bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association study for proliferative diabetic retinopathy in Africans
Authors: Liu Chang , Chen Guanjie , Bentley Amy R. , Doumatey Ayo , Zhou Jie , Adeyemo Adebowale , Yang Jinkui , Rotimi Charles 
Published: August 2019

AbstractProliferative diabetic retinopathy (PDR) is a sight-threatening complication of diabetes that is associated with longer duration of diabetes and poor glycemic control under a genetic susceptibility background. Although GWAS of PDR have been conducted in Europeans and Asians, none has been done in continental Africans, a population at increased risk for PDR. Here, we report a GWAS of PDR among Africans. PDR cases (n = 64) were T2D patients with neovascularization in the retina and/or retinal detachment. Controls (n = 227) were T2D patients without listed eye complications despite high risk (T2D duration ≥10 years and fasting blood glucose >169 mg/dl). Replication was assessed in African Americans enrolled in the ARIC study. We identified 4 significant loci: WDR72, HLA-B, GAP43/RP11-326J18.1, and AL713866.1. At WDR72 the most strongly associated SNPs were rs12906891 (MAF = 0.071; p = 9.68 × 10-10; OR = 1.46, 95% CI [1.30,1.64]) and rs11070992 (MAF = 0.14; p = 4.23 × 10−8; OR = 1.28, 95%CI [1.17–1.40]). rs11070992 replicated in African Americans (p = 0.04). Variants in this gene have been associated with diabetic retinopathy, glycemic control, revascularization, and kidney disease.
UASOL, a large-scale high-resolution outdoor stereo dataset
Authors: Bauer Zuria , Gomez-Donoso Francisco , Cruz Edmanuel , Orts-Escolano Sergio , Cazorla Miguel 
Published: August 2019

AbstractIn this paper, we propose a new dataset for outdoor depth estimation from single and stereo RGB images. The dataset was acquired from the point of view of a pedestrian. Currently, the most novel approaches take advantage of deep learning-based techniques, which have proven to outperform traditional state-of-the-art computer vision methods. Nonetheless, these methods require large amounts of reliable ground-truth data. Despite there already existing several datasets that could be used for depth estimation, almost none of them are outdoor-oriented from an egocentric point of view. Our dataset introduces a large number of high-definition pairs of color frames and corresponding depth maps from a human perspective. In addition, the proposed dataset also features human interaction and great variability of data, as shown in this work.
NLRP3 inflammasome is attenuated in patients with Mycobacterium avium complex lung disease and correlated with decreased interleukin-1β response and host susceptibility
Authors: Wu Ming-Fang , Shu Chin-Chung , Wang Jann-Yuan , Yan Bo-Shiun , Lai Hsin-Chih , Chiang Bor-Luen , Wu Lawrence Shih-Hsin , Yu Chong-Jen 
Published: August 2019

AbstractThe incidence of nontuberculous mycobacteria lung disease (NTM-LD) is increasing in patients without human immunodeficiency virus. Mycobacterium avium complex (MAC) is one of the most common pathogenic species. The presence of MAC has a clinical relevance of around 35~42%, indicating the possibility of host susceptibility. Previous studies have shown that interleukin (IL)-1β and IL-1-receptor knock-out mice are susceptible to mycobacterial infections; however, the role of inflammasome-driven interleukin (IL)-1β has not been studied in MAC-LD. We enrolled patients with MAC-LD and healthy controls. Peripheral blood mononuclear cells (PBMCs), monocytes, and monocyte-derived macrophages were stimulated by MAC bacilli. The responses of interleukin(IL)-1β and the expression of inflammasome and toll-like receptors (TLRs) were measured. Single nucleotide polymorphisms (SNPs) were also examined for NLRP3 and TLR2 genes. In the patients with MAC-LD, the IL-1β responses decreased in PBMCs, monocytes, and macrophages assayed by MAC bacilli in comparison to the healthy controls. In addition, the level of caspase-1 after stimulation was lower in the MAC-LD group, although the mRNA level of IL-1β was not significantly lower. In surveying the activation of IL-1β, the MAC-LD group had an attenuated mRNA level of NLRP3 but similar levels of AIM2 and ASC compared with the controls. The SNPs rs3806268 and rs34298354 in NLRP3 for females and rs3804100 in TLR2 for males were associated with MAC-LD. In conclusion, our patients with MAC-LD had attenuated IL-1β production, which may have been due to lower activation of the NLRP3-caspase-1 axis. Two SNPs of NLRP3 and one of TLR2 were correlated with MAC-LD, possibly indicating host susceptibility.
Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing
Authors: Rzechorzek Nina M. , Saunders Olivia M. , Hiscox Lucy V. , Schwarz Tobias , Marioni-Henry Katia , Argyle David J. , Schoenebeck Jeffrey J. , Freeman Tom C. 
Published: August 2019

AbstractStructural ‘brain age’ is a valuable but complex biomarker for several brain disorders. The dog is an unrivalled comparator for neurological disease modeling, however canine brain morphometric diversity creates computational and statistical challenges. Using a data-driven approach, we explored complex interactions between patient metadata, brain morphometry, and neurological disease. Twenty-four morphometric parameters measured from 286 canine brain magnetic resonance imaging scans were combined with clinical parameters to generate 9,438 data points. Network analysis was used to cluster patients according to their brain morphometry profiles. An ‘aged-brain’ profile, defined by a small brain width and volume combined with ventriculomegaly, was revealed in the Boxer breed. Key features of this profile were paralleled in neutered female dogs which, relative to un-neutered females, had an 11-fold greater risk of developing brain tumours. Boxer dog and geriatric dog groups were both enriched for brain tumour diagnoses, despite a lack of geriatric Boxers within the cohort. Our findings suggest that advanced brain ageing enhances brain tumour risk in dogs and may be influenced by oestrogen deficiency—a risk factor for dementia and brain tumours in humans. Morphometric features of brain ageing in dogs, like humans, might better predict neurological disease risk than patient chronological age.
Prophage protein RacR activates lysozyme LysN, causing the growth defect of E. coli JM83
Authors: Tang Qiongwei , Feng Meilin , Hou Bingbing , Ye Jiang , Wu Haizhen , Zhang Huizhan 
Published: August 2019

AbstractProphage enriched the prokaryotic genome, and their transcriptional factors improved the protein expression network of the host. In this study, we uncovered a new prophage-prophage interaction in E. coli JM83. The Rac prophage protein RacR (GenBank accession no. AVI55875.1) directly activated the transcription of φ80dlacZΔM15 prophage lysozyme encoding gene 19 (GenBank accession no. ACB02445.1, renamed it lysN, lysozyme nineteen), resulting in the growth defect of JM83. This phenomenon also occurred in DH5α, but not in BL21(DE3) and MG1655 due to the genotype differences. However, deletion of lysN could not completely rescued JM83 from the growth arrest, indicating that RacR may regulate other related targets. In addition, passivation of RacR regulation was found in the late period of growth of JM83, and it was transmissible to daughter cells. Altogether, our study revealed part of RacR regulatory network, which suggested some advanced genetic strategies in bacteria.
NaCl induced salt adaptive changes and enhanced accumulation of 20-hydroxyecdysone in the in vitro shoot cultures of Spinacia oleracea (L.)
Authors: Muchate Niramaya S. , Rajurkar Nilima S. , Suprasanna Penna , Nikam Tukaram D. 
Published: August 2019

AbstractSpinach (Spinacia oleracea L.) is a vegetable plant with high nutritional properties. In the present work, we studied responses of in vitro shoot cultures to salt stress (0 (control), 100, 200 and 300 mM NaCl) and salt stress-induced accumulation of 20-hydroxyecdysone (20E). Our results revealed that effect of low to moderate level of salinity stress (100–200 mM) was less pronounced on growth and tissue water content (TWC) of shoot cultures compared to higher salinity level (300 mM). The salt treated shoot cultures showed better osmotic adjustment in terms of significant accumulation of compatible solutes and total soluble sugars and also higher antioxidant enzyme activity. As the NaCl stress was increased, there was a corresponding linear raise in the Na+ accumulation while the contents of both K+ and Ca2+ decreased significantly. We also studied salt-stress induced accumulation of a bioactive compound; 20E and results showed that 200 mM salt treated shoot cultures accumulated significantly 2.9 fold higher 20E as compared to untreated shoot cultures. The results suggest that Spinacia oleracea exhibits considerable salt tolerance with better osmotic adjustment and can be considered a suitable candidate for the production of bioactive secondary metabolite.
Role of fundoplication in treatment of patients with symptoms of hiatal hernia
Authors: Li Zhi-tong , Ji Feng , Han Xin-wei , Yuan Li-li , Wu Zheng-yang , Xu Miao , Peng De-lu , Wang Zhong-gao 
Published: August 2019

AbstractGastroesophageal reflux disease (GERD) is often associated with hiatal hernia (HH). However, the need for fundoplication during hiatal hernia repair (HHR) remains controversial. The objective of this study was to evaluate the effect of HHR with concomitant laparoscopic Nissen fundoplication (HHR-LNF) in HH patients. A total of 122 patients with symptomatic HH were randomized to receive either HHR (n = 61) or HHR-LNF (n = 61). The measures of evaluating outcomes included DeMeester scores (DMS), complications, Reflux Diagnostic Questionnaire and patients’ satisfaction 24 months following surgery. Despite comparable values in both groups at randomization, the DMS, total numbers of reflux episodes and percentage of time with pH < 4 were significantly higher in HHR group than in HHR-LNF group (P = 0.017, P = 0.002 and P = 0.019, respectively) at 6 months after surgery. One months postoperatively, complications were higher in the HHR-LNF group than in the HHR group (all P < 0.001), and there was no difference between the two groups at 6 months. By the end of the 2-year follow-up, HHR-LNF group showed a significantly lower reflux syndrome frequency-intensity score and greater percentage of satisfaction compared with HHR group (all P < 0.001). Laparoscopic HHR should be combined with a fundoplication in GERD patients with HH. HHR-LNF is safe and effective, not only improve reflux-related symptom, but also reduce the incidence of complications.
Self-reduction of the native TiO2 (110) surface during cooling after thermal annealing – in-operando investigations
Authors: Rogala M. , Bihlmayer G. , Dabrowski P. , Rodenbücher C. , Wrana D. , Krok F. , Klusek Z. , Szot K. 
Published: August 2019

AbstractWe investigate the thermal reduction of TiO2 in ultra-high vacuum. Contrary to what is usually assumed, we observe that the maximal surface reduction occurs not during the heating, but during the cooling of the sample back to room temperature. We describe the self-reduction, which occurs as a result of differences in the energies of defect formation in the bulk and surface regions. The findings presented are based on X-ray photoelectron spectroscopy carried out in-operando during the heating and cooling steps. The presented conclusions, concerning the course of redox processes, are especially important when considering oxides for resistive switching and neuromorphic applications and also when describing the mechanisms related to the basics of operation of solid oxide fuel cells.
Extreme levels of fallout radionuclides and other contaminants in glacial sediment (cryoconite) and implications for downstream aquatic ecosystems
Authors: Owens Philip N. , Blake William H. , Millward Geoffrey E. 
Published: August 2019

AbstractGlaciers in most parts of the world are retreating, releasing water and sediments to downstream rivers. Studies have found elevated levels of fallout radionuclides (FRNs) and other contaminants in glacial sediments, especially cryoconite, in European glaciers and Greenland. However, there are no equivalent studies for glaciers in North America. We report concentrations of FRNs (i.e. 137Cs, 210Pbun and 241Am) and other contaminants (i.e. metal(loids), phosphorus) in cryoconite and proglacial sediments from a glacier in British Columbia, Canada, and compare values to suspended sediments from the downstream river. The mean concentrations of 137Cs, 210Pbun and 241Am in cryoconite were 2,123 ± 74, 7,535 ± 224 and 11.5 ± 3.0 Bq kg−1, respectively, which are an order of magnitude greater than those for most soils and surficial materials. FRNs were much lower in suspended sediments and decreased with distance away from the glacier. Geochemical elements were enriched in cryoconite relative to local clastic materials and upper continental crust. Concentrations of FRNs in cryoconite were correlated with organic matter, which suggests this is important in controlling the scavenging of hydrophobic contaminants in glacial meltwater. Low concentrations of FRNs and contaminants in suspended sediments suggest that glacial meltwater and the delivery of cryoconite have limited impact on downstream aquatic ecosystems.
Evaluation of uterine receptivity after gonadotropin releasing hormone agonist administration as an oocyte maturation trigger: a rodent model
Authors: Ezoe Kenji , Murata Nana , Yabuuchi Akiko , Kobayashi Tamotsu , Kato Keiichi 
Published: August 2019

AbstractIn natural cycle or minimal stimulation cycle IVF, buserelin acetate (buserelin), a gonadotropin-releasing hormone agonist, is often used as a maturation trigger; however, its effect on pregnancy outcomes remains unclear. Therefore, in the present study, we compared uterine receptivity in buserelin-administered mice with that in human chorionic gonadotropin (hCG)-administered mice during the peri-implantation period. Implantation, decidualisation, and term-pregnancy were impaired following hCG, but not buserelin administration. hCG stimulated the synthesis and secretion of progesterone and oestradiol, whereas ovarian steroidogenesis in the buserelin-treated group was comparable with that in the control group. Furthermore, similar to the observation in controls, the buserelin-treated group exhibited activation of progesterone receptor signalling and inhibition of oestrogen receptor signalling in the endometrial epithelium on the day of implantation. However, epithelial progesterone signalling was not detected, and a high expression of genes downstream to oestrogen was observed on day 4 following hCG administration. These results suggest that buserelin administration does not impact uterine receptivity as it did not affect ovarian steroidogenesis and endometrial steroid signalling. Therefore, buserelin is preferred as an oocyte maturation trigger to optimise uterine receptivity during treatments involving timed intercourse, intrauterine insemination, or fresh embryo transfer following in vitro fertilisation.
A high-throughput screen to identify novel synthetic lethal compounds for the treatment of E-cadherin-deficient cells
Authors: Beetham Henry , Chen Augustine , Telford Bryony J. , Single Andrew , Jarman Kate E. , Lackovic Kurt , Luxenburger Andreas , Guilford Parry 
Published: August 2019

AbstractThe cell-cell adhesion protein E-cadherin (CDH1) is a tumor suppressor that is required to maintain cell adhesion, cell polarity and cell survival signalling. Somatic mutations in CDH1 are common in diffuse gastric cancer (DGC) and lobular breast cancer (LBC). In addition, germline mutations in CDH1 predispose to the autosomal dominant cancer syndrome Hereditary Diffuse Gastric Cancer (HDGC). One approach to target cells with mutations in specific tumor suppressor genes is synthetic lethality. To identify novel synthetic lethal compounds for the treatment of cancers associated with E-cadherin loss, we have undertaken a high-throughput screening campaign of ~114,000 lead-like compounds on an isogenic pair of human mammary epithelial cell lines – with and without CDH1 expression. This unbiased approach identified 12 novel compounds that preferentially harmed E-cadherin-deficient cells. Validation of these compounds using both real-time and end-point viability assays identified two novel compounds with significant synthetic lethal activity, thereby demonstrating that E-cadherin loss creates druggable vulnerabilities within tumor cells. In summary, we have identified novel synthetic lethal compounds that may provide a new strategy for the prevention and treatment of both sporadic and hereditary LBC and DGC.
Nitrogen-based gas molecule adsorption of monolayer phosphorene under metal functionalization
Authors: Lei Shuangying , Gao Ran , Sun Xiaolong , Guo Sijia , Yu Hong , Wan Neng , Xu Feng , Chen Jie 
Published: August 2019

AbstractUsing the first-principles calculation based on density functional theory (DFT), the adsorption properties of nitrogen-based gases molecules (NH3, NO, NO2) on various metal (Li, Na, K, Rb, Cs, Ca, Sr, Ba, Ni, La, Tl) decorated phosphorene systems have been studied systematically. The results show that all metal decorations can improve the adsorption strength of phosphorene to nitrogen-based gases molecules except for Tl decoration. Especially, the adsorption energy of NH3 molecule on Ni decorated phosphorene is 1.305 eV, and the adsorption energies of NO and NO2 on La decorated phosphorene can be up to 2.475 and 3.734 eV, respectively. In addition, after NO and NO2 adsorptions, the electronic and magnetic properties of some metal decorated phosphorenes change, indicating that the metal decorated phosphorenes have great potential in NO and NO2 detection.
A major sea-level drop briefly precedes the Toarcian oceanic anoxic event: implication for Early Jurassic climate and carbon cycle
Authors: Krencker François-Nicolas , Lindström Sofie , Bodin Stéphane 
Published: August 2019

AbstractSea-level change is an important parameter controlling the expansion of oxygen-depleted conditions in neritic settings during oceanic anoxic events (OAEs). Despite this fundamental role, it remains on a short timescale (<1 Myr) one of the least constrained parameters for numerous OAEs. Here we present sedimentological and geochemical evidence from Morocco and East Greenland showing that a forced regression shortly precedes (ca.102 kyr) the major transgression associated with the Toarcian OAE. The forced regression can be correlated over distances greater than 3000 km in numerous Tethyan and Boreal basins, indicating that the relative sea-level change was driven by eustastic fluctuations. The major amplitude (>50 m) and short duration of the forced regression suggests that it was most likely related to the transient waxing and waning of polar ice sheet. We suggest that this short-lived glaciation might have a genetic link with the inception of the Toarcian OAE. Indeed, during the deglaciation and the accompanying sea-level rise, the thawing permafrost may have released important quantities of methane into the atmosphere that would have contributed to the Toarcian OAE rapid warming and its characteristic negative carbon isotope excursion. This study offers a hypothesis on how some hyperthermal events might be rooted in short-lived “cold-snap” episodes.
Respiration of permeabilized cardiomyocytes from mice: no sex differences, but substrate-dependent changes in the apparent ADP-affinity
Authors: Karro Niina , Laasmaa Martin , Vendelin Marko , Birkedal Rikke 
Published: August 2019

AbstractSex differences in cardiac physiology are getting increased attention. This study assessed whether isolated, permeabilized cardiomyocytes from male and female C57BL/6 mice differ in terms of their respiration with multiple substrates and overall intracellular diffusion restriction estimated by the apparent ADP-affinity of respiration. Using respirometry, we recorded 1) the activities of respiratory complexes I, II and IV, 2) the respiration rate with substrates fuelling either complex I, II, or I + II, and 3) the apparent ADP-affinity with substrates fuelling complex I and I + II. The respiration rates were normalized to protein content and citrate synthase (CS) activity. We found no sex differences in CS activity (a marker of mitochondrial content) normalized to protein content or in any of the respiration measurements. This suggests that cardiomyocytes from male and female mice do not differ in terms of mitochondrial respiratory capacity and apparent ADP-affinity. Pyruvate modestly lowered the respiration rate, when added to succinate, glutamate and malate. This may be explained by intramitochondrial compartmentalization caused by the formation of supercomplexes and their association with specific dehydrogenases. To our knowledge, we show for the first time that the apparent ADP-affinity was substrate-dependent. This suggests that substrates may change or regulate intracellular barriers in cardiomyocytes.
Prediction of Site Preference of Implanted Transition Metal Dopants in Rock-salt Oxides
Authors: Misra Debolina , Yadav Satyesh K. 
Published: August 2019

AbstractTransition metals (TMs) implanted in oxides with rock-salt crystal structures (for example MgO and BaO) are assumed to substitute cations (Mg in case of MgO) from the lattice sites. We show that not all implanted TMs substitute cations but can be stable in interstitial sites as well. Stability of TM (Sc–Zn) dopants in various charge states in MgO and BaO has been investigated in the framework of density functional theory. We propose an effective way to calculate stability of implanted metals that let us predict site preference (interstitial or substitution) of the dopant in the host. We find that two factors govern the preference for an interstitial site: (i) relative ionic radius and (ii) relative oxygen affinity of cation and the TM dopants. If the radius of the cation is much larger than TM dopant, as in BaO, TM atoms always sit at interstitial sites. On the other hand, if the radius of the cation is comparable to that of the dopant TM, as in case of MgO, the transition of the preferred defect site, from substituting lattice Mg atom (Sc to Mn) to occupying interstitial site (Fe to Zn) is observed. This transition can be attributed to the change in the oxygen affinity of the TM atoms from Sc to Zn. Our results also explain experiments on Ni and Fe atoms implanted in MgO. TM dopants at interstitial sites could show substantially different and new properties from substitutionally doped stable compounds.