Miracle-dz/UniFAR-FTUs huggingface dataset:
Personalized vaccines for cancer immunotherapy

Cancer is characterized by an accumulation of genetic alterations. Somatic mutations can generate cancer-specific neoepitopes that are recognized by autologous T cells as foreign and constitute ideal cancer vaccine targets. Every tumor has its own unique composition of mutations, with only a small fraction shared between patients. Technological advances in genomics, data science, and cancer immunotherapy now enable the rapid mapping of the mutations within a genome, rational selection of vaccine targets, and on-demand production of a therapy customized to a patient’s individual tumor. First-in-human clinical trials of personalized cancer vaccines have shown the feasibility, safety, and immunotherapeutic activity of targeting individual tumor mutation signatures. With vaccination development being promoted by emerging innovations of the digital age, vaccinating a patient with individual tumor mutations may become the first truly personalized treatment for cancer.
ComNSense

Recently, point clouds have been efficiently utilized for medical imaging, modeling urban environments, and indoor modeling. In this realm, several mobile platforms, such as Google Tango and Apple ARKit, have been released leveraging 3D mapping, augmented reality, etc. In modeling applications, these modern mobile devices opened the door for crowd-sourcing point clouds to distribute the overhead of data collection. However, uploading these large points clouds from resources-constrained mobile devices to the back-end servers consumes excessive energy. Accordingly, participation rates in such crowd-sensing systems can be negatively influenced. To tackle this challenge, this paper introduces our ComNSense approach that dramatically reduces the energy consumption of processing and uploading point clouds. To this end, ComNSense reports only a set of extracted geometrical data to the servers. To optimize the geometry extraction, ComNSense leverages formal grammars which encode design-time knowledge, i.e. structural information. To demonstrate the effectiveness of ComNSense, we performed several experiments of collecting point clouds from two different buildings to extract the walls location, as a case study. We also assess the performance of ComNSense relative to a grammar-free method. The results showed a significant reduction of the energy consumption while achieving a comparable detection accuracy.
Semi-Discrete Galerkin Finite Element Method for the Diffusive Peterlin Viscoelastic Model

Abstract In this paper, a semi-discrete Galerkin finite element method is applied to the two-dimensional diffusive Peterlin viscoelastic model which can describe the unsteady behavior of some incompressible ploymeric fluids. For the derived semi-discrete finite element spatial discretization scheme, the a priori bounds are given that does not rely on the mesh width restriction. Further, with the help of the a priori error bounds of the Stokes and Ritz projections, optimal error estimates for the velocity, the conformation tensor and the pressure are presented, respectively. Finally, in order to implement the proposed semi-discrete numerical scheme, we derive three kinds of fully discrete schemes, e.g., Newton’s iterative scheme, Picard’s iterative scheme and implicit-explicit time-stepping scheme. Finally, several numerical experiments are conducted to confirm our theoretical results.
A multidisciplinary learning experience contributing to mental health rehabilitation

Abstract Purpose People who access health services often have a range of needs that require the involvement of members from a multidisciplinary team. Teaching future health professionals about the importance of a multidisciplinary approach can be challenging. The aim of this paper is to describe a project called Recovery Camp that enhanced multidisciplinary health education through experiential and immersive engagement with people experiencing mental illness. Method Future health professionals and people with a lived experience of mental illness took part in Recovery Camp — an innovative five-day therapeutic recreation initiative in the Australian bush. Results are presented in a case study format and provide the reflective quotes of participants. The quotes were analyzed using a content analysis to identify core concepts. Results Analyses identified a common appreciation of multidisciplinary learning. The interactions among students and between students and consumers, promoted inter-professional practice and a holistic understanding of mental health care. Conclusions An immersive multidisciplinary approach, embedded within a recovery-based programme, enhances students’ understanding of the significance of multidisciplinary mental health care and treatment. Implications for Rehabilitation People with a lived experience of mental illness have a range of complex needs that require involvement of members from a multidisciplinary rehabilitation team. This study suggested a multidisciplinary, experiential, immersive health education experience — drawing on the principles of therapeutic recreation — can promote inter-professional rehabilitative practice and an appreciation for holistic mental health care.
Streptococcus dysgalactiae subsp. dysgalactiae isolated from milk of the bovine udder as emerging pathogens: In vitro and in vivo infection of human cells and zebrafish as biological models

Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) is a major cause of bovine mastitis and has been regarded as an animal‐restricted pathogen, although rare infections have been described in humans. Previous studies revealed the presence of virulence genes encoded by phages of the human pathogen Group A Streptococcus pyogenes (GAS) in SDSD isolated from the milk of bovine udder with mastitis. The isolates SDSD VSD5 and VSD13 could adhere and internalize human primary keratinocyte cells, suggesting a possible human infection potential of bovine isolates. In this work, the in vitro and in vivo potential of SDSD to internalize/adhere human cells of the respiratory track and zebrafish as biological models was evaluated. Our results showed that, in vitro, bovine SDSD strains could interact and internalize human respiratory cell lines and that this internalization was dependent on an active transport mechanism and that, in vivo, SDSD are able to cause invasive infections producing zebrafish morbidity and mortality. The infectious potential of these isolates showed to be isolate‐specific and appeared to be independent of the presence or absence of GAS phage‐encoded virulence genes. Although the infection ability of the bovine SDSD strains was not as strong as the human pathogenic S. pyogenes in the zebrafish model, results suggested that these SDSD isolates are able to interact with human cells and infect zebrafish, a vertebrate infectious model, emerging as pathogens with zoonotic capability.
Reading Between the Menu Lines: Are Restaurants’ Descriptions of “Healthy” Foods Unappealing?

Objective: As obesity rates continue to climb in America, much of the blame has fallen on the high-calorie meals at popular chain restaurants. Many restaurants have responded by offering “healthy” menu options. Yet menus’ descriptions of healthy options may be less attractive than their descriptions of less healthy, standard options. This study examined the hypothesis that the words describing items in healthy menu sections are less appealing than the words describing items in standard menu sections. Method: Menus from the top-selling American casual-dining chain restaurants with dedicated healthy submenus (N = 26) were examined, and the library of words from health-labeled items (N = 5,873) was compared to that from standard menu items (N = 38,343) across 22 qualitative themes (e.g., taste, texture). Results: Log-likelihood ratios revealed that restaurants described healthy items with significantly less appealing themes and significantly more health-related themes. Specifically, healthy items were described as less exciting, fun, traditional, American regional, textured, provocative, spicy hot, artisanal, tasty, and indulgent than standard menu items, but were described with significantly more foreign, fresh, simple, macronutrient, deprivation, thinness, and nutritious words. Conclusion: Describing the most nutritious menu options in less appealing terms may perpetuate beliefs that healthy foods are not flavorful or indulgent, and may undermine customers’ choice of healthier dining options. From a public health perspective, incorporating more appealing descriptive language to boost the appeal of nutritious foods may be one avenue to improve dietary health.
Factors influencing the toxicity of Headline® fungicides to terrestrial stage toads

Amphibians are susceptible to exposure from contaminants via multiple pathways. Pyraclostrobin fungicides have been shown to be toxic to terrestrial amphibians at environmentally relevant concentrations; however, these studies did not account for factors that may influence exposure and effects, such as fungicide formulation, age of the individual, exposure route, and physiological state of the individual. We examined Headline® and Headline AMP® fungicide toxicity to adult Anaxyrus cognatus and Anaxyrus woodhousii by direct overspray, as well as acute toxicity of Headline AMP to juvenile A. cognatus through direct overspray, previously exposed soils, and diet. We also assessed effects of hydration state on fungicide toxicity in juvenile A. cognatus and sublethal effects of fungicide exposure on prey‐orientation ability of juvenile A. cognatus. Neither formulation of Headline caused mortality of adult A. cognatus and A. woodhousii at up to 5 times the maximum label rate in North American corn (1052 and 879 mL formulation/ha for Headline AMP and Headline fungicides, respectively, corresponding to 1.52 and 2.2 μg pyraclostrobin/cm2, respectively). Exposures of juvenile A. cognatus to Headline AMP via direct overspray and previously exposed soils (2 types) resulted in median lethal rate (LR50) values of 2.4, 3.34, and 3.61 μg pyraclostrobin/cm2, respectively. Dietary Headline AMP exposure was not toxic, prey‐orientations were not influenced by exposure, and effects were similar between dehydrated and hydrated treatments (LR50 = 2.4 and 2.3 μg pyraclostrobin/cm2, respectively). These results, combined with exposure concentrations reported in previous studies, suggest that risk of acute mortality for amphibians in terrestrial environments is low and is dictated by body size and site‐specific factors influencing exposure. Environ Toxicol Chem 2017;36:2679–2688. © 2017 SETAC
Youth reports of parents' romantic relationship quality: Links to physical health.

OBJECTIVE Prior work has shown that negative aspects (e.g., conflict) of marriage or marriage-like relationships are associated with poor health of offspring, but much less is known about the effects of positive aspects (e.g., affection) of parental romantic relationships. This study investigated links between conflict and affection within parents' romantic relationships and the health of youth with asthma. METHOD Eighty youths with asthma aged 10-17 answered daily questions over a 4-day period about conflict and affection within their parents' romantic relationship, as well as their own daily mood, asthma symptoms, and expiratory peak flow. RESULTS Multiple regression analyses revealed that romantic affection-but not conflict-was directly associated with higher expiratory peak flow. Further, there was a significant indirect effect of romantic affection via youth positive affect on lower asthma symptoms. CONCLUSION These results are the first to our knowledge to demonstrate that youth-reported positive characteristics of parents' romantic relationships are associated with better health among youth with asthma. (PsycINFO Database Record
First‐year growth in children with Noonan syndrome: Associated with feeding problems?

Children with Noonan syndrome show rapid decline of growth in the first year of life and feeding problems are present in over 50%. The aim of this study was to explore whether growth decelerates because of feeding problems or other Noonan syndrome‐related factors. We performed a retrospective, longitudinal cohort study of clinically and genetically diagnosed subjects with Noonan syndrome (n = 143). Questionnaires about the phenotypic–genotypic profile and reported feeding problems were sent to eligible subjects. Data on first‐year growth was obtained from growth charts. Ninety‐one participants were excluded because of different criteria. A total of 52 subjects with Noonan syndrome were included. The largest decline in weight and length standard deviation score (SDS) occurred in the first 2.5 months after birth (−1.93 and −1.15, respectively), with feeding problems causing a decline of 0.57 SDS in the remaining months. At 1 year, children with feeding problems were on average 290 g lighter and 0.8 cm shorter than children without feeding problems. Weight gain was also negatively influenced by having a PTPN11 mutation (n = 39) and a higher gestational age, whereas children of parents with Noonan syndrome and with a higher birth weight gained more weight. Growth in length was reduced by having cardiac surgery and a higher gestational age, but positively influenced by birth length and maternal height. Growth in children with Noonan syndrome is impaired right after birth and only partially associated with feeding problems. In addition, several specific Noonan syndrome‐related factors seem to influence growth in the first year.
Examination of a 19th Century Daguerreotype Photograph using High Resolution Scanning Transmission Electron Microscopy for 2D and 3D Nanoscale Imaging and Analysis

In 1839, the daguerreotype photographic process was first presented to the scientific community in France. The technology spread rapidly and was widely used around the globe until roughly 1860. Image formation can be generalized into four steps: 1) exposing silver-plated copper to an iodine plus or minus another halogen vapor(s), 2) further exposing the sensitized plate to visible light within a camera, 3) development of an image after the plate is treated with heated mercury vapor, and 4) deposition of a gilding layer via gold chloride solution and heating [1].
To Grow or to Reproduce? The Role of Life‐History Plasticity in Food Web Dynamics

The size of an individual is a key feature influencing and determined by a species' life history and ecology. Here, I consider how life‐history plasticity within a single species can influence the outcome of food web interactions along a productivity gradient. An individual can either reproduce early but remain susceptible to predators throughout its life (strategy 1) or delay reproduction and grow to a predator‐invulnerable size refuge (strategy 2). At low productivity, strategy 1 is favored because the probability of growing to a size refuge is low compared to the probability of being eaten. Here, the system is consumer controlled, and predators have large effects on the food web. At high productivity, strategy 2 is favored because high food availability increases the probability of prey attaining size refuge before being eaten. Consequently, the system becomes less consumer controlled, and predators have weaker effects on food web dynamics. At intermediate productivity, either strategy 1 or strategy 2 can be favored, depending on the initial conditions of the system. Field and laboratory experiments with a common freshwater snail Helisoma trivolis and its insect predator Belostoma flumineum support both the key assumptions and predictions of the models.
Misleading First Impressions

Studies on first impressions from facial appearance have rapidly proliferated in the past decade. Almost all of these studies have relied on a single face image per target individual, and differences in impressions have been interpreted as originating in stable physiognomic differences between individuals. Here we show that images of the same individual can lead to different impressions, with within-individual image variance comparable to or exceeding between-individuals variance for a variety of social judgments (Experiment 1). We further show that preferences for images shift as a function of the context (e.g., selecting an image for online dating vs. a political campaign; Experiment 2), that preferences are predictably biased by the selection of the images (e.g., an image fitting a political campaign vs. a randomly selected image; Experiment 3), and that these biases are evident after extremely brief (40-ms) presentation of the images (Experiment 4). We discuss the implications of these findings for studies on the accuracy of first impressions.
Light exercise heart rate on‐kinetics: a comparison of data fitted with sigmoidal and exponential functions and the impact of fitness and exercise intensity

This study examined the suitability of sigmoidal (SIG) and exponential (EXP) functions for modeling HR kinetics at the onset of a 5‐min low‐intensity cycling ergometer exercise test (5MT). The effects of training status, absolute and relative workloads, and high versus low workloads on the accuracy and reliability of these functions were also examined. Untrained participants (UTabs; n = 13) performed 5MTs at 100W. One group of trained participants (n = 10) also performed 5MTs at 100W (ETabs). Another group of trained participants (n = 9) performed 5MTs at 45% and 60% V˙O2 max (ET45 and ET60, respectively). SIG and EXP functions were fitted to HR data from 5MTs. A 30‐s lead‐in time was included when fitting SIG functions. Functions were compared using the standard error of the regression (SER), and test‐retest reliability of curve parameters. SER for EXP functions was significantly lower than for SIG functions across all groups. When residuals from the 30‐s lead‐in time were omitted, EXP functions only outperformed SIG functions in ET60 (EXP, 2.7 ± 1.2 beats·min−1; SIG, 3.1 ± 1.1 beats·min−1: P < 0.05). Goodness of fit and test–retest reliability of curve parameters were best in ET60 and comparatively poor in UTabs. Overall, goodness of fit and test–retest reliability of curve parameters favored functions fitted to 5MTs performed by trained participants at a high and relative workload, while functions fitted to data from untrained participants exercising at a low and absolute workload were less accurate and reliable.
geneEx - A Novel Tool to Assess Differential Expression from Gene and Exon Sequencing Data

The widespread of Next Generation Sequencing technologies accounted in recent years for the possibility to evaluate gene expression with great accuracy. Moreover, it allowed assessing differential gene expression among biological conditions with high sensitivity. However, state-of-the-art bioinformatics methodologies for differential gene expression evaluation from RNA Sequencing data still suffer from several drawbacks such as reduced specificity. In this paper we propose geneEx, a novel methodology and tool for differential gene expression evaluation from RNA Sequencing reads. By combining gene and exon expression evaluation and BioMart information, geneEX provides users with annotated lists of highly reliable differentially expressed genes. The results obtained in Sequencing Quality Control dataset proven the importance of a novel approach to lower False Positive predictions from current methodologies and the strength of the proposed methodological approach to increase the sensitivity of differentially expressed gene identification.
A library to modularly control asynchronous executions

Asynchronous programming style has been widely adopted for a variety of reasons one such being the rise of Web applications. Using non-blocking operations is a major approach to enforcing asynchronous programming. A non-blocking operation requires decomposing a module that consists of a set of blocking operations into more than two modules, in turn, leading to a variety of challenges such as callback spaghetti and callback hell. This paper presents SyncAS, a library specification to address these two problems. This library specification follows the ECMAScript standard; indeed, we provide a prototype implementation for ActionScript3. SyncAS proposes a novel approach that enables programmers to virtually block a program execution and restart it at arbitrary points of the program, instead of waiting for a callback execution. As a result, programmers do not need to decompose a module even if non-blocking operations are adopted. SyncAS uses aspect-oriented programming to control the program execution in an oblivious manner.
Phosphoproteomic profiling reveals ABA‐responsive phosphosignaling pathways in Physcomitrella patens

Abscisic acid (ABA) and its signaling system are important for land plants to survive in terrestrial conditions. Here, we took a phosphoproteomic approach to elucidate the ABA signaling network in Physcomitrella patens, a model species of basal land plants. Our phosphoproteomic analysis detected 4630 phosphopeptides from wild-type P. patens and two ABA-responsive mutants, a disruptant of group-A type-2C protein phosphatase (PP2C; ppabi1a/b) and AR7, a defective mutant in ARK, identified as an upstream regulator of SnRK2. Quantitative analysis detected 143 ABA-responsive phosphopeptides in P. patens. The analysis indicated that SnRK2-mediated phosphorylation and target motifs were partially conserved in bryophytes. Our data demonstrate that the PpSnRK2B and AREB/ABF-type transcription factors are phosphorylated in vivo in response to ABA under the control of ARK. On the other hand, our data also revealed the following: (i) the entire ABA-responsive phosphoproteome in P. patens is quite diverse; (ii) P. patens PP2C affects additional pathways other than the known ABA signaling pathway; and (iii) ARK is mainly involved in ABA signaling. Taken together, we propose that the core ABA signaling pathway is essential in all land plants; however, some ABA-responsive phosphosignaling uniquely developed in bryophytes during the evolutionary process.
Visual-Inertial Teach and Repeat for Aerial Inspection

Industrial facilities often require periodic visual inspections of key installations. Examining these points of interest is time consuming, potentially hazardous or require special equipment to reach. MAVs are ideal platforms to automate this expensive and tedious task. In this work we present a novel system that enables a human operator to teach a visual inspection task to an autonomous aerial vehicle by simply demonstrating the task using a handheld device. To enable robust operation in confined, GPS-denied environments, the system employs the Google Tango visual-inertial mapping framework as the only source of pose estimates. In a first step the operator records the desired inspection path and defines the inspection points. The mapping framework then computes a feature-based localization map, which is shared with the robot. After take-off, the robot estimates its pose based on this map and plans a smooth trajectory through the way points defined by the operator. Furthermore, the system is able to track the poses of other robots or the operator, localized in the same map, and follow them in real-time while keeping a safe distance.