bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Diagnostic Accuracy of PET(CT) in Patients With Neuroblastoma: A Meta-Analysis and Systematic Review
Authors: Li Huai-Feng , Mao Hai-Jia , Zhao Li , Guo Dan-Ling , Chen Bo , Yang Jian-Feng 
Published: January 2020

Objective
The objective of this study was to evaluate the overall diagnostic value of PET(CT) in patients with neuroblastoma (NB) based on qualified studies.

Methods
PubMed, Cochrane, and Embase database were searched by the index words to identify the qualified studies, and relevant literature sources were also searched. The latest research was performed in April 2019. Heterogeneity of the included studies was tested, which was used to select proper effect model to calculate pooled weighted sensitivity, specificity, and diagnostic odds ratio (DOR). Summary receiver operating characteristic (SROC) analyses were also performed.

Results
Eleven studies with 580 patients were involved in the meta-analysis to explore the diagnostic accuracy of PET(CT) for NB. PET(CT) has high diagnostic accuracy of NB: the global sensitivity was 91% (95% confidence interval [CI], 86%–94%), the global specificity was 78% (95% CI, 66%–86%), the global positive likelihood ratio was 4.07 (95% CI, 2.54–6.50), the global negative likelihood ratio was 0.12 (95% CI, 0.08–0.18), the global DOR was 27.43 (95% CI, 14.45–52.07), and the area under the SROC was high (area under the curve, 0.93; 95% CI, 0.90–0.95). Besides this, PET(CT) has high diagnostic accuracy of primary NB: the global sensitivity was 86% (95% CI, 73%–93%), the global specificity was 82% (95% CI, 57%–94%), the global positive likelihood ratio was 4.90 (95% CI, 1.63–14.72), the global negative likelihood ratio was 0.17 (95% CI, 0.07–0.40), the global DOR was 25.427 (95% CI, 3.988–162.098), and the area under the SROC was high (area under the curve, 0.91; 95% CI, 0.88–0.93). However, there has no significant accuracy of PET(CT) in NB with bone marrow.

Conclusions
This study provides a systematic review and meta-analysis of diagnostic accuracy studies of PET(CT) for NB. The results indicated that PET(CT) is a highly accurate diagnostic tool for NB.
In-SilicoInvestigation of Luminol, Its Analogues and Improved Mechanism of Chemiluminescence for Blood Identification Beyond Forensics
Authors: Fatoki Toluwase Hezekiah 
Published: January 2020

ABSTRACTThis study aimed to discover chemiluminescent analogues of luminol, understand their molecular binding to hemoglobin of bloodstains in the household crime, and the mechanism of chemiluminescence. Similarity and clustering analyses of luminol analogues were conducted, and molecular docking was carried out on hemoglobin fromHomo sapiensand other four domestic organism namelyGallus gallus, Drosophila melanogaster, Rattus norvegicus,andCanis familiaris. The results show that the order of overall binding score isD. melanogaster > H. sapiens > C. familiaris > R. norvegicus > G. gallus. Seven compounds namely ZINC16958228, ZINC17023010, ZINC19915427, ZINC34928954, ZINC19915369, ZINC19915444, and ZINC82294978, were found to be consistently stable in binding to diverse hemoglobin and possibly have chemiluminescence than luminol. The amino acid residues involved in the interaction of human hemoglobin with the 30 test compounds, show that His45, Lys61, Asn68, Val73, Met76, Pro77, Ala79, Ala82, Leu83, Pro95, Phe98, Lys99, Ser102, Ser133, Ala134, and Thr134 are significant in the mechanism of action of presumptive test compounds. The improved mechanism of chemiluminescent identification of blood hypothesized that nitrite interact with the Fe(II) heme, with the cleavage of a hydroxide ion and the formation of the nitrosonium cation in peroxidase reaction. It was proposed that degradation of rhombic heme complex to fluorescent products is possibly inhibited by nitric oxide from the test compound luminol. This study provides novel insight on the luminol and its actual mechanism for broader possible applications of luminol with careful development of new methodologies.
Ribo-ODDR: Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs in Ribo-seq
Authors: Alkan Ferhat , Silva Joana , Barberà Eric Pintó , Faller William J. 
Published: January 2020

AbstractRibosome profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet, several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of ribosomal RNA (rRNA) fragments, which frequently make up more than 90% of sequencing reads if not depleted. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, such kits may perform suboptimally in Ribo-seq. There is therefore potential to significantly increase the information that can be gleaned from Ribo-seq experiments. Here we show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a “one-size-fits-all” approach may result in inefficient rRNA depletion. In order to overcome this, it is possible to use custom-designed biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos. We have developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We show that Ribo-ODDR designed oligos lead to a significant increase in rRNA depletion, and increased sequencing depth as a result, providing substantial information that would otherwise have been lost. Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR
Windows out of Africa: A 300,000-year chronology of climatically plausible human contact with Eurasia
Authors: Beyer Robert M. , Krapp Mario , Eriksson Anders , Manica Andrea 
Published: January 2020

AbstractWhilst an African origin for Anatomically Modern Humans is well established1, the timings of their expansions into Eurasia are the subject to heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA2. Here, we estimate potential timings and routes out of Africa by deriving anthropologically and ecologically plausible precipitation requirements for human existence, and applying them to high-resolution palaeoclimate reconstructions for the past 300k years. We find that exit routes and timings previously suggested based on archaeological and genetic evidence coincide precisely with the presence of sufficiently wet corridors into Eurasia, while the gaps between the proposed exit timings co-occur with periods of insufficient rainfall. This demonstrates the key role that palaeoclimatic conditions played for out-of-Africa expansions. The challenging environmental conditions outside of Africa that occurred between windows of potential contact, coupled with the lack of a demographic rescue effect from migration and possible competition with other hominins, likely explain the demise of early colonists prior to the large-scale colonisation of the world beginning from ∼65kya.
The Nigro-Thalamic Projection contributes to the Control of Action Initiation Timing
Authors: Catanese Julien , Jaeger Dieter 
Published: January 2020

ABSTRACTThe nigro-thalamic pathway is one of the main outputs from the basal ganglia, known to be involved in action selection, learning motor skills, and/or control the vigor of actions. However, the specific function of the nigral input to the motor thalamus remains unclear. Using a combination of in vivo electrophysiological recordings from motor thalamic neurons and optogenetic activation of nigral inputs in behaving head-fixed mice, we determined that this pathway is primarily involved in the proper timing of the release of goal directed actions. At the behavioral level, we were able to reduce the amount of impulsive licking by activating thalamic terminals. We describe changes in thalamic neuronal activity explaining this effect and propose a parsimonious model to account for our observations. These results provide new insight in the circuitry for timing control, a critical part of motor planning, and reveal a potential new target to modulate impulsivity.
Dissociation of connectivity for syntactic irregularity and perceptual ambiguity in musical chord stimuli
Authors: Kim Chan Hee , Jin Seung-Hyun , Kim June Sic , Kim Youn , Yi Suk Won , Chung Chun Kee 
Published: January 2020

AbstractPreviously syntactic irregularity has been most studied with chord sequences. However, the same chord may be interpreted as having different harmonic functions, implying perceptual ambiguity. Hence, syntactic irregularity and perceptual ambiguity may be processed simultaneously. We devised 3 different 5-chord sequences in which the ending chord differed with the tonic (T), submediant (SM), and supertonic (ST). In terms of syntactic regularity, T is most regular, ST is most irregular. However, in terms of perceptual ambiguity, the most irregular ST had the salient highest voice. Therefore, the SM was the most ambiguous condition. We investigated how the human brain separates syntactic irregularity and perceptual ambiguity in terms of effective connectivity in bilateral inferior frontal gyri (IFGs) and superior temporal gyri (STGs) with magnetoencephalography in 19 subjects. Correct rate was lower for the most ambiguous chord (SM) (P= 0.020) as expected. Connectivity from the right to the left IFG was enhanced for the most irregular chord (ST) (P= 0.024, false discovery rate (FDR) corrected), whereas connectivity from the right to the left STG was enhanced for the most ambiguous chord (SM) (P< 0.001, FDR corrected). The correct rate was negatively correlated with connectivity in the STG, further reflecting perceptual ambiguity (P= 0.026). We found that syntactic irregularity and perceptual ambiguity in music are dissociated in connectivity between bilateral IFGs and STGs, respectively.Significance StatementWe provide the first neurophysiological evidence of the processing of perceptual ambiguity, other than syntactic irregularity, implied in musical chords. We found that the notion of “perceptually ambiguity” is applicable to musical chord stimuli different in syntactic irregularity, and that perceptual ambiguity is separate from syntactic irregularity. Our data demonstrate that the brain interprets the three conditions of musical chords as both “from regular to irregular” and “from ambiguous to unambiguous” conditions simultaneously. This study is the first to unveil dissociation of connectivity by syntactic irregularity and perceptual ambiguity involved in musical chord stimuli.
Cross-sectional volumes and trajectories of the human brain, gray matter, white matter and cerebrospinal fluid in 9,473 typically aging adults
Authors: Irimia Andrei 
Published: January 2020

AbstractAccurate knowledge of adult human brain volume (BV) is critical for studies of aging- and disease-related brain alterations, and for monitoring the trajectories of neural and cognitive functions in conditions like Alzheimer’s disease and traumatic brain injury. This scoping meta-analysis aggregates normative reference values for BV and three related volumetrics—gray matter volume (GMV), white matter volume (WMV) and cerebrospinal fluid volume (CSFV)—from typically-aging adults studied cross-sectionally using magnetic resonance imaging (MRI). Drawing from an aggregate sample of 9,473 adults, this study provides (A) regression coefficientsβdescribing the age-dependent trajectories of volumetric measures by sex within the range from 20 to 70 years based on both linear and quadratic models, and (B) average values for BV, GMV, WMV and CSFV at the representative ages of 20 (young age), 45 (middle age) and 70 (old age). The results provided synthesize ∼20 years of brain volumetrics research and allow one to estimate BV at any age between 20 and 70. Importantly, however, such estimates should be used and interpreted with caution because they depend on MRI hardware specifications (e.g. scanner manufacturer, magnetic field strength), data acquisition parameters (e.g. spatial resolution, weighting), and brain segmentation algorithms. Guidelines are proposed to facilitate future meta- and mega-analyses of brain volumetrics.Disclosure statementThe author declares that he has no actual or potential conflicts of interest.
Patch size distribution and network connectivity affect species invasion dynamics in dendritic networks
Authors: Holenstein Kathrin , Harvey Eric , Altermatt Florian 
Published: January 2020

AbstractBiological invasions are globally affecting ecosystems, causing local species loss and altering ecosystem functioning. Understanding the success and unfolding of such biological invasions is thus of high priority. Both local properties and the spatial network structure have been shown to be determinants of invasion success, and the identification of spatial invasion hubs directly promoting invasion dynamics is gaining attention. Spatial dynamics, however, could also indirectly alter invasion success by shaping local community structure: in many ecosystems, such as riverine networks, regional properties such as patch size distribution are known drivers of local community structures, which themselves may affect the establishment success of invading species. Using microcosm experiments in dendritic networks, we disentangled how patch size distribution and dispersal along specific network topologies shaped local communities, and, subsequently, affected the establishment success of invading species. We find that inherent patch size distributions shaped composition and diversity of local communities, and, subsequently, modulated invasion success. Specifically, the relationship between local diversity and invasion success changed across an increasing patch size gradient from a negative to a positive correlation, while overall increasing patch size reduced invasion success. Connectivity did not have a direct effect on invasion success but indirectly affected invasions by shaping diversity patterns in the whole network. Our results emphasize the relevance of indirect, landscape-level effects on species invasions, which need to be considered in the management of spatial habitat networks.
Spatially organized genomic and physiological heterogeneity of the olfactory bulb mitral cell layer
Authors: Paseltiner Daniel , Loeffler Henry , Andonian Alex , Leberman Abigail , Gould Travis J. , Castro Jason B. 
Published: January 2020

AbstractSensory inputs to the dorsal vs ventral olfactory bulb derive from distinct receptor families, and drive distinct behaviors. To address whether second-order OB neurons and circuits exhibit matching heterogeneity for input-specific readout, we clustered spatial expression profiles of >2,000 genes from the mitral cell layer (MCL). We observed clear dorsal and ventral clusters, together with dorsoventral differences in mitral cell physiology. Bulbar circuits may therefore be tuned for zone-specific computation.
Toward an understanding of the relation between gene regulation and 3D genome organization
Authors: Tian Hao , Yang Ying , Liu Sirui , Quan Hui , Gao Yi Qin 
Published: January 2020

AbstractThe development and usage of chromosome conformation capture technologies have provided great details on 3D genome organization and provide great opportunities to understand how gene regulation is affected by the 3D chromatin structure. Previously, we identified two types of sequence domains, CGI forest and CGI prairie, which tend to segregate spatially, but to different extent in different tissues/cell states. To further quantify the association of domain segregation with gene regulation and differentiation, we analyzed in this study the distribution of genes of different tissue specificities along the linear genome, and found that the distribution patterns are distinctly different in forests and prairies. The tissue-specific genes (TSGs) are significantly enriched in the latter but not in the former and genes of similar expression profiles among different cell types (co-activation/repression) also tend to cluster in specific prairies. We then analyzed the correlation between gene expression and the spatial contact revealed in Hi-C measurement. Tissue-specific forest-prairie contact formation was found to correlate with the regulation of the TSGs, in particular those in the prairie domains, pointing to the important role gene positioning, in the linear DNA sequence as well as in 3D chromatin structure, plays in gene regulatory network formation.
Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes
Authors: Mutte Sumanth Kumar , Weijers Dolf 
Published: January 2020

ABSTRACTProtein oligomerization is a fundamental process to build complex functional modules. Domains that facilitate the oligomerization process are diverse and widespread in nature across all kingdoms of life. One such domain is the Phox and Bem1 (PB1) domain, which is functionally (relatively) well understood in the animal kingdom. However, beyond animals, neither the origin nor the evolutionary patterns of PB1-containing proteins are understood. While PB1 domain proteins have been found in other kingdoms, including plants, it is unclear how these relate to animal PB1 proteins.To address this question, we utilized large transcriptome datasets along with the proteomes of a broad range of species. We discovered eight PB1 domain-containing protein families in plants, along with three each in Protozoa and Chromista and four families in Fungi. Studying the deep evolutionary history of PB1 domains throughout eukaryotes revealed the presence of at least two, but likely three, ancestral PB1 copies in the Last Eukaryotic Common Ancestor (LECA). These three ancestral copies gave rise to multiple orthologues later in evolution. Tertiary structural models of these plant PB1 families, combined with Random Forest based classification, indicated family-specific differences attributed to the length of PB1 domain and the proportion of β-sheets.This study identifies novel PB1 families and reveals considerable complexity in the protein oligomerization potential at the origin of eukaryotes. The newly identified relationships provide an evolutionary basis to understand the diverse functional interactions of key regulatory proteins carrying PB1 domains across eukaryotic life.
Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis
Authors: Xue Yue , Yang Ying , Tian Hao , Quan Hui , Liu Sirui , Zhang Ling , Gao Yi Qin 
Published: January 2020

AbstractThe three-dimensional (3D) chromatin structure, together with DNA methylation and other epigenetic marks, profoundly affects gene expression and displays abnormal behaviors in cancer cells. We elucidated the chromatin architecture remodeling in carcinogenesis from the perspective of spatial interactions between CGI forest and prairie domains, which are two types of megabase-sized domains defined by different sequence features but show distinct epigenetic and transcriptional patterns. DNA sequence strongly affects chromosome spatial interaction, DNA methylation and gene expression. Globally, forests and prairies show enhanced spatial segregation in cancer cells and such structural changes are accordant with the alteration of CGI interactions and domain boundary insulation, which could affect vital cancer-related properties. As the cancer progresses, a gradual increase of the DNA methylation difference between the two types of DNA domains is also observed for many different types of cancers. These observations are consistent with the change of transcriptional level differences of genes in these two domains, suggesting a highly-connected global structural, epigenetic and transcriptional activity changes in carcinogenesis.
A genome-wide association study highlights a regulatory role forIFNG-AS1contributing to cutaneous leishmaniasis in Brazil
Authors: Castellucci Léa C. , Almeida Lucas , Cherlin Svetlana , Fakiola Michaela , Carvalho Edgar , Figueiredo Amanda B. , Cavalcanti Clara M. , Alves Natalia S. , Dutra Walderez O. , Gollob Kenneth J. , Cordell Heather J. , Blackwell Jenefer M. 
Published: January 2020

AbstractBackgroundCutaneous leishmaniasis (CL) caused byLeishmania braziliensisremains an important public health problem in Brazil. The goal of this study was to identify genetic risk factors for CL.MethodsGenome-wide analysis was undertaken using DNAs from 956 CL cases and 868 controls (phase 1) and 1110 CL cases and 1178 controls (phase 2) genotyped using Illumina HumanCoreExome BeadChips. Imputation against 1000G data provided 4,498,586 quality-controlled single nucleotide variants (SNVs) common across phase 1 and phase 2 samples. Linear mixed models in FastLMM were used to take account of genetic diversity/ethnicity/admixture. Cellular cytokines were measured using flow cytometry.ResultsCombined analysis across cohorts found no associations that achieved genome-wide significance, commonly accepted asP<5×10-8. Support for variants at wound-healing genes previously studied as candidate genes for CL includedSMAD2(rs115582038/rs75753347;Pimputed_1000G=1.47×10-4). Top novel GWAS hits at P<5×10-5in plausible candidate genes for CL includedSERPINB10(rs62097497;Pimputed_1000G=2.67×10-6),CRLF3(rs75270613;Pimputed_1000G=5.12×10-6),STX7(rs144488134;Pimputed_1000G=6.06×10-6),KRT80(rs10783496Pimputed_1000G=6.58×10-6),LAMP3(rs74285558;Pimputed_1000G=6.54×10-6) andIFNG-AS1(rs4913269;Pimputed_1000G=1.32×10-5). Of these,LAMP3(Padjusted=9.25×10-12; +6-fold),STX7(Padjusted=7.62×10-3; +1.3-fold) andCRLF3(Padjusted=9.19×10-9; +1.97-fold) were all expressed more highly in CL biopsies compared to normal skin, whereas expression ofKRT80(Padjusted=3.07×10-8; −3-fold) was lower. Notably, the percent peripheral blood CD3+T cells making interferon-γ in response toLeishmaniaantigen differed significantly byIFNG-AS1genotype.ConclusionsIn addition to supporting variants in wound-healing genes as genetic risk factors for CL, our GWAS results provide important novel leads to understanding pathogenesis of CL including through the regulation of interferon-γ responses.