bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rethinking Measures of Functional Connectivity via Feature Extraction
Authors: Mohanty Rosaleena , Sethares William A. , Nair Veena A. , Prabhakaran Vivek 
Published: January 2020

AbstractFunctional magnetic resonance imaging (fMRI)-based functional connectivity (FC) commonly characterizes the functional connections in the brain. Conventional quantification of FC by Pearson's correlation captures linear, time-domain dependencies among blood-oxygen-level-dependent (BOLD) signals. We examined measures to quantify FC by investigating: (i) Is Pearson's correlation sufficient to characterize FC? (ii) Can alternative measures better quantify FC? (iii) What are the implications of using alternative FC measures? FMRI analysis in healthy adult population suggested that: (i) Pearson's correlation cannot comprehensively capture BOLD inter-dependencies. (ii) Eight alternative FC measures were similarly consistent between task and resting-state fMRI, improved age-based classification and provided better association with behavioral outcomes. (iii) Formulated hypotheses were: first, in lieu of Pearson’s correlation, an augmented, composite and multi-metric definition of FC is more appropriate; second, canonical large-scale brain networks may depend on the chosen FC measure. A thorough notion of FC promises better understanding of variations within a given population.
Visceral fat metabolic activity evaluated by preoperative 18F-FDG PET/CT significantly affects axillary lymph node metastasis in postmenopausal luminal breast cancer
Authors: Pahk Kisoo , Joung Chanmin , Kim Sungeun 
Published: January 2020

AbstractObesity is known to increase breast cancer risk and aggressiveness in postmenopausal luminal breast cancer and obesity-driven dysfunctional metabolic activity in visceral adipose tissue (VAT) is considered as one of the principal underlying mechanism. We aimed to investigate the relationship between VAT metabolic activity evaluated by preoperative 18F-FDG PET/CT and axillary lymph node (ALN) metastasis in postmenopausal luminal breast cancer patients. In total, 173 patients were enrolled in study. They all underwent preoperative 18F-FDG PET/CT and surgery. VAT metabolic activity was defined as the maximum standardized uptake value (SUVmax) of VAT divided by the SUVmax of subcutaneous adipose tissue (V/S ratio). In luminal breast cancer, the patients with ALN metastasis showed significantly higher V/S ratio than the patients without ALN metastasis. Furthermore, V/S ratio was significantly associated with ALN metastasis in luminal breast cancer patients. Erythrocyte sedimentation rate, which reflect the systemic inflammation, was significantly higher in ALN metastasis group than the negative ALN metastasis group in luminal breast cancer patients and showed significant positive correlation with V/S ratio. V/S ratio significantly affects the ALN metastasis status in postmenopausal luminal breast cancer patients and it may be useful as a potential biomarker of obesity-driven systemic inflammation associated with tumor aggressiveness.
Jedi-1 deficiency increases sensory neuron excitability through a non-cell autonomous mechanism
Authors: Trevisan Alexandra J. , Bauer Mary Beth , Brindley Rebecca L. , Currie Kevin P. M. , Carter Bruce D. 
Published: January 2020

AbstractThe dorsal root ganglia (DRG) house the primary afferent neurons responsible for somatosensation, including pain. We previously identified Jedi-1 (PEAR1/MEGF12) as a phagocytic receptor expressed by satellite glia in the DRG involved in clearing apoptotic neurons during development. Here, we further investigated the function of this receptor in vivo using Jedi-1 null mice. In addition to satellite glia, we found Jedi-1 expression in perineurial glia and endothelial cells, but not in sensory neurons. We did not detect any morphological or functional changes in the glial cells or vasculature of Jedi-1 knockout mice. Surprisingly, we did observe changes in DRG neuron activity. In neurons from Jedi-1 knockout (KO) mice, there was an increase in the fraction of capsaicin-sensitive cells relative to wild type (WT) controls. Patch-clamp electrophysiology revealed an increase in excitability, with a shift from phasic to tonic action potential firing patterns in KO neurons. We also found alterations in the properties of voltage-gated sodium channel currents in Jedi-1 null neurons. These results provide new insight into the expression pattern of Jedi-1 in the peripheral nervous system and indicate that loss of Jedi-1 alters DRG neuron activity indirectly through an intercellular interaction between non-neuronal cells and sensory neurons.
A computational analysis of retinal image quality in eyes with keratoconus
Authors: Nilagiri Vinay Kumar , Metlapally Sangeetha , Schor Clifton M. , Bharadwaj Shrikant R. 
Published: January 2020

AbstractHigher-order aberrations (HOA’s) are exaggerated in eyes with keratoconus but little is known about their impact on the retinal image quality (IQ) of these eyes. This computational study determined changes in IQ [peak IQ, best focus and depth of focus (DOF)] of 12 subjects with manifest keratoconus in both eyes (KCE cohort), 9 subjects with very asymmetric ectasia (VAE cohort) with and without their Rigid Gas Permeable contact lenses (RGP CL’s) and 20 age-matched controls, using a HOA-based through-focus analysis performed on the logNS IQ metric over 5 mm pupil diameter following cycloplegia. All IQ parameters were significantly worse in the KCE cohort with their native HOA’s, relative to controls and in the ectatic eye of the VAE cohort, relative to the fellow non-ectatic eye (p ≤ 0.008 for all). Reduction in HOA’s of these eyes with RGP CL’s resulted in a significant improvement in all IQ parameters but they all remained significantly poorer than controls (p ≤ 0.02 for all). The inter-subject variability of best focus and the DOF range were inversely related to peak IQ in these eyes (r = 0.85; p < 0.001). These results provide the optical basis for two clinical observations on keratoconus: (1) optical performance of keratoconic eyes are significantly better with RGP CL’s than with spectacles or unaided conditions and (2) the endpoint of subjective refraction is elusive in keratoconic eyes, relative to healthy controls or to the non-ectatic eye in bilaterally asymmetric ectasia.
Internal short circuit detection in Li-ion batteries using supervised machine learning
Authors: Naha Arunava , Khandelwal Ashish , Agarwal Samarth , Tagade Piyush , Hariharan Krishnan S. , Kaushik Anshul , Yadu Ankit , Kolake Subramanya Mayya , Han Seongho , Oh Bookeun 
Published: January 2020

AbstractWith the proliferation of Li-ion batteries in smart phones, safety is the main concern and an on-line detection of battery faults is much wanting. Internal short circuit is a very critical issue that is often ascribed to be a cause of many accidents involving Li-ion batteries. A novel method that can detect the Internal short circuit in real time based on an advanced machine leaning approach, is proposed. Based on an equivalent electric circuit model, a set of features encompassing the physics of Li-ion cell with short circuit fault are identified and extracted from each charge-discharge cycle. The training feature set is generated with and without an external short-circuit resistance across the battery terminals. To emulate a real user scenario, internal short is induced by mechanical abuse. The testing feature set is generated from the battery charge-discharge data before and after the abuse. A random forest classifier is trained with the training feature set. The fault detection accuracy for the testing dataset is found to be more than 97%. The proposed algorithm does not interfere with the normal usage of the device, and the trained model can be implemented in any device for online fault detection.
Biomarker discovery for chronic liver diseases by multi-omics – a preclinical case study
Authors: Veyel Daniel , Wenger Kathrin , Broermann Andre , Bretschneider Tom , Luippold Andreas H. , Krawczyk Bartlomiej , Rist Wolfgang , Simon Eric 
Published: January 2020

AbstractNonalcoholic steatohepatitis (NASH) is a major cause of liver fibrosis with increasing prevalence worldwide. Currently there are no approved drugs available. The development of new therapies is difficult as diagnosis and staging requires biopsies. Consequently, predictive plasma biomarkers would be useful for drug development. Here we present a multi-omics approach to characterize the molecular pathophysiology and to identify new plasma biomarkers in a choline-deficient L-amino acid-defined diet rat NASH model. We analyzed liver samples by RNA-Seq and proteomics, revealing disease relevant signatures and a high correlation between mRNA and protein changes. Comparison to human data showed an overlap of inflammatory, metabolic, and developmental pathways. Using proteomics analysis of plasma we identified mainly secreted proteins that correlate with liver RNA and protein levels. We developed a multi-dimensional attribute ranking approach integrating multi-omics data with liver histology and prior knowledge uncovering known human markers, but also novel candidates. Using regression analysis, we show that the top-ranked markers were highly predictive for fibrosis in our model and hence can serve as preclinical plasma biomarkers. Our approach presented here illustrates the power of multi-omics analyses combined with plasma proteomics and is readily applicable to human biomarker discovery.
CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes
Authors: Bayati Masroor , Rabiee Hamid R. , Mehrbod Mehrdad , Vafaee Fatemeh , Ebrahimi Diako , Forrest Alistair R. R. , Alinejad-Rokny Hamid 
Published: January 2020

AbstractAnalysis of cancer mutational signatures have been instrumental in identification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly interface for analysis of cancer mutational signatures is necessary. In this manuscript we introduce CANCERSIGN, which enables users to identify 3-mer and 5-mer mutational signatures within whole genome, whole exome or pooled samples. Additionally, this tool enables users to perform clustering on tumor samples based on the proportion of mutational signatures in each sample. Using CANCERSIGN, we analysed all the whole genome somatic mutation datasets profiled by the International Cancer Genome Consortium (ICGC) and identified a number of novel signatures. By examining signatures found in exonic and non-exonic regions of the genome using WGS and comparing this to signatures found in WES data we observe that WGS can identify additional non-exonic signatures that are enriched in the non-coding regions of the genome while the deeper sequencing of WES may help identify weak signatures that are otherwise missed in shallower WGS data.
Probiotics and Maternal Mental Health: A Randomised Controlled Trial among Pregnant Women with Obesity
Authors: Dawe Julia P. , McCowan Lesley M. E. , Wilson Jess , Okesene-Gafa Karaponi A. M. , Serlachius Anna S. 
Published: January 2020

AbstractPoor maternal mental health has been associated with a myriad of pregnancy and child health complications. Obesity in pregnancy is known to increase one’s risk of experiencing poor maternal mental health and associated physical and mental health complications. Probiotics may represent a novel approach to intervene in poor mental health and obesity. We conducted this pre-specified secondary analysis of the Healthy Mums and Babies (HUMBA) randomised controlled trial to investigate whether probiotics would improve maternal mental health outcomes up to 36 weeks of pregnancy. Two-hundred-and-thirty pregnant women with obesity (BMI ≥ 30.0 kg/m2) were recruited and randomised to receive probiotic (Lactobacillus rhamnosus GG and Bifidobacterium lactis BB12, minimum 6.5 × 109 CFU) or placebo capsules. Depression, anxiety, and functional health and well-being were assessed at baseline (120−176 weeks’ gestation) and 36 weeks of pregnancy. Depression scores remained stable and did not differ between the probiotic (M = 7.18, SD = 3.80) and placebo groups (M = 6.76, SD = 4.65) at 36 weeks (p-values > 0.05). Anxiety and physical well-being scores worsened over time irrespective of group allocation, and mental well-being scores did not differ between the two groups at 36 weeks. Probiotics did not improve mental health outcomes in this multi-ethnic cohort of pregnant women with obesity.
Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues
Authors: Mehani Bharati , Narta Kiran , Paul Deepanjan , Raj Anurag , Kumar Deepak , Sharma Anchal , Kaurani Lalit , Nayak Subhashree , Dash Debasis , Suri Ashish , Sarkar Chitra , Mukhopadhyay Arijit 
Published: January 2020

AbstractFusion transcripts can contribute to diversity of molecular networks in the human cortex. In this study, we explored the occurrence of fusion transcripts in normal human cortex along with single neurons and astrocytes. We identified 1305 non-redundant fusion events from 388 transcriptomes representing 59 human cortices and 329 single cells. Our results indicate while the majority of fusion transcripts in human cortex are intra-chromosomal (85%), events found in single neurons and astrocytes were primarily inter-chromosomal (80%). The number of fusions in single neurons was significantly higher than that in single astrocytes (p < 0.05), indicating fusion as a possible contributor towards transcriptome diversity in neuronal cells. The identified fusions were largely private and 4 specific recurring events were found both in cortex and in single neurons but not in astrocytes. We found a significant increase in the number of fusion transcripts in human brain with increasing age both in single cells and whole cortex (p < 0.0005 and < 0.005, respectively). This is likely one of the many possible contributors for the inherent plasticity of the adult brain. The fusion transcripts in fetal brain were enriched for genes for long-term depression; while those in adult brain involved genes enriched for long-term potentiation pathways. Our findings demonstrate fusion transcripts are naturally occurring phenomenon spanning across the health-disease continuum, and likely contribute to the diverse molecular network of human brain.
GABA potentiate the immunoregulatory effects of Lactobacillus brevis BGZLS10-17 via ATG5-dependent autophagy in vitro
Authors: Bajić Svetlana Soković , Đokić Jelena , Dinić Miroslav , Tomić Sergej , Popović Nikola , Brdarić Emilija , Golić Nataša , Tolinački Maja 
Published: January 2020

AbstractThe characterization of mechanisms involved in the positive effects of probiotic bacteria in various pathophysiological conditions is a prerogative for their safe and efficient application in biomedicine. We have investigated the immunological effects of live bacteria-free supernatant collected from GABA-producing Lactobacillus brevis BGZLS10-17 on Concanavalin A-stimulated mesenteric lymph node cells (MLNC), an in vitro model of activated immune cells. We have shown that GABA containing and GABA-free supernatant of Lactobacillus brevis BGZLS10-17 have strong immunoregulatory effects on MLNC. Further, GABA produced by this strain exhibit additional inhibitory effects on proliferation, IFN-γ and IL-17 production by MLNC, and the expression of MHCII and CD80 on antigen presenting cells. At the other hand, GABA-containing supernatants displayed the strongest stimulatory effects on the expression of immunoregulatory molecules, such as Foxp3+, IL-10, TGF-β, CTLA4 and SIRP-α. By looking for the mechanisms of actions, we found that supernatants produced by BGZLS10-17 induce autophagy in different MLNC, such as CD4+ and CD8+ T lymphocytes, NK and NKT cells, as well as antigen presenting cells. Further, we showed that the stimulation of Foxp3+, IL-10 and TGF-β expression by BGZLS10-17 produced GABA is completely mediated by the induction of ATG5 dependent autophagy, and that other molecules in the supernatants display GABA-, ATG5-, Foxp3+-, IL-10- and TGF-β- independent, immunoregulatory effects.
The mechanism of how CD95/Fas activates the Type I IFN/STAT1 axis, driving cancer stemness in breast cancer
Authors: Qadir Abdul S. , Stults Austin M. , Murmann Andrea E. , Peter Marcus E. 
Published: January 2020

AbstractCD95/Fas is an apoptosis inducing death receptor. However, it also has multiple nonapoptotic activities that are tumorigenic. Chronic stimulation of CD95 on breast cancer cells can increase their cancer initiating capacity through activation of a type I interferon (IFN-I)/STAT1 pathway when caspases are inhibited. We now show that this activity relies on the canonical components of the CD95 death-inducing signaling complex, FADD and caspase-8, and on the activation of NF-κB. We identified caspase-2 as the antagonistic caspase that downregulates IFN-I production. Once produced, IFN-Is bind to their receptors activating both STAT1 and STAT2 resulting in upregulation of the double stranded (ds)RNA sensor proteins RIG-I and MDA5, and a release of a subset of endogenous retroviruses. Thus, CD95 is part of a complex cell autonomous regulatory network that involves activation of innate immune components that drive cancer stemness and contribute to therapy resistance.
Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia
Authors: Oswald Jessica A. , Allen Julie M. , LeFebvre Michelle J. , Stucky Brian J. , Folk Ryan A. , Albury Nancy A. , Morgan Gary S. , Guralnick Robert P. , Steadman David W. 
Published: January 2020

AbstractQuaternary paleontological and archaeological evidence often is crucial for uncovering the historical mechanisms shaping modern diversity and distributions. We take an interdisciplinary approach using multiple lines of evidence to understand how past human activity has shaped long-term animal diversity in an island system. Islands afford unique opportunities for such studies given their robust fossil and archaeological records. Herein, we examine the only non-volant terrestrial mammal endemic to the Bahamian Archipelago, the hutiaGeocapromys ingrahami. This capromyine rodent once inhabited many islands but is now restricted to several small cays. Radiocarbon dated fossils indicate that hutias were present on the Great Bahama Bank islands before humans arrived at AD ~800–1000; all dates from other islands post-date human arrival. Using ancient DNA from a subset of these fossils, along with modern representatives of Bahamian hutia and related taxa, we develop a fossil-calibrated phylogeny. We found little genetic divergence among individuals from within either the northern or southern Bahamas but discovered a relatively deep North-South divergence (~750 ka). This result, combined with radiocarbon dating and archaeological evidence, reveals a pre-human biogeographic divergence, and an unexpected human role in shaping Bahamian hutia diversity and biogeography across islands.
Task-dependent fMRI decoder with the power to extend Gabor patch results to Natural images
Authors: Tsushima Yoshiaki , Sawahata Yasuhito , Komine Kazuteru 
Published: January 2020

AbstractScientists are often asked to what extent a simple finding in a laboratory can be generalized to complicated phenomena in our daily lives. The same is equally true of vision science; numerous critical discoveries about our visual system have been made using very simple visual images, such as Gabor patches, but to what extent can these findings be applied to more natural images? Here, we used the fMRI decoding technique and directly tested whether the findings obtained with primitive visual stimuli (Gabor patches) were applicable to natural images. In the fMRI experiments, participants performed depth and resolution tasks with both Gabor patches and natural images. We created a fMRI decoder made from the results of the Gabor patch experiments that classified a brain activity pattern into the depth or resolution task, and then examined how successful the task-dependent decoder could sort a brain activity pattern in the natural image experiment into the depth or resolution task. As a result, we found that the task-dependent decoder constructed from Gabor patch experiments could predict which task (depth or resolution task) a participant was engaged in the natural image experiments, especially in the V3 and middle temporal (MT+) areas of the brain. This is consistent with previous researches on the cortical activation relating to depth perception rather than perceptual processing of display resolution. These results provide firm evidence that fMRI decoding technique possesses the power to evaluate the application of Gabor patch results (laboratory findings) to the natural images (everyday affairs), representing a new approach for studying the mechanism of visual perception.
In Vitro Functional and Structural Characterization of A Synthetic Clinical Pulmonary Surfactant with Enhanced Resistance to Inhibition
Authors: Echaide Mercedes , Autilio Chiara , López-Rodríguez Elena , Cruz Antonio , Pérez-Gil Jesús 
Published: January 2020

AbstractCHF5633 is a novel synthetic clinical pulmonary surfactant preparation composed by two phospholipid species, dipalmitoyl phosphatidylcholine (DPPC) and palmitoyloleoyl phosphatidylglycerol (POPG), and synthetic analogues of the hydrophobic surfactant proteins SP-B and SP-C. In this study, the interfacial properties of CHF5633 in the absence and in the presence of inhibitory serum proteins have been assessed in comparison with a native surfactant purified from porcine lungs and with poractant alpha, a widely used clinical surfactant preparation. The study of the spreading properties of CHF5633 in a Wilhelmy balance, its ability to adsorb and accumulate at air-liquid interfaces as revealed by a multiwell fluorescence assay, and its dynamic behavior under breathing-like compression-expansion cycling in a Captive Bubble Surfactometer (CBS), all revealed that CHF5633 exhibits a good behavior to reduce and sustain surface tensions to values below 5 mN/m. CHF5633 shows somehow slower initial interfacial adsorption than native surfactant or poractant alpha, but a better resistance to inhibition by serum proteins than the animal-derived clinical surfactant, comparable to that of the full native surfactant complex. Interfacial CHF5633 films formed in a Langmuir-Blodgett balance coupled with epifluorescence microscopy revealed similar propensity to segregate condensed lipid domains under compression than films made by native porcine surfactant or poractant alpha. This ability of CHF5633 to segregate condensed lipid phases can be related with a marked thermotropic transition from ordered to disordered membrane phases as exhibited by differential scanning calorimetry (DSC) of CHF5633 suspensions, occurring at similar temperatures but with higher associated enthalpy than that shown by poractant alpha. The good interfacial behavior of CHF5633 tested under physiologically meaningful conditions in vitro and its higher resistance to inactivation by serum proteins, together with its standardized and well-defined composition, makes it a particularly useful therapeutic preparation to be applied in situations associated with lung inflammation and edema, alone or in combined strategies to exploit surfactant-facilitated drug delivery.