Miracle-dz/UniFAR-FTUs huggingface dataset:
Bullying and Victimization in Overweight and Obese Outpatient Children and Adolescents: An Italian Multicentric Study

Objective Being overweight or obese is one of the most common reasons that children and adolescents are teased at school. We carried out a study in order to investigate: i) the relation between weight status and school bullying and ii) the relation between weight status categories and types of victimization and bullying in an outpatient sample of Italian children and adolescents with different degrees of overweight from minimal overweight up to severe obesity. Participants/Methods Nine-hundred-forty-seven outpatient children and adolescents (age range 6.0–14.0 years) were recruited in 14 hospitals distributed over the country of Italy. The participants were classified as normal-weight (N = 129), overweight (N = 126), moderately obese (N = 568), and severely obese (N = 124). The nature and extent of verbal, physical and relational bullying and victimization were assessed with an adapted version of the revised Olweus bully-victim questionnaire. Each participant was coded as bully, victim, bully-victim, or not involved. Results Normal-weight and overweight participants were less involved in bullying than obese participants; severely obese males were more involved in the double role of bully and victim. Severely obese children and adolescents suffered not only from verbal victimization but also from physical victimization and exclusion from group activities. Weight status categories were not directly related to bullying behaviour; however severely obese males perpetrated more bullying behaviour compared to severely obese females. Conclusions Obesity and bullying among children and adolescents are of ongoing concern worldwide and may be closely related. Common strategies of intervention are needed to cope with these two social health challenges.
The TAF10-containing TFIID and SAGA transcriptional complexes are dispensable for early somitogenesis in the mouse embryo

During development, tightly regulated gene expression programs control cell fate and patterning. A key regulatory step in eukaryotic transcription is the assembly of the pre-initiation complex (PIC) at promoters. PIC assembly has mainly been studied in vitro, and little is known about its composition during development. In vitro data suggest that TFIID is the general transcription factor that nucleates PIC formation at promoters. Here we show that TAF10, a subunit of TFIID and of the transcriptional co-activator SAGA, is required for the assembly of these complexes in the mouse embryo. We performed Taf10 conditional deletions during mesoderm development and show that Taf10 loss in the presomitic mesoderm (PSM) does not prevent cyclic gene transcription or PSM segmental patterning, whereas lateral plate differentiation is profoundly altered. During this period, global mRNA levels are unchanged in the PSM, with only a minor subset of genes dysregulated. Together, our data strongly suggest that the TAF10-containing canonical TFIID and SAGA complexes are dispensable for early paraxial mesoderm development, arguing against the generic role in transcription proposed for these fully assembled holo-complexes. Summary:TAF10 is important for the assembly of TFIID and SAGA complexes in the embryo but in its absence, global transcription is not affected in the presomitic mesoderm at E9.5.
Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.
Optimistic Localization: Avoiding Location Ambiguity in Wireless Ad-hoc Networks

Accurate self-localization is a key enabling technique for many pervasive applications. Existing approaches, most of which are multilateration based, often suffer ambiguities, resulting in unbounded positioning errors. To address this problem, previous approaches discard those positioning results with possible flip ambiguities, trading the performance for robustness. However, the high false positive rate of flip prediction incorrectly rejects many reliable location estimates. By exploiting the characteristics of flip ambiguity, which causes either huge or zero error, we propose the concept of optimistic localization and design an algorithm, OFA, that employs a global consistency check and a location correction phase in the localization process. We evaluate this design through extensive simulations. The results show that OFA obtains robustness with extremely low performance cost, so as to reduce the requirement on average degree from 25 to 10 for robustly localizing a network.
Performance analysis of coherently detected FFH/BPSK with maximal ratio combining receiver over Rayleigh fading channel with multitone jamming and imperfect channel estimation

Fast frequency hopping (FFH) system is an effective method to combat jamming in military applications. In FFH system over fading channels, noncoherent detected frequency shift keying (FSK) is commonly used. In this paper, we derived the error performance of a FFH system based on coherently detected binary phase shift keying (BPSK) over Rayleigh fading channel. The jamming type is assumed to be multitone jamming (MTJ). The channel estimation is assumed to be affected by additive while Gaussian noise (AWGN) and MTJ.
Evaluation of a high-resolution patient-specific model of the electrically stimulated cochlea

Abstract. Cochlear implants (CIs) are surgically implanted medical devices used to treat individuals with severe-to-profound sensorineural hearing loss. Although these devices have been remarkably successful at restoring audibility, many patients experience poor outcomes. Our group has developed the first image-guided CI programming technique where the electrode positions are found in CT images and used to estimate neural activation patterns, which is unique information that audiologists can use to define patient-specific processor settings. Currently, neural activation is estimated using only the distance from each electrode to the neural activation sites, which might be less accurate than using high-resolution electro-anatomical models (EAMs) to perform physics-based estimations of neural activation. We propose a patient-customized EAM approach where the EAM is spatially and electrically adapted to a patient-specific configuration. Spatial adaptation is done through nonrigid registration of the model with the patient CT image. Electrical adaptation is done by adjusting tissue resistivity parameters, so the intracochlear voltage distributions predicted by the model best match those directly measured for the patient via their implant. We found that our approach, demonstrated for N=7 patients, results in mean percent differences between direct and simulated measurements of voltage distributions of 10.9%.
Summarization of User-Generated Sports Video by Using Deep Action Recognition Features

Automatically generating a summary of a sports video poses the challenge of detecting interesting moments, or highlights, of a game. Traditional sports video summarization methods leverage editing conventions of broadcast sports video that facilitate the extraction of high-level semantics. However, user-generated videos are not edited and, thus, traditional methods are not suitable to generate a summary. In order to solve this problem, this paper proposes a novel video summarization method that uses players’ actions as a cue to determine the highlights of the original video. A deep neural-network-based approach is used to extract two types of action-related features and to classify video segments into interesting or uninteresting parts. The proposed method can be applied to any sports in which games consist of a succession of actions. Especially, this paper considers the case of Kendo (Japanese fencing) as an example of a sport to evaluate the proposed method. The method is trained using Kendo videos with ground truth labels that indicate the video highlights. The labels are provided by annotators possessing a different experience with respect to Kendo to demonstrate how the proposed method adapts to different needs. The performance of the proposed method is compared with several combinations of different features, and the results show that it outperforms previous summarization methods.
A Large-Scale Software-Generated Face Composite Sketch Database

Numerous algorithms that can identify suspects depicted in sketches following eyewitness descriptions of criminals are currently being developed because of their potential importance in forensics investigations. Yet, despite the prevalent use of software-generated composite sketches by law enforcement agencies, there still exist few such sketches which can be used by researchers to adequately evaluate face photo- sketch recognition algorithms when using these composites. The main contribution of this paper is the creation of the University of Malta Software- Generated Face Sketch (UoM-SGFS) database that is publicly available and which contains the largest number of viewed software-generated sketches, that also exhibit several deformations and exaggerations to mimic sketches obtained in real- world investigations. Further, in contrast to other databases, all sketches in this new database are represented in colour. {Lastly, state-of-the- art recognition algorithms are found to perform worse on the software-generated composites than on hand-drawn sketches, while recognition accuracies still lag far behind those achieved for traditional photo-to-photo comparisons.
Hardware-Sensitive Scan Operator Variants for Compiled Selection Pipelines

: The ever-increasing demand for performance on huge data sets forces database systems to tweak the last bit of performance out of their operators. Especially query compiled plans allow for several tuning opportunities that can be applied depending on the query plan and the underlying data. Apart from classical query optimization opportunities, it includes to tune the code using code optimizations for processor specifics, e
Effect of Origanum vulgare essential oil on biofilm formation and motility capacity of Pseudomonas fluorescens strains isolated from discoloured Mozzarella cheese

The study was focused on Pseudomonas fluorescens strains isolated from Mozzarella cheese, with the aim of evaluating the effects of Origanum vulgare L. essential oil (OEO) on the biofilm formation and eradication, as well as on the motility and blue pigment production at 10°C.
Truncating variants of the DLG4 gene are responsible for intellectual disability with marfanoid features

Marfanoid habitus (MH) combined with intellectual disability (ID) is a genetically and clinically heterogeneous group of overlapping disorders. We performed exome sequencing in 33 trios and 31 single probands to identify novel genes specific to MH‐ID. After the search for variants in known disease‐causing genes and non‐disease‐causing genes with classical approaches, we searched for variants in non‐disease‐causing genes whose pLI was above 0.9 (ExAC Consortium data), in which truncating variants were found in at least 3 unrelated patients. Only DLG4 gene met these criteria. Data from the literature and various databases also indicated its implication in ID. DLG4 encodes post‐synaptic density protein 95 (PSD‐95), a protein expressed in various tissues, including the brain. In neurons, PSD‐95 is located at the post‐synaptic density, and is associated with glutamatergic receptor signaling (NMDA and AMPA). PSD‐95 probably participates in dendritogenesis. Two patients were heterozygous for de novo frameshift variants and one patient carried a a consensus splice site variant. Gene expression studies supported their pathogenicity through haploinsufficiency and loss‐of‐function. Patients exhibited mild‐to‐moderate ID, similar marfanoid features, including a long face, high‐arched palate, long and thin fingers, pectus excavatum, scoliosis and ophthalmological manifestations (nystagmus or strabismus). Our study emphasizes the role of DLG4 as a novel post‐synaptic‐associated gene involved in syndromic ID associated with MH.
Delay in Diagnosis of Testicular Cancer; A Need for Awareness Programs

Background Aim To gain insight into patient and doctor delay in testicular cancer (TC) and factors associated with delay. Materials and Methods Sixty of the 66 eligible men; median age 26 (range 17–45) years, diagnosed with TC at the University Medical Center Groningen completed a questionnaire on patients’ delay: interval from symptom onset to first consultation with a general practitioner (GP) and doctors’ delay: interval between GP and specialist visit. Results Median patient reported delay was 30 (range 1–365) days. Patient delay and TC tumor stage were associated (p = .01). Lower educated men and men embarrassed about their scrotal change reported longer patient delay (r = -.25, r = .79 respectively). Age, marital status, TC awareness, warning signals, nor perceived limitations were associated with patient delay. Median patient reported time from GP to specialist (doctors’ delay) was 7 (range 0–240) days. Referral time and disease stage were associated (p = .04). Six patients never reported a scrotal change. Of the 54 patients reporting a testicular change, 29 (54%) patients were initially ‘misdiagnosed’, leading to a median doctors’ delay of 14 (1–240) days, which was longer (p< .001) than in the 25 (46%) patients whose GP suspected TC (median doctors’ delay 1(0–7 days). Conclusions High variation in patients’ and doctors’ delay was found. Most important risk variables for longer patient delay were embarrassment and lower education. Most important risk variable in GP’s was ‘misdiagnosis’. TC awareness programs for men and physicians are required to decrease delay in the diagnosis of TC and improve disease free survival.
TUM: Towards ubiquitous multi-device localization for cross-device interaction

Cross-device interaction is becoming an increasingly hot topic as we often have multiple devices at our immediate disposal in this era of mobile computing. Various cross-device applications such as file sharing, multi-screen display, and cross-device authentication have been proposed and investigated. However, one of the most fundamental enablers remains unsolved: How to achieve ubiquitous multi-device localization? Though pioneer efforts have resorted to gesture-assisted or sensing-assisted localization, they either require extensive user participation or impose some strong assumptions on device sensing abilities. This introduces extra costs and constraints, and thus degrades their practicality. To overcome these limitations, we propose TUM, an acoustic-assisted localization scheme Towards Ubiquitous Multi-device localization. The basic idea of TUM is to utilize the dual-microphones and speakers to obtain distance cues among devices. At the same time it resolves the location ambiguity with the help of MEMS sensors. We devise techniques for distance constraint extraction, static localization, continuous localization, and multi-device localization, and build a prototype that runs on commodity devices. Extensive experiments show that TUM provides a real-time 3D relative localization service under 10cm mean error for both static and continuous localization.
Prestin-Dependence of Outer Hair Cell Survival and Partial Rescue of Outer Hair Cell Loss in Prestin V499G/Y501H Knockin Mice

A knockin (KI) mouse expressing mutated prestin V499G/Y501H (499 prestin) was created to study cochlear amplification. Recordings from isolated outer hair cells (OHC) in this mutant showed vastly reduced electromotility and, as a consequence, reduced hearing sensitivity. Although 499 prestin OHCs were normal in stiffness and longer than OHCs lacking prestin, accelerated OHC death was unexpectedly observed relative to that documented in prestin knockout (KO) mice. These observations imply an additional role of prestin in OHC maintenance besides its known requirement for mammalian cochlear amplification. In order to gain mechanistic insights into prestin-associated OHC loss, we implemented several interventions to improve survival. First, 499 prestin KI’s were backcrossed to Bak KO mice, which lack the mitochondrial pro-apoptotic gene Bak. Because oxidative stress is implicated in OHC death, another group of 499 prestin KI mice was fed the antioxidant diet, Protandim. 499 KI mice were also backcrossed onto the FVB murine strain, which retains excellent high-frequency hearing well into adulthood, to reduce the compounding effect of age-related hearing loss associated with the original 499 prestin KIs. Finally, a compound heterozygous (chet) mouse expressing one copy of 499 prestin and one copy of KO prestin was also created to reduce quantities of 499 prestin protein. Results show reduction in OHC death in chets, and in 499 prestin KIs on the FVB background, but only a slight improvement in OHC survival for mice receiving Protandim. We also report that improved OHC survival in 499 prestin KIs had little effect on hearing phenotype, reaffirming the original contention about the essential role of prestin’s motor function in cochlear amplification.
Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals

Eukaryotic genomes must accomplish the tradeoff between compact packaging for genome stability and inheritance, and accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3 and H4), and by deploying histone variants with specialized chromatin functions. While some histone variants are highly conserved across eukaryotes, others carry out lineage-specific functions. Here, we characterize the evolution of male germline-specific “short H2A variants”, which wrap shorter DNA fragments than canonical H2A. In addition to three previously described H2A.B, H2A.L and H2A.P variants, we describe a novel, extremely short H2A histone variant: H2A.Q. We show that H2A.B, H2A.L, H2A.P and H2A.Q are most closely related to a novel, more canonical mmH2A variant found only in monotremes and marsupials. Using phylogenomics, we trace the origins and early diversification of short histone variants into four distinct clades to the ancestral X chromosome of placental mammals. We show that short H2A variants further diversified by repeated lineage-specific amplifications and losses, including pseudogenization of H2A.L in many primates. We also uncover evidence for concerted evolution of H2A.B and H2A.L genes by gene conversion in many species, involving loci separated by large distances. Finally, we find that short H2As evolve more rapidly than any other histone variant, with evidence that positive selection has acted upon H2A.P in primates. Based on their X chromosomal location and pattern of genetic innovation, we speculate that short H2A histone variants are engaged in a form of genetic conflict involving the mammalian sex chromosomes.
Frequency and clinical correlates of elevated plasma Epstein‐Barr virus DNA at diagnosis in peripheral T‐cell lymphomas

Epstein‐Barr virus (EBV)‐encoded RNAs (EBER) in tumor tissue and cell‐free plasma EBV‐DNA (pEBVd) are detected in EBV‐associated lymphomas. Studies have suggested that EBER+ peripheral T‐cell lymphomas (PTCL) have worse prognosis but the role of EBV in these neoplasms remains unclear. pEBVd is quantitative and more easily amenable to standardization than EBER, but frequency of pEBVd detection, clinical impact and agreement with EBER status in PTCL are unknown. We retrospectively assessed frequency of detectable pre‐treatment pEBVd, presence of EBER in tumor tissue, and outcomes in 61 of 135 EBV‐assessable PTCL patients. Fifteen of 61 patients (24.5%, 95% CI: 14–37%) were pre‐treatment pEBVd+, with no significant differences in baseline characteristics or treatment between pEBVd+ and pEBVd− patients. EBER‐ISH was performed on 10 pEBVd+ and 35 pEBVd− tumors. All 10 pEBVd+ patients were EBER+, but 9 pEBVd− patients were also EBER+. With median follow up of 24 months (range 1–96), overall survival (OS) was shorter in pEBVd+ compared to pEBVd− patients (13 vs. 72 months; p = 0.04). In our retrospective study, pre‐treatment pEBVd was elevated in 25% of PTCL patients, was highly specific for EBER+ tumors, and was associated with shorter survival. pEBVd should be further explored as a prognostic variable and tumor biomarker in PTCL.
Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

Avian malaria parasites are prevalent around the world and infect a wide diversity of bird species. Here, we report the sequencing and analysis of high-quality draft genome sequences for two avian malaria species, Plasmodium relictum and Plasmodium gallinaceum. We identify 50 genes that are specific to avian malaria, located in an otherwise conserved core of the genome that shares gene synteny with all other sequenced malaria genomes. Phylogenetic analysis suggests that the avian malaria species form an outgroup to the mammalian Plasmodium species, and using amino acid divergence between species, we estimate the avian- and mammalian-infective lineages diverged in the order of 10 million years ago. Consistent with their phylogenetic position, we identify orthologs of genes that had previously appeared to be restricted to the clades of parasites containing Plasmodium falciparum and Plasmodium vivax, the species with the greatest impact on human health. From these orthologs, we explore differential diversifying selection across the genus and show that the avian lineage is remarkable in the extent to which invasion-related genes are evolving. The subtelomeres of the P. relictum and P. gallinaceum genomes contain several novel gene families, including an expanded surf multigene family. We also identify an expansion of reticulocyte binding protein homologs in P. relictum, and within these proteins, we detect distinct regions that are specific to nonhuman primate, humans, rodent, and avian hosts. For the first time in the Plasmodium lineage, we find evidence of transposable elements, including several hundred fragments of LTR-retrotransposons in both species and an apparently complete LTR-retrotransposon in the genome of P. gallinaceum.