bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnosis of thyroid nodules for ultrasonographic characteristics indicative of malignancy using random forest
Authors: Chen Dan , Hu Jun , Zhu Mei , Tang Niansheng , Yang Yang , Feng Yuran 
Published: September 2020

AbstractBackgroundVarious combinations of ultrasonographic (US) characteristics are increasingly utilized to classify thyroid nodules. But they lack theories, and heavily depend on radiologists’ experience, and cannot correctly classify thyroid nodules. Hence, our main purpose of this manuscript is to select the US characteristics significantly associated with malignancy and to develop an efficient scoring system for facilitating ultrasonic clinicians to correctly identify thyroid malignancy.MethodsA logistic regression (LR) model is utilized to identify the potential thyroid malignancy, and the least absolute shrinkage and selection operator (LASSO) method is adopted to simultaneously select US characteristics significantly associated with malignancy and estimate parameters in LR model. Based on the selected US characteristics, we calculate the probability for each of thyroid nodules via random forest (RF) and extreme learning machine (ELM), and develop a scoring system to classify thyroid nodules. For comparison, we also consider eight state-of-the-art methods such as support vector machine (SVM), neural network (NET), etc. The area under the receiver operating characteristic curve (AUC) is employed to measure the accuracy of various classifiers.ResultsThe US characteristics: nodule size, AP/T≥1, solid component, micro-calcifications, hackly border, hypoechogenicity, presence of halo, unclear border, irregular margin, and central vascularity are selected as the significant predictors associated with thyroid malignancy via the LASSO LR (LLR). Using the developed scoring system, thyroid nodules are classified into the following four categories: benign, low suspicion, intermediate suspicion, and high suspicion, whose rates of malignancy correctly identified for RF (ELM) method on the testing dataset are 0.0% (4.3%), 14.3% (50.0%), 58.1% (59.1%) and 96.1% (97.7%), respectively.ConclusionLLR together with RF performs better than other methods in identifying malignancy, especially for abnormal nodules, in terms of risk scores. The developed scoring system can well predict the risk of malignancy and guide medical doctors to make management decisions for reducing the number of unnecessary biopsies for benign nodules.
Conserved and distinct morphological aspects of the salivary glands of sand fly vectors of leishmaniasis: an anatomical and ultrastructural study
Authors: Nacif-Pimenta Rafael , Pinto Luciana C. , Volfova Vera , Volf Petr , Pimenta Paulo F. P. , Secundino Nagila F. C. 
Published: September 2020

AbstractBackgroundSand flies are vectors ofLeishmaniaspp., the causative agents of leishmaniasis in vertebrates, including man. The sand fly saliva contains powerful pharmacologically active substances that prevent hemostasis and enhanceLeishmaniaspp. infections. On the other hand, salivary proteins can protect vaccinated mice challenged with parasites. Therefore, sand fly salivary proteins are relevant for the epidemiology of leishmaniasis and can be a potential target for a vaccine against leishmaniasis. Despite this, studies on sand fly salivary glands (SGs) are limited.MethodsThe present study analyzes, in detail, the morphology, anatomy and ultrastructure of the SGs of sand fly vectors of the generaLutzomyiaandPhlebotomus. We used histology, transmission and scanning electron microscopy and lectin labeling associated with confocal laser microscopy.ResultsThe SGs have conserved and distinct morphological aspects according to the distinct sand fly species. Each SG has a single rounded lobe constituting ofc.100–120 secretory cells. The SG secretory cells, according to their ultrastructure and lectin binding, were classified into five different subpopulations, which may differ in secretory pathways.ConclusionsTo the best of our knowledge, these morphological details of sand fly salivary glands are described for the first time. Further studies are necessary to better understand the role of these different cell types and better relate them with the production and secretion of the saliva substances, which has a fundamental role in the interaction of the sand fly vectors withLeishmania.
The draft genome of Labeo catla
Authors: Sahoo Lakshman , Das Paramananda , Sahoo Bismay , Das Gargee , Meher Prem Kumar , Udit Uday Kumar , Mahapatra Kanta Das , Sundaray Jitendra Kumar 
Published: September 2020

Abstract
Objective
Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar. Its higher growth rate and compatibility with other major carps, specific surface feeding habit, and consumer preference have increased its popularity in carp polyculture systems among the fish farmers in Indian subcontinent. Recent advancement in sequencing technology coupled with massive parallel sequencing platforms has facilitated accelerated genetic improvement in aquaculture species through integration of genomics tools. A draft genome and allied resources are lacking in catla. Therefore, in the present study, we have performed de-novo assembly of Labeo catla for the first time.

Data description
A male farm reared catla was used for extracting high molecular weight genomic DNA followed by sequencing in Oxford Nanopore and Illumina platforms. Approximately, 80× coverage of sequence data was assembled adopting the hybrid assembly strategy. The assembled genome size of catla was 1.01 Gb containing 5345 scaffolds with N50 value 0.7 Mb and more than 92% BUSCO completeness. Gene annotation resulted in 25,812 predicted genes.
Evaluation of immunophenotypic markers and clinico-hematological profile in chronic lymphocytic leukemia: implications for prognosis
Authors: Bagheri Marziye , Vosoughi Tina , Hosseinzadeh Mehran , Saki Najmaldin 
Published: September 2020

Abstract
Objective
Chronic lymphocytic leukemia (CLL) is an adult leukemia presented with clonal accumulation of lymphocytes. Immunophenotypic changes can be effective in predicting clinical course, the survival of patients, and determining first-line treatment. This is a study of the association between immunophenotypic markers with complete blood cell count (CBC) values and clinical parameters.

Results
Peripheral blood samples were collected from 35 newly diagnosed CLL patients. The expression of immunophenotypic markers and CBC were evaluated. Platelet counts and hemoglobin concentration had a significant, inverse association with Rai staging, modified Rai staging, Binet staging systems (all p < 0.001 in both parameters), and splenomegaly (p = 0.001 and 0.007, respectively). The platelet/lymphocyte ratio (PLR) had a significant, inverse association with Rai staging (p = 0.014), modified Rai staging (p = 0.024), Binet staging systems (p = 0.027), and splenomegaly (p = 0.033). However, CD38, CD25, and double-positive CD56/CD117 expression, group 3 of innate lymphocyte cells (ILC3s), had no significant association with clinical parameters. In regression analysis, that ILC3s has an inverse correlation with neutrophil/lymphocyte ratio (r = −0.340, p = 0.046). Given that there is an inverse association between PLR and advanced clinical stages, it seems that PLR may have prognostic value in CLL.
Draft genome sequence of Clostridium jeddahense EE-R19 isolated from an anaerobic digester
Authors: Ziganshina Elvira E. , Mohammed Waleed S. , Ziganshin Ayrat M. 
Published: September 2020

Abstract
Objectives
Clostridium species of the order Clostridiales are mostly strictly anaerobic rod-shaped bacteria. They can be detected in a variety of environments, including the intestines of humans and animals, soil, water, and biogas reactors. Species of the genus Clostridium are widely used in various biotechnological processes, but several of them have been identified as significant human pathogens. Therefore, investigation at the genome level is necessary to provide valuable information about the ecology, genetics, and phylogenetic diversity of various Clostridium species.

Data description
In the present study, we report the whole genome sequence of Clostridium jeddahense strain EE-R19, which was isolated from a mesophilic anaerobic digester. The draft genome of C. jeddahense EE-R19 consisted of 59 contigs (> 500 bp), which amounted to 3,562,974 with an overall G + C content of 51.79%. The whole genome shotgun project of C. jeddahense EE-R19 has been deposited at DDBJ/ENA/GenBank under the accession number JAAVNF000000000.
Association between NPPA promoter methylation and hypertension: results from Gusu cohort and replication in an independent sample
Authors: Li Jing , Zhu Jinhua , Ren Liyun , Ma Shengqi , Shen Bin , Yu Jia , Zhang Rongyan , Zhang Mingzhi , He Yan , Peng Hao 
Published: September 2020

Abstract
Background
Atrial natriuretic peptide (ANP), one of the main members of the natriuretic peptides system, has been associated with hypertension and related complications, but the underlying molecular mechanisms are not very clear. Here, we aimed to examine whether DNA methylation, a molecular modification to the genome, of the natriuretic peptide A gene (NPPA), the coding gene of ANP, was associated with hypertension.

Methods
Peripheral blood DNA methylation of NPPA promoter was quantified by target bisulfite sequencing in 2498 community members (mean aged 53 years, 38% men) as a discovery sample and 1771 independent participants (mean aged 62 years, 54% men) as a replication sample. In both samples, we conducted a single CpG association analysis, followed by a gene-based association analysis, to examine the association between NPPA promoter methylation and hypertension, adjusting for age, sex, education level, cigarette smoking, alcohol consumption, obesity, fasting glucose, and lipids. Multiple testing was controlled by the false discovery rate approach.

Results
Of the 9 CpG loci assayed, hypermethylation at 5 CpGs (CpG1, CpG3, CpG6, CpG8, and CpG9) was significantly associated with a lower odds of prevalent hypertension in the discovery sample, and one CpG methylation (CpG1 located at Chr1:11908353) was successfully replicated in the replication sample (OR = 0.82, 95%CI 0.74–0.91, q = 0.002) after adjusting for covariates and multiple testing. The gene-based analysis found that DNA methylation of the 9 CpGs at NPPA promoter as a whole was significantly associated with blood pressure and prevalent hypertension in both samples (all P < 0.05).

Conclusions
DNA methylation levels at NPPA promoter were decreased in Chinese adults with hypertension. Aberrant DNA methylation of the NPPA gene may participate in the mechanisms of hypertension.
Inflammatory cutaneous lesions and pulmonary manifestations in a new patient with autosomal recessive ISG15 deficiency case report
Authors: Buda Guadalupe , Valdez Rita María , Biagioli German , Olivieri Federico A. , Affranchino Nicolás , Bouso Carolina , Lotersztein Vanesa , Bogunovic Dusan , Bustamante Jacinta , Martí Marcelo A. 
Published: September 2020

AbstractInterferon-stimulated gene 15 (ISG15) was the first ubiquitin-like modifier protein identified that acts by protein conjugation (ISGylation) and is thought to modulate IFN-induced inflammation. Here, we report a new patient from a non-consanguineous Argentinian family, who was followed for recurrent ulcerative skin lesions, cerebral calcifications and lung disease. Whole Exome Sequencing (WES) revealed two novel compound heterozygous variants (c.285del and c.299_312del, NM_005101.4 GRCh37(hg19), both classified as pathogenic according to ACMG criteria) in the ISG15 gene, resulting in a complete deficiency due to disruption of the second ubiquitin domain of the corresponding protein. The clinical phenotype of this patient is unique given the presence of recurrent pulmonary manifestations and the absence of mycobacterial infections, thus resulting in a phenotype distinct from that previously described in patients with biallelic loss-of-function (LOF) ISG15 variants. This case highlights the role of ISG15 as an immunomodulating factor whose LOF variants result in heterogeneous clinical presentations.
“Immune Boosting” in the time of COVID: selling immunity on Instagram
Authors: Wagner Darren N. , Marcon Alessandro R. , Caulfield Timothy 
Published: September 2020

Abstract“Immune boosting” is a trending topic during the COVID-19 pandemic. The concept of “immune boosting” is scientifically misleading and often used to market unproven products and therapies. This paper presents an analysis of popular immune-boosting posts from Instagram. Of the sampled posts, all promoted “immune boosting” as beneficial, nearly all involved commercial interests, and many used scientific and medical rhetoric in their messaging.
A non-viral genome editing platform for site-specific insertion of large transgenes
Authors: Chaudhari Namrata , Rickard Amanda M. , Roy Suki , Dröge Peter , Makhija Harshyaa 
Published: September 2020

Abstract
Background
The precise, functional and safe insertion of large DNA payloads into host genomes offers versatility in downstream genetic engineering-associated applications, spanning cell and gene therapies, therapeutic protein production, high-throughput cell-based drug screening and reporter cell lines amongst others. Employing viral- and non-viral-based genome engineering tools to achieve specific insertion of large DNA—despite being successful in E. coli and animal models—still pose challenges in the human system. In this study, we demonstrate the applicability of our lambda integrase-based genome insertion tool for human cell and gene therapy applications that require insertions of large functional genes, as exemplified by the integration of a functional copy of the F8 gene and a Double Homeobox Protein 4 (DUX4)-based reporter cassette for potential hemophilia A gene therapy and facioscapulohumeral muscular dystrophy (FSHD)-based high-throughput drug screening purposes, respectively. Thus, we present a non-viral genome insertion tool for safe and functional delivery of large seamless DNA cargo into the human genome that can enable novel designer cell-based therapies.

Methods
Previously, we have demonstrated the utility of our phage λ-integrase platform to generate seamless vectors and subsequently achieve functional integration of large-sized DNA payloads at defined loci in the human genome. To further explore this tool for therapeutic applications, we used pluripotent human embryonic stem cells (hESCs) to integrate large seamless vectors comprising a ‘gene of interest’. Clonal cell populations were screened for the correct integration events and further characterized by southern blotting, gene expression and protein activity assays. In the case of our hemophilia A-related study, clones were differentiated to confirm that the targeted locus is active after differentiation and actively express and secrete Factor VIII.

Results
The two independent approaches demonstrated specific and functional insertions of a full-length blood clotting F8 expression cassette of ~ 10 kb and of a DUX4 reporter cassette of ~ 7 kb in hESCs.

Conclusion
We present a versatile tool for site-specific human genome engineering with large transgenes for cell/gene therapies and other synthetic biology and biomedical applications.
Overexpressing TGF-β1 in mesenchymal stem cells attenuates organ dysfunction during CLP-induced septic mice by reducing macrophage-driven inflammation
Authors: Liu Feng , Xie Jianfeng , Zhang Xiwen , Wu Zongsheng , Zhang Shi , Xue Ming , Chen Jianxiao , Yang Yi , Qiu Haibo 
Published: September 2020

Abstract
Background
Sepsis remains a leading cause of death in critically ill patients. It is well known that mesenchymal stem cells (MSCs) are a promising therapy partly due to their paracrine-mediated immunoregulatory function. Previous study demonstrated that transforming growth factor-beta1 (TGF-β1) is an important cytokine secreted by MSCs and that it participates in MSC-mediated macrophage phenotype switch from pro-inflammatory to pro-resolution. In addition, the transformation of macrophage phenotype may be a potential treatment for sepsis. However, the therapeutic effect of overexpressing TGF-β1 in MSCs (MSC-TGF-β1) on sepsis is not well understood. Therefore, this study aimed to evaluate the effects of TGF-β1 overexpressing MSCs on organ injury in cecal ligation and puncture (CLP)-induced septic mice and to detect the changes in macrophage phenotype during this process.

Methods
Mouse MSCs stably transfected with TGF-β1 were constructed and injected into CLP-induced septic mice via tail vein. After 24 h, the mice were sacrificed; then, the histopathology of the organ was evaluated by hematoxylin-eosin (H&E) staining. Inflammatory cytokines were detected by ELISA. Macrophage infiltration and phenotype transformation in the tissues were determined by immunohistochemistry and flow cytometry. In addition, we performed adoptive transfer of mouse peritoneal macrophage pretreated with TGF-β1 overexpressing MSCs in septic mice.

Results
We found that infusion of TGF-β1 overexpressing MSCs attenuated the histopathological impairment of the organ, decreased the pro-inflammatory cytokine levels and inhibited macrophage infiltration in tissues. TGF-β1 overexpressing MSCs induced macrophage phenotypes changed from pro-inflammatory to pro-resolution in inflammatory environment. The adoptive transfer of mouse peritoneal macrophages pretreated with TGF-β1 overexpressing MSCs also relieved organ damage in CLP-induced septic mice.

Conclusion
Under septic conditions, TGF-β1 overexpressing MSCs can enhance the therapeutic effects of MSCs on organ injury and inflammation as a result of reduced macrophage infiltration and induced macrophages transformation, the adoptive transfer of macrophages treated with TGF-β1 overexpressing MSCs also relieved organ damage. This will provide new hope for the treatment of sepsis.
Regional probabilistic tsunami hazard assessment associated with active faults along the eastern margin of the Sea of Japan
Authors: Mulia Iyan E. , Ishibe Takeo , Satake Kenji , Gusman Aditya Riadi , Murotani Satoko 
Published: September 2020

AbstractWe analyze the regional tsunami hazard along the Sea of Japan coast associated with 60 active faults beneath the eastern margin of the Sea of Japan. We generate stochastic slip distribution using a Monte Carlo approach at each fault, and the total number of required earthquake samples is determined based on convergence analysis of maximum coastal tsunami heights. The earthquake recurrence interval on each fault is estimated from observed seismicity. The variance parameter representing aleatory uncertainty for probabilistic tsunami hazard analysis is determined from comparison with the four historical tsunamis, and a logic-tree is used for the choice of the values. Using nearshore tsunami heights at the 50 m isobath and an amplification factor by the Green’s law, hazard curves are constructed at 154 locations for coastal municipalities along the Sea of Japan coast. The highest maximum coastal tsunamis are expected to be approximately 3.7, 7.7, and 11.5 m for the return periods of 100-, 400-, and 1000-year, respectively. The results indicate that the hazard level generally increases from southwest to northeast, which is consistent with the number and type of the identified fault systems. Furthermore, the deaggregation of hazard suggests that tsunamis in the northeast are predominated by local sources, while the southwest parts are likely affected by several regional sources.
Microarray data analysis reveals gene expression changes in response to ionizing radiation in MCF7 human breast cancer cells
Authors: Bai Jing , Luo Youzhen , Zhang Shengchu 
Published: September 2020

Abstract
Background
The aim of this study was to identify potential therapeutic target genes for breast cancer (BC) by the investigation of gene expression changes after ionizing radiation (IR) in BC cells. Gene expression profile GSE21748, including BC cell line MCF-7 samples at different time points after IR treatment, were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified in different time points following IR compared with cell samples before IR, respectively. Gene ontology functions and The Kyoto Encyclopedia of Genes and Genomes pathways of the overlapping DEGs were enriched using DAVID. Transcription factor (TFs)-encoding genes were identified from the overlapping DEGs, followed by construction of transcriptional regulatory network and co-expression network.

Results
A total of 864 overlapping DEGs were identified, which were significantly enriched in regulation of cell proliferation and apoptosis, and cell cycle process. We found that FOXD1, STAT6, XBP1, STAT2, LMO2, TFAP4, STAT3, STAT1 were hub nodes in the transcriptional regulatory network of the overlapping DEGs. The co-expression network of target genes regulated by STAT3, STAT1, STAT6 and STAT2 included some key genes such as BCL2L1.

Conclusion
STAT1, STAT2, STAT3, STAT6, XBP1, BCL2L1, CYB5D2, ESCO2, and PARP2 were significantly affected by IR and they may be used as therapeutic gene targets in the treatment of BC.
Understanding stakeholders’ perspectives on implementing deprescribing for older people living in long-term residential care homes: the STOPPING study protocol
Authors: Warmoth Krystal , Day Jo , Cockcroft Emma , Reed Donald Nigel , Pollock Lucy , Coxon George , Heneker Julia , Walton Bridget , Stein Ken 
Published: September 2020

Abstract
Background
Older people with multimorbidity often experience polypharmacy. Taking multiple medicines can be beneficial; however, some older adults are prescribed multiple medicines when they are unlikely to improve clinical outcomes and may lead to harm. Deprescribing means reducing or stopping prescription medicines which may no longer be providing benefit. While appropriate deprescribing may usually be safely undertaken, there is a lack of guidance about how to implement it in practice settings such as care homes. Implementing deprescribing in care homes is often challenging, due to differing concerns of residents, staff, clinicians, friends/family members and carers along with differences in care home structures. The STOPPING study will support the development of better deprescribing practice in care homes, considering different views and environments. This paper aims to introduce the research protocol.

Methods
We will use qualitative approaches informed by the widely accepted Consolidated Framework for Implementation Research (CFIR) to aid analysis. To understand the barriers, facilitators, and contextual factors influencing deprescribing in care homes, we will employ individual interviews with care home residents and family members, focus groups with care home staff and healthcare professionals, and observations from care homes. Then, we will examine acceptability, feasibility, and suitability of existing deprescribing approaches using cognitive interviews with care home staff and healthcare professionals. Lastly, we will use narrative synthesis to integrate findings and develop guidance for implementing a deprescribing approach for care homes.

Discussion
This research will support the development of implementable approaches to deprescribing in care homes. The insights from this project will be shared with various stakeholders: care home residents, staff, pharmacists, general practitioners, nurses, and other health professionals, carers, researchers, and the public. This work will support deprescribing to be implemented effectively in care homes to benefit residents and the wider health economy.