Miracle-dz/UniFAR-FTUs huggingface dataset:
Inference in Deep Gaussian Processes using Stochastic Gradient Hamiltonian Monte Carlo

Deep Gaussian Processes (DGPs) are hierarchical generalizations of Gaussian Processes that combine well calibrated uncertainty estimates with the high flexibility of multilayer models. One of the biggest challenges with these models is that exact inference is intractable. The current state-of-the-art inference method, Variational Inference (VI), employs a Gaussian approximation to the posterior distribution. This can be a potentially poor unimodal approximation of the generally multimodal posterior. In this work, we provide evidence for the non-Gaussian nature of the posterior and we apply the Stochastic Gradient Hamiltonian Monte Carlo method to generate samples. To efficiently optimize the hyperparameters, we introduce the Moving Window MCEM algorithm. This results in significantly better predictions at a lower computational cost than its VI counterpart. Thus our method establishes a new state-of-the-art for inference in DGPs.
A CsTu‐TS1 regulatory module promotes fruit tubercule formation in cucumber

Summary The fruit epidermal features such as the size of tubercules are important fruit quality traits for cucumber production. But the mechanisms underlying tubercule formation remain elusive. Here, tubercule size locus CsTS1 was identified by map‐based cloning and was found to encode an oleosin protein. Allelic variation was identified in the promoter region of CsTS1, resulting in low expression of CsTS1 in all 22 different small‐warty or nonwarty cucumber lines. High CsTS1 expression levels were closely correlated with increased fruit tubercule size among 44 different cucumber lines. Transgenic complementation and RNAi‐mediated gene silencing of CsTS1 in transgenic cucumber plants demonstrated that CsTS1 positively regulates the development of tubercules. CsTS1 is highly expressed in the peel at fruit tubercule forming and enlargement stage. Auxin content and expression of three auxin signalling pathway genes were altered in the 35S:CsTS1 and CsTS1‐RNAi fruit tubercules, a result that was supported by comparing the cell size of the control and transgenic fruit tubercules. CsTu, a C2H2 zinc finger domain transcription factor that regulates tubercule initiation, binds directly to the CsTS1 promoter and promotes its expression. Taken together, our results reveal a novel mechanism in which the CsTu‐TS1 complex promotes fruit tubercule formation in cucumber.
Has Something Changed Here? Autonomous Difference Detection for Security Patrol Robot s

This paper presents a system for autonomous change detection with a security patrol robot. In an initial step a reference model of the environment is created and changes are then detected with respect to the reference model as differences in coloured 3D point clouds, which are obtained from a 3D laser range scanner and a CCD camera. The suggested approach introduces several novel aspects, includin g a registration method that utilizes local visual features to determine point correspondences (thus essentially working without an initial pose estimate) and the 3D-NDT representation with adaptive cell size to efficiently represent both the spatial and colour aspects of the reference model. Apart from a detailed description of the individual parts of the difference detection system, a qualitative experimental evaluation in an indoor lab environment is presented, which demonstrates that the suggested system is able register and detect changes in spatial 3D data and also to detect changes that occur in colour space and are not observable using range values only.
White matter correlates of different aspects of facial affect recognition impairment following traumatic brain injury

ABSTRACT Although facial affect recognition deficits are well documented in individuals with moderate-to-severe traumatic brain injury (TBI), little research has examined the neural mechanisms underlying these impairments. Here, we use diffusion tensor imaging (DTI), specifically the scalars fractional anisotropy (FA), mean diffusivity (MD), and radial diffusivity (RD), to examine relationships between regional white-matter integrity and two facial affect sub-skills: perceptual affect recognition abilities (measured by an affect matching task) and verbal categorization of facial affect (measured by an affect labeling task). Our results showed that, within the TBI group, higher levels of white-matter integrity in tracts involved in affect recognition (inferior fronto-occipital, inferior longitudinal, and uncinate fasciculi) were associated with better performance on both tasks. Verbal categorization skills were specifically and positively correlated with integrity of the left uncinate fasciculus. Moreover, we observed a striking lateralization effect, with perceptual abilities having an almost exclusive relationship with integrity of right hemisphere tracts, while verbal abilities were associated with both left and right hemisphere integrity. The findings advance our understanding of the neurobiological mechanisms that underlie subcomponents of facial affect recognition and lead to different patterns of facial affect recognition impairment in adults with TBI.
Red Cell Distribution Width and Mortality in Patients With Acute Coronary Syndrome: A Meta-Analysis on Prognosis

Background Red cell distribution width (RDW), a routine component of the complete blood count (CBC), measures variation in the size of circulating erythrocytes. It has been associated with several clinical outcomes in cardiovascular disease. We sought to strengthen the association between RDW and mortality in patients admitted for acute coronary syndrome (ACS) by pooling together data from available studies. Methods Studies that fulfilled the following were identified for analysis: 1) observational; 2) included patients admitted for ACS; 3) reported data on all-cause or cardiovascular (CV) mortality in association with a low or high RDW; and 4) used logistic regression analysis to control for confounders. Using MEDLINE, Clinical Key, ScienceDirect, Scopus, and Cochrane Central Register of Controlled Trials databases, a search for eligible studies was conducted until January 9, 2017. The quality of each study was evaluated using the Newcastle-Ottawa Quality Assessment Scale. Our primary outcome of interest was all-cause or CV mortality. We also investigated the impact of RDW on major adverse cardiovascular events (MACEs) for the studies that reported these outcomes. Review Manager (RevMan) 5.3 was utilized to perform Mantel-Haenzel analysis of random effects and compute for relative risk. Results We identified 13 trials involving 10,410 patients, showing that in ACS, a low RDW is associated with a statistically significant lower all-cause or CV mortality (RR 0.35, (95% CI 0.30 to 0.40), P < 0.00001, I2 = 53%), a finding that was consistent both in the short- and long-term. Conclusions A low RDW is also associated with lower risk for MACEs after an ACS (RR 0.56, (95% CI 0.51 to 0.61), P < 0.00001, I2 = 91%). A low RDW during an ACS is associated with lower all-cause or CV mortality and lower risk of subsequent MACEs, providing us with a convenient and inexpensive risk stratification tool in ACS patients.
Effect of Temperature on the Development, Survival, and Fecundity of Heliothis viriplaca (Lepidoptera: Noctuidae)

Abstract Heliothis viriplaca (Hüfnagel) (Lepidoptera: Noctuidae) is worldwide an important economic pest of major agricultural crops. The effect of temperature on the biology, in particular the duration of the different developmental stages, of this insect pest was examined.The development, survival, and fecundity of H. viriplaca at five different temperatures (22, 25, 28, 31, and 34°C) were investigated, and experimental population life tables calculated.The results show that the developmental time of larvae, pupae, pre-oviposition, adults, and the entire generation decreases with increasing temperature. Larvae emerged fastest from the eggs at 28°C.The percentage of larvae that reached the seventh instar stage was 32.69, 38.60, 19.67, 3.61, and 20.88% at 22, 25, 28, 31, and 34°C, respectively.The developmental threshold temperature of the eggs, larvae, pupae, pre-oviposition and total pre-oviposition period was 10.53, 12.34, 5.60, 11.47, and 10.01°C, respectively.The effective accumulative temperature was 42.90, 239.68, 309.19, 77.72, and 767.64 degree-days, respectively.The population trend index (I) and the intrinsic rate of increase (r) of H. viriplaca were the highest at 31°C (133.97 and 0.12 d-1, respectively). The results of this study may be useful for predicting the population dynamics of H. viriplaca and thus provides information on this important insect pest that may assist in its management.
Beyond Bags of Words: Inferring Systemic Nets

Textual analytics based on representations of documents as bags of words have been reasonably successful. However, analysis that requires deeper insight into language, into author properties, or into the contexts in which documents were created requires a richer representation. Systemic nets are one such representation. They have not been extensively used because they required human effort to construct. We show that systemic nets can be algorithmically inferred from corpora, that the resulting nets are plausible, and that they can provide practical benefits for knowledge discovery problems. This opens up a new class of practical analysis techniques for textual analytics.
Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine.

BACKGROUND Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use. METHODS We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer (KRAS c.35G>A, p.Gly12Asp, from hereon termed G12D) by evaluating potential sources of uncertainty that influence dPCR measurement. RESULTS Concentration values for samples of KRAS G12D and wild-type plasmid templates varied by <1.2-fold when measured using 5 different assays with varying detection chemistry (hydrolysis, scorpion probes, and intercalating dyes) and <1.3-fold with 4 commercial dPCR platforms. Measurement trueness of a selected dPCR assay and platform was validated by comparison with an orthogonal method (inductively coupled plasma mass spectrometry). The candidate dPCR reference measurement procedure showed linear quantification over a wide range of copies per reaction and high repeatability and interlaboratory reproducibility (CV, 2%-8% and 5%-10%, respectively). CONCLUSIONS This work validates dPCR as an SI-traceable reference measurement procedure based on enumeration and demonstrates how it can be applied for assignment of copy number concentration and fractional abundance values to DNA reference materials in an aqueous solution. High-accuracy measurements using dPCR will support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.
Prognostic Implications of Gadolinium Enhancement of Skull Base Chordomas

BACKGROUND AND PURPOSE: Skull base chordomas often demonstrate variable MR imaging characteristics, and there has been limited prior research investigating the potential clinical relevance of this variability. The purpose of this retrospective study was to assess the prognostic implications of signal intensity on standard imaging techniques for the biologic behavior of skull base chordomas. MATERIALS AND METHODS: Medical records were retrospectively reviewed for 22 patients with pathologically confirmed skull base chordomas. Clinical data were recorded, including the degree of surgical resection, the presence or absence of radiation therapy, and time to progression/recurrence of the tumor or time without progression/recurrence of the tumor following initial treatment. Pretreatment imaging was reviewed for the presence or absence of enhancement and the T2 signal characteristics. Tumor-to-brain stem signal intensity ratios on T2, precontrast T1, and postcontrast T1 spin-echo sequences were also calculated. Statistical analysis was then performed to assess correlations between imaging characteristics and tumor progression/recurrence. RESULTS: Progression/recurrence of skull base chordomas was seen following surgical resection in 11 of 14 (78.6%) patients with enhancing tumors and in zero of 8 patients with nonenhancing tumors. There was a statistically significant correlation between skull base chordoma enhancement and subsequent tumor progression/recurrence (P < .001), which remained significant after controlling for differences in treatment strategy (P < .001). There was also a correlation between postcontrast T1 signal intensity (as measured by postcontrast T1 tumor-to-brain stem signal intensity ratios) and recurrence/progression (P = .02). While T2 signal intensity was higher in patients without tumor progression (median tumor-to-brain stem signal intensity ratios on T2 = 2.27) than in those with progression (median tumor-to-brain stem signal intensity ratios on T2 = 1.78), this association was not significant (P = .12). CONCLUSIONS: Enhancement of skull base chordomas is a risk factor for tumor progression/recurrence following surgical resection.
Two Novel, Distantly Related Papillomaviruses Isolated from Healthy Skin of the Timor Deer (Rusa timorensis)

ABSTRACT We report the complete genome sequences of Rusa timorensis papillomavirus 1 (RtimPV1) and Rusa timorensis papillomavirus 2 (RtimPV2), isolated from hair follicles of asymptomatic skin from the same Timor deer specimen. RtimPV1 and RtimPV2 are evolutionarily only distantly related. RtimPV1 lacks a canonical E2-binding site, and RtimPV2 does not carry an E6 gene.
Association Between Portable Music Player Use and Hearing Loss Among Children of School Age in the Netherlands

Importance Portable music player use may have harmful effects on hearing. The magnitude and effect of frequent music exposure, especially at younger ages, on hearing are unclear. Objectives To examine the prevalence of noise-induced hearing loss in a 9- to 11-year-old population and associations with portable music player use and sociodemographic factors. Design, Setting, and Participants A cross-sectional study within an ongoing, prospective, birth cohort study within Rotterdam, the Netherlands was conducted. Between ages 9 and 11 years, 5355 children underwent their first audiometric evaluation. Children were excluded if they had missing or failed tympanometry results. The study was conducted from April 16, 2012, to October 25, 2015. Exposures Portable music player (PMP) use and sociodemographic factors assessed via parental questionnaires. Main Outcomes and Measures Hearing acuity measured by pure-tone audiometry at 0.5 to 8 kHz. Possible noise-induced hearing loss was contingent on a high-frequency notch and/or high-frequency hearing loss in the audiogram, or reported hearing-related symptoms. Results The final sample included 3116 participants who were a mean (interquartile range) age of 9.7 (9.6-9.9) years and equally distributed between boys (1550 [49.7%]) and girls (1566 [50.3%]). Of these, 1244 (39.9%) reported no PMP use, 577 (18.5%) reported use 1 or 2 days per week, 254 (8.2%) reported use 3 or more days per week, and for 1041 (33.4%), PMP use was not reported. Audiometric notches and high-frequency hearing loss were present in 443 (14.2%) of all children; 140 (4.5%) fulfilled the criteria of a notch, 238 (7.6%) of high-frequency hearing loss, and 65 (2.1%) of both. Of the cohort, 52 (1.7%) showed bilateral impairment. Hearing-related symptoms were reported for 232 (11.3%) of the respondents, and 831 (40.0%) of the respondents used portable music players. Portable music player use was associated with high-frequency hearing loss (odds ratio [OR], 2.88; 95% CI, 1.36-6.980 for 1 or 2 days per week and OR, 2.74; 95% CI, 1.22-6.96 for ≥3 days per week), but listening time and duration were not. There was no association of music exposure with high-frequency notches. Conclusions and Relevance In this study, 14.2% of school-aged children showed audiometric notches or high-frequency hearing loss. This hearing impairment is already present prior to exposure to known noise hazards, such as club and concert attendance, and may have lifelong consequences. Repeated measurements are needed to confirm the association of portable music player use with hearing impairment in children.
Improved method for the determination of 12 non-nutritive sweeteners and monitoring in various foods using liquid chromatography–tandem mass spectrometry

ABSTRACT An improved and highly sensitive method was developed and validated for the determination of 12 (7 permitted and 5 non-permitted in Korea) non-nutritive sweeteners in various foods using liquid chromatography-electrospray ionisation-tandem mass spectrometry. The chromatographic separation was performed on an Xbridge BEH C18 column (3 mm × 100 mm, 2.5 μm) with gradient elution using 10 mM ammonium acetate in water and 10 mM ammonium acetate in methanol. Sample preparation consisted of simple dilution, homogenisation, centrifugation and purification with a C18 cartridge prior to analysis. The relative matrix effect (%ME) was within ±20% for all sweeteners. The method also showed good linearity (R2 > 0.99). The limit of detection and limit of quantification values in sample were in the range of 0.02–2.66 and 0.06–8.05 mg kg−1, respectively. The recoveries at three concentration levels ranged between 80% and 119%, with relative standard deviation values below 10%. In addition, the expanded uncertainties determined for 12 sweeteners in 5 different food matrices were confirmed to be <14%. Finally, the method was successfully applied to the analysis of sweeteners in 681 food samples purchased in Korea, Australia and Turkey. These results demonstrate that the method is suitable for the simultaneous determination of multiple-sweeteners in a variety of foods.
Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR

DNA methylation is one of the most important epigenetic modifications in the regulation of gene transcription. The current gold standard to study this modification is bisulfite sequencing. Although multiple commercial bisulfite treatment kits provide good conversion efficiencies, DNA loss and especially DNA fragmentation remain troublesome. This hampers DNA methylation profiling of long DNA sequences. Here, we explored the performance of twelve commercial bisulfite kits by an in-depth comparison of DNA fragmentation using gel electrophoresis, qPCR and digital PCR, DNA recovery by spectroscopic measurements and digital PCR and conversion efficiency by next generation sequencing. The results show a clear performance difference between the bisulfite kits, and depending on the specific goal of the study, the most appropriate kit might differ. Moreover, we demonstrated that digital PCR is a valuable method to monitor both DNA fragmentation as well as DNA recovery after bisulfite treatment.
SemAxis: A Lightweight Framework to Characterize Domain-Specific Word Semantics Beyond Sentiment

Because word semantics can substantially change across communities and contexts, capturing domain-specific word semantics is an important challenge. Here, we propose SemAxis, a simple yet powerful framework to characterize word semantics using many semantic axes in word-vector spaces beyond sentiment. We demonstrate that SemAxis can capture nuanced semantic representations in multiple online communities. We also show that, when the sentiment axis is examined, SemAxis outperforms the state-of-the-art approaches in building domain-specific sentiment lexicons.
Stable and High Piezoelectric Output of GaN Nanowire-Based Lead-Free Piezoelectric Nanogenerator by Suppression of Internal Screening

A piezoelectric nanogenerator (PNG) that is based on c-axis GaN nanowires is fabricated on flexible substrate. In this regard, c-axis GaN nanowires were grown on GaN substrate using the vapor-liquid-solid (VLS) technique by metal organic chemical vapor deposition. Further, Polydimethylsiloxane (PDMS) was coated on nanowire-arrays then PDMS matrix embedded with GaN nanowire-arrays was transferred on Si-rubber substrate. The piezoelectric performance of nanowire-based flexible PNG was measured, while the device was actuated using a cyclic stretching-releasing agitation mechanism that was driven by a linear motor. The piezoelectric output was measured as a function of actuation frequency ranging from 1 Hz to 10 Hz and a linear tendency was observed for piezoelectric output current, while the output voltages remained constant. A maximum of piezoelectric open circuit voltages and short circuit current were measured 15.4 V and 85.6 nA, respectively. In order to evaluate the feasibility of our flexible PNG for real application, a long term stability test was performed for 20,000 cycles and the device performance was degraded by less than 18%. The underlying reason for the high piezoelectric output was attributed to the reduced free carriers inside nanowires due to surface Fermi-level pinning and insulating metal-dielectric-semiconductor interface, respectively; the former reduced the free carrier screening radially while latter reduced longitudinally. The flexibility and the high aspect ratio of GaN nanowire were the responsible factors for higher stability. Such higher piezoelectric output and the novel design make our device more promising for the diverse range of real applications.
Assisted Reproductive Technology, Comorbidities, and Cardiovascular Risk: The Experience of an Italian Center.

BACKGROUND A growing number of infertile women undergo assisted reproductive technology (ART). Older maternal age and the presence of comorbidities may affect cardiovascular (CV) women health. Safety aspects are central in risk assessment; we report the experience of internal medicine clinical setting at the ART center. MATERIALS AND METHODS we investigated 243 infertile women (110 autologous and 133 oocyte donation [OD]); cardiometabolic parameters and CV risk factors were investigated during the clinical evaluation. RESULTS We observed high prevalence of dyslipidemia (62.9%), smoking habit (27.5%), and body mass index (26.7%). Waist ≥80 cm was present in 65%, and waist to hip ratio (WHR) value >0.80 in 60.5% of women. The prevalence of migraine with aura, hypertension, and diabetes was 5.3%, 4.9%, and 4.5%, respectively. By evaluating variables according to autologous or OD ART, we observed that OD women were older than autologous, p < 0.0001. Overweight and obesity prevalence was higher in OD group; waist and WHR were significantly higher in autologous than in OD group (75% vs. 57%, p = 0.005, and 91.8% vs. 34.6%, p = 0.01, respectively). We observed a statistically significant unfavorable risk profile in OD in comparison to autologous women (p = 0.003); in particular, 60% of OD women carried 3-5 CV risk factors, and 8.3% carried at least six CV risk factors. CONCLUSIONS The experience of an internal medicine clinic at the ART center strongly underlies the relevance of a careful medical evaluation before attempting ART, and suggests the opportuneness of a structured internal medicine clinic in every gynecology setting to better frame risk profile.