bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significant Diel Variation of Soil Respiration Suggests Aboveground and Belowground Controls in a Tropical Moist Forest in Puerto Rico
Authors: Gutiérrez del Arroyo Omar , Wood Tana E. 
Published: March 2020

AbstractSoil respiration in tropical forests represents a major source of carbon dioxide (CO2) to the atmosphere. The magnitude of this large flux is projected to change in response to climate change, with global implications due to the disproportionate role of tropical forests in the carbon cycle. Evaluating diel patterns of soil respiration concomitantly with biophysical drivers is a valuable approach for elucidating the mechanisms controlling soil respiration. We measured hourly soil respiration rates in a tropical moist forest in Puerto Rico over a 3‐year period using automated chambers, as well as soil temperature/moisture, air temperature, relative humidity, and photosynthetically active radiation. Hourly soil respiration exhibited as much as threefold variation on diel time scales (monthly diel amplitude ranged from 1 to 7 μmol CO2 m−2 s−1), and both the magnitude and shape of diel patterns changed significantly from month to month. Soil respiration peaked in the morning and late afternoon with a midday decline that was evident during the warmest summer months. The relationship between soil respiration and soil temperature differed during daytime versus the night, with a nonlinear relationship in the daytime but a significant positive linear relationship at night. These findings suggest factors other than/in addition to temperature could be controlling soil respiration during the day; however, soil respiration did not correlate with any of the other measured biophysical variables. Overall, our results highlight the potential role of aboveground processes as drivers of soil respiration at diel time scales, especially in closed canopy tropical forests with low diel variation in soil temperature/moisture.
Assessing auditory processing endophenotypes associated with Schizophrenia in individuals with 22q11.2 deletion syndrome
Authors: Francisco Ana A. , Foxe John J. , Horsthuis Douwe J. , DeMaio Danielle , Molholm Sophie 
Published: March 2020

Abstract22q11.2 Deletion Syndrome (22q11.2DS) is the strongest known molecular risk factor for schizophrenia. Brain responses to auditory stimuli have been studied extensively in schizophrenia and described as potential biomarkers of vulnerability to psychosis. We sought to understand whether these responses might aid in differentiating individuals with 22q11.2DS as a function of psychotic symptoms, and ultimately serve as signals of risk for schizophrenia. A duration oddball paradigm and high-density electrophysiology were used to test auditory processing in 26 individuals with 22q11.2DS (13–35 years old, 17 females) with varying degrees of psychotic symptomatology and in 26 age- and sex-matched neurotypical controls (NT). Presentation rate varied across three levels, to examine the effect of increasing demands on memory and the integrity of sensory adaptation. We tested whether N1 and mismatch negativity (MMN), typically reduced in schizophrenia, related to clinical/cognitive measures, and how they were affected by presentation rate. N1 adaptation effects interacted with psychotic symptomatology: Compared to an NT group, individuals with 22q11.2DS but no psychotic symptomatology presented larger adaptation effects, whereas those with psychotic symptomatology presented smaller effects. In contrast, individuals with 22q11.2DS showed increased effects of presentation rate on MMN amplitude, regardless of the presence of symptoms. While IQ and working memory were lower in the 22q11.2DS group, these measures did not correlate with the electrophysiological data. These findings suggest the presence of two distinct mechanisms: One intrinsic to 22q11.2DS resulting in increased N1 and MMN responses; another related to psychosis leading to a decreased N1 response.
Cdc42 subcellular relocation in response to VEGF/NRP1 engagement is associated with the poor prognosis of colorectal cancer
Authors: Ma Li-li , Guo Li-li , Luo Yang , Liu Guang-long , Lei Yan , Jing Fang-yan , Zhang Yun-li , Tong Gui-hui , Jing Zhi-Liang , Shen Lan , Tang Min-shan , Ding Yan-qing , Deng Yong-jian 
Published: March 2020

AbstractMicroscopic indications of malignancy and hallmark molecules of cancer are pivotal to determining cancer patient prognosis and subsequent medical intervention. Here, we found that compared to apical expression of Cdc42, which indicated that basal expression of Cdc42 occurred at the migrating cell front, glandular basal expression of Cdc42 (cell division cycle 42) in tissues indicated poorer prognoses for colorectal cancer (CRC) patients. The current study shows that activated Cdc42 was rapidly recruited to the migrating CRC cell front after VEGF stimulation through engagement of membrane-anchored neuropilin-1 (NRP1). When VEGF signalling was blocked with NRP1 knockdown or ATWLPPR (A7R, antagonist of VEGF/NRP1 interaction), Cdc42 activation and relocation to the cell front was attenuated, and filopodia and invadopodia formation was inhibited. The VEGF/NRP1 axis regulates directional migration, invasion, and metastasis through Cdc42 activation and relocation resulting from actin filament polymerisation of the extensions of membrane protrusions. Collectively, the immuno-micromorphological pattern of subcellular Cdc42 at the cell front indicated aggressive behaviours and predicted poor prognosis in CRC patients. Disruption of the intra- and extracellular interactions of the VEGF/NRP1 axis or Cdc42 relocation could be performed in clinical practice because it might inhibit cancer cell motility and metastasis.
Structural basis of ligand binding modes at the human formyl peptide receptor 2
Authors: Chen Tong , Xiong Muya , Zong Xin , Ge Yunjun , Zhang Hui , Wang Mu , Won Han Gye , Yi Cuiying , Ma Limin , Ye Richard D. , Xu Yechun , Zhao Qiang , Wu Beili 
Published: March 2020

AbstractThe human formyl peptide receptor 2 (FPR2) plays a crucial role in host defense and inflammation, and has been considered as a drug target for chronic inflammatory diseases. A variety of peptides with different structures and origins have been characterized as FPR2 ligands. However, the ligand-binding modes of FPR2 remain elusive, thereby limiting the development of potential drugs. Here we report the crystal structure of FPR2 bound to the potent peptide agonist WKYMVm at 2.8 Å resolution. The structure adopts an active conformation and exhibits a deep ligand-binding pocket. Combined with mutagenesis, ligand binding and signaling studies, key interactions between the agonist and FPR2 that govern ligand recognition and receptor activation are identified. Furthermore, molecular docking and functional assays reveal key factors that may define binding affinity and agonist potency of formyl peptides. These findings deepen our understanding about ligand recognition and selectivity mechanisms of the formyl peptide receptor family.
The electronic structure of benzene from a tiling of the correlated 126-dimensional wavefunction
Authors: Liu Yu , Kilby Phil , Frankcombe Terry J. , Schmidt Timothy W. 
Published: March 2020

AbstractThe electronic structure of benzene is a battleground for competing viewpoints of electronic structure, with valence bond theory localising electrons within superimposed resonance structures, and molecular orbital theory describing delocalised electrons. But, the interpretation of electronic structure in terms of orbitals ignores that the wavefunction is anti-symmetric upon interchange of like-spins. Furthermore, molecular orbitals do not provide an intuitive description of electron correlation. Here we show that the 126-dimensional electronic wavefunction of benzene can be partitioned into tiles related by permutation of like-spins. Employing correlated wavefunctions, these tiles are projected onto the three dimensions of each electron to reveal the superposition of Kekulé structures. But, opposing spins favour the occupancy of alternate Kekulé structures. This result succinctly describes the principal effect of electron correlation in benzene and underlines that electrons will not be spatially paired when it is energetically advantageous to avoid one another.
Gate controlled valley polarizer in bilayer graphene
Authors: Chen Hao , Zhou Pinjia , Liu Jiawei , Qiao Jiabin , Oezyilmaz Barbaros , Martin Jens 
Published: March 2020

AbstractSign reversal of Berry curvature across two oppositely gated regions in bilayer graphene can give rise to counter-propagating 1D channels with opposite valley indices. Considering spin and sub-lattice degeneracy, there are four quantized conduction channels in each direction. Previous experimental work on gate-controlled valley polarizer achieved good contrast only in the presence of an external magnetic field. Yet, with increasing magnetic field the ungated regions of bilayer graphene will transit into the quantum Hall regime, limiting the applications of valley-polarized electrons. Here we present improved performance of a gate-controlled valley polarizer through optimized device geometry and stacking method. Electrical measurements show up to two orders of magnitude difference in conductance between the valley-polarized state and gapped states. The valley-polarized state displays conductance of nearly 4e2/h and produces contrast in a subsequent valley analyzer configuration. These results pave the way to further experiments on valley-polarized electrons in zero magnetic field.
Prevalence, comorbidity, and breed differences in canine anxiety in 13,700 Finnish pet dogs
Authors: Salonen Milla , Sulkama Sini , Mikkola Salla , Puurunen Jenni , Hakanen Emma , Tiira Katriina , Araujo César , Lohi Hannes 
Published: March 2020

AbstractBehaviour problems and anxieties in dogs decrease their quality of life and may lead to relinquishment or euthanasia. Considering the large number of pet dogs and the commonness of these problematic behaviours, a better understanding of the epidemiology and related molecular and environmental factors is needed. We have here studied the prevalence, comorbidity, and breed specificity of seven canine anxiety-like traits: noise sensitivity, fearfulness, fear of surfaces and heights, inattention/impulsivity, compulsion, separation related behaviour and aggression with an online behaviour questionnaire answered by dog owners. Our results show that noise sensitivity is the most common anxiety-related trait with a prevalence of 32% in 13,700 Finnish pet dogs. Due to the high prevalence of noise sensitivity and fear, they were the most common comorbidities. However, when comparing the relative risk, the largest risk ratios were seen between hyperactivity/inattention, separation related behaviour and compulsion, and between fear and aggression. Furthermore, dog breeds showed large differences in prevalence of all anxiety-related traits, suggesting a strong genetic contribution. As a result, selective breeding focusing on behaviour may reduce the prevalence of canine anxieties. Anxious animals may suffer from chronic stress and thus, modified breeding policies could improve the welfare of our companion dogs.
Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms
Authors: Bhogireddy Sailaja , Xavier Abishek , Garg Vanika , Layland Nancy , Arias Renee , Payton Paxton , Nayak Spurthi N. , Pandey Manish K. , Puppala Naveen , Varshney Rajeev K. 
Published: March 2020

AbstractDrought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. A multi-seasonal phenotypic analysis of 10 peanut genotypes revealed C76-16 (C-76) and Valencia-C (Val-C) as the best and poor performers under deficit irrigation (DI) in West Texas, respectively. In order to decipher transcriptome changes under DI, RNA-seq was performed in C-76 and Val-C. Approximately 369 million raw reads were generated from 12 different libraries of two genotypes subjected to fully irrigated (FI) and DI conditions, of which ~329 million (90.2%) filtered reads were mapped to the diploid ancestors of peanut. The transcriptome analysis detected 4,508 differentially expressed genes (DEGs), 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms (SNPs) among the identified DEGs. The comparative analysis between the two genotypes revealed higher and integral tolerance in C-76 through activation of key genes involved in ABA and sucrose metabolic pathways. Interestingly, one SNP from the gene coding F-box protein (Araip.3WN1Q) and another SNP from gene coding for the lipid transfer protein (Aradu.03ENG) showed polymorphism in selected contrasting genotypes. These SNPs after further validation may be useful for performing early generation selection for selecting drought-responsive genotypes.
Comparison of Target Enrichment Platforms for Circulating Tumor DNA Detection
Authors: Lam So Ngo , Zhou Ying Chun , Chan Yee Man , Foo Ching Man , Lee Po Yi , Mok Wing Yeung , Wong Wing Sum , Fung Yan Yee , Wong Kit Yee , Huang Jun Yuan , Chow Chun Kin 
Published: March 2020

AbstractCancer-related mortality of solid tumors remains the major cause of death worldwide. Circulating tumor DNA (ctDNA) released from cancer cells harbors specific somatic mutations. Sequencing ctDNA opens opportunities to non-invasive population screening and lays foundations for personalized therapy. In this study, two commercially available platforms, Roche’s Avenio ctDNA Expanded panel and QIAgen’s QIAseq Human Comprehensive Cancer panel were compared for (1) panel coverage of clinically relevant variants; (2) target enrichment specificity and sequencing performance; (3) the sensitivity; (4) concordance and (5) sequencing coverage using the same human blood sample with ultra-deep next-generation sequencing. Our finding suggests that Avenio detected somatic mutations in common cancers in over 70% of patients while QIAseq covered nearly 90% with a higher average number of variants per patient (Avenio: 3; QIAseq: 8 variants per patient). Both panels demonstrated similar on-target rate and percentage of reads mapped. However, Avenio had more uniform sequencing coverage across regions with different GC content. Avenio had a higher sensitivity and concordance compared with QIAseq at the same sequencing depth. This study identifies a unique niche for the application of each of the panel and allows the scientific community to make an informed decision on the technologies to meet research or application needs.
Functionally Enigmatic Genes in Cancer: Using TCGA Data to Map the Limitations of Annotations
Authors: Maertens Alexandra , Tran Vy P. , Maertens Mikhail , Kleensang Andre , Luechtefeld Thomas H. , Hartung Thomas , Paller Channing J. 
Published: March 2020

AbstractCancer is a comparatively well-studied disease, yet despite decades of intense focus, we demonstrate here using data from The Cancer Genome Atlas that a substantial number of genes implicated in cancer are relatively poorly studied. Those genes will likely be missed by any data analysis pipeline, such as enrichment analysis, that depends exclusively on annotations for understanding biological function. There is no indication that the amount of research - indicated by number of publications - is correlated with any objective metric of gene significance. Moreover, these genes are not missing at random but reflect that our information about genes is gathered in a biased manner: poorly studied genes are more likely to be primate-specific and less likely to have a Mendelian inheritance pattern, and they tend to cluster in some biological processes and not others. While this likely reflects both technological limitations as well as the fact that well-known genes tend to gather more interest from the research community, in the absence of a concerted effort to study genes in an unbiased way, many genes (and biological processes) will remain opaque.
Rhizodegradation of Petroleum Oily Sludge-contaminated Soil Using Cajanus cajan Increases the Diversity of Soil Microbial Community
Authors: Allamin Ibrahim Alkali , Halmi Mohd Izuan Effendi , Yasid Nur Adeela , Ahmad Siti Aqlima , Abdullah Siti Rozaimah Sheikh , Shukor Yunus 
Published: March 2020

AbstractMost components of petroleum oily sludge (POS) are toxic, mutagenic and cancer-causing. Often bioremediation using microorganisms is hindered by the toxicity of POS. Under this circumstance, phytoremediation is the main option as it can overcome the toxicity of POS. Cajanus cajan a legume plant, was evaluated as a phyto-remediating agent for petroleum oily sludge-spiked soil. Culture dependent and independent methods were used to determine the rhizosphere microorganisms’ composition. Degradation rates were estimated gravimetrically. The population of total heterotrophic bacteria (THRB) was significantly higher in the uncontaminated soil compared to the contaminated rhizosphere soil with C. cajan, but the population of hydrocarbon-utilizing bacteria (HUB) was higher in the contaminated rhizosphere soil. The results show that for 1 to 3% oily sludge concentrations, an increase in microbial counts for all treatments from day 0 to 90 d was observed with the contaminated rhizosphere CR showing the highest significant increase (p  < 0.05) in microbial counts compared to other treatments. The metagenomic study focused on the POS of 3% (w/w) and based on the calculated bacterial community abundance indices showed an increase in the values for Ace, Cho, Shannon (Shannon-Weaver) and the Simpson’s (measured as InvSimpson) indices in CR3 compared to CN3. Both the Simpson’s and the Shannon values for CR3 were higher than CN3 indicating an increase in diversity upon the introduction of C. cajan into the contaminated soil. The PCoA plot revealed community-level differences between the contaminated non-rhizosphere control and contaminated rhizosphere microbiota. The PCoA differentiated the two treatments based on the presence or absence of plant. The composition and taxonomic analysis of microbiota-amplified sequences were categorized into eight phyla for the contaminated non-rhizosphere and ten phyla for the contaminated rhizosphere. The overall bacterial composition of the two treatments varied, as the distribution shows a similar variation between the two treatments in the phylum distribution. The percentage removal of total petroleum hydrocarbon (TPH) after 90 days of treatments with 1, 2, 3, 4, and 5% (w/w) of POS were 92, 90, 89, 68.3 and 47.3%, respectively, indicating removal inhibition at higher POS concentrations. As the search for more eco-friendly and sustainable remediating green plant continues, C. cajan shows great potential in reclaiming POS contaminated soil. Our findings will provide solutions to POS polluted soils and subsequent re-vegetation.
Development of glass micro-electrodes for local electric field, electrical conductivity, and pH measurements
Authors: Doi Kentaro , Asano Naoki , Kawano Satoyuki 
Published: March 2020

AbstractIn micro- and nanofluidic devices, liquid flows are often influenced by ionic currents generated by electric fields in narrow channels, which is an electrokinetic phenomenon. Various technologies have been developed that are analogous to semiconductor devices, such as diodes and field effect transistors. On the other hand, measurement techniques for local electric fields in such narrow channels have not yet been established. In the present study, electric fields in liquids are locally measured using glass micro-electrodes with 1-μm diameter tips, which are constructed by pulling a glass tube. By scanning a liquid poured into a channel by glass micro-electrodes, the potential difference in a liquid can be determined with a spatial resolution of the size of the glass tip. As a result, the electrical conductivity of sample solutions can be quantitatively evaluated. Furthermore, combining two glass capillaries filled with buffer solutions of different concentrations, an ionic diode that rectifies the proton conduction direction is constructed, and the possibility of pH measurement is also demonstrated. Under constant-current conditions, pH values ranging from 1.68 to 9.18 can be determined more quickly and stably than with conventional methods that depend on the proton selectivity of glass electrodes under equilibrium conditions.
Post-treatment FDG PET-CT in head and neck carcinoma: comparative analysis of 4 qualitative interpretative criteria in a large patient cohort
Authors: Zhong Jim , Sundersingh Moses , Dyker Karen , Currie Stuart , Vaidyanathan Sriram , Prestwich Robin , Scarsbrook Andrew 
Published: March 2020

AbstractThere is no consensus regarding optimal interpretative criteria (IC) for Fluorine-18 fluorodeoxyglucose (FDG) Positron Emission Tomography – Computed Tomography (PET-CT) response assessment following (chemo)radiotherapy (CRT) for head and neck squamous cell carcinoma (HNSCC). The aim was to compare accuracy of IC (NI-RADS, Porceddu, Hopkins, Deauville) for predicting loco-regional control and progression free survival (PFS). All patients with histologically confirmed HNSCC treated at a specialist cancer centre with curative-intent non-surgical treatment who underwent baseline and response assessment FDG PET-CT between August 2008 and May 2017 were included. Metabolic response was assessed using 4 different IC harmonised into 4-point scales (complete response, indeterminate, partial response, progressive disease). IC performance metrics (sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy) were compared. Kaplan-Meier and Cox proportional hazards regression analyses were performed for survival analysis. 562 patients were included (397 oropharynx, 53 hypopharynx, 48 larynx, 64 other/unknown primary). 420 patients (75%) received CRT and 142 (25%) had radiotherapy alone. Median follow-up was 26 months (range 3–148). 156 patients (28%) progressed during follow-up. All IC were accurate for prediction of primary tumour (mean NPV 85.0% (84.6–85.3), PPV 85.0% (82.5–92.3), accuracy 84.9% (84.2–86.0)) and nodal outcome (mean NPV 85.6% (84.1–86.6), PPV 94.7% (93.8–95.1), accuracy 86.8% (85.6–88.0)). Number of indeterminate scores for NI-RADS, Porceddu, Deauville and Hopkins were 91, 25, 20, 13 and 55, 70, 18 and 3 for primary tumour and nodes respectively. PPV was significantly reduced for indeterminate uptake across all IC (mean PPV primary tumour 36%, nodes 48%). Survival analyses showed significant differences in PFS between response categories classified by each of the four IC (p <0.001). All four IC have similar diagnostic performance characteristics although Porceddu and Deauville scores offered the best trade off of minimising indeterminate outcomes whilst maintaining a high NPV.