bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Main Course Was Mealworms: The Epistemics of Art and Science in Public Engagement
Authors: Bevan Bronwyn , Mejias Sam , Rosin Mark , Wong Jen 
Published: February 2020

Abstract
The authors share an emerging analytical approach to designing and studying STEAM programs that focuses on how programs integrate the respective epistemic practices—the ways in which knowledge is constructed—of science and art. They share the rationale for moving beyond surface features of STEAM programs (e.g. putting textiles and electronics on the same table) to the discipline-specific ways in which participants engage in creative inquiry and production. They share a brief example from a public STEAM event to demonstrate the ways in which this approach can foster reflection and intentionality in the design and implementation of STEAM programs.
Collective Currents: Exploring Sustainability through a Collaborative and Interactive Installation
Authors: Brunvand Erik , Wischer Wendy 
Published: February 2020

Abstract
Water issues in the western United States include a long history of struggle, controversy and politics. Collaboration and compromise are required to achieve desirable outcomes in water quality and water rights. Collective Currents is an interactive art installation, developed collaboratively by a computer engineer and a multimedia artist, that explores the idea of cooperative experience in both literal and conceptual ways and creates an environment that makes reference to and engages the viewer to think about our ability to understand and solve environmental issues, specifically water quality and conservation, through collaboration.
Importance of Laplacian of Low-Level Warming for the Response of Precipitation to Climate Change over Tropical Oceans
Authors: Duffy Margaret L. , O’Gorman Paul A. , Back Larissa E. 
Published: February 2020

AbstractSeveral physical mechanisms have been proposed for projected changes in mean precipitation in the tropics under climate warming. In particular, the “wet-get-wetter” mechanism describes an amplification of the pattern of precipitation in a moister atmosphere, and the “warmer-get-wetter” mechanism describes enhanced upward motion and precipitation in regions where the increase in SST exceeds the tropical-mean increase. Studies of the current climate have shown that surface convergence over the tropical oceans is largely driven by horizontal gradients of low-level temperature, but the influence of these gradients on the precipitation response under climate warming has received little attention. Here, a simple model is applied to give a decomposition of changes in precipitation over tropical oceans in twenty-first-century climate model projections. The wet-get-wetter mechanism and changes in surface convergence are found to be of widespread importance, whereas the warmer-get-wetter mechanism is primarily limited to negative anomalies in the tropical southern Pacific. Furthermore, surface convergence is linked to gradients of boundary layer temperature using an atmospheric mixed layer model. Changes in surface convergence are found to be strongly related to changes in the Laplacian of boundary layer virtual temperature, and, to a lesser extent, the Laplacian of SST. Taken together, these results suggest that a “Laplacian-of-warming” mechanism is of comparable importance to wet get wetter and warmer get wetter for the response of precipitation to climate change over tropical oceans.
Impact of the Boreal Summer Intraseasonal Oscillation on the Diurnal Cycle of Precipitation near and over the Island of Luzon
Authors: Chudler Kyle , Xu Weixin , Rutledge Steven A. 
Published: February 2020

AbstractDuring the boreal summer, satellite-based precipitation estimates indicate a distinct maximum in rainfall off the west coast of the island of Luzon in the Philippines. Also occurring during the summer months is the boreal summer intraseasonal oscillation (BSISO), a main driver of intraseasonal variability in the region. This study investigates the diurnal variability of convective intensity, morphology, and precipitation coverage offshore and over the island of Luzon. The results are then composited by BSISO activity. Results of this study indicate that offshore precipitation is markedly increased during active BSISO phases, when strong low-level southwesterly monsoon winds bring increased moisture and enhanced convergence upwind of the island’s high terrain. A key finding of this work is the existence of an afternoon maximum in convection over Luzon even during active BSISO phases, when solar heating and instability are apparently reduced due to enhanced cloud cover. This result is important, as previous studies have shown in other areas of the tropics afternoon convection over landmasses is a key component to offshore precipitation. Although offshore precipitation is maximized in the evening hours during active phases, results indicate that precipitation frequently occurs over the ocean around the clock (both as organized systems and isolated, shallow showers), possibly owing to an increase in sensible and latent heat fluxes, vertical wind shear, and convergence of the monsoon flow with land features.
Overview of Castleman disease
Authors: Dispenzieri Angela , Fajgenbaum David C. 
Published: February 2020

AbstractCastleman disease (CD) describes a group of at least 4 disorders that share a spectrum of characteristic histopathological features but have a wide range of etiologies, presentations, treatments, and outcomes. CD includes unicentric CD (UCD) and multicentric CD (MCD), the latter of which is divided into idiopathic MCD (iMCD), human herpes virus-8 (HHV8)-associated MCD (HHV8-MCD), and polyneuropathy, organomegaly, endocrinopathy, monoclonal plasma cell disorder, skin changes (POEMS)-associated MCD (POEMS-MCD). iMCD can be further subclassified into iMCD–thrombocytopenia, ascites, reticulin fibrosis, renal dysfunction, organomegaly (iMCD-TAFRO) or iMCD–not otherwise specified (iMCD-NOS). Advances in diagnosis, classification, pathogenesis, and therapy are substantial since the original description of UCD by Benjamin Castleman in 1954. The advent of effective retroviral therapy and use of rituximab in HHV8-MCD have improved outcomes in HHV8-MCD. Anti–interleukin-6–directed therapies are highly effective in many iMCD patients, but additional therapies are required for refractory cases. Much of the recent progress has been coordinated by the Castleman Disease Collaborative Network (CDCN), and further progress will be made by continued engagement of physicians, scientists, and patients. Progress can also be facilitated by encouraging patients to self-enroll in the CDCN’s ACCELERATE natural history registry (#NCT02817997; www.CDCN.org/ACCELERATE).
New developments in diagnosis, prognostication, and treatment of advanced systemic mastocytosis
Authors: Reiter Andreas , George Tracy I. , Gotlib Jason 
Published: February 2020

AbstractSystemic mastocytosis (SM) has greatly benefited from the broad application of precision medicine techniques to hematolymphoid neoplasms. Sensitive detection of the recurrent KIT D816V mutation and use of next-generation sequencing (NGS) panels to profile the genetic landscape of SM variants have been critical adjuncts to the diagnosis and subclassification of SM, and development of clinical-molecular prognostic scoring systems. Multilineage KIT involvement and multimutated clones are characteristic of advanced SM (advSM), especially SM with an associated hematologic neoplasm (AHN). A major challenge is how to integrate conventional markers of mast cell disease burden (percentage of bone marrow mast cell infiltration and serum tryptase levels) with molecular data (serial monitoring of both KIT D816V variant allele frequency and NGS panels) to lend more diagnostic and prognostic clarity to the heterogeneous clinical presentations and natural histories of advSM. The approval of the multikinase/KIT inhibitor midostaurin has validated the paradigm of KIT inhibition in advSM, and the efficacy and safety of second-generation agents, such as the switch-control inhibitor ripretinib (DCC-2618) and the D816V-selective inhibitor avapritinib (BLU-285) are being further defined in ongoing clinical trials. Looking forward, perhaps the most fruitful marriage of the advances in molecular genetics and treatment will be the design of adaptive basket trials that combine histopathology and genetic profiling to individualize treatment approaches for patients with diverse AHNs and relapsed/refractory SM.
Pathobiology and treatment of lymphomatoid granulomatosis, a rare EBV-driven disorder
Authors: Melani Christopher , Jaffe Elaine S. , Wilson Wyndham H. 
Published: February 2020

Abstract
Lymphomatoid granulomatosis (LYG) is a rare Epstein-Barr virus (EBV)–driven B-cell lymphoproliferative disease (LPD). This disease is hypothesized to result from defective immune surveillance of EBV, with most patients showing evidence of immune dysfunction, despite no known primary immunodeficiency. Pathologically, LYG is graded by the number and density of EBV+ atypical B cells, and other characteristic findings include an angioinvasive/angiodestructive reactive T-cell infiltrate and various degrees of necrosis. Clinically, LYG universally involves the lungs with other common extranodal sites, including skin, central nervous system, liver, and kidneys. Nodal and/or bone marrow involvement is extremely rare and, if present, suggests an alternative diagnosis. Treatment selection is based on histologic grade and underlying pathobiology with low-grade disease hypothesized to be immune-dependent and typically polyclonal and high-grade disease to be immune-independent and typically oligoclonal or monoclonal. Methods of augmenting the immune response to EBV in low-grade LYG include treatment with interferon-α2b, whereas high-grade disease requires immunochemotherapy. Given the underlying defective immune surveillance of EBV, patients with high-grade disease may have a recurrence in the form of low-grade disease after immunochemotherapy, and those with low-grade disease may progress to high-grade disease after immune modulation, which can be effectively managed with crossover treatment. In patients with primary refractory disease or in those with multiple relapses, hematopoietic stem cell transplantation may be considered, but its efficacy is not well established. This review discusses the pathogenesis of LYG and highlights distinct histopathologic and clinical features that distinguish this disorder from other EBV+ B-cell LPDs and lymphomas. Treatment options, including immune modulation and combination immunochemotherapy, are discussed.
Daratumumab for systemic AL amyloidosis: prognostic factors and adverse outcome with nephrotic-range albuminuria
Authors: Kimmich Christoph R. , Terzer Tobias , Benner Axel , Dittrich Tobias , Veelken Kaya , Carpinteiro Alexander , Hansen Timon , Goldschmidt Hartmut , Seckinger Anja , Hose Dirk , Jauch Anna , Wörner Stefan , Beimler Jörg , Müller-Tidow Carsten , Hegenbart Ute , Schönland Stefan O. 
Published: February 2020

Abstract
Daratumumab has shown promising first results in systemic amyloid light-chain (AL) amyloidosis. We analyzed a consecutive series of 168 patients with advanced AL receiving either daratumumab/dexamethasone (DD, n = 106) or daratumumab/bortezomib/dexamethasone (DVD, n = 62). DD achieved a remission rate (RR) of 64% and a very good hematologic remission (VGHR) rate of 48% after 3 months. Median hematologic event-free survival (hemEFS) was 11.8 months and median overall survival (OS) was 25.6 months. DVD achieved a 66% RR and a 55% VGHR rate. Median hemEFS was 19.1 months and median OS had not been reached. Cardiac organ responses were noted in 22% with DD and 26% with DVD after 6 months. Infectious complications were common (Common Terminology Criteria [CTC] grade 3/4: DD 16%, DVD 18%) and likely related to a high rate of lymphocytopenia (CTC grade 3/4: DD 20%, DVD 17%). On univariable analysis, hyperdiploidy and gain 1q21 conferred an adverse factor for OS and hemEFS with DD, whereas translocation t(11;14) was associated with a better hemEFS. N-terminal prohormone of brain natriuretic peptide &gt;8500 ng/L could not be overcome for survival with each regimen. Multivariable Cox regression analysis revealed plasma cell dyscrasia (difference between serum free light chains [dFLC]) &gt;180 mg/L as an overall strong negative prognostic factor. Additionally, nephrotic-range albuminuria with an albumin-to-creatinine-ratio (ACR) &gt;220 mg/mmol was a significantly adverse factor for hemEFS (hazard ratio, 2.1 and 3.1) with DD and DVD. Daratumumab salvage therapy produced good results and remission rates challenging any therapy in advanced AL. Outcome is adversely influenced by the activity of the underlying plasma cell dyscrasia (dFLC) and nephrotic-range albuminuria (ACR).
A prospective phase 2 trial of daratumumab in patients with previously treated systemic light-chain amyloidosis
Authors: Roussel Murielle , Merlini Giampaolo , Chevret Sylvie , Arnulf Bertrand , Stoppa Anne Marie , Perrot Aurore , Palladini Giovanni , Karlin Lionel , Royer Bruno , Huart Antoine , Macro Margaret , Morel Pierre , Frenzel Laurent , Touzeau Cyrille , Boyle Eileen , Dorvaux Véronique , Le Bras Fabien , Lavergne David , Bridoux Frank , Jaccard Arnaud 
Published: February 2020

Abstract
Daratumumab is a human monoclonal antibody targeting CD38, an antigen uniformly expressed by plasma cells in multiple myeloma and light-chain amyloidosis (AL). We report the results of a prospective multicenter phase 2 study of daratumumab monotherapy in AL (NCT02816476). Forty previously treated AL patients with a difference between involved and uninvolved free light chains (dFLC) &gt;50 mg/L were included in 15 centers between September of 2016 and April of 2018. Patients received 6 28-day cycles of IV daratumumab, every week for cycles 1 and 2 and every 2 weeks for cycles 3 through 6. Median age was 69 years (range, 45-83). Twenty-six patients had ≥2 organs involved, with heart in 24 and kidney in 26. Median time from diagnosis to enrollment was 23 months (interquartile range, 4-122), with a median of 3 prior therapies (range, 1-5). At data cutoff (September of 2019), all patients discontinued therapy; 33 received the planned 6 cycles. Overall, 22 patients had hematological response, and 19 patients (47.5%) achieved very good partial response (dFLC &lt;40 mg/L) or better. Median time to hematological response was 1 week. Patients with no response after 4 doses were unlikely to respond further. Renal and cardiac responses occurred in 8 and 7 patients, respectively. Daratumumab was well tolerated, with no unexpected adverse events. With a median follow-up of 26 months, the 2-year overall survival rate was 74% (95% confidence interval, 62-81). Daratumumab monotherapy is associated with deep and rapid hematological responses in previously treated AL patients, with a good safety profile. Further studies of daratumumab in combination regimens are warranted.
Ferrostatin-1 alleviates lipopolysaccharide-induced acute lung injury via inhibiting ferroptosis
Authors: Liu Pengfei , Feng Yetong , Li Hanwei , Chen Xin , Wang Guangsuo , Xu Shiyuan , Li Yalan , Zhao Lei 
Published: February 2020

AbstractBackgroundFerroptosis is a newly recognized type of cell death, which is different from traditional necrosis, apoptosis or autophagic cell death. However, the position of ferroptosis in lipopolysaccharide (LPS)-induced acute lung injury (ALI) has not been explored intensively so far. In this study, we mainly analyzed the relationship between ferroptosis and LPS-induced ALI.MethodsIn this study, a human bronchial epithelial cell line, BEAS-2B, was treated with LPS and ferrostatin-1 (Fer-1, ferroptosis inhibitor). The cell viability was measured using CCK-8. Additionally, the levels of malondialdehyde (MDA), 4-hydroxynonenal (4-HNE), and iron, as well as the protein level of SLC7A11 and GPX4, were measured in different groups. To further confirm the in vitro results, an ALI model was induced by LPS in mice, and the therapeutic action of Fer-1 and ferroptosis level in lung tissues were evaluated.ResultsThe cell viability of BEAS-2B was down-regulated by LPS treatment, together with the ferroptosis markers SLC7A11 and GPX4, while the levels of MDA, 4-HNE and total iron were increased by LPS treatment in a dose-dependent manner, which could be rescued by Fer-1. The results of the in vivo experiment also indicated that Fer-1 exerted therapeutic action against LPS-induced ALI, and down-regulated the ferroptosis level in lung tissues.ConclusionsOur study indicated that ferroptosis has an important role in the progression of LPS-induced ALI, and ferroptosis may become a novel target in the treatment of ALI patients.
Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates
Authors: Harris R. Alan , Raveendran Muthuswamy , Worley Kim C. , Rogers Jeffrey 
Published: February 2020

Abstract
Background
Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression.

Results
We examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential.

Conclusions
The pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.
The use of taxon-specific reference databases compromises metagenomic classification
Authors: R. Marcelino Vanessa , Holmes Edward C. , Sorrell Tania C. 
Published: February 2020

AbstractA recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of samples. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan’s fungal reference database with one containing genome sequences of amphibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxon-specific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.
Transcriptome analysis reveals the defense mechanism of cotton against Verticillium dahliae in the presence of the biocontrol fungus Chaetomium globosum CEF-082
Authors: Zhang Yun , Yang Na , Zhao Lihong , Zhu Heqin , Tang Canming 
Published: February 2020

Abstract
Background
Verticillium wilt of cotton is a serious soil-borne disease that causes a substantial reduction in cotton yields. A previous study showed that the endophytic fungus Chaetomium globosum CEF-082 could control Verticillium wilt of cotton, and induce a defense response in cotton plants. However, the comprehensive molecular mechanism governing this response is not yet clear.

Results
To study the signalling mechanism induced by CEF-082, the transcriptome of cotton seedlings pretreated with CEF-082 was sequenced. The results revealed 5638 DEGs at 24 h post inoculation with CEF-082, and 2921 and 2153 DEGs at 12 and 48 h post inoculation with Verticillium dahliae, respectively. At 24 h post inoculation with CEF-082, KEGG enrichment analysis indicated that the DEGs were enriched mainly in the plant-pathogen interaction, MAPK signalling pathway-plant, flavonoid biosynthesis, and phenylpropanoid biosynthesis pathways. There were 1209 DEGs specifically induced only in cotton plants inoculated with V. dahliae in the presence of the biocontrol fungus CEF-082, and not when cotton plants were only inoculated with V. dahliae. GO analysis revealed that these DEGs were enriched mainly in the following terms: ROS metabolic process, H2O2 metabolic process, defense response, superoxide dismutase activity, and antioxidant activity. Moreover, many genes, such as ERF, CNGC, FLS2, MYB, GST and CML, that regulate crucial points in defense-related pathways were identified and may contribute to V. dahliae resistance in cotton. These results provide a basis for understanding the molecular mechanism by which the biocontrol fungus CEF-082 increases the resistance of cotton to Verticillium wilt.

Conclusions
The results of this study showed that CEF-082 could regulate multiple metabolic pathways in cotton. After treatment with V. dahliae, the defense response of cotton plants preinoculated with CEF-082 was strengthened.