Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing Hollow-Channel Gold Nanoflowers as Trimodal Intracellular Nanoprobes

Gold nanoparticles-enabled intracellular surface-enhanced Raman spectroscopy (SERS) provides a sensitive and promising technique for single cell analysis. Compared with spherical gold nanoparticles, gold nanoflowers, i.e., flower-shaped gold nanostructures, can produce a stronger SERS signal. Current exploration of gold nanoflowers for intracellular SERS has been considerably limited by the difficulties in preparation, as well as background signal and cytotoxicity arising from the surfactant capping layer. Recently, we have developed a facile and surfactant-free method for fabricating hollow-channel gold nanoflowers (HAuNFs) with great single-particle SERS activity. In this paper, we investigate the cellular uptake and cytotoxicity of our HAuNFs using a RAW 264.7 macrophage cell line, and have observed effective cellular internalization and low cytotoxicity. We have further engineered our HAuNFs into SERS-active tags, and demonstrated the functionality of the obtained tags as trimodal nanoprobes for dark-field and fluorescence microscopy imaging, together with intracellular SERS.
A Phase-coded Aperture Camera with Programmable Optics

We propose a novel computational imaging system that en-ables the generation of Point Spread Functions (PSFs) of user-speciﬁed geometry. Key ingredient of our system is a phase-coded aperture which manipulates the phase distribution of the pupil function by inserting a phase modulator. We use a reﬂective phase-only liquid crystal-based Spatial Light Modulator (SLM) for phase modulation. Via encoding a grayscale image on the SLM, the refractive index of each cell can be altered. Phase patterns of PSFs with different shapes are optimized by the Gerchberg-Saxton algorithm. A number of non-trivial, complex shaped PSFs has been captured. We further demonstrate how such a system can realize refocusing through encoding a Fresnel lens phase pattern to shift the focal plane.
A Visual Analytics Approach for User Behaviour Understanding through Action Sequence Analysis

Analysis of action sequence data provides new opportunities to understand and model user behaviour. Such data are often in the form of timestamped and labelled series of atomic user actions. Cyber security is one of the domains that show the value of the analysis of these data. Elaborate and specialised models of user-behaviour are desired for effective decision making during investigation of cyber threats. However, due to their complex nature, activity sequences are not yet well-exploited within cyber security systems. In this paper, we describe the initial phases of a visual analytics approach that aims to enable a rich understanding of user behaviour through the analysis of user activity sequences. First, we discuss a motivating case study and discuss a number of high level requirements as derived from a series of workshops within an ongoing research project. We then present the components of a visual analytics approach that constitutes a novel combination of ``action space'' analysis, pattern mining, and the interactive visual analysis of multiple sequences to take the initial steps towards a comprehensive understanding of user behaviour.
Touch the Time: Touch-Centered Interaction Paradigms for Time-Oriented Data

We present novel direct-touch centered paradigms for exploring time series data visualized in a coordinated multi-view display. The views can be easily and ﬂexibly conﬁgured by choosing from various adapted or enhanced time-oriented visualizations. A vocabulary of robust direct-touch gestures enables the user to create, ﬁlter, derive, and focus on subsets of time-oriented data within the temporal dimension as well as the (data) records dimension. Our two-dimensional Focus&Context technique works particularly well with our extension to horizon graphs, which enables interactive scaling from area charts to multiply folded Horizon Graphs down to pixel-based visualizations and back.
Ivy1 is a negative regulator of Gtr-dependent TORC1 activation

ABSTRACT The highly conserved TORC1 complex controls cell growth in response to nutrients, especially amino acids. The EGO complex activates TORC1 in response to glutamine and leucine. Here, we demonstrate that the I-BAR domain-containing protein Ivy1 colocalizes with Gtr1 and Gtr2, a heterodimer of small GTPases that are part of the EGO complex. Ivy1 is a negative regulator of Gtr-induced TORC1 activation, and is contained within puncta associated with the vacuolar membrane in cells grown in nutrient-rich medium or after brief nitrogen starvation. Addition of glutamine to nitrogen-starved cells leads to dissipation of Ivy1 puncta and redistribution of Ivy1 throughout the vacuolar membrane. Continued stimulation with glutamine results in concentration of Ivy1 within vacuolar membrane invaginations and its spatial separation from the EGO complex components Gtr1 and Gtr2. Disruption of vacuolar membrane invagination is associated with persistent mislocalization of Ivy1 across the vacuolar membrane and inhibition of TORC1 activity. Together, our findings illustrate a novel negative-feedback pathway that is exerted by Ivy1 on Gtr-dependent TORC1 signaling and provide insight into a potential molecular mechanism underlying TORC1 activation by vacuolar membrane remodeling. Summary: The I-BAR domain-containing protein Ivy1 colocalizes with the EGO complex components Gtr1 and Gtr2 and regulates their activation.
Modeling the implementation of population-level isoniazid preventive therapy for tuberculosis control in a high HIV-prevalence setting

Background: We model the epidemiological impact of providing isoniazid preventive therapy (IPT) to South African adolescents, among whom HIV prevalence is low, latent tuberculosis (TB) prevalence is high, and school-based programs may enable population-level coverage. Methods: We simulate a dynamic compartmental model of age-structured HIV and TB coepidemics in South Africa. HIV dynamics are modeled by infection status, CD4+ cell count, and antiretroviral therapy; TB dynamics are modeled by disease stage, diagnosis, treatment, and IPT status. We analyze the effects of continuous IPT coverage among adolescents from 5 (baseline) to 90%. Results: Our model is calibrated to WHO and the Joint United Nations Programme on HIV/AIDS epidemiological estimates. In simulations, increasing IPT coverage to 50% among adolescents reduced active TB incidence by 5–34%. Increasing coverage to 90% led to a 9–40% reduction in active TB incidence. Expanded IPT access causes TB incidence to decline in the general population of HIV-positive individuals, as well as in adult HIV-positive individuals. Conclusion: Targeting IPT to a secondary school population with high latent TB prevalence and low-HIV prevalence, in which risk of false-negative diagnosis of active TB is low and IPT benefits are more established, could have substantial benefits to adolescents and spillover benefits to the adult population.
Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.
Monteggia fracture with unreducable anterior dislocation of the radial head and a lesion of the external collateral ligament of the elbow

Monteggia described a fracture of the proximal third of the ulna with anterior dislocation of the radial head from both the proximal radioulnar and radiocapitellar joints. The key treatment principle in Monteggia fractures is stable anatomic alignment of the ulna. We present an uncommon case of a Monteggia fracture-dislocation with an unreducable anterior dislocation of the radial head and associated with a lesion of the lateral collateral ligament of the elbow. The patient in our report had a successful clinical outcome and functional range of motion after rigid fixation of the ulnar shaft fracture and exploration of the elbow joint, reduction of the radial head and repair of the lateral collateral ligament. This case is unusual because of the association of a complete tear of the external collateral ligament of the elbow.
Receptor recognition by the peroxisomal AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p

The receptor cycle of type I peroxisomal matrix protein import is completed by ubiquitination of the membrane-bound peroxisome biogenesis factor 5 (Pex5p) and its subsequent export back to the cytosol. The receptor export is the only ATP-dependent step of the whole process and is facilitated by two members of the AAA family of proteins (ATPases associated with various cellular activities), namely Pex1p and Pex6p. To gain further insight into substrate recognition by the AAA complex, we generated an N-terminally linked ubiquitin–Pex5p fusion protein. This fusion protein displayed biological activity because it is able to functionally complement a PEX5-deletion in Saccharomyces cerevisiae. In vitro assays revealed its interaction at WT level with the native cargo protein Pcs60p and Pex14p, a constituent of the receptor docking complex. We also demonstrate in vitro deubiquitination by the deubiquitinating enzyme Ubp15p. In vitro pulldown assays and cross-linking studies demonstrate that Pex5p recognition by the AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p.
A 3 Cent Recognizer: Simple and Effective Retrieval and Classification of Mid-air Gestures from Single 3D Traces

In this paper we present a simple 3D gesture recognizer based on trajectory matching, showing its good performances in classification and retrieval of command gestures based on single hand trajectories. We demonstrate that further simplifications in porting the classic "1 dollar" algorithm approach from the 2D to the 3D gesture recognition and retrieval problems can result in very high classification accuracy and retrieval scores even on datasets with a large number of different gestures executed by different users. Furthermore, recognition can be good even with heavily subsampled path traces and with incomplete gestures.
Radiation Dose Does Indeed Matter: Proof That Invalidates The Linear No-Threshold Model

1779 Objectives: We aimed to make use of non-local mean (NLM) and median (NLEM) methods, with and without anatomy information, to significantly enhance quality and quantitative accuracy of PET images, with special focus on amyloid imaging. Methods: Using anatomy information to enhance PET images has been a popular strategy, but many previous works have incorporated too much anatomy information, biasing PET images. In this study, we only use the anatomy regions as masks to restrict the search window in non-local type methods. We investigated two methods, namely non-local means (NLM) and non-local Euclidean medians (NLEM): NLM and NLM-A compute the mean of the patches in the search window to update the center pixel of the patch in the original image, while NLEM and NLEM-A use the Euclidean median. To further improve the PET images, we also implemented the anatomy-incorporated counterparts (NLM-A and NLEM-A), utilizing the anatomical region masks to restrict the search window, thus restricting usage of non-local information to voxels that belong to the same tissue. We set the overall search window size to 21[asterisk]21 and patch size to 7[asterisk]7 within a given slice. We performed two studies to evaluate these four methods. First, we utilized the classical NEMA NU-2 image quality phantom with six spheres of different diameters (10, 13, 17, 22, 28 and 37 mm). Second, we subsequently performed realistic amyloid PET simulations based on real data from human amyloid dynamic PET (11C-PIB) and MRI studies. We labeled regions including GM, WM, CSF, caudate, putamen and thalamus, as areas of interest for Alzheimer9s disease research. We incorporated realistic clinical data activity distributions in our simulation studies based on participant images. Results: Compared with the no-anatomy versions, anatomy-guided methods performed better in both studies, specifically in visual image and image roughness (spatial variance) performance. At matched noise levels, anatomy-based non-local methods (both NLM-A and NLEM-A) significantly lowered bias. For example, in GM of NLEM-A, at matched 20% noise (image roughness), the bias was reduced by 88%, and at 25% noise, the bias was lowered by 66%, and at 35% noise, the bias was lowered by 48%. The ensemble variance of these four methods looked relatively matched. In general, the effectiveness and trend of the four methods are not greatly affected by noise levels. For high noise levels, NLEM and NLEM-A perform somewhat more effectively than NLM and NLM-A in some regions (e.g. thalamus, WM), because the median operator (instead of mean operator) is less impacted by the presence of outliers. Furthermore, without anatomy guidance, NLM and NLEM use information from a very wide search window to update the image, and this can result in additional bias in the resulting image estimates. Conclusion: Overall, we have demonstrated that non-local methods in combination with anatomic guidance have a significant potential to improve quality and quantitative accuracy of amyloid PET images.
Social and emotional loneliness in Korsakoff’s syndrome

ABSTRACT Introduction: Loneliness is the subjective negative evaluation of social participation and isolation. Emotional loneliness reflects the absence of close relationships, and social loneliness the absence of a social network. Although loneliness is a growing problem in modern society, studies about loneliness in patients with Korsakoff’s syndrome (KS) in need of chronic care are currently missing. Methods: Sixty-three KS patients in long-term care and their primary caregivers reported loneliness of the patients on the De Jong Gierveld Loneliness Scale. Results: A majority of KS patients reliably reported to feel lonely on both a social and emotional level of loneliness. The caregiving professionals rated loneliness of the patients even higher. Patients that had stayed in the clinic for a longer time tended to report less social loneliness, while caregivers reported less emotional loneliness in those patients. The KS-specific neuropsychiatric symptom of confabulations and a lack of social visits had a negative impact on social loneliness as perceived by the caregivers. Conclusion: Loneliness is a large problem in patients with KS that live in a long term care facility. Social loneliness can be positively influenced by creating possibilities to interact with other people, although the severity of the neuropsychiatric aspects of KS could compromise the presence of those interactions.
ConTraffic Visual Analytics in Support to Customs Risk-Analysis

Customs risk analysis is crucial for detecting fraud and contraband goods in the massive ﬂows of internationally traded goods. Most of non-bulk goods are transported in shipping containers and, as customs can control only about 2% of them, efﬁcient customs risk analysis is crucial. In support to EU customs, the Joint Research Centre of the European Commission has developed the ConTrafﬁc visual analytics research prototype. This paper presents the main architectural elements of the application and some visualization and user-interaction techniques selected to enable the route-based risk analysis of large number of shipping containers
Cardiac Computed Tomography Radiomics: A Comprehensive Review on Radiomic Techniques

Radiologic images are vast three-dimensional data sets in which each voxel of the underlying volume represents distinct physical measurements of a tissue-dependent characteristic. Advances in technology allow radiologists to image pathologies with unforeseen detail, thereby further increasing the amount of information to be processed. Even though the imaging modalities have advanced greatly, our interpretation of the images has remained essentially unchanged for decades. We have arrived in the era of precision medicine where even slight differences in disease manifestation are seen as potential target points for new intervention strategies. There is a pressing need to improve and expand the interpretation of radiologic images if we wish to keep up with the progress in other diagnostic areas. Radiomics is the process of extracting numerous quantitative features from a given region of interest to create large data sets in which each abnormality is described by hundreds of parameters. From these parameters datamining is used to explore and establish new, meaningful correlations between the variables and the clinical data. Predictive models can be built on the basis of the results, which may broaden our knowledge of diseases and assist clinical decision making. Radiomics is a complex subject that involves the interaction of different disciplines; our objective is to explain commonly used radiomic techniques and review current applications in cardiac computed tomography imaging.
Treatment interventions for diarrhoea in HIV-infected and HIV-exposed children: a systematic review

Introduction Seventy percent of an estimated 10 million children less than five years of age in developing countries die each year of acute respiratory infections, diarrhoea, measles, malaria, malnutrition or a combination of these conditions. Children living with Human immunodeficiency virus (HIV) are at risk of diarrhoea because of drug interactions with antiretroviral therapy and bottle feeding. This may be aggravated by malnutrition and other infectious diseases which are frequent in children living with HIV. Objective: to evaluate treatment interventions for diarrhoea in HIV infected and exposed children. Methods A comprehensive search was conducted on 02 June 2016 to identify relevant studies for inclusion. We included randomised controlled trials of HIV infected or exposed children under 15 years of age with diarrhoea. Two authors independently selected studies for inclusion, assessed risk of bias (RoB) and extracted data using a pre-designed data extraction form. Results We included two studies (Amadi 2002 and Mda 2010) that each enrolled 50 participants. The RoB was assessed as low-risk for both included studies. There was no difference in clinical cure and all-cause mortality between nitazoxanide and placebo for cryptosporidial diarrhoea in Amadi 2002. In Mda 2010, there was a reduction in duration of hospitalisation in the micronutrient supplement group (P < 0.005) although there was no difference in all-cause mortality. Conclusion There is low certainty evidence on the effectiveness of nitazoxanide for treating cryptosporidial diarrhoea and micronutrient supplementation in children with diarrhoea. Adequately powered trials are needed to assess micronutrients and nitazoxanide, as well as other interventions, for diarrhoea in HIV-infected and-exposed children.
Meta-optimization of bio-inspired algorithms for antenna array design

In this article, a technique called Meta-Optimization is used to enhance the eﬀectiveness of bio-inspired algorithms that solve antenna array synthesis problems. This technique consists on a second optimization layer that ﬁnds the best behavioral parameters for a given algo-rithm, which allows to achieve better results. Bio-inspired computational methods are useful to solve complex multidimensional problems such as the design of antenna arrays. However, their performance depends heavily on the initial parameters. In this paper, the distances be-tween antenna array elements are calculated in order to reduce electromagnetic interference from undesired sources. The results are compared to previous works, showing an improvement on the performance of bio-inspired optimization algorithms such as Particle Swarm Optimization and Diﬀerential Evolution. These results are found to be statistically signiﬁcant based on the Wilcoxon’s rank sum test as compared to these methods using the standard parameters proposed in the literature. Furthermore, graphical representations of the Meta-Optimization process called meta-landscapes are presented, showing the behavior of these algorithms for a range of diﬀerent parameters, providing the best parameter combinations for each antenna problem.
Estimating the number of people living with HIV and the undiagnosed fraction in Spain in 2013

Objective: We aim to estimate the number of people living with HIV and the undiagnosed fraction in Spain, where coverage of the HIV surveillance system has only recently become complete. Methods: The reconstruction of all HIV diagnoses and infections was obtained by combining HIV and AIDS surveillance data. The imputation of the diagnoses and back-calculation of the infection incidence are integrated in a Bayesian framework to take into account the uncertainty associated with unavailable data. Results: An estimated 141 000 [95% credible interval (CI) 128 000–155 000] persons were living with HIV by the end of 2013, in Spain and 18% (95% CI 14.3–22.1%) were unaware of it. A similar fraction of undiagnosed infections was obtained in men who have sex with men and heterosexuals (18.8 and 20.1%, respectively), but for injection drug users, this fraction was 3.5%. Conclusion: This study provides the first estimates of the number of people living with HIV and the undiagnosed fraction in Spain, using routine surveillance data. The proposed method could be useful for countries where the geographical coverage of the HIV surveillance system is partial or was completed only recently.
Autophagy processes are dependent on EGF receptor signaling

Autophagy is a not well-understood conserved mechanism activated during nutritional deprivation in order to maintain cellular homeostasis. In the present study, we investigated the correlations between autophagy, apoptosis and the MAPK pathways in melanoma cell lines. We demonstrated that during starvation the EGF receptor mediated signaling activates many proteins involved in the MAPK pathway. Our data also suggest a previously unidentified link between the EGFR and Beclin-1 in melanoma cell line. We demonstrated that, following starvation, EGFR binds and tyrosine-phosphorylates Beclin-1, suggesting that it may play a key inhibitory role in the early stage of starvation, possibly through the Beclin-1 sequestration. Furthermore, EGFR releases Beclin-1 and allows initiating steps of the autophagic process. Interestingly enough, when the EGFR pathway was blocked by anti-EGF antibodies, immunoprecipitated Beclin-1 did not bind the phospho-EGFR. In addition, an extended binding of p-Bcl2 either with Beclin-1 or with Bax was observed with a decreased activation of the stress-induced JNK kinase, thus avoiding the transduction pathways that activate autophagy and apoptosis, respectively. For this reason, we advance the hypothesis that the activation of the EGFR is a necessary event that allows the ignition and progression of the autophagic process, at least in melanoma cells.