-Adognravi Olga 
Published: July 2020

ABSTRACTTumor microenvironment contains the parenchyma, blood vessels, and infiltrating immune cells, including tumor-associated macrophages (TAMs). TAMs affect the developing tumor and drive cancer inflammation.Hyperglycemic patients have a higher risk of developing breast cancer (BC). We have identified a novel miRNA-dependent pathway activated by hyperglycemia that promotes BC angiogenesis and inflammation supporting BC growth. miR-467 is upregulated in endothelial cells (EC), macrophages, BC cells, and in BC tumors. A target of miR-467, thrombospondin-1 (TSP-1), inhibits angiogenesis and promotes resolution of inflammation. Systemic injections of a miR-467 antagonist in mouse models of hyperglycemia resulted in decreased BC growth (P<.001). Tumors from hyperglycemic mice had a 2-fold increase in macrophage accumulation compared to normoglycemic controls (P<.001), and TAM infiltration was prevented by the miR-467 antagonist (P<.001). BC specimens from hyperglycemic patients had increased miR-467 levels, increased angiogenesis, decreased levels of TSP-1, and increased TAM infiltration in malignant breast tissue in hyperglycemic vs normoglycemic patients (2.17-fold,P=.002) and even in normal breast tissue from hyperglycemic patients (2.18-fold inc.,P=.04). In malignant BC tissue, miR-467 levels were upregulated 258-fold in hyperglycemic patients compared to normoglycemic patients (P<.001) and increased 56-fold in adjacent normal tissue (P=.008).Our results suggest that miR-467 accelerates tumor growth by inducing angiogenesis and promoting the recruitment of TAMs to drive hyperglycemia-induced cancer inflammation.
The Small GTPase OsRac1 forms two distinct immune receptor complexes containing the PRR OsCERK1 and the NLR Pit
Authors: Akamatsu Akira , Fujiwara Masayuki , Hamada Satoshi , Wakabayashi Megumi , Yao Ai , Wang Qiong , Kosami Ken-ichi , Dang Thu Thi , Kaneko-Kawano Takako , Shimamoto Ko , Kawano Yoji 
Published: July 2020

AbstractPlants employ two different types of immune receptors, cell surface pattern recognition receptors (PRRs) and intracellular nucleotide-binding and Leucine-rich repeat-containing proteins (NLRs), to cope with pathogen invasion. Both immune receptors often share similar downstream components and responses but it remains unknown whether a PRR and an NLR assemble into the same protein complex or two distinct receptor complexes. We have previously found that the small GTPase OsRac1 plays key roles in the signaling of OsCERK1, a PRR for fungal chitin, and of Pit, an NLR for rice blast fungus, and associates directly and indirectly with both of these immune receptors. In this study, using biochemical and bioimaging approaches, we reveal that OsRac1 formed two distinct receptor complexes with OsCERK1 and with Pit. Supporting this result, OsCERK1 and Pit utilized different transport systems for anchorage to the plasma membrane. Activation of OsCERK1 and Pit led to OsRac1 activation and, concomitantly, OsRac1 shifted from a small to a large protein complex fraction. We also found that the chaperone Hsp90 contributed to the proper transport of Pit to the plasma membrane and the immune induction of Pit. These findings illuminate how the PRR OsCERK1 and the NLR Pit orchestrate rice immunity through the small GTPase OsRac1.
Characterization of Bacterial Isolates in Vermicompost Produced from a Mixture of Cow dung, Straw, Neem leaf and Vegetable Wastes
Authors: Satpathy Jyotismita , Saha Mirkashim H. , Mishra Aditya S. , Mishra Sujit K. 
Published: July 2020

ABSTRACTVermicomposting is a non-thermophilic biological oxidation process of composting where certain species of earthworm are used to enhance the process of conversion of organic waste to compost. Earthworm helps in influencing the growth of certain microbial species, and also improves the physical and chemical properties of the soil. The microbial population present in vermicompost play an important role in increasing the productivity of crop as well as maintain the structural stability of the soil. Different types of bacteria found in vermicompost and is depends on the environmental condition and the raw materials used in vermicomposting. Owing to this, a study was carried out to identify the bacteria exist in vermicompost produced from cow dungs, straw, neem leafs and vegetable wastes. The phenotypic studies such as colony morphology, microscopic studies, and biochemical characterization have identified eight bacterial species namelyActinomyces israelli, Azotobacter, Micrococus luteus, Bacillus cereus, Bacillus subtillis, Pseudomonas aeruginosa, Enterobacterin the vermicompost. All these bacteria were present in the gut ofEesenia Foetidaand found beneficial for the soil and crop plants.
Activation of prodynorphin neurons in the dorsomedial hypothalamus inhibits food intake and promotes positive valence
Authors: Imoto Daigo , Yamamoto Izumi , Matsunaga Hirokazu , Yonekura Toya , Lee Ming-Liang , Kato Kan X , Yamasaki Takeshi , Otsuguro Ken-ichi , Horiuchi Motohiro , Iijima Norifumi , Kimura Kazuhiro , Toda Chitoku 
Published: July 2020

AbstractThe regulation of food intake is one of the major research areas in the study of metabolic syndromes such as obesity. Gene targeting studies have clarified the roles of hypothalamic neurons in feeding behaviour. However, our understanding of neural function under physiological conditions is still limited. Immediate early genes, such as activity-regulated cytoskeleton-associated protein (Arc/Arg3.1), are useful markers of neuronal activity. Here, we investigated the role of Arc/Arg3.1 gene-expressing neurons in the hypothalamus after refeeding using the targeted recombination in active populations method. We identified refeeding-responsive prodynorphin/cholecystokinin neurons in the dorsomedial hypothalamus that project to the paraventricular hypothalamic nucleus. Chemogenetic activation of these neurons decreased food intake and promoted positive valence. Our findings provide insight into the role of newly identified hedonic neurons in the process of feeding-induced satiety.
Concurrent depletion of Vps37 proteins evokes ESCRT-I destabilization and profound cellular stress responses
Authors: Kolmus Krzysztof , Erdenebat Purevsuren , Stewig Blair , Szymańska Ewelina , Goryca Krzysztof , Derezińska-Wołek Edyta , Szumera-Ciećkiewicz Anna , Brewińska-Olchowik Marta , Piwocka Katarzyna , Prochorec-Sobieszek Monika , Mikula Michał , Miączyńska Marta 
Published: July 2020

ABSTRACTMolecular details of how endocytosis contributes to oncogenesis remain elusive. Ourin silicoanalysis of colorectal cancer (CRC) patients revealed stage-dependent alterations in the expression of 113 endocytosis-related genes. Among them transcription of the Endosomal Sorting Complex Required for Transport (ESCRT)-I componentVPS37Bwas decreased in the advanced stages of CRC. Expression of other ESCRT-I core subunits remained unchanged in the investigated dataset. We analyzed an independent cohort of CRC patients showing also reducedVPS37AmRNA and protein abundance. Transcriptomic profiling of CRC cells revealed non-redundant functions of Vps37 proteins. Knockdown ofVPS37AandVPS37Btriggered p21-mediated inhibition of cell proliferation and sterile inflammatory response driven by the Nuclear Factor (NF)-κB transcription factor and associated with mitogen-activated protein kinase signaling. Co-silencing ofVPS37Cfurther potentiated activation of these independently induced processes. The type and magnitude of transcriptional alterations correlated with the differential ESCRT-I stability upon individual and concurrent Vps37 depletion. Our study provides novel insights into cancer cell biology by describing cellular stress responses that are associated with ESCRT-I destabilization, which might occur in CRC patients.SUMMARY STATEMENTEndosomal Sorting Complex Required for Transport (ESCRT)-I destabilization upon concurrent depletion of Vps37 proteins is linked to the activation of sterile inflammatory response and cell growth inhibition.
The impact of allometry on vomer shape and its implications for the taxonomy and cranial kinesis of crown-group birds
Authors: Plateau Olivia , Foth Christian 
Published: July 2020

AbstractCrown birds are subdivided into two main groups, Palaeognathae and Neognathae, that can be distinguished, among other means, by the organization of the bones in their pterygoidpalatine complex (PPC). Shape variation of the vomer, which is the most anterior part of the PPC, was recently analysed with help of geometric morphometrics to discover morphological differences between palaeognath and neognath birds. Based on this study, the vomer was identified as sufficient to distinguish the two main groups (and even some inclusive neognath groups) and their cranial kinetic system. As there are notable size differences between the skulls of Palaeognathae and Neognathae, we here investigate the impact of allometry on vomeral shape and its implication for taxonomic classification by re-analysing the data of the previous study. Different types of multivariate statistical analyses reveal that taxonomic identification based on vomeral shape is strongly impaired by allometry, as the error of correct identification is high when shape data is corrected for size. This finding is evidenced by a great overlap between palaeognath and neognath subclades in morphospace. Correct taxonomic identification is further impeded by the convergent presence of a flattened vomeral morphotype in multiple neognath subclades. As the evolution of cranial kinesis has been linked to vomeral shape in the original study, the correlation between shape and size of the vomer across different bird groups found in the present study questions this conclusion. In fact, cranial kinesis in crown birds results from the loss of the jugal-postorbital bar in the temporal region and ectopterygoid in the PPC and the combination of a mobilized quadratezygomatic arch complex and a flexible PPC. Therefore, we can conclude that vomer shape itself is not a suitable proxy for exploring the evolution of cranial kinesis in crown birds and their ancestors. In contrast, the evolution of cranial kinesis needs to be viewed in context of the braincase, quadrate-zygomatic arch and the whole pterygoid-palatine complex.