bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamic Stability and Structural Insights for CH3NH3Pb1−xSixI3, CH3NH3Pb1−xGexI3, and CH3NH3Pb1−xSnxI3 Hybrid Perovskite Alloys: A Statistical Approach from First Principles Calculations
Authors: Guedes-Sobrinho Diego , Guilhon Ivan , Marques Marcelo , Teles Lara K. 
Published: July 2019

AbstractThe recent reaching of 20% of conversion efficiency by solar cells based on metal hybrid perovskites (MHP), e.g., the methylammonium (MA) lead iodide, CH3NH3PbI3(MAPbI3), has excited the scientific community devoted to the photovoltaic materials. However, the toxicity of Pb is a hindrance for large scale commercial of MHP and motivates the search of another congener eco-friendly metal. Here, we employed first-principles calculations via density functional theory combined with the generalized quasichemical approximation to investigate the structural, thermodynamic, and ordering properties of MAPb1−xSixI3, MAPb1−xGexI3, and MAPb1−xSnxI3alloys as pseudo-cubic structures. The inclusion of a smaller second metal, as Si and Ge, strongly affects the structural properties, reducing the cavity volume occupied by the organic cation and limitating the free orientation under high temperature effects. Unstable and metaestable phases are observed at room temperature for MAPb1−xSixI3, whereas MAPb1−xGexI3is energetically favored for Pb-rich in ordered phases even at very low temperatures. Conversely, the high miscibility of Pb and Sn into MAPb1−xSnxI3yields an alloy energetically favored as a pseudo-cubic random alloy with tunable properties at room temperature.
Evidence of different climatic adaptation strategies in humans and non-human primates
Authors: Buck L. T. , De Groote I. , Hamada Y. , Hassett B. R. , Ito T. , Stock J. T. 
Published: July 2019

AbstractTo understand human evolution it is critical to clarify which adaptations enabled our colonisation of novel ecological niches. For any species climate is a fundamental source of environmental stress during range expansion. Mammalian climatic adaptations include changes in size and shape reflected in skeletal dimensions and humans fit general primate ecogeographic patterns. It remains unclear however, whether there are also comparable amounts of adaptation in humans, which has implications for understanding the relative importance of biological/behavioural mechanisms in human evolution. We compare cranial variation between prehistoric human populations from throughout Japan and ecologically comparable groups of macaques. We compare amounts of intraspecific variation and covariation between cranial shape and ecological variables. Given equal rates and sufficient time for adaptation for both groups, human conservation of non-human primate adaptation should result in comparable variation and patterns of covariation in both species. In fact, we find similar amounts of intraspecific variation in both species, but no covariation between shape and climate in humans, contrasting with strong covariation in macaques. The lack of covariation in humans may suggest a disconnect in climatic adaptation strategies from other primates. We suggest this is due to the importance of human behavioural adaptations, which act as a buffer from climatic stress and were likely key to our evolutionary success.
Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points
Authors: McGrath Krista , Rowsell Keri , Gates St-Pierre Christian , Tedder Andrew , Foody George , Roberts Carolynne , Speller Camilla , Collins Matthew 
Published: July 2019

AbstractToday, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology.
Bruton’s tyrosine kinase is at the crossroads of metabolic adaptation in primary malignant human lymphocytes
Authors: Sharif-Askari Bahram , Doyon Daniel , Paliouras Miltiadis , Aloyz Raquel 
Published: July 2019

AbstractIn this work we explored metabolic aspects of human primary leukemic lymphocytes that hold a potential impact on the treatment of Bruton tyrosine kinase (BTK)-driven diseases. Our results suggest that there is crosstalk between Bruton tyrosine kinase (BTK) signaling and bioenergetic stress responses. In primary chronic lymphocytic leukemia (CLL) lymphocytes, pharmacological interference with mitochondrial ATP synthesis or glucose metabolism affects BTK activity. Conversely, an inhibitor of BTK used clinically (ibrutinib) induces bioenergetic stress responses that in turn affect ibrutinib resistance. Although the detailed molecular mechanisms are still to be defined, our work shows for the first time that in primary B cells, metabolic stressors enhance BTK signaling and suggest that metabolic rewiring to hyperglycemia affects ibrutinib resistance in TP53 deficient chronic lymphocytic leukemia (CLL) lymphocytes.
The effect of labor and delivery mode on electrocortical and brainstem autonomic function during neonatal transition
Authors: Mulkey Sarah B. , Kota Srinivas , Govindan Rathinaswamy B. , Al-Shargabi Tareq , Swisher Christopher B. , Eze Augustine , Hitchings Laura , Russo Stephanie , Herrera Nicole , McCarter Robert , Maxwell G. Larry , Baker Robin , du Plessis Adre J. 
Published: July 2019

AbstractDelivery of the newborn occurs either vaginally or via caesarean section. It is not known whether the mode of delivery and exposure to labor affects early autonomic nervous system (ANS) function, as measured by heart rate variability (HRV), or cortical electroencephalogram (EEG) activity. The objective of the study was to determine if autonomic function in newborns differs by mode of delivery. Simultaneous recording of EEG and electrocardiogram were collected in low-risk term newborns at <72 hours of age to measure HRV, the asymmetry index, and EEG power. Newborns were compared by delivery type: vaginal delivery (VD), cesarean section (CS) after labor (L-CS), or elective CS (E-CS). Quantile Regression controlled for gestational age, postnatal age, and percent active states. One hundred and eighteen newborns were studied at 25.2 (11.4) hours of age. Sixty-two (52.5%) were born by VD, 22 by L-CS (18.6%), and 34 by E-CS (28.8%). HRV metrics didn’t differ by delivery mode. Asymmetry index was higher in L-CS compared to VD and E-CS (P = 0.03). On EEG, L-CS newborns showed lower relative gamma power compared to VD and E-CS (P = 0.005). The study found that overall ANS tone is not altered by mode of delivery in low-risk term newborns.
A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line
Authors: Genov Nikolai , Basti Alireza , Abreu Mónica , Astaburuaga Rosario , Relógio Angela 
Published: July 2019

AbstractThe circadian clock regulates key cellular processes and its dysregulation is associated to several pathologies including cancer. Although the transcriptional regulation of gene expression by the clock machinery is well described, the role of the clock in the regulation of post-transcriptional processes, including splicing, remains poorly understood. In the present work, we investigated the putative interplay between the circadian clock and splicing in a cancer context. For this, we applied a computational pipeline to identify oscillating genes and alternatively spliced transcripts in time-course high-throughput data sets from normal cells and tissues, and cancer cell lines. We investigated the temporal phenotype of clock-controlled genes and splicing factors, and evaluated their impact in alternative splice patterns in the Hodgkin Lymphoma cell line HD-MY-Z. Our data points to a connection between clock-controlled genes and splicing factors, which correlates with temporal alternative splicing in several genes in the HD-MY-Z cell line. These include the genes DPYD, SS18, VIPR1 and IRF4, involved in metabolism, cell cycle, apoptosis and proliferation. Our results highlight a role for the clock as a temporal regulator of alternative splicing, which may impact malignancy in this cellular model.
Multicentre evaluation of Xpert MTB/RIF assay in detecting urinary tract tuberculosis with urine samples
Authors: Chen Yu , Wu Peng , Fu Liang , Liu Yu-hong , Zhang Yao , Zhao Yanping 
Published: July 2019

AbstractGenitourinary tuberculosis (GUTB) accounts for up to 40% of extrapulmonary tuberculosis cases. Rapid tests for GUTB are urgently needed because it is often associated with delayed health-care seeking, leading to serious consequences. This study evaluated the performance of the Xpert MTB/RIF assay in the rapid diagnosis of urinary tract tuberculosis (UTB) and rifampicin-resistant tuberculosis with urine specimens. In all, 302 patients were included from four hospitals in China. Suspected UTB patients were tested with Xpert, smear, and MGIT 960 culture. Drug susceptibility testing (DST) was conducted for culture-positive cases. The performance of the assays was evaluated against MGIT 960 culture and a composite reference standard (CRS). Among all participants, 150 (49.7%) had CRS-positive UTB, of whom 36 (24.0%) were culture-confirmed. Against culture, Xpert and smear achieved a sensitivity of 94.4% (95% CI: 81.3–99.3%) and 22.2% (95% CI: 10.1–39.2%), respectively. Against CRS, the sensitivity of Xpert, smear and culture was 41.3% (95% CI: 33.4–49.7%), 7.3% (95% CI: 3.7–12.7%), and 24.0% (95% CI: 17.4–31.6%). Xpert had better performance than smear and culture in detecting UTB from urine samples and could be considered for the diagnosis of UTB. Moreover, Xpert showed better performance than MGIT 960-based DST using urine culture.
Resistance of in natura and torrefied wood chips to xylophage fungi
Authors: Castro Vinícius Resende de , de Castro Freitas Matheus Perdigão , Zanuncio Antônio José Vinha , Zanuncio José Cola , Surdi Paula Gabriella , Carneiro Angélica de Cássia Oliveira , Vital Benedito Rocha 
Published: July 2019

AbstractThe diversity of fungi allows for their colonisation in different environments, including wood destined for power generation, with an ability to degrade or hinder its use. Torrefaction or pre-carbonisation, a low oxygenation heat treatment with temperatures between 200 and 300 °C, accumulates carbon and lignin, decreases hygroscopicity, increases energy efficiency and reduces the wood attractiveness to xylophagous microorganisms. This work aimed to study the resistance of Eucalyptus urophylla wood chips, submitted to torrefaction temperatures of 180, 220 and 260 °C for 20 minutes, to xylophagous fungi, according to the ASTM D-2017 method (2005). The white rot fungi Phanerochaete chrysosporium, Pleurotus ostreatus and Trametes versicolor and the brown rot fungus Gloeophyllum trabeum were used. After 12 weeks of exposure, the mass losses of wood samples in natura and torrified at 180 °C attacked by Pleurotus ostreatus and Trametes versicolor was higher. Torrefaction increased the resistance to fungi; the treatment at 260 °C was the most efficient with lower mass losses caused by fungi attacks and, consequently, greater resistance to the fungi tested.
Deregulation of TLR4 signaling pathway characterizes Bicuspid Aortic valve syndrome
Authors: Balistreri Carmela R. , Marullo Antonino G. M. , Madonna Michele , Cavarretta Elena , Allegra Alberto , Cesarini Valeriana , Iaccarino Alessandra , Schiavon Sonia , Peruzzi Mariangela , Greco Ernesto , Sciarretta Sebastiano , Pisano Calogera , Ruvolo Giovanni , Torella Michele , Frati Giacomo 
Published: July 2019

AbstractBicuspid aortic valve (BAV) disease is recognized to be a syndrome with a complex and multifaceted pathophysiology. Its progression is modulated by diverse evolutionary conserved pathways, such as Notch-1 pathway. Emerging evidence is also highlighting the key role of TLR4 signaling pathway in the aortic valve pathologies and their related complications, such as sporadic ascending aorta aneurysms (AAA). Consistent with these observations, we aimed to evaluate the role of TLR4 pathway in both BAV disease and its common complication, such as AAA. To this aim, 70 subjects with BAV (M/F 50/20; mean age: 58.8 ± 14.8 years) and 70 subjects with tricuspid aortic valve (TAV) (M/F 35/35; mean age: 69.1 ± 12.8 years), with and without AAA were enrolled. Plasma assessment, tissue and gene expression evaluations were performed. Consistent with data obtained in the previous study on immune clonotypic T and B altered responses, we found reduced levels of systemic TNF-α, IL-1, IL-6, IL-17 cytokines in BAV cases, either in the presence or absence of AAA, than TAV cases (p < 0.0001 by ANOVA test). Interestingly, we also detected reduced levels of s-TLR4 in BAV cases with or without AAA in comparison to the two groups of TAV subjects (p < 0.0001 by ANOVA test). These results may suggest a deregulation in the activity or in the expression of TLR4 signaling pathway in all BAV cases. Portrait of these data is, indeed, the significantly decreased gene expression of inflammatory cytokines and TLR4, in both normal and aneurysmatic tissue samples, from BAV with AAA than TAV with AAA. In conclusion, our study demonstrates that subjects with BAV display a significant deregulation of TLR4 signaling pathway paralleled by a deregulation of Notch-1 pathway, as previously showed. This data suggests that the crosstalk between the Notch-1 and TLR4 signaling pathways may play a crucial role in both physiological embryological development, and homeostasis and functionality of aortic valve in adult life.
Functionalization of Brain Region-specific Spheroids with Isogenic Microglia-like Cells
Authors: Song Liqing , Yuan Xuegang , Jones Zachary , Vied Cynthia , Miao Yu , Marzano Mark , Hua Thien , Sang Qing-Xiang Amy , Guan Jingjiao , Ma Teng , Zhou Yi , Li Yan 
Published: July 2019

AbstractCurrent brain spheroids or organoids derived from human induced pluripotent stem cells (hiPSCs) still lack a microglia component, the resident immune cells in the brain. The objective of this study is to engineer brain region-specific organoids from hiPSCs incorporated with isogenic microglia-like cells in order to enhance immune function. In this study, microglia-like cells were derived from hiPSCs using a simplified protocol with stage-wise growth factor induction, which expressed several phenotypic markers, including CD11b, IBA-1, CX3CR1, and P2RY12, and phagocytosed micron-size super-paramagnetic iron oxides. The derived cells were able to upregulate pro-inflammatory gene (TNF-α) and secrete anti-inflammatory cytokines (i.e., VEGF, TGF-β1, and PGE2) when stimulated with amyloid β42 oligomers, lipopolysaccharides, or dexamethasone. The derived isogenic dorsal cortical (higher expression of TBR1 and PAX6) and ventral (higher expression of NKX2.1 and PROX1) spheroids/organoids displayed action potentials and synaptic activities. Co-culturing the microglia-like cells (MG) with the dorsal (D) or ventral (V) organoids showed differential migration ability, intracellular Ca2+signaling, and the response to pro-inflammatory stimuli (V-MG group had higher TNF-α and TREM2 expression). Transcriptome analysis exhibited 37 microglia-related genes that were differentially expressed in MG and D-MG groups. In addition, the hybrid D-MG spheroids exhibited higher levels of immunoreceptor genes in activating members, but the MG group contained higher levels for most of genes in inhibitory members (except SIGLEC5 and CD200). This study should advance our understanding of the microglia function in brain-like tissue and establish a transformative approach to modulate cellular microenvironment toward the goal of treating various neurological disorders.
Relationship between semiquantitative 18F-fluorodeoxyglucose positron emission tomography metrics and necrosis in classical Hodgkin lymphoma
Authors: Kahle X. U. , Montes de Jesus F. M. , Kwee T. C. , van Meerten T. , Diepstra A. , Rosati S. , Glaudemans A. W. J. M. , Noordzij W. , Plattel W. J. , Nijland M. 
Published: July 2019

AbstractSemiquantitative 18F-fluoro-2-deoxy-D-glucose positron emission tomography (18F-FDG PET) parameters have been proposed as prognostic markers in classical Hodgkin lymphoma (cHL). In non-Hodgkin lymphoma necrosis as assessed by 18F-FDG PET or computed tomography (CT) (necrosisvisual) correlates with an adverse prognosis. We investigated whether semiquantitative 18F-FDG PET metrics correlate with necrosisvisual, determined the incidence of necrosisvisual and explored the prognostic impact of these factors in cHL. From 87 cHL cases treated with ABVD, (escalated) BEACOPP or CHOP chemotherapy between 2010 and 2017, 71 had both a NEDPAS/EARL accredited 18F-FDG PET and a contrast enhanced CT scan. Semiquantitative 18F-FDG PET parameters were determined using Hermes Hybrid 3D software. Necrosisvisual, defined by photopenic tumor areas on 18F-FDG PET and attenuation values between 10 and 30 Hounsfield units (HUs) on CT, was assessed blinded to outcome. Univariate Cox regression survival analyses of progression free survival (PFS) were performed. Necrosisvisual was observed in 18.3% of cHL patients. Bulky disease (tumor mass >10 cm in any direction) (P = 0.002) and TLG (P = 0.041) but no other semiquantitative parameters were significantly associated with necrosisvisual. In exploratory univariate survival analysis for PFS the covariates IPS, bulky disease, MTV and TLG were prognostic, while necrosisvisual was not.
Musical interaction is influenced by underlying predictive models and musical expertise
Authors: Heggli Ole A. , Konvalinka Ivana , Kringelbach Morten L. , Vuust Peter 
Published: July 2019

AbstractMusical interaction is a unique model for understanding humans’ ability to align goals, intentions, and actions, which also allows for the manipulation of participants’ internal predictive models of upcoming events. Here we used polyrhythms to construct two joint finger tapping tasks that even when rhythmically dissimilar resulted in equal inter-tap intervals (ITIs). Thus, behaviourally a dyad of two musicians tap isochronously at the same rate, yet with their own distinct rhythmical context model (RCM). We recruited 22 highly skilled musicians (in 11 dyads) and contrasted the effect of having a shared versus non-shared RCM on dyads’ synchronization behaviour. As expected, tapping synchronization was significantly worse at the start of trials with non-shared models compared to trials with a shared model. However, the musicians were able to quickly recover when holding dissimilar predictive models. We characterised the directionality in the tapping behaviour of the dyads and found patterns mostly of mutual adaptation. Yet, in a subset of dyads primarily consisting of drummers, we found significantly different synchronization patterns, suggesting that instrument expertise can significantly affect synchronization strategies. Overall, this demonstrates that holding different predictive models impacts synchronization in musicians performing joint finger tapping.
The lytic transglycosylase, LtgG, controls cell morphology and virulence in Burkholderia pseudomallei
Authors: Jenkins Christopher H. , Wallis Russell , Allcock Natalie , Barnes Kay B. , Richards Mark I. , Auty Joss M. , Galyov Edouard E. , Harding Sarah V. , Mukamolova Galina V. 
Published: July 2019

AbstractBurkholderia pseudomallei is the causative agent of the tropical disease melioidosis. Its genome encodes an arsenal of virulence factors that allow it, when required, to switch from a soil dwelling bacterium to a deadly intracellular pathogen. With a high intrinsic resistance to antibiotics and the ability to overcome challenges from the host immune system, there is an increasing requirement for new antibiotics and a greater understanding into the molecular mechanisms of B. pseudomallei virulence and dormancy. The peptidoglycan remodeling enzymes, lytic transglycosylases (Ltgs) are potential targets for such new antibiotics. Ltgs cleave the glycosidic bonds within bacterial peptidoglycan allowing for the insertion of peptidoglycan precursors during cell growth and division, and cell membrane spanning structures such as flagella and secretion systems. Using bioinformatic analysis we have identified 8 putative Ltgs in B. pseudomallei K96243. We aimed to investigate one of these Ltgs, LtgG (BPSL3046) through the generation of deletion mutants and biochemical analysis. We have shown that LtgG is a key contributor to cellular morphology, division, motility and virulence in BALB/c mice. We have determined the crystal structure of LtgG and have identified various amino acids likely to be important in peptidoglycan binding and catalytic activity. Recombinant protein assays and complementation studies using LtgG containing a site directed mutation in aspartate 343, confirmed the essentiality of this amino acid in the function of LtgG.
Assembling real networks from synthetic and unstructured subsets: the corporate reporting case
Authors: Viegas Eduardo , Goto Hayato , Takayasu Misako , Takayasu Hideki , Jensen Henrik Jeldtoft 
Published: July 2019

AbstractThe analysis of interfirm business transaction networks provides invaluable insight into the trading dynamics and economic structure of countries. However, there is a general scarcity of data available recording real, accurate and extensive information for these types of networks. As a result, and in common with other types of network studies - such as protein interactions for instance - research tends to rely on partial and incomplete datasets, i.e. subsets, with less certain conclusions. Here, we make use of unstructured financial and corporate reporting data in Japan as the base source to construct a financial reporting network, which is then compared and contrasted to the wider real business transaction network. The comparative analysis between these two rich datasets - the proxy, partially derived network and the real, complete network at macro as well as local structural levels - provides an enhanced understanding of the non trivial relationships between partial sampled subsets and fully formed networks. Furthermore, we present an elemental agent based pruning algorithm that reconciles and preserves key structural differences between these two networks, which may serve as an embryonic generic framework of potentially wider use to network research, enabling enhanced extrapolation of conclusions from partial data or subsets.