bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test-retest reliability of the human functional connectome over consecutive days: identifying highly reliable portions and assessing the impact of methodological choices
Authors: Tozzi Leonardo , Fleming Scott L. , Taylor Zachary D. , Raterink Cooper D. , Williams Leanne M. 
Published: May 2020

Abstract
Countless studies have advanced our understanding of the human brain and its organization by using functional magnetic resonance imaging (fMRI) to derive network representations of human brain function. However, we do not know to what extent these “functional connectomes” are reliable over time. In a large public sample of healthy participants (N = 833) scanned on two consecutive days, we assessed the test-retest reliability of fMRI functional connectivity and the consequences on reliability of three common sources of variation in analysis workflows: atlas choice, global signal regression, and thresholding. By adopting the intraclass correlation coefficient as a metric, we demonstrate that only a small portion of the functional connectome is characterized by good (6–8%) to excellent (0.08–0.14%) reliability. Connectivity between prefrontal, parietal, and temporal areas is especially reliable, but also average connectivity within known networks has good reliability. In general, while unreliable edges are weak, reliable edges are not necessarily strong. Methodologically, reliability of edges varies between atlases, global signal regression decreases reliability for networks and most edges (but increases it for some), and thresholding based on connection strength reduces reliability. Focusing on the reliable portion of the connectome could help quantify brain trait-like features and investigate individual differences using functional neuroimaging.
Response of specialized birds to reed-bed aging in a Mediterranean wetland: Significant changes in bird biomass after two decades
Authors: Battisti Corrado , Grosso Giacomo , Ioni Susanna , Zullo Francesco , Cerfolli Fulvio 
Published: May 2020

Abstract
Traditional fish farming carried out in wetland is declining in many countries of Mediterranean Europe. This decline can lead to a lack of management of the reeds that tend to age progressively. In this work we compared, through a wide temporal range (2001-2019), the densities of four habitat-specialized birds (warblers), strictly linked to Phragmites australis reed-beds in a coastal wetland on the Tyrrhenian central Italy. In this wetland, following the abandonment of fish farming, the average density of reeds significantly decreased, and both the average reed diameter and habitat heterogeneity showed a significant increase. Comparing 2001 to 2019, we observed an increase in the total density of breeding warblers. The two species of Acrocephalus (scirpaceus and arundinaceus), and Cettia cetti showed a marked increase in density, while Cisticola juncidis showed a clear decrease. More particularly, a significant increase in Cettia cetti (p < 0.001) and a decrease in Cisticola juncidis (p < 0.05) emerged when comparing bird biomasses. Species diversity and evenness were more high in 2019 than in 2001. Our data suggest that: (i) these species could be considered indicators of long-term reed-bed changes and (ii) their biomass may be used as a more effective metric when compared to abundance.
Best Practice Strategies for Process Studies Designed to Improve Climate Modeling
Authors: Sprintall Janet , Coles Victoria J. , Reed Kevin A. , Butler Amy H. , Foltz Gregory R. , Penny Stephen G. , Seo Hyodae 
Published: May 2020

AbstractProcess studies are designed to improve our understanding of poorly described physical processes that are central to the behavior of the climate system. They typically include coordinated efforts of intensive field campaigns in the atmosphere and/or ocean to collect a carefully planned set of in situ observations. Ideally the observational portion of a process study is paired with numerical modeling efforts that lead to better representation of a poorly simulated or previously neglected physical process in operational and research models. This article provides a framework of best practices to help guide scientists in carrying out more productive, collaborative, and successful process studies. Topics include the planning and implementation of a process study and the associated web of logistical challenges; the development of focused science goals and testable hypotheses; and the importance of assembling an integrated and compatible team with a diversity of social identity, gender, career stage, and scientific background. Guidelines are also provided for scientific data management, dissemination, and stewardship. Above all, developing trust and continual communication within the science team during the field campaign and analysis phase are key for process studies. We consider a successful process study as one that ultimately will improve our quantitative understanding of the mechanisms responsible for climate variability and enhance our ability to represent them in climate models.
Why Does the Deep Western Boundary Current “Leak” around Flemish Cap?
Authors: Solodoch Aviv , McWilliams James C. , Stewart Andrew L. , Gula Jonathan , Renault Lionel 
Published: May 2020

AbstractThe southward-flowing deep limb of the Atlantic meridional overturning circulation is composed of both the deep western boundary current (DWBC) and interior pathways. The latter are fed by “leakiness” from the DWBC in the Newfoundland Basin. However, the cause of this leakiness has not yet been explored mechanistically. Here the statistics and dynamics of the DWBC leakiness in the Newfoundland Basin are explored using two float datasets and a high-resolution numerical model. The float leakiness around Flemish Cap is found to be concentrated in several areas (hot spots) that are collocated with bathymetric curvature and steepening. Numerical particle advection experiments reveal that the Lagrangian mean velocity is offshore at these hot spots, while Lagrangian variability is minimal locally. Furthermore, model Eulerian mean streamlines separate from the DWBC to the interior at the leakiness hot spots. This suggests that the leakiness of Lagrangian particles is primarily accomplished by an Eulerian mean flow across isobaths, though eddies serve to transfer around 50% of the Lagrangian particles to the leakiness hot spots via chaotic advection, and rectified eddy transport accounts for around 50% of the offshore flow along the southern face of Flemish Cap. Analysis of the model’s energy and potential vorticity budgets suggests that the flow is baroclinically unstable after separation, but that the resulting eddies induce modest modifications of the mean potential vorticity along streamlines. These results suggest that mean uncompensated leakiness occurs mostly through inertial separation, for which a scaling analysis is presented. Implications for leakiness of other major boundary current systems are discussed.
Preliminary Study of Land–Sea Microphysics Associated with the East Asian Summer Monsoon Rainband and Its Application to GPM DPR
Authors: Zhang Yun , Wu Zuhang , Zhang Lifeng , Xie Yanqiong , Huang Yanbin , Zheng Hepeng 
Published: May 2020

AbstractRaindrop size distribution (DSD) characteristics during the East Asian summer monsoon (EASM) were studied, using measurements from three OTT Particle Size Velocity (Parsivel) disdrometers in Nanjing, Chuzhou, and the northwestern Pacific (NWP), respectively. Western and eastern parts of the monsoon rainband were separated for a comparative study of the DSD variability. Along with disdrometer data, GPM Dual-Frequency Precipitation Radar (DPR), Fengyun-2E (FY-2E), MODIS, GPCP, ERA-Interim, and in situ radiosonde datasets are combined to illustrate the possible microphysical mechanisms for the significant DSD variability in two parts, in terms of convective intensity, cloud structure, and aerosol effects. The DSD characteristics of six rain-rate classes and two rainfall categories (convective and stratiform) were studied. The western part has larger mass-weighted mean diameter Dm while smaller normalized intercept log10(Nw) than the eastern part, and the convective clusters of the western part (land) could be identified more maritime-like than continental-like due to moisture transport from the tropical ocean, while that of the eastern part (sea) is between maritime-like and continental-like. Cross validation of GPM rainfall products are implemented based on surface disdrometer observations. DPR products manifest better performance over sea than land areas of the EASM rainband. Empirical Dm–Ze and Nw–Dm relations were also derived preliminarily to improve the GPM rain-retrieval algorithms in the EASM season.
External Sector: Between Congestion and Sanctions—‘Syrian Economy Case, 1987–2018’
Authors: Suliman Forat , Khwanda Homam 
Published: May 2020

Since the outbreak of the Syrian crisis in March 2011, the USA, European Union, Arab League and several other regulatory entities imposed negative economic sanctions on Syria—some of the most comprehensive ever implemented. This article first provides an assessment of Syrian foreign trade sector during the reform period of the 2000s and its impact on economic growth. Second, it estimates the impact of sanctions and conflict on the trade sector of the Syrian economy. The analysis is conducted using a panel-gravity model between Syria and 78 trading partners (1987–2017). Multilateral sanctions and conflict-related disruptions demonstrate a large significant negative impact on Syria-bilateral trade flow by 65 per cent. We attempt to find out whether the Syrian economy was able to divert trade away from Europe and/or conduct de-Europeanisation. Findings confirm that the Syrian economy was unable to divert trade flow to Asian and other countries due to the conflict-related congestion and distance factor. JEL: C33, F10
Secondary myelodysplastic syndrome and leukemia in acquired aplastic anemia and paroxysmal nocturnal hemoglobinuria
Authors: Sun Lova , Babushok Daria V. 
Published: May 2020

AbstractAcquired aplastic anemia (AA) and paroxysmal nocturnal hemoglobinuria (PNH) are pathogenically related nonmalignant bone marrow failure disorders linked to T-cell–mediated autoimmunity; they are associated with an increased risk of secondary myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Approximately 15% to 20% of AA patients and 2% to 6% of PNH patients go on to develop secondary MDS/AML by 10 years of follow-up. Factors determining an individual patient’s risk of malignant transformation remain poorly defined. Recent studies identified nearly ubiquitous clonal hematopoiesis (CH) in AA patients. Similarly, CH with additional, non-PIGA, somatic alterations occurs in the majority of patients with PNH. Factors associated with progression to secondary MDS/AML include longer duration of disease, increased telomere attrition, presence of adverse prognostic mutations, and multiple mutations, particularly when occurring early in the disease course and at a high allelic burden. Here, we will review the prevalence and characteristics of somatic alterations in AA and PNH and will explore their prognostic significance and mechanisms of clonal selection. We will then discuss the available data on post-AA and post-PNH progression to secondary MDS/AML and provide practical guidance for approaching patients with PNH and AA who have CH.
Impact of Myc in HIV-associated non-Hodgkin lymphomas treated with EPOCH and outcomes with vorinostat (AMC-075 trial)
Authors: Ramos Juan C. , Sparano Joseph A. , Chadburn Amy , Reid Erin G. , Ambinder Richard F. , Siegel Eric R. , Moore Page C. , Rubinstein Paul G. , Durand Christine M. , Cesarman Ethel , Aboulafia David , Baiocchi Robert , Ratner Lee , Kaplan Lawrence , Capoferri Adam A. , Lee Jeannette Y. , Mitsuyasu Ronald , Noy Ariela 
Published: May 2020

Abstract
EPOCH (etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin) is a preferred regimen for HIV-non-Hodgkin lymphomas (HIV-NHLs), which are frequently Epstein-Barr virus (EBV) positive or human herpesvirus type-8 (HHV-8) positive. The histone deacetylase (HDAC) inhibitor vorinostat disrupts EBV/HHV-8 latency, enhances chemotherapy-induced cell death, and may clear HIV reservoirs. We performed a randomized phase 2 study in 90 patients (45 per study arm) with aggressive HIV-NHLs, using dose-adjusted EPOCH (plus rituximab if CD20+), alone or with 300 mg vorinostat, administered on days 1 to 5 of each cycle. Up to 1 prior cycle of systemic chemotherapy was allowed. The primary end point was complete response (CR). In 86 evaluable patients with diffuse large B-cell lymphoma (DLBCL; n = 61), plasmablastic lymphoma (n = 15), primary effusion lymphoma (n = 7), unclassifiable B-cell NHL (n = 2), and Burkitt lymphoma (n = 1), CR rates were 74% vs 68% for EPOCH vs EPOCH-vorinostat (P = .72). Patients with a CD4+ count &lt;200 cells/mm3 had a lower CR rate. EPOCH-vorinostat did not eliminate HIV reservoirs, resulted in more frequent grade 4 neutropenia and thrombocytopenia, and did not affect survival. Overall, patients with Myc+ DLBCL had a significantly lower EFS. A low diagnosis-to-treatment interval (DTI) was also associated with inferior outcomes, whereas preprotocol therapy had no negative impact. In summary, EPOCH had broad efficacy against highly aggressive HIV-NHLs, whereas vorinostat had no benefit; patients with Myc-driven DLBCL, low CD4, and low DTI had less favorable outcomes. Permitting preprotocol therapy facilitated accruals without compromising outcomes. This trial was registered at www.clinicaltrials.gov as #NCT0119384.
Clinical outcomes of older patients with AML receiving hypomethylating agents: a large population-based study in the United States
Authors: Zeidan Amer M. , Wang Rong , Wang Xiaoyi , Shallis Rory M. , Podoltsev Nikolai A. , Bewersdorf Jan P. , Huntington Scott F. , Neparidze Natalia , Giri Smith , Gore Steven D. , Davidoff Amy J. , Ma Xiaomei 
Published: May 2020

Abstract
The hypomethylating agents (HMAs) azacitidine and decitabine have been the de facto standard of care for patients with acute myeloid leukemia (AML) who are unfit for intensive therapy. Using the Surveillance, Epidemiology, and End Results-Medicare linked database, we identified 2263 older adults (age ≥66 years) diagnosed with AML during 2005-2015 who received a first-line HMA; 1154 (51%) received azacitidine, and 1109 (49%) received decitabine. Median survival from diagnosis was 7.1 and 8.2 months (P &lt; .01) for azacitidine- and decitabine-treated patients, respectively. Mortality risk was higher with azacitidine vs decitabine (hazard ratio [HR], 1.11; 95% confidence interval [CI], 1.01-1.21; P = .02). The findings were similar when evaluating only patients completing ≥4 cycles (42% of patients treated with either azacitidine or decitabine). These findings lost significance when evaluating those completing a standard 7-day schedule of azacitidine (34%) vs 5-day schedule for decitabine (66%) (HR, 0.95; 95% CI, 0.83-1.08; P = .43). Red blood cell (RBC) transfusion independence (TI) was achieved in one-third of patients with no difference between the 2 HMAs. In conclusion, the majority of older AML patients did not receive the minimum of 4 cycles of HMA often needed to elicit clinical benefit. We observed no clinically meaningful differences between azacitidine- and decitabine-treated patients in their achievement of RBC TI or survival.
Cloning of Hynobius lichenatus (Tohoku hynobiid salamander) p53 and analysis of its expression in response to radiation
Authors: Kamada Toshiki , Une Yumi , Matsui Kumi , Fuma Shoichi , Ikeda Teruo , Okamoto Mariko 
Published: May 2020

Abstract
Background
Caudata species such as salamanders are easily affected by environmental changes, which can drastically reduce their population. The effects of acute X-rays and chronic γ-irradiation on Hynobius lichenatus, the Japanese Tohoku hynobiid salamander, are known. However, the expression of radiation-inducible genes, such as the DNA-damage checkpoint response gene p53, has not been analyzed in H. lichenatus. This has not occurred because there is no established method for mRNA quantification in H. lichenatus due to a lack of information on available nucleotide sequences corresponding to both radiation-inducible genes and endogenous control genes such as ACTB (β-actin).

Results
In this study, we aimed to evaluate the effects of radiation on gene expression in H. lichenatus. Using RNA extracted from irradiated salamanders, we performed rapid amplification of cDNA ends (RACE) and cloned H. lichenatus β-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and p53. We confirmed that the cloned cDNAs were able to synthesize salamander proteins by western blotting after transfection into cultured HEK293 cells. Proliferation assays using HEK293 cells stably expressing H. lichenatus p53 protein showed that this protein has antiproliferative effects, similar to that of mammalian p53. Furthermore, RT-qPCR analysis using gene-specific primers revealed that p53 mRNA expression in H. lichenatus was upregulated upon exposure to radiation.

Conclusion
Our results suggest that H. lichenatus p53 protein take an important role in regulating the cellular responses to various stimuli as mammalian p53 does. Furthermore, our study provides novel data to select appropriate primers to analyze internal control mRNA expression in H. lichenatus and to evaluate p53 expression as a marker of radiation and environmental stimuli.
Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing
Authors: Parveen Alia , Jackson Christa D. , Dey Shatovisha , Tarrant Katy , Anthony Nicholas , Rhoads Douglas D. 
Published: May 2020

Abstract
Background
Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations.

Results
The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype.

Conclusions
The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.
New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions
Authors: De Meur Quentin , Deutschbauer Adam , Koch Matthias , Bayon-Vicente Guillaume , Cabecas Segura Paloma , Wattiez Ruddy , Leroy Baptiste 
Published: May 2020

Abstract
Background
The great metabolic versatility of the purple non-sulfur bacteria is of particular interest in green technology. Rhodospirillum rubrum S1H is an α-proteobacterium that is capable of photoheterotrophic assimilation of volatile fatty acids (VFAs). Butyrate is one of the most abundant VFAs produced during fermentative biodegradation of crude organic wastes in various applications. While there is a growing understanding of the photoassimilation of acetate, another abundantly produced VFA, the mechanisms involved in the photoheterotrophic metabolism of butyrate remain poorly studied.

Results
In this work, we used proteomic and functional genomic analyses to determine potential metabolic pathways involved in the photoassimilation of butyrate. We propose that a fraction of butyrate is converted to acetyl-CoA, a reaction shared with polyhydroxybutyrate metabolism, while the other fraction supplies the ethylmalonyl-CoA (EMC) pathway used as an anaplerotic pathway to replenish the TCA cycle. Surprisingly, we also highlighted a potential assimilation pathway, through isoleucine synthesis and degradation, allowing the conversion of acetyl-CoA to propionyl-CoA. We tentatively named this pathway the methylbutanoyl-CoA pathway (MBC). An increase in isoleucine abundance was observed during the early growth phase under butyrate condition. Nevertheless, while the EMC and MBC pathways appeared to be concomitantly used, a genome-wide mutant fitness assay highlighted the EMC pathway as the only pathway strictly required for the assimilation of butyrate.

Conclusion
Photoheterotrophic growth of Rs. rubrum with butyrate as sole carbon source requires a functional EMC pathway. In addition, a new assimilation pathway involving isoleucine synthesis and degradation, named the methylbutanoyl-CoA (MBC) pathway, could also be involved in the assimilation of this volatile fatty acid by Rs. rubrum.