Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between Variant Y402H in Age-Related Macular Degeneration (AMD) Susceptibility Gene CFH and Treatment Response of AMD: A Meta-Analysis

Purpose To investigate the association between polymorphism rs1061170 (T1277C, Y402H) in age-related macular degeneration (AMD) susceptibility gene Complement Factor H (CFH) and treatment response of neovascular AMD. Methods We performed a literature-based meta-analysis including 10 published association studies involving 1,510 patients. Treatments included anti-VEGF (bevacizumab and ranibizumab) or photodynamic therapy. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using fixed- and random-effects models. Q-statistic test was used to assess heterogeneity. Results Polymorphism rs1061170 showed a significant summary OR of 1.68 (95% CI, 1.09 to 2.60; P = 0.020; CC versus TT; random-effects) for treatment response of neovascular AMD with heterogeneity of 0.09. In subgroup analysis, rs1061170 was more likely to be a predictor of response to anti-VEGF therapy (P = 0.011). However, heterozygous TC genotype was not associated with altered treatment response (OR = 1.18, 95% CI, 0.95 to 1.47; P = 0.145; fixed-effects). Influence analysis indicated the robustness of our findings. Conclusions rs1061170 might be associated with treatment response of neovascular AMD, especially for the anti-VEGF agents. It might be the first meta-analytically confirmed genetic marker predictive for AMD treatment response though a further validation in larger studies is needed.
A review of chemical vapour deposition of graphene on copper

The discovery of uniform deposition of high-quality single layered graphene on copper has generated significant interest. That interest has been translated into rapid progress in terms of large area deposition of thin films via transfer onto plastic and glass substrates. The opto-electronic properties of the graphene thin films reveal that they are of very high quality with transmittance and conductance values of >90% and 30Ω/sq, both are comparable to the current state-of-the-art indium tin oxide transparent conductor. In this Feature Article, we provide a detailed and up to date description of the literature on the subject as well as highlighting challenges that must be overcome for the utilization of graphene deposited on copper substrates by chemical vapour deposition.
Protective Effects of Alkaloid Compounds from Nelumbinis Plumula on tert-Butyl Hydroperoxide-Induced Oxidative Stress

This study was conducted to investigate the effect of Nelumbinis Plumula total alkaloid (NPA) and its main alkaloid components on oxidative stress induced by tert-butyl hydroperoxide (t-BHP) in the human hepatocellular HepG2 cell line. According to HPLC analysis, several major alkaloid compounds such as liensinine, isoliensinine and neferine were present in NPA. The cytotoxic effects in 0.55 mM t-BHP-induced HepG2 cells were significantly inhibited by NPA and the major compound in NPA, neferine, showed the strongest activities. The protective effect of neferine against oxidative stress induced by t-BHP may be associated with decreased ROS formation, TBARS generation, LDH release and increased GSH levels, suggesting their involvement of the cytoprotective on oxidative stress. The effects were comparable with quercetin, which was used as positive control. Overall, total alkaloid and alkaloid compounds from Nelumbinis Plumula displayed a significant cytoprotective effect against oxidative stress. Further study is needed to elucidate the relationship between the chemical structures of the components in NPA and their protective effect on oxidative stress.
von Hippel-Lindau tumor suppressor mutants faithfully model pathological hypoxia-driven angiogenesis and vascular retinopathies in zebrafish

SUMMARY Biallelic inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene predisposes human patients to the development of highly vascularized neoplasms in multiple organ systems. We show that zebrafish vhl mutants display a marked increase in blood vessel formation throughout the embryo, starting at 2 days post-fertilization. The most severe neovascularization is observed in distinct areas that overlap with high vegfa mRNA expression, including the vhl mutant brain and eye. Real-time quantitative PCR revealed increased expression of the duplicated VEGFA orthologs vegfaa and vegfab, and of vegfb and its receptors flt1, kdr and kdr-like, indicating increased vascular endothelial growth factor (Vegf) signaling in vhl mutants. Similar to VHL-associated retinal neoplasms, diabetic retinopathy and age-related macular degeneration, we show, by tetramethyl rhodamine-dextran angiography, that vascular abnormalities in the vhl−/− retina lead to vascular leakage, severe macular edema and retinal detachment. Significantly, vessels in the brain and eye express cxcr4a, a marker gene expressed by tumor and vascular cells in VHL-associated hemangioblastomas and renal cell carcinomas. VEGF receptor (VEGFR) tyrosine kinase inhibition (through exposure to sunitinib and 676475) blocked vhl−/−-induced angiogenesis in all affected tissues, demonstrating that Vegfaa, Vegfab and Vegfb are key effectors of the vhl−/− angiogenic phenotype through Flt1, Kdr and Kdr-like signaling. Since we show that the vhl−/− angiogenic phenotype shares distinct characteristics with VHL-associated vascular neoplasms, zebrafish vhl mutants provide a valuable in vivo vertebrate model to elucidate underlying mechanisms contributing to the development of these lesions. Furthermore, vhl mutant zebrafish embryos carrying blood vessel-specific transgenes represent a unique and clinically relevant model for tissue-specific, hypoxia-induced pathological angiogenesis and vascular retinopathies. Importantly, they will allow for a cost-effective, non-invasive and efficient way to screen for novel pharmacological agents and combinatorial treatments.
Dysfunctional Inhibitory Mechanisms in Locus Coeruleus Neurons of the Wistar Kyoto Rat

Background: The noradrenergic nucleus locus coeruleus (LC) has functional relevance in several psychopathologies such as stress, anxiety, and depression. In addition to glutamatergic and GABAergic synaptic inputs, the activation of somatodendritic α2-adrenoceptors is the main responsible for LC activity regulation. The Wistar Kyoto (WKY) rat exhibits depressive- and anxiety-like behaviors and hyperresponse to stressors. Thus, the goal of the present study was to investigate in vitro the sensitivity of α2-adrenoceptors, as well as the glutamatergic and GABAergic synaptic activity on LC neurons of the WKY strain. Methods: For that purpose patch-clamp whole-cell recordings were done in LC slices. Results: The α2-adrenoceptors of LC neurons from WKY rats were less sensitive to the effect induced by the agonist UK 14 304 as compared to that recorded in the Wistar (Wis) control strain. In addition, the GABAergic input to LC neurons of WKY rats was significantly modified compared to that in Wis rats, since the amplitude of spontaneous GABAergic postsynaptic currents was reduced and the half-width increased. On the contrary, no significant alterations were detected regarding glutamatergic input to LC neurons between rat strains. Conclusions: These results point out that in WKY rats the inhibitory control exerted by α2-adrenoceptors and GABAergic input onto LC neurons is dysregulated. Overall, this study supports in this animal model the hypothesis that claims an imbalance between the glutamatergic-GABAergic systems as a key factor in the pathophysiology of depression.
Relative Contributions of Agricultural Drift, Para-Occupational, and Residential Use Exposure Pathways to House Dust Pesticide Concentrations: Meta-Regression of Published Data

Background: Increased pesticide concentrations in house dust in agricultural areas have been attributed to several exposure pathways, including agricultural drift, para-occupational, and residential use. Objective: To guide future exposure assessment efforts, we quantified relative contributions of these pathways using meta-regression models of published data on dust pesticide concentrations. Methods: From studies in North American agricultural areas published from 1995 to 2015, we abstracted dust pesticide concentrations reported as summary statistics [e.g., geometric means (GM)]. We analyzed these data using mixed-effects meta-regression models that weighted each summary statistic by its inverse variance. Dependent variables were either the log-transformed GM (drift) or the log-transformed ratio of GMs from two groups (para-occupational, residential use). Results: For the drift pathway, predicted GMs decreased sharply and nonlinearly, with GMs 64% lower in homes 250 m versus 23 m from fields (interquartile range of published data) based on 52 statistics from seven studies. For the para-occupational pathway, GMs were 2.3 times higher [95% confidence interval (CI): 1.5, 3.3; 15 statistics, five studies] in homes of farmers who applied pesticides more recently or frequently versus less recently or frequently. For the residential use pathway, GMs were 1.3 (95% CI: 1.1, 1.4) and 1.5 (95% CI: 1.2, 1.9) times higher in treated versus untreated homes, when the probability that a pesticide was used for the pest treatment was 1–19% and ≥ 20%, respectively (88 statistics, five studies). Conclusion: Our quantification of the relative contributions of pesticide exposure pathways in agricultural populations could improve exposure assessments in epidemiologic studies. The meta-regression models can be updated when additional data become available. Citation: Deziel NC, Beane Freeman LE, Graubard BI, Jones RR, Hoppin JA, Thomas K, Hines CJ, Blair A, Sandler DP, Chen H, Lubin JH, Andreotti G, Alavanja MC, Friesen MC. 2017. Relative contributions of agricultural drift, para-occupational, and residential use exposure pathways to house dust pesticide concentrations: meta-regression of published data. Environ Health Perspect 125:296–305; http://dx.doi. org/10.1289/EHP426
Occupational Asthma

Occupational asthma is an important diagnosis to make, as it is one of the few instances when an individual can be cured of his or her asthma after they are no longer exposed to the causal agent. The diagnosis should always be considered in any adult with new onset asthma or an unexplained deterioration in a known asthmatic. Over 300 agents have been implicated as causes of occupational asthma and with the introduction of new chemicals in the workplace, as industrial processes change, it is likely that more will be identified.
Physical Interpretations of Rotating Radio Transients

Nearly a dozen of Rotating RAdio Transients (RRATs) have been discovered recently. These objects share similar spin parameters with normal radio pulsars but distinguish themselves from normal pulsars by being quiescent most of the time and only becoming radio bright occasionally. We discuss two possible interpretations to the phenomenon. The first model suggests that these objects are pulsars slightly below the radio emission “death line”, and become active occasionally when the conditions for pair production and coherent emission are satisfied. The second model invokes a radio emission direction reversal in normal pulsars, as has been introduced to interpret the peculiar mode changing phenomenon in PSR B1822-09. In this picture, our line of sight misses the main radio emission beam of RRATs but happens to sweep the emission beam when the radio emission direction is reversed. RRATs are therefore the other half of the normal “nulling” pulsars. We suggest that X-ray observations can provide clues to differentiate these two possibilities. Subject headings: stars: pulsars X-ray: observation radiation mechanism: coherent radio
Denser than the densest subgraph: extracting optimal quasi-cliques with quality guarantees

Finding dense subgraphs is an important graph-mining task with many applications. Given that the direct optimization of edge density is not meaningful, as even a single edge achieves maximum density, research has focused on optimizing alternative density functions. A very popular among such functions is the average degree, whose maximization leads to the well-known densest-subgraph notion. Surprisingly enough, however, densest subgraphs are typically large graphs, with small edge density and large diameter. In this paper, we define a novel density function, which gives subgraphs of much higher quality than densest subgraphs: the graphs found by our method are compact, dense, and with smaller diameter. We show that the proposed function can be derived from a general framework, which includes other important density functions as subcases and for which we show interesting general theoretical properties. To optimize the proposed function we provide an additive approximation algorithm and a local-search heuristic. Both algorithms are very efficient and scale well to large graphs. We evaluate our algorithms on real and synthetic datasets, and we also devise several application studies as variants of our original problem. When compared with the method that finds the subgraph of the largest average degree, our algorithms return denser subgraphs with smaller diameter. Finally, we discuss new interesting research directions that our problem leaves open.
Unprecedented Utilization of Pelargonidin and Indole for the Biosynthesis of Plant Indole Alkaloids

Nudicaulins are a group of indole alkaloid glycosides responsible for the color of yellow petals of Papaver nudicaule (Iceland poppy). The unique aglycone scaffold of these alkaloids attracted our interest as one of the most unusual flavonoid‐indole hybrid structures that occur in nature. Stable isotope labeling experiments with sliced petals identified free indole, but not tryptamine or l‐tryptophan, as one of the two key biosynthetic precursors of the nudicaulin aglycone. Pelargonidin was identified as the second key precursor, contributing the polyphenolic unit to the nudicaulin molecule. This finding was inferred from the temporary accumulation of pelargonidin glycosides in the petals during flower bud development and a drop at the point in time when nudicaulin levels start to increase. The precursor‐directed incorporation of cyanidin into a new 3′‐hydroxynudicaulin strongly supports the hypothesis that anthocyanins are involved in the biosynthesis of nudicaulins.
Topographic influences on ring widths of trees and shrubs across alpine treelines in southwest Yukon

ABSTRACT Growth responses of trees and shrubs to climate often exhibit unexplained variation in alpine regions, making it difficult to predict how they will respond to future changes in climate. We sought to characterize and explain this variability in southwest Yukon, a topographically complex region of subarctic Canada. We collected cores and sections from 360 spruce trees and 480 willow shrubs across treelines on north and south aspects in six valleys spanning two mountain ranges. We compared growth rates, growth patterns, and climate-growth responses between species and topographic factors. South aspects had wider tree rings and higher tree and shrub interseries correlations than north aspects, likely because of shallow active layers on the latter. Growth patterns and responses to climate did not vary between aspects or elevations but differed slightly between mountain ranges, likely because of differences in spring soil moisture content between ranges. Growth responses of both species to summer temperature were positive, but tree growth was negatively correlated to spring temperature and shrub growth was negatively correlated to summer precipitation, both of which are projected to increase along with summer temperature. Future changes in climate could therefore reduce the growth of one or both species in southwest Yukon.
Whole-brain atrophy in multiple sclerosis measured by automated versus semiautomated MR imaging segmentation.

BACKGROUND AND PURPOSE Semiautomated and automated methods are used to measure whole-brain atrophy in multiple sclerosis (MS), but their comparative reliability, sensitivity, and validity are unknown. METHODS Brain parenchymal fraction (BPF) was measured in patients with MS (n = 52) and healthy control subjects (n = 17) by four methods: semiautomated or automated segmentation and 2D or 3D pulse sequences. Linear measures of atrophy, whole-brain lesion volumes, and clinical data were used to explore validity. RESULTS The 2D automated method yielded unreliable segmentation and was discarded. The three other BPF methods produced data that were highly intercorrelated and indistinguishable by analysis of variance. In the MS group, semiautomated (2D: 0.84 +/- 0.04, P <.001; 3D: 0.84 +/- 0.05, P =.04) and automated 3D (0.83 +/- 0.05, P =.002) BPFs were lower than controls (semiautomated 2D: 0.88 +/- 0.02; 3D: 0.88 +/- 0.03; automated 3D: 0.88 +/- 0.03). In the MS group, the semiautomated (r = -.79 to -.82) and automated 3D (r = -.81) BPFs inversely correlated with third ventricular width and showed similarly robust correlations with the bicaudate ratio (all r = -.74). The semiautomated and automated BPFs showed similar, moderate correlations with T1 hypointense and FLAIR hyperintense lesion volume, physical disability (Expanded Disability Status Scale) score, and disease duration and similar differences between secondary progressive and relapsing-remitting patients. The intraobserver, interobserver, and test-retest reliability was somewhat higher for the automated than for the semiautomated methods. CONCLUSION These automated and semiautomated measures of whole-brain atrophy provided similar and nearly interchangeable data regarding MS. They discriminated MS from healthy individuals and showed similar relationships to established disease variables.
Sources of Variation in Social Networks

What explains the large variation in the number of contacts (degree) that different participants of social networks have: age, randomness, or some unobservable fitness measure? To answer this question, I extend the model presented in Jackson and Rogers (2007) to allow individuals to vary in their ability to attract contacts. I estimate the parameters of the extended model, using a social network of citations among high-energy physics papers, and find that the extended Jackson–Rogers model can parsimoniously fit the degree distribution of each age cohort. Moreover, both the length of time spent in the network and the unobservable fitness measure are important in explaining the observed variation in participantsʼ degrees.
A Comparison of the Functional Traits of Common Reed (Phragmites australis) in Northern China: Aquatic vs. Terrestrial Ecotypes

Common reed (Phragmites australis (Cav.) Trin. ex Steud. ) is distributed widely throughout the world with various ecotypes. This research compares the functional traits and biomass allocation patterns of two contrasting reed ecotypes. Twelve pairs of aquatic and terrestrial reed samples were collected in northern China. Significant differences in functional traits between the two reed ecotypes were observed, while biomass allocation patterns of reed organs did not differ significantly except for at the root. The dry matter content (DMC) in the whole of the reed plant, leaf, root, and rhizome was higher; while the specific leaf area (SLA) and specific root length (SRL) were lower in terrestrial versus aquatic reed. The biomass allocation in organs of the two forms of reed was isometric, only root in the terrestrial habitat increased faster with an increase in the whole plant biomass. It can be affirmed that aquatic and terrestrial reed that adapt to different environments generally has distinct leaf and root functional traits but isometric biomass allocation patterns. This suggests different resource acquisition strategies: (1) aquatic reed grows faster with high SLA and SRL and is more responsive to the environment, while (2) terrestrial reed with high DMC grows slower and is less responsive to the adverse environment (e.g. dry soil conditions).
De novo triple segmental aneuploid of 1p, 1q, and 4q in a girl with hypertrophic cardiomyopathy, muscle hypotonia, and multiple congenital anomalies

De novo Triple Segmental Aneuploid of 1p, 1q, and 4q in a Girl With Hypertrophic Cardiomyopathy, Muscle Hypotonia, and Multiple Congenital Anomalies Gwo-Chin Ma, Yu-Yuan Ke, Meng-Luen Lee, Long-Yen Tsao, Dong-Jay Lee, Chin-Wen Yang, Shou-Jen Kuo, Han-Yao Chiu,** and Ming Chen* Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan Institute of Biochemistry and Biotechnology, Chung Shan Medical University, Taichung, Taiwan Department of Pediatrics, Changhua Christian Hospital, Changhua, Taiwan Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan Department of Respiratory Care, Chang Jung Christian University, Tainan, Taiwan Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan Department of Obstetrics and Gynecology, College of Medicine and Hospital, National Taiwan University, Taipei, Taiwan Department of Medical Genetics, College of Medicine and Hospital, National Taiwan University, Taipei, Taiwan
Giant landslide displacement analysis using a point cloud set conflict technique: a case in Xishancun landslide, Sichuan, China

ABSTRACT Landslides, threatening millions of human lives, are geological phenomena on earth, occurred frequently. An increasing number of techniques are being used to monitor landslide deformation. Among these, Light Detection and Ranging (LiDAR) stands out for its high efficiency and accuracy in displacement detection, particularly for giant landslides. In this work, we collected two temporal datasets of terrain laser scanning and proposed a flowchart for giant landslide displacement analysis using the point cloud set conflict（PCSC） technique. First, the terrestrial points were obtained by performing registration and off-terrain point filtering. Second, the landslide displacement field was acquired using the proposed method based on its surface roughness. The displacement results from our established methodological system are comparable with the ones of Interferometric Synthetic Aperture Radar (InSAR)-derived deformations. The differences estimated from two systems are at the centimetre level. Cross-analysis on the trigger factor with landslide occurred mechanism could be achieved based on the results as well. Therefore, this work provides a novel system to analyse the displacement of a giant landslide in the future study.
Rose-K contact lens for keratoconus.

AIM To report clinical experience and the comparative value of axial and instantaneous topography data in fitting Rose-K design contact lenses in moderate and severe keratoconus. MATERIALS AND METHODS Thirty-eight eyes (of 23 patients) with keratoconus were fitted with Rose-K design contact lenses and followed up for at least six months or more. Visual acuity with habitual vision correction available was measured. Axial and instantaneous topography maps for each eye were recorded. Contact lens wear comfort was graded on a ten point rating scale every three months. RESULTS Fourteen (100%) moderate keratoconus eyes (average Sim K 48.61 +/- 1.24D) and 23 of 24 (96%) of severe keratoconus eyes (average Sim K 60.88 +/- 5.31D) were successfully fitted with the Rose-K lenses. Final fit contact lenses in severe keratoconus had statistically significant steeper base curves compared to average axial corneal curvature than in moderate keratoconus eyes. Average simulated corneal curvature on axial maps predicted final fit contact lens base curves significantly better than on instantaneous maps. Thirty-three of the 37 eyes fitted with contact lenses maintained wear comfort over average follow up period of 13 +/- 3.5 months. CONCLUSIONS Rose-K design rigid contact lenses are successful in visually rehabilitating 100% of moderate and 96% of severe keratoconus eyes. Most patients (90%) maintained contact lens wear comfort. Corneal curvature on axial maps is a better predictive of base curve of final fit contact lens.