bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization Enabled Black Hole Entropic Fuzzy Clustering Approach for Medical Data
Authors: Rani A Jaya Mabel , Pravin A 
Published: April 2021

Abstract
Medical data clustering is an important part of medical decision systems as it refines highly sensitive information from the huge medical datasets. Medical data clustering includes processes, like determine random clusters, set data into specified clusters and handle data clusters dynamically. Hence, handling of medical data streams and clustering remains a challenging issue. This paper proposes a technique, namely Rider-based sunflower optimization (RSFO) for medical data clustering. Initially, the significant features are selected using the Tversky index with holoentropy that is established from the input data. The holo-entropy is utilized to analyze the relationship between the attributes and features. Here, the clustering is done by a Black Hole Entropic Fuzzy Clustering (BHEFC) algorithm, where the optimal cluster centroids are selected by the proposed RSFO algorithm. The proposed RSFO is designed by incorporating the Rider optimization algorithm (ROA) and sunflower optimization (SFO). The effectiveness of the proposed BHEFC+RSFO algorithm is analyzed by the Dermatology Data Set, and the proposed method has the maximal accuracy of 94.480%, Jaccard coefficient of 94.224% and Rand coefficient of 91.307%, respectively.
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease
Authors: Khan Farhat , Radovanovic Aleksandar , Gojobori Takashi , Kaur Mandeep 
Published: April 2021

Abstract
To date, research on inflammatory bowel disease (IBD, encompassing Crohn’s disease and ulcerative colitis), a chronic complex disorder, has generated a large amount of data scattered across published literature (1 06 333) listed in PubMed on 14 October 2020, and no dedicated database currently exists that catalogues information on genes associated with IBD. We aimed to manually curate 289 genes that are experimentally validated to be linked with IBD and its known phenotypes. Furthermore, we have developed an integrated platform providing information about different aspects of these genes by incorporating several resources and an extensive text-mined knowledgebase. The curated IBD database (IBDDB) allows the selective display of collated 34 subject-specific concepts (listed as columns) exportable through a user-friendly IBDDB portal. The information embedded in concepts was acquired via text-mining of PubMed (manually cleaned and curated), accompanied by data-mining from varied resources. The user can also explore different biomedical entities and their co-occurrence with other entities (about one million) from 11 curated dictionaries in the indexed PubMed records. This functionality permits the user to generate and cross-examine a new hypothesis that is otherwise not easy to comprehend by just reading the published abstracts and papers. Users can download required information using various file formats and can display information in the form of networks. To our knowledge, no curated database of IBD-related genes is available so far. IBDDB is free for academic users and can be accessed at https://www.cbrc.kaust.edu.sa/ibd/.
Tripal MegaSearch: a tool for interactive and customizable query and download of big data
Authors: Jung Sook , Cheng Chun-Huai , Buble Katheryn , Lee Taein , Humann Jodi , Yu Jing , Crabb James , Hough Heidi , Main Dorrie 
Published: April 2021

Abstract
Tripal MegaSearch is a Tripal module for querying and downloading biological data stored in Chado. This module allows site users to select data types, restrict the dataset by applying various filters and then customizing fields to view and download through a single interface. Set by site administrators, example data types include gene, germplasm, marker, map, QTL, genotype, phenotype and expression data. When querying for genes, users can restrict the gene dataset using various filters such as name, chromosome position and functional annotation. They can then customize fields to download, such as name, organism, type, chromosome position, various functional annotations such as BLAST, KEGG, InterPro and GO term. FASTA files can also be downloaded for the sequence data. Site administrators can choose from two different data sources to serve data: Tripal MegaSearch materialized views or Chado tables. If neither data source is desired, administrators may also create their own materialized views and serve them through the flexible dynamic Tripal MegaSearch query form. Tripal MegaSearch is currently implemented in several databases including the Genome Database for Rosaceae www.rosaceae.org and TreeGenes www.https://treegenesdb.org/.
Rank-invariance conditions for the comparison of volatility forecasts
Authors: Palandri Alessandro 
Published: April 2021

Summary
The paper derives four conditions that guarantee rank-invariance, i.e., that the empirical rankings (based on measurement error-affected variance proxies) of competing volatility forecasts be consistent with the true rankings (based on the unobservable conditional variance). The first three establish bounds beyond which the separation between the forecasts is enough for their rankings not to be affected by the measurement error. The conditions’ ability to establish rank-invariance with respect to forecast characteristics, such as bias, variance and correlation, is studied via Monte Carlo simulations. An additional moment condition identifies the functional forms of the triplet {model, estimation criterion, loss} for which the effects of measurement errors on the rankings cancel altogether. Both theoretical and empirical results show the extension of admissible loss functions achieving ranking consistency in forecast evaluations.
Platypnea and orthodeoxia syndrome as an uncommon clinical indication for a challenging percutaneous patent foramen ovale closure: a case report
Authors: Dipasquale Francesco , Musto Carmine , Pennacchi Mauro , De Felice Francesco 
Published: April 2021

AbstractBackgroundPlatypnea and Orthodeoxia Syndrome (POS) is a rare clinical condition characterized by positional dyspnoea and arterial desaturation. Various mechanisms are related to this syndrome. The simultaneous presence of abnormal anatomical findings [aortic root dilatation, atrial septal aneurysm (ASA), Lipomatous septum, and patent foramen ovale (PFO)] and an occurring ventilation/perfusion mismatch can modify intracardiac haemodynamics leading to POS in elderly patients.Case summaryA 70-year-old man was admitted to our emergency department suffering from neurological symptoms. A brain computed tomography scan showed a subdural haematoma and the patient underwent surgical evacuation. Some days later, he experienced an acute pulmonary insufficiency (SpO2 63%) due to parenchymal basal pneumonia treated with endotracheal intubation. Two weeks later, despite pneumonia resolution, the patient’s dyspnoea became worse, experiencing deep hypoxia as soon as the patient sat up with a partial resolution on recumbent position. A transoesophageal echocardiogram with bubble-test was performed showing aortic root dilatation and a lipomatous interatrial septum characterized by the presence of tunnel-like PFO with large ASA resulting in a big right to left shunt at rest with no signs of pulmonary hypertension. The patient underwent PFO percutaneous closure intervention and a few days later O2 therapy was reduced and the patient decannulated.DiscussionThis case illustrates how the presence of both intracardiac and extracardiac factors may facilitate the onset of POS in aged patients. Platypnea and Orthodeoxia Syndrome should be considered in patients with unexplained dyspnoea and arterial desaturation related to orthostatism. It has a good prognosis with an improvement of quality of life if the causal factor can be treated.
Rotatripsy: synergistic effects of complementary technologies: a case report
Authors: Kaur Navjyot , Pruthvi C R , Sharma Yashpaul , Gupta Himanshu 
Published: April 2021

Abstract

Background
Percutaneous coronary intervention (PCI) to calcified coronary lesions (CCLs) remains one of the most complex procedures. Latest modality to modify calcium, intravascular lithotripsy (IVL), has shown good safety and efficacy in preliminary research. However, it may be associated with acute complications, and as standalone therapy, is not sufficient for all CCLs.

Case summary
Eighty-two-year-old man, known case of coronary artery disease and multiple comorbidities, presented with worsening angina of 1 month duration. Coronary angiography revealed heavily calcified triple vessel disease with critical distal left main (LM) involvement. Owing to high surgical risk, he was offered intravascular ultrasound (IVUS) guided PCI with intra-aortic balloon support. While the diffuse, circumferential calcified lesions in LM and left anterior descending (LAD) artery were modified with rotablation (RA) followed by IVL with 3.5 and 3.0 mm balloons; ostial-proximal lesion in left circumflex (LCX) artery was treated with 3.0 mm IVL balloon as a standalone therapy. During second cycle of shockwave therapy in LCX, the 3.0 mm IVL balloon ruptured with type C dissection extending upto LM ostium which required emergent LM bifurcation stenting. We had a good angiographic result which was confirmed with IVUS.

Discussion
ntravascular lithotripsy and RA are complementary technologies in treating CCLs. Rotablation with a relatively small-sized burr is safe and can favourably modify superficial calcium which helps in smooth delivery of IVL balloon and ensures safe shockwave therapy, if required. Unselected upfront use of IVL without intravascular imaging may be associated with complications as described in this case.
Clinical utility of two-phase computed tomography angiography for the detection of myocardial perfusion defects related to acute coronary syndrome in patients with acute chest pain: a case series
Authors: Vallejo Enrique , Buelna-Cano Christian 
Published: April 2021

Abstract

Background
Evaluation of acute chest pain (ACP) in the emergency department is a major health issue and differential diagnosis remains challenging for the physician, particularly in patients with atypical symptoms and inconclusive changes in electrocardiogram (ECG) or biomarkers levels.

Case summary
We present the potential value of the two-phase computed tomography angiography (TP-CTA) imaging protocol done in six different patients evaluated with ACP and underwent non-gated or gated computed tomography angiography (CTA) to exclude pulmonary embolism (PE), acute aortic syndrome (AAS), or acute coronary syndrome (ACS). All patients had new-onset chest pain and atypical clinical presentation with non-diagnostic ECG and initially negative or near-normal cardiac biomarkers.

Discussion
The evaluation of myocardial computed tomography perfusion (MCTP) using TP-CTA imaging protocol might open a new diagnostic approach to evaluate MCTP in patients with ACP related to PE, AAS, or ACS.
Differences Attract: An Experimental Study of Focusing in Economic Choice
Authors: Andersson Ola , Carlson Jim Ingebretsen , Wengström Erik 
Published: April 2021

AbstractSeveral behavioural models of choice assume that decision makers place more weight on attributes where options differ more, an assumption we test in a set of experiments. We find that subjects are more likely to choose an option when we add options increasing the maximal difference in the original option’s strongest attribute, suggesting that the decision maker’s focus is drawn to attributes with a high spread. Additional experiments corroborate this finding. Still, we document that the focusing effect diminishes when options are presented using numbers instead of graphs or when subjects are forced to wait before submitting their answers.
The effect of intravenous ferric carboxymaltose on health-related quality of life in iron-deficient patients with acute heart failure: the results of the AFFIRM-AHF study
Authors: Jankowska Ewa A , Kirwan Bridget-Anne , Kosiborod Mikhail , Butler Javed , Anker Stefan D , McDonagh Theresa , Dorobantu Maria , Drozdz Jarosław , Filippatos Gerasimos , Keren Andre , Khintibidze Irakli , Kragten Hans , Martinez Felipe A , Metra Marco , Milicic Davor , Nicolau José C , Ohlsson Marcus , Parkhomenko Alexander , Pascual-Figal Domingo A , Ruschitzka Frank , Sim David , Skouri Hadi , van der Meer Peter , Lewis Basil S , Comin-Colet Josep , von Haehling Stephan , Cohen-Solal Alain , Danchin Nicolas , Doehner Wolfram , Dargie Henry J , Motro Michael , Friede Tim , Fabien Vincent , Dorigotti Fabio , Pocock Stuart , Ponikowski Piotr 
Published: April 2021

Abstract

Aims
Patients with heart failure (HF) and iron deficiency experience poor health-related quality of life (HRQoL). We evaluated the impact of intravenous (IV) ferric carboxymaltose (FCM) vs. placebo on HRQoL for the AFFIRM-AHF population.

Methods and results
The baseline 12-item Kansas City Cardiomyopathy Questionnaire (KCCQ-12), which was completed for 1058 (535 and 523) patients in the FCM and placebo groups, respectively, was administered prior to randomization and at Weeks 2, 4, 6, 12, 24, 36, and 52. The baseline KCCQ-12 overall summary score (OSS) mean ± standard error was 38.7 ± 0.9 (FCM group) and 37.1 ± 0.8 (placebo group); corresponding values for the clinical summary score (CSS) were 40.9 ± 0.9 and 40.1 ± 0.9. At Week 2, changes in OSS and CSS were similar for FCM and placebo. From Week 4 to Week 24, patients assigned to FCM had significantly greater improvements in OSS and CSS scores vs. placebo [adjusted mean difference (95% confidence interval, CI) at Week 4: 2.9 (0.5–5.3, P = 0.018) for OSS and 2.8 (0.3–5.3, P = 0.029) for CSS; adjusted mean difference (95% CI) at Week 24: 3.0 (0.3–5.6, P = 0.028) for OSS and 2.9 (0.2–5.6, P = 0.035) for CSS]. At Week 52, the treatment effect had attenuated but remained in favour of FCM.

Conclusion
In iron-deficient patients with HF and left ventricular ejection fraction &lt;50% who had stabilized after an episode of acute HF, treatment with IV FCM, compared with placebo, results in clinically meaningful beneficial effects on HRQoL as early as 4 weeks after treatment initiation, lasting up to Week 24.
Visualization of intestinal infections with astro- and sapovirus in mink (Neovison vison) kits byin situhybridization
Authors: Birch Julie Melsted , Leijon Mikael , Nielsen Søren Saxmose , Struve Tina , Jensen Henrik Elvang 
Published: April 2021

ABSTRACTClarification of the infection microbiology remains a challenge in the pre-weaning diarrhea (PWD) syndrome in farmed mink (Neovison vison). Duodenal, jejunal and colon sections from 36 mink kits with PWD were systematically examined by chromogen in situ hybridization targeting two incriminated viruses: mink astrovirus and mink sapovirus. Using the RNAscope® 2.5 HD Duplex Assay, astrovirus and sapovirus were visualized and simultaneously demonstrated in the gut tissue. Both viruses infect enterocytes in the small intestine with a specific localization pattern; astrovirus affects the two apical thirds of the villi, whereas sapovirus generally affects the basal parts of the villi. Furthermore, we demonstrated that astrovirus in mink does not target the goblet cells. This is the first time astro- and calicivirus have been visualized in mink kit gut tissue, and these findings might be important in clarification of the impact of these viruses in the PWD syndrome.
Public Preferences for Longleaf Pine Restoration Programs in the Southeastern United States
Authors: Oluoch Sydney , Lal Pankaj , Wolde Bernabas , Susaeta Andres , Soto Josè R , Smith Meghann , Adams Damian C 
Published: April 2021

Abstract
Longleaf pine (LLP) (Pinus palustris Mill.) is well known for its role in supporting healthy ecosystems in the southeastern (SE) United States (US). The decline of LLP forest ecosystems has led to a consensus among stakeholders that restoration efforts are needed. However, there is still a lack of robust understanding of the utilization of nonmarket ecosystem services of LLP forests. These challenges have presented major barriers to landowner acceptance of subsidized LLP restoration programs. Understanding the tradeoffs between forest ecosystem services is critical to restoring LLP in the SE US. This study employs the best-worst choice (BWC) method to assess public preferences toward hypothetical LLP restoration programs that consider ecosystem services such as recreation, timber production, carbon sequestration, water yield, and wildlife diversity. We surveyed a representative sample of n = 953 respondents from Alabama, Mississippi, Georgia, and Florida, and results showed that residents in all four states are willing to pay for LLP restoration, with the highest average willingness to pay (WTP) for forest recreation ($20.39), followed by red-cockaded woodpecker (RCW) conservation ($13.37) and carbon sequestration ($13.32). This research provides important public preference information on ecosystem services that is critical in forming sustainable LLP restoration programs.
Gut Microbiota Represent a Major Thermogenic Biomass
Authors: Riedl Ruth A , Burnett Colin M L , Pearson Nicole A , Reho John J , Mokadem Mohamad , Edwards Robert A , Kindel Tammy L , Kirby John R , Grobe Justin L 
Published: April 2021

Abstract
Evidence supports various roles for microbial metabolites in the control of multiple aspects of host energy flux including feeding behaviors, digestive efficiency, and energy expenditure, but few studies have quantified the energy utilization of the biomass of the gut microbiota itself. Because gut microbiota exist in an anoxic environment, energy flux is expected to be anaerobic; unfortunately, commonly utilized O2/CO2 respirometry-based approaches are unable to detect anaerobic energy flux. To quantify the contribution of the gut microbial biomass to whole-animal energy flux, we examined the effect of surgical reduction of gut biomass in C57BL/6J mice via cecectomy and assessed energy expenditure using methods sensitive to anaerobic flux, including bomb and direct calorimetry. First, we determined that cecectomy caused an acceleration of weight gain over several months due to a reduction in combined total host plus microbial energy expenditure, as reflected by an increase in energy efficiency (ie, weight gained per calorie absorbed). Second, we determined that under general anesthesia, cecectomy caused immediate changes in heat dissipation that were significantly modified by short-term pretreatment with dietary or pharmaceutical interventions known to modify the microbiome, and confirmed that these effects were undetectable by respirometry. We conclude that while the cecum only contributes approximately 1% of body mass in the mouse, this organ contributes roughly 8% of total resting energy expenditure, that this contribution is predominantly anaerobic, and that the composition and abundance of the cecal microbial contents can significantly alter its contribution to energy flux.
Meta-GWAS for quantitative trait loci identification in soybean
Authors: Shook Johnathon M , Zhang Jiaoping , Jones Sarah E , Singh Arti , Diers Brian W , Singh Asheesh K 
Published: April 2021

Abstract
We report a meta-Genome Wide Association Study involving 73 published studies in soybean [Glycine max L. (Merr.)] covering 17,556 unique accessions, with improved statistical power for robust detection of loci associated with a broad range of traits. De novo GWAS and meta-analysis were conducted for composition traits including fatty acid and amino acid composition traits, disease resistance traits, and agronomic traits including seed yield, plant height, stem lodging, seed weight, seed mottling, seed quality, flowering timing, and pod shattering. To examine differences in detectability and test statistical power between single- and multi-environment GWAS, comparison of meta-GWAS results to those from the constituent experiments were performed. Using meta-GWAS analysis and the analysis of individual studies, we report 483 peaks at 393 unique loci. Using stringent criteria to detect significant marker-trait associations, 59 candidate genes were identified, including 17 agronomic traits loci, 19 for seed-related traits, and 33 for disease reaction traits. This study identified potentially valuable candidate genes that affect multiple traits. The success in narrowing down the genomic region for some loci through overlapping mapping results of multiple studies is a promising avenue for community-based studies and plant breeding applications.
A head-to-head comparison of ribodepletion and polyA selection approaches for Caenorhabditis elegans low input RNA-sequencing libraries
Authors: Barrett Alec , McWhirter Rebecca , Taylor Seth R , Weinreb Alexis , Miller David M , Hammarlund Marc 
Published: April 2021

Abstract
A recent and powerful technique is to obtain transcriptomes from rare cell populations, such as single neurons in Caenorhabditis elegans, by enriching dissociated cells using fluorescent sorting. However, these cell samples often have low yields of RNA that present challenges in library preparation. This can lead to PCR duplicates, noisy gene expression for lowly expressed genes, and other issues that limit endpoint analysis. Furthermore, some common resources, such as sequence-specific kits for removing ribosomal RNA, are not optimized for nonmammalian samples. To advance library construction for such challenging samples, we compared two approaches for building RNAseq libraries from less than 10 nanograms of C. elegans RNA: SMARTSeq V4 (Takara), a widely used kit for selecting poly-adenylated transcripts; and SoLo Ovation (Tecan Genomics), a newly developed ribodepletion-based approach. For ribodepletion, we used a custom kit of 200 probes designed to match C. elegans rRNA gene sequences. We found that SoLo Ovation, in combination with our custom C. elegans probe set for rRNA depletion, detects an expanded set of noncoding RNAs, shows reduced noise in lowly expressed genes, and more accurately counts expression of long genes. The approach described here should be broadly useful for similar efforts to analyze transcriptomics when RNA is limiting.
A gap in knowledge surrounding urban housing interventions: a call for gender redistribution
Authors: Perri Melissa , O’Campo Patricia 
Published: April 2021

AbstractUsing gender-sensitive (ensures that resource distribution considers gender) and gender-redistributive (aims to develop balanced gendered relationships through redistributing resources) analytic lenses in urban health interventions is long overdue. The social construction of gender and its impact on the health of marginalized women, especially women who experience homelessness within urban settings is frequently overlooked. Housing research, programs, and policies too often fail to utilize gender redistributive frameworks—perpetuating gendered harm for many. This article provides an update of current practices around consideration of gender in housing interventions and literature while advocating for the necessary incorporation of gender-redistributive practices in housing research and program implementation. Addressing these gaps will address the longstanding neglect that has led to disparities among women who experience homelessness or housing insecurity.