Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multicenter Clinical Evaluation of Data Logging in Cochlear Implant Recipients Using Automated Scene Classification Technologies

Currently, there are no studies assessing everyday use of cochlear implant (CI) processors by recipients by means of objective tools. The Nucleus 6 sound processor features a data logging system capable of real-time recording of CI use in different acoustic environments and under various categories of loudness levels. In this study, we report data logged for the different scenes and different loudness levels of 1,366 CI patients, as recorded by SCAN. Monitoring device use in cochlear implant recipients of all ages provides important information about the listening conditions encountered in recipients' daily lives that may support counseling and assist in the further management of their device settings. The findings for this large cohort of active CI users confirm differences between age groups concerning device use and exposure to various noise environments, especially between the youngest and oldest age groups, while similar levels of loudness were observed.
Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age

Following up on the encouraging results of residue‐residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of 34 groups for 38 domains classified as free modeling targets which are not accessible to homology‐based modeling due to a lack of structural templates. CASP11 saw a rise of coevolution‐based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12. In more than half of the targets, especially those with many homologous sequences accessible, precisions above 90% were achieved with the best predictors reaching a precision of 100% in some cases. We furthermore tested the impact of using these contacts as restraints in ab initio modeling of 14 single‐domain free modeling targets using Rosetta. Adding contacts to the Rosetta calculations resulted in improvements of up to 26% in GDT_TS within the top five structures.
A Multi-Layered Framework for color pastel painting

We present a computerized framework for producing color pastel painting from the visual information extracted from a photograph. To express color pastel painting, we propose a multi-layered framework where each layer possesses pastel stroke patterns of different colors. The stroke patterns in the separate layers are merged by a rendering equation based on a participating media rendering scheme. To produce the stroke patterns in each layer, we review the physical properties of pastels and the mechanism of a convolution framework, which is the most widely used scheme to simulate stick-shaped media such as pencils. We devise the following computational models to extend the convolution framework to produce pastel strokes: a bold noise model, which mimics heavy and clustered deposition of pigment, and a thick convolution filter model, which produces various pastel stroke patterns. We also design a stochastic color coordination scheme to mimic pastel artists’ color expression and to separate strokes in different layers. To demonstrate the soundness of approach, we conduct several experiments using the models and compare the results with existing works or real pastel paintings. We present the results for several pastel paintings to demonstrate the excellent performance of our framework.
DZNep represses Bcl-2 expression and modulates apoptosis sensitivity in response to Nutlin-3a

ABSTRACT MDM2 antagonists stabilize and activate wild-type p53, and histone methyltransferase (HMT) inhibitors reduce methylation on histone lysines and arginines. Both MDM2 antagonists and HMT inhibitors are being developed as cancer therapeutics. Wild-type p53 expressing HCT116 colon cancer cells were resistant to apoptosis in response to the MDM2 antagonist Nutlin-3a. However, co-treatment with the HMT inhibitor DZNep sensitized the cells to Nutlin-3a-induced apoptosis. This sensitization resulted from reduced activity of the Bcl-2 gene promoter and a reduction in Bcl-2 mRNA and protein. Surprisingly, DZNep reduced Bcl-2 expression in other colon cancer cell lines (RKO, SW48, and LoVo) but failed to sensitize them to Nutlin-3a. We found these cell lines express elevated levels of Bcl-2 or other Bcl-2-family proteins, including Bcl-xL, Mcl-1, and Bcl-w. Knockdown of Mcl-1 and/or treatment with specific or pan Bcl-2-family inhibitors (BH3 mimetics) sensitized RKO, SW48, and LoVo cells to apoptosis by Nutlin-3a. The results demonstrate 1) DZNep represses the Bcl-2 gene promoter and affects apoptosis sensitivity by reducing Bcl-2 protein expression, and 2) elevated expression of pro-survival Bcl-2 family members protects colon cancer cells from Nutlin-3a-induced apoptosis. Targeting Bcl-2 proteins via DZNep or BH3 mimetics could increase the therapeutic potential of MDM2-antagonists like Nutlin-3a in colon cancer.
Flow boiling of halogenated olefins inside a square cross-section microchannel

New experimental heat transfer coefficients measured during flow boiling of HFO-1234ze(E) and HFO-1234yf inside a square cross-section microchannel having a hydraulic diameter of 1.23 mm are presented. The test runs have been performed with mass flux ranging between 200 and 500 kg m−2 s−1 and heat flux between 20 and 170 kW m−2. The local heat transfer coefficients are compared against the values previously measured using the same refrigerants in a 1 mm diameter tube, with the aim of highlighting the effect of the noncircular shape of the cross-section. The experimental data are compared against predicting models available in the literature to suggest possible design methods for evaporators adopting hydrofluoroolefins in microchannels.
Offline Interturn Fault Diagnosis Method for Induction Motors by Impedance Analysis

In this paper, a new offline interturn fault (ITF) diagnosis method for induction motors is presented. The proposed method is based on impedance imbalance in the stationary d-q plane. First, to show the impedance imbalance, an induction motor model is presented with an ITF circuit loop and fault resistance. Then, six impedance components in the stationary d-q plane are defined, depending on the excited phase windings. With fast Fourier transform (FFT) filtering applied to the six impedance components in the d-q plane, the second-order impedance magnitudes are obtained. From the magnitude, the ITF and the faulty phase can easily be detected. Moreover, a specific faulty winding among the faulty phase windings can be identified. To verify the proposed method, finite-element analysis (FEA) and experimental results are presented for an induction motor having an ITF.
Safety of Simultaneous Bilateral Pulmonary Resection for Metastatic Lung Tumors.

AIM We investigated the safety of simultaneous bilateral lung resection for lung metastases. PATIENTS AND METHODS We retrospectively analyzed 185 patients with pulmonary metastases who underwent unilateral or bilateral pulmonary resection from August 2009 to December 2016 at a single institution. RESULTS Single-stage bilateral lung resection was undertaken in 19 patients, and the other 166 patients underwent unilateral pulmonary resection, including 20 patients who underwent repeated resections for synchronous or metachronous metastases. Operative time and drainage days in the bilateral group were significantly longer than those in the unilateral group (220±20 vs. 152±6.9 min: p<0.01, and 2.79±0.3 vs. 2.08±0.1 days: p<0.01). Incidence of postoperative complications and postoperative in-hospital days did not differ between the two groups (p=0.33 and 0.66, respectively). The bilateral group was further divided into two groups, namely, those who underwent wedge resection on both sides (WW) and those who underwent wedge resection on one side and segmentectomy or lobectomy on an opposite side (WSL). Operative time in the WSL group was significantly longer than that in the WW group (260±19 vs. 201±18 min: p=0.03). However, there was no significant difference in duration of chest tube use and postoperative hospital days between the two groups (p=0.26 and p=0.89). No severe postoperative complications occurred in either group. CONCLUSION One-stage bilateral pulmonary metastasectomy appears to be safe as long as only wedge resection is performed on at least one side.
Local-Scale Drivers of Tree Survival in a Temperate Forest

Tree survival plays a central role in forest ecosystems. Although many factors such as tree size, abiotic and biotic neighborhoods have been proposed as being important in explaining patterns of tree survival, their contributions are still subject to debate. We used generalized linear mixed models to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree survival in an old-growth temperate forest in northeastern China at three levels (community, guild and species). Tree size and both abiotic and biotic neighborhood variables influenced tree survival under current forest conditions, but their relative importance varied dramatically within and among the community, guild and species levels. Of the variables tested, tree size was typically the most important predictor of tree survival, followed by biotic and then abiotic variables. The effect of tree size on survival varied from strongly positive for small trees (1–20 cm dbh) and medium trees (20–40 cm dbh), to slightly negative for large trees (>40 cm dbh). Among the biotic factors, we found strong evidence for negative density and frequency dependence in this temperate forest, as indicated by negative effects of both total basal area of neighbors and the frequency of conspecific neighbors. Among the abiotic factors tested, soil nutrients tended to be more important in affecting tree survival than topographic variables. Abiotic factors generally influenced survival for species with relatively high abundance, for individuals in smaller size classes and for shade-tolerant species. Our study demonstrates that the relative importance of variables driving patterns of tree survival differs greatly among size classes, species guilds and abundance classes in temperate forest, which can further understanding of forest dynamics and offer important insights into forest management.
Exposure and dose modelling in occupational epidemiology

Complex and dynamic physiologic processes underlie the exposure-response relations that occupational and environmental epidemiologists study. Simple summary measures of exposure such as the average, cumulative exposure, or duration of exposure, can be applied suitably in exposure-response analyses in many instances. However, there are situations where these metrics may not be directly proportional to risk, in which case their use will result in misclassification and biased estimates of exposure-response associations. We outline methods for developing exposure or dose metrics which may reduce misclassification, as illustrated with some recent examples. Selecting better exposure or dose metrics can be thought of as a problem of choosing appropriate weights on the exposure history of each cohort member. Dosimetric modeling involves choosing exposure weights based on formal hypotheses about underlying physiologic or pathogenetic processes. Dosimetric modeling is still not widely used in epidemiology, and so the forms of mathematical models and the criteria for choosing one model over another are not yet standardized. We hope to stimulate further applications through this presentation.
Computationally-Optimized Bone Mechanical Modeling from High-Resolution Structural Images

Image-based mechanical modeling of the complex micro-structure of human bone has shown promise as a non-invasive method for characterizing bone strength and fracture risk in vivo. In particular, elastic moduli obtained from image-derived micro-finite element (μFE) simulations have been shown to correlate well with results obtained by mechanical testing of cadaveric bone. However, most existing large-scale finite-element simulation programs require significant computing resources, which hamper their use in common laboratory and clinical environments. In this work, we theoretically derive and computationally evaluate the resources needed to perform such simulations (in terms of computer memory and computation time), which are dependent on the number of finite elements in the image-derived bone model. A detailed description of our approach is provided, which is specifically optimized for μFE modeling of the complex three-dimensional architecture of trabecular bone. Our implementation includes domain decomposition for parallel computing, a novel stopping criterion, and a system for speeding up convergence by pre-iterating on coarser grids. The performance of the system is demonstrated on a dual quad-core Xeon 3.16 GHz CPUs equipped with 40 GB of RAM. Models of distal tibia derived from 3D in-vivo MR images in a patient comprising 200,000 elements required less than 30 seconds to converge (and 40 MB RAM). To illustrate the system's potential for large-scale μFE simulations, axial stiffness was estimated from high-resolution micro-CT images of a voxel array of 90 million elements comprising the human proximal femur in seven hours CPU time. In conclusion, the system described should enable image-based finite-element bone simulations in practical computation times on high-end desktop computers with applications to laboratory studies and clinical imaging.
Impact of Antihypertensive Treatment on Maternal and Perinatal Outcomes in Pregnancy Complicated by Chronic Hypertension: A Systematic Review and Meta‐Analysis

Background Chronic hypertension complicates around 3% of all pregnancies. There is evidence that treating severe hypertension reduces maternal morbidity. This study aimed to systematically review randomized controlled trials of antihypertensive agents treating chronic hypertension in pregnancy to determine the effect of this intervention. Methods and Results Medline (via OVID), Embase (via OVID) and the Cochrane Trials Register were searched from their earliest entries until November 30, 2016. All randomized controlled trials evaluating antihypertensive treatments for chronic hypertension in pregnancy were included. Data were extracted and analyzed in Stata (version 14.1). Fifteen randomized controlled trials (1166 women) were identified for meta‐analysis. A clinically important reduction in the incidence of severe hypertension was seen with antihypertensive treatment versus no antihypertensive treatment/placebo (5 studies, 446 women; risk ratio 0.33, 95%CI 0.19‐0.56; I2 0.0%). There was no difference in the incidence of superimposed pre‐eclampsia (7 studies, 727 women; risk ratio 0.74, 95%CI 0.49‐1.11; I2 28.1%), stillbirth/neonatal death (4 studies, 667 women; risk ratio 0.37, 95%CI 0.11‐1.26; I2 0.0%), birth weight (7 studies, 802 women; weighted mean difference −60 g, 95%CI −200 to 80 g; I2 0.0%), or small for gestational age (4 studies, 369 women; risk ratio 1.01, 95%CI 0.53‐1.94; I2 0.0%) with antihypertensive treatment versus no treatment/placebo. Conclusions Antihypertensive treatment reduces the risk of severe hypertension in pregnant women with chronic hypertension. A considerable paucity of data exists to guide choice of antihypertensive agent. Adequately powered head‐to‐head randomized controlled trials of commonly used antihypertensive agents are required to inform prescribing.
Perpetrating Violence Increases Identification With Violent Groups: Survey Evidence From Former Combatants

Heightened group identification motivates individuals to perpetrate violence, but can perpetrating violence—in and of itself—increase identification with violent groups? I test this idea using archival surveys of ex-combatants. In Liberia, where many combatants joined their violent group willingly, the data show a positive association between perpetrating violence and identification with one’s violent group (Study 1). These results hold even when controlling for potentially confounding variables such as being abducted into the group versus joining willingly, length of time in the group, and personally experiencing violence. Study 2 replicates and extends this finding with data from ex-combatants in Uganda who were abducted into their group, using a natural experiment in which some abductees were forced to perpetrate violence whereas other abductees were not. These findings support a cycle of violence in which perpetrating violence increases identification with violent groups and heightened identification increases future violent behavior.
Natural Functions of PLIN2 Mediating Wnt/LiCl Signaling and Glycogen Synthase Kinase 3 (GSK3)/GSK3 Substrate-Related Effects Are Modulated by Lipid

ABSTRACT Belonging to the PLIN family, PLIN2 associates with lipid storage droplets (LSDs), but other functions of PLIN2 remain unclear. Here, we suggest that PLIN2 mediates Wnt signaling because PLIN2 small interfering RNA (siRNA) suppresses activation of Wnt/coreceptor pathways. The mediation in the Wnt/Frizzled pathway seems to occur from Dishevelleds to axin/glycogen synthase kinase 3(GSK3)/β-catenin complexes (AGβC) as Wnt decreases Dishevelled/PLIN2 but increases AGβC/PLIN2 associations. Augmenting cellular LSDs that affect PLIN2 associations with these proteins, oleic acid (OA) treatment inhibits Wnt-increased AGβC/PLIN2 associations and β-catenin T-cell factor signaling (β-CTS). Revealing that PLIN2 is a GSK3-associated protein, the study explored PLIN2-mediated effects on GSK3/GSK3 substrates. PLIN2 siRNA reduces inhibitory GSK3 levels and lithium chloride (LiCl)-upregulated β-catenin or CCAAT/enhancer binding protein α (c/EBPα) expression. OA treatment decreases LiCl-increased c/EBPα via PLIN2-c/EBPα dissociation. In addition to PLIN2 overexpression increasing β-CTS, PLIN2 depletion or overexpression drops or adds expression of GSK3 substrates, such as β-catenin, c/EBPα,c-Myc, cyclin D1, and insulin receptor substrate 1, and cell growth/survival. PLIN2 N or C terminus overexpression that is associated with higher levels of the substrates suggests that those substrates bind to specific regions of PLIN2. Mimicking the possible high lipid concentrations in cells in the human body under conditions of hyperlipidemia/obesity, OA-treated cells gain or reduce GSK3 substrate expression in parallel with a decrease (a Wnt-like effect) or increase in GSK3 activity, likely regulated by GSK3/PLIN2/GSK3 substrate associations.
Hexokinase 2 is a molecular bridge linking telomerase and autophagy

Autophagy is systematically regulated by upstream factors and nutrients. Recent studies reported that telomerase and hexokinase 2 [HK2) regulate autophagy through mTOR and that telomerase has the capacity to bind to the HK2 promoter. However, the molecular linkage among telomerase, HK2, and autophagy is not fully understood. Here, we show that HK2 connects telomerase to autophagy. HK2 inhibition in HepG2 cells suppressed TERT-induced autophagy activation and further enhancement by glucose deprivation. The HK2 downstream factor mTOR was responsible for the TERT-induced autophagy activation under glucose deprivation, implying that TERT promotes autophagy through an HK2-mTOR pathway. TERC played a role similar to that of TERT, and simultaneous expression of TERT and TERC synergistically enhanced HK2 expression and autophagy. At the gene level, TERT bound to the HK2 promoter at a specific region harboring the telomerase-responsive sequence ‘TTGGG. ’ Mutagenesis of TERC and the TERT-responsive element in the HK2 promoter revealed that TERC is required for the binding of TERT to the HK2 promoter. We demonstrate the existence of a telomerase-HK2-mTOR-autophagy axis and suggest that inhibition of the interaction between telomerase and the HK2 promoter diminishes glucose starvation-induced autophagy.
AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula[OPEN]

The AspWood large-scale data set comprises high-spatial-resolution RNA-seq transcriptome profiles collected across the phloem-cambium-xylem developmental zone of aspen trees. Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula. The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies. The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.
Forestry Alters Foraging Efficiency and Crop Contents of Aphid-Tending Red Wood Ants, Formica aquilonia

Forest management alters species behaviours, distributions and interactions. To evaluate forestry effects on ant foraging performance, we compared the quality and quantity of honeydew harvested by ants among clear-cuts, middle-aged and mature spruce-dominated stands in boreal forests in Sweden. Honeydew quality was examined using honeydew collected by squeezing the gasters of laden Formica aquilonia workers. We used fifteen laden individuals at each study site (four replicates of each stand age) and analysed honeydew chemical composition with gas chromatography-mass spectroscopy. To compare the quantity of honeydew collected by individual ants, we collected and weighed five ants moving up and five ants moving down each of ten trees at the twelve sites (totally 1200 ants). The concentration of trehalose in honeydew was lower in clear-cuts compared with middle aged and mature stands, and similar trends were shown for sucrose, raffinose and melezitose, indicating poorer honeydew quality on clear cuts. Concentrations of the amino acid serine were higher on clear-cuts. The same trend occurred for glutamine, suggesting that increased N-uptake by the trees after clear cutting is reflected in the honeydew of aphids. Ants in mature stands had larger heads and carried proportionally more honeydew and may therefore be more efficient foragers. Human alternation of habitats through clear-cutting thus affects food quality and worker condition in F. aquilonia. This is the first study to show that honeydew quality is affected by anthropogenic disturbances, likely contributing to the reduction in size and abundance of F. aquilonia workers and mounds after clear cutting.