Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of intensity modulated radiation therapy on survival in anal cancer.

Background This study was designed to investigate the impact of intensity modulated radiation therapy (IMRT) on overall survival (OS) in patients treated with chemoradiation (CRT) for anal cancer (AC). Methods We performed a case-control, propensity score (PS) matched analysis of the National Cancer Data Base (NCDB) of patients diagnosed with non-metastatic AC from 2004 to 2013. Only patients receiving concurrent CRT were included. Patients were stratified into two groups based on the RT technique: IMRT vs. non-IMRT. Multivariate analysis (MVA) and Kaplan-Meier (KM) plots for OS were obtained for the matched and unmatched groups. Results A total of 8,108 patients diagnosed between 2004 and 2013 were eligible for the study, of which 3,307 (40.8%) and 4,801 (59.2%) were in the IMRT and non-IMRT groups, respectively. Median follow-up for all patients was 54.4 months. After PS matching, MVA for OS showed that IMRT was associated with improved OS compared to non-IMRT (HR 0.83, 95% CI: 0.74-0.94; P=0.002). Adjusted KM analysis showed that the 5-year OS for patients treated with IMRT was 74.6% vs. 70.5% (P=0.0022). Conclusions To our knowledge, this is the largest study to date that evaluates the impact of IMRT on OS for patients with AC. Our investigation shows that IMRT based concurrent CRT for non-metastatic AC is associated with improved survival when compared to similar patients treated with non-IMRT based therapy. In the absence of randomized evidence, our analysis might provide additional support for increasing the use of IMRT for patients with AC receiving concurrent CRT.
Fabrication of a Food Nano-Platform Sensor for Determination of Vanillin in Food Samples

Herein, we describe the fabrication of NiO decorated single wall carbon nanotubes (NiO-SWCNTs) nanocomposites using the precipitation method. The synthesized NiO-SWCNTs nanocomposites were characterized by X-ray diffraction (XRD) and Transmission electron microscopy (TEM). Remarkably, NiO-SWCNTs and 1-butylpyridinium hexafluorophosphate modified carbon paste electrode (CPE/NiO-SWCNTs/BPrPF6) were employed for the electrochemical detection of vanillin. The vanillin sensor showed an ultra-high sensitivity of 0.3594 μA/μM and a low detection limit of 0.007 μM. In the final step, the NiO-SWCNTs/BPrPF6 was used as the suitable tool for food analysis.
Percent Body Fat Change in Chinese Women After Adjuvant Chemotherapy for Breast Cancer

Background Weight gain is a common side effect observed in breast cancer (BC) patients undergoing adjuvant chemotherapy, although the characteristics and mechanism are not been fully understood. This study aimed to investigate percent body fat (%BF) change, and identify the associated risk factors among Chinese women receiving chemotherapy for BC. Material/Methods A prospective longitudinal study was conducted on a cohort of 140 Chinese female patients with BC between June 2016 and October 2017. Data on demographic and clinical features were collected using a standard protocol. Anthropometric parameters including body weight and %BF were measured before and after chemotherapy. Multiple logistic analysis was performed to identify the risk factors for %BF change. Results A total of 52.9% and 58.6% of the 140 patients experienced gains in weight and %BF after chemotherapy, respectively, with mean increases of 2.1±1.9 kg and 1.3±2.2%, respectively. Fifty-eight patients gained %BF over 2.5% of the baseline value. Moreover, premenopausal women had a greater mean %BF gain than postmenopausal women (P=0.018). Logistic analysis showed that premenopausal status, younger age, multi-agent chemotherapy regimen, high-calorie diet, and decreased physical activity were independent variables that inducted %BF gain. Conclusions %BF gain occurred frequently in Chinese women after adjuvant chemotherapy for BC, especially in premenopausal women. An effort should be made to the management of %BF.
Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies

Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer’s disease. The soluble, oligomeric forms of hIAPP are the most toxic to β-cells in the pancreas. However, the structure of these oligomeric forms is difficult to characterise because of their intrinsic disorder and their tendency to rapidly aggregate into insoluble fibrils. Experimental studies of hIAPP have generally used non-physiological conditions to prevent aggregation, and they have been unable to describe its soluble monomeric and oligomeric structure at physiological conditions. Molecular dynamics (MD) simulations offer an alternative for the detailed characterisation of the monomeric structure of hIAPP and its aggregation in aqueous solution. This paper reviews the knowledge that has been gained by the use of MD simulations, and its relationship to experimental data for both hIAPP and rat IAPP. In particular, the influence of the choice of force field and water models, the choice of initial structure, and the configurational sampling method used, are discussed in detail. Characterisation of the solution structure of hIAPP and its mechanism of oligomerisation is important to understanding its cellular toxicity and its role in disease states, and may ultimately offer new opportunities for therapeutic interventions.
Airbot: using a work flow model for proactive assistance in public spaces

We investigate how a task-sensitive personal assistant on smartphones can support users in public space. Therefore, we designed, implemented, and evaluated airbot, a mobile chatbot providing air travelers with proactive information during flight relevant tasks. We tested the application on passengers at a major airport (N = 101). The results of our evaluation study suggest, firstly, that airbot's utility is acknowledged by its users and, secondly, that its use affects the perception of passengers' airport service experience, both positively and negatively.
Pressure-sensitive zooming-out interfaces for one-handed mobile interaction

We present new alternative interfaces for zooming out on a mobile device: Bounce Back and Force Zoom. These interfaces are designed to be used with a single hand. They use a pressure-sensitive multitouch technology in which the pressure itself is used to zoom. Bounce Back senses the intensity of pressure while the user is pressing down on the display. When the user releases his or her finger, the view is bounced back to zoom out. Force Zoom also senses the intensity of pressure, and the zoom level is associated with this intensity. When the user presses down on the display, the view is scaled back according to the intensity of the pressure. We conducted a user study to investigate the efficiency and usability of our interfaces by comparing with previous pressure-sensitive zooming interface and Google Maps zooming interface as a baseline. Results showed that Bounce Back and Force Zoom was evaluated as significantly superior to that of previous research; number of operations was significantly lower than default mobile Google Maps interface and previous research.
In Vitro Activity of PBTZ169 against Multiple Mycobacterium Species

In this study, we demonstrate that PBTZ169 exhibits significant differences in in vitro activity against multiple Mycobacterium species. The amino acid polymorphism at codon 387 of decaprenylphosphoryl-beta-d-ribose oxidase (DprE1) can be used as a surrogate marker for in vitro susceptibility to PBTZ169 in mycobacteria. ABSTRACT In this study, we demonstrate that PBTZ169 exhibits significant differences in in vitro activity against multiple Mycobacterium species. The amino acid polymorphism at codon 387 of decaprenylphosphoryl-beta-d-ribose oxidase (DprE1) can be used as a surrogate marker for in vitro susceptibility to PBTZ169 in mycobacteria. In addition, the amino acid substitution at codon 154 in DprE1 may be associated with acquired resistance to PBTZ169 in the Mycobacterium fortuitum mutants.
Traits correlate with invasive success more than plasticity: A comparison of three Centaurea congeners

Abstract The importance of phenotypic plasticity for successful invasion by exotic plant species has been well studied, but with contradictory and inconclusive results. However, many previous studies focused on comparisons of native and invasive species that co‐occur in a single invaded region, and thus on species with potentially very different evolutionary histories. We took a different approach by comparing three closely related Centaurea species: the highly invasive C. solstitialis, and the noninvasive but exotic C. calcitrapa and C. sulphurea. These species have overlapping distributions both in their native range of Spain and in their non‐native range of California. We collected seeds from 3 to 10 populations from each region and species and grew them in common garden greenhouse conditions to obtain an F1 generation in order to reduce maternal effects. Then, F1 seeds were grown subjected to simulated herbivory, variation in nutrient availability, and competition, to explore plasticity in the responses to these conditions. We found little variation in phenotypic plasticity among species and regions, but C. solstitialis plants from California produced more biomass in competition than their Spanish conspecifics. This species also had the highest relative growth rates when in competition and when grown under low nutrient availability. Noninvasive congeners produced intermediate or opposite patterns.
Stabilization of the CD81 Large Extracellular Loop with De Novo Disulfide Bonds Improves Its Amenability for Peptide Grafting

Tetraspan proteins are significantly enriched in the membranes of exosomal vesicles (EVs) and their extracellular domains are attractive targets for engineering towards specific antigen recognition units. To enhance the tolerance of a tetraspanin fold to modification, we achieved significant thermal stabilization of the human CD81 large extracellular loop (hCD81 LEL) via de novo disulfide bonds. The best mutants were shown to exhibit a positive shift in the melting temperature (Tm) of up to 25 °C. The combination of two most potent disulfide bonds connecting different strands of the protein resulted in a mutant with a Tm of 109 °C, 43 °C over the Tm of the wild-type hCD81 LEL. A peptide sequence binding to the human transferrin receptor (hTfr) was engrafted into the D-segment of the hCD81 LEL, resulting in a mutant that still exhibited a compact fold. Grafting of the same peptide sequence between helices A and B resulted in a molecule with an aberrant profile in size exclusion chromatography (SEC), which could be improved by a de novo cysteine bond connecting both helices. Both peptide-grafted proteins showed an enhanced internalization into the cell line SK-BR3, which strongly overexpresses hTfr. In summary, the tetraspan LEL fold could be stabilized to enhance its amenability for engineering into a more versatile protein scaffold.
Filtered Medial Surface Based Approach for 3D Collision-Free Path Planning Problem

This paper introduces an original 3D path planning approach for Unmanned Aerial Vehicle (UAV) applications. More specifically, the core idea is to generate a smooth and collision-free path with respect to the vehicle dimension. Given a 3D grid representation of the environment, the Generalized Voronoi Graph (GVG) is first approximated using a filtered medial surface (FMS) algorithm on the corresponding navigable space. Based on an efficient pruning criterion, the produced FMS excludes GVG portions corresponding to narrow passages unfitting safe UAV navigation constraints, and thus it defines a set of guaranteed safe trajectories within the environment. Given a set of starting and destination coordinates, an adapted A-star algorithm is then applied to compute the shortest path on the FMS. Finally, an optimization process ensures the smoothness of the final path by fitting a set of 3D Bézier curves to the initial path. For a comparative study, the A-star algorithm is applied directly on the input environment representation and relevant comparative criteria are defined to assert the proposed approach using simulation results.
Neural Correlates of Giving Social Support: Differences Between Giving Targeted Versus Untargeted Support

Objective Giving support contributes to the link between social ties and health; however, the neural mechanisms are not known. Giving support in humans may rely on neural regions implicated in parental care in animals. The current studies, therefore, assess the contribution of parental care–related neural regions to giving support in humans and, as a further theoretical test, examine whether the benefits of giving targeted support to single, identifiable individuals in need extend to giving untargeted support to larger societal causes. Methods For study 1 (n = 45, M (SD) age = 21.98 (3.29), 69% females), participants completed a giving support task, followed by an emotional faces task in the functional magnetic resonance imaging scanner. For study 2 (n = 382, M (SD) age = 43.03 (7.28), 52% females), participants self-reported on their giving support behavior and completed an emotional faces task in the functional magnetic resonance imaging scanner. Results In study 1, giving targeted (versus untargeted) support resulted in greater feelings of social connection and support effectiveness. Furthermore, greater septal area activity, a region centrally involved in parental care in animals, to giving targeted support was associated with less right amygdala activity to an emotional faces task (r = −.297, 95% confidence interval = −.547 to −.043). Study 2 replicated and extended this association to show that self-reports of giving targeted support were associated with less amygdala activity to a different emotional faces task, even when adjusting for other social factors (r = −.105, 95% confidence interval = −.200 to −.011). Giving untargeted support was not related to amygdala activity in either study. Conclusions Results highlight the unique benefits of giving targeted support and elucidate neural pathways by which giving support may lead to health.
Sphere-Formation Assay: Three-Dimensional in vitro Culturing of Prostate Cancer Stem/Progenitor Sphere-Forming Cells

Cancer Stem Cells (CSCs) are a sub-population of cells, identified in most tumors, responsible for the initiation, recurrence, metastatic potential, and resistance of different malignancies. In prostate cancer (PCa), CSCs were identified and thought to be responsible for the generation of the lethal subtype, commonly known as Castration-Resistant Prostate Cancer (CRPC). In vitro models to investigate the properties of CSCs in PCa are highly required. Sphere-formation assay is an in vitro method commonly used to identify CSCs and study their properties. Here, we report the detailed methodology on how to generate and propagate spheres from PCa cell lines and from murine prostate tissue. This model is based on the ability of stem cells to grow in non-adherent serum-free gel matrix. We also describe how to use these spheres in histological and immuno-fluorescent staining assays to assess the differentiation potential of the CSCs. Our results show the sphere-formation Assay (SFA) as a reliable in vitro assay to assess the presence and self-renewal ability of CSCs in different PCa models. This platform presents a useful tool to evaluate the effect of conventional or novel agents on the initiation and self-renewing properties of different tumors. The effects can be directly evaluated through assessment of the sphere-forming efficiency (SFE) over five generations or other downstream assays such as immuno-histochemical analysis of the generated spheres.
Comparison of the Performance Between Sepsis-1 and Sepsis-3 in ICUs in China: A Retrospective Multicenter Study

ABSTRACT The definition of sepsis was updated to sepsis-3 in February 2016. However, the performance of the previous and new definition of sepsis remains unclear in China. This was a retrospective multicenter study in six intensive care unit (ICUs) from five university-affiliated hospitals to compare the performance between sepsis-1 and sepsis-3 in China. From May 1, 2016 to June 1, 2016, 496 patients were enrolled consecutively. Data were extracted from the electronic clinical records. We evaluated the performance of sepsis-1 and sepsis-3 by measuring the area under the receiver operating characteristic curves (AUROC) to predict 28-day mortality rates. Of 496 enrolled patients, 186 (37.5%) were diagnosed with sepsis according to sepsis-1, while 175 (35.3%) fulfilled the criteria of sepsis-3. The AUROC of systemic inflammatory response syndrome (SIRS) is significantly smaller than that of sequential organ failure assessment (SOFA) (0.55 [95% confidence interval, 0.46–0.64] vs. 0.69 (95% confidence interval, 0.61–0.77], P = 0.008) to predict 28-day mortality rates of infected patients. Moreover, 5.9% infected patients (11 patients) were diagnosed as sepsis according to sepsis-1 but not to sepsis-3. The APACHE II, SOFA scores, and mortality rate of the 11 patients were significantly lower than of patients whose sepsis was defined by both the previous and new criteria (8.6±3.5 vs. 16.3±6.2, P = < 0.001; 1 (0–1) vs. 6 (4–8), P = <0.001; 0.0 vs. 33.1%, P = 0.019). In addition, the APACHE II, length of stay in ICU, and 28-day mortality rate of septic patients rose gradually corresponding with the raise in SOFA score (but not the SIRS score). Sepsis-3 performed better than sepsis-1 in the study samples in ICUs in China.
Patterns and Inconsistencies in Collaborative Tagging Systems: An Examination of Tagging Practices

This paper analyzes the tagging patterns exhibited by users of del.icio. us, to assess how collaborative tagging supports and enhances traditional ways of classifying and indexing documents. Using frequency data and co-word analysis matrices analyzed by multi-dimensional scaling, the authors discovered that tagging practices to some extent work in ways that are continuous with conventional indexing. Small numbers of tags tend to emerge by unspoken consensus, and inconsistencies follow several predictable patterns that can easily be anticipated. However, the tags also indicated intriguing practices relating to time and task which suggest the presence of an extra dimension in classification and organization, a dimension which conventional systems are unable to facilitate. (The paper is available from http://eprints.rclis.org/archive/00008315/)
YouTube needs: understanding user's motivations to watch videos on mobile devices

Watching online videos on mobile devices has been massively present in people's daily activities. However, different users can watch the same video for different purposes, and hence develop different expectations for their experience. Understanding people's motivations for watching videos on mobile can help address this problem by giving designers the information needed to craft the whole watching journey better adapting to user's expectations. To obtain this understanding, a comprehensive framework of viewer motivations is necessary. We present research that provides several contributions to understanding mobile video watchers: a thorough framework of user motivations to watch videos on mobile devices, a detailed procedure for collecting and categorizing these motivations, a set of challenges that viewers experience to address each motivation, insights on usage of mobile and non-mobile devices, and design recommendations for video sharing systems.
Virtual reality on the go?: a study on social acceptance of VR glasses

Virtual reality (VR) glasses enable to be present in an environment while the own physical body is located in another place. Recent mobile VR glasses enable users to be present in any environment they want at any time and physical place. Still, mobile VR glasses are rarely used. One explanation is that it is not considered socially acceptable to immerse in another environment in certain situations. We conducted an online experiment that investigates the social acceptance of VR glasses in six different contexts. Our results confirm that social acceptability depends on the situation. In the bed, in the metro, or in a train, mobile VR glasses seem to be acceptable. However, while being surrounded by other people where a social interaction between people is expected, such as in a living room or a public cafe, the acceptance of mobile VR glasses is significantly reduced. If one or two persons wear glasses seems to have a negligible effect. We conclude that social acceptability of VR glasses depends on the situation and is lower when the user is supposed to interact with surrounding people.
A new method for curvilinear text line extraction and straightening of arabic handwritten text

Line extraction is a critical step from one of the main subtasks of Document Image Analysis, which is layout analysis. This paper presents a new method for curvilinear text line extraction and straightening in Arabic handwritten documents. The proposed method is based on a strategy that consists of two distinct steps. First, text line is extracted based on morphological dilation operation. Secondly, the extracted text line is straighten in two sub-steps: Course tuning of text line orientation based on Hough transform, then fine tuning based on centroid alignment of the connected component that forms the text line. The proposed approach has been extensively experimented on samples from the benchmark datasets of KFUPM Handwritten Arabic TexT (KHATT) and Arabic Handwriting DataBase (AHDB). Experimental results show that, the proposed method is capable of detecting and straightening curvilinear text lines even on challenging Arabic handwritten documents.
Characterization of a Novel Thermostable Enzyme from Thermus sp. 2.9 with Phospholipase and Acyltransferase Activities

Phospholipases are classified in different enzyme families according to the ester bond they cleave within phospholipids. The use of phospholipases in industrial processes has prompted the search for new enzymes with differential properties. A gene encoding a novel phospholipase (PLP_2.9) was identified in the genome of the thermophilic strain Thermus sp. 2.9. The analysis of the primary sequence unveiled a patatin-like domain. The alignment of the amino acid sequence of PLP_2.9 to other bacterial patatin-related proteins showed that the four blocks characteristic of this type of phospholipases and the amino acids representing the catalytic dyad are conserved in this protein. PLP_2.9 was overexpressed in Escherichia coli and the purified enzyme was characterized biochemically. PLP_2.9 hydrolyzed p-nitrophenyl palmitate at alkaline pH over a wide range of temperatures (55–80°C), showing high thermostability. PLP_2.9 displayed phospholipase A and acyltransferase activities on egg yolk phosphatidylcholine. Due to its high thermostability, PLP_2.9 has potential applications as a catalyst in several industrial processes.