Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Multi-Slice Inputs to Convolutional Neural Networks for Medical Image Segmentation

PURPOSE When using convolutional neural networks (CNNs) for segmentation of organs and lesions in medical images, the conventional approach is to work with inputs and outputs either as single slice [two-dimensional (2D)] or whole volumes [three-dimensional (3D)]. One common alternative, in this study denoted as pseudo-3D, is to use a stack of adjacent slices as input and produce a prediction for at least the central slice. This approach gives the network the possibility to capture 3D spatial information, with only a minor additional computational cost. METHODS In this study, we systematically evaluate the segmentation performance and computational costs of this pseudo-3D approach as a function of the number of input slices, and compare the results to conventional end-to-end 2D and 3D CNNs, and to triplanar orthogonal 2D CNNs. The standard pseudo-3D method regards the neighboring slices as multiple input image channels. We additionally design and evaluate a novel, simple approach where the input stack is a volumetric input that is repeatably convolved in 3D to obtain a 2D feature map. This 2D map is in turn fed into a standard 2D network. We conducted experiments using two different CNN backbone architectures and on eight diverse data sets covering different anatomical regions, imaging modalities, and segmentation tasks. RESULTS We found that while both pseudo-3D methods can process a large number of slices at once and still be computationally much more efficient than fully 3D CNNs, a significant improvement over a regular 2D CNN was only observed with two of the eight data sets. triplanar networks had the poorest performance of all the evaluated models. An analysis of the structural properties of the segmentation masks revealed no relations to the segmentation performance with respect to the number of input slices. A post hoc rank sum test which combined all metrics and data sets yielded that only our newly proposed pseudo-3D method with an input size of 13 slices outperformed almost all methods. CONCLUSION In the general case, multislice inputs appear not to improve segmentation results over using 2D or 3D CNNs. For the particular case of 13 input slices, the proposed novel pseudo-3D method does appear to have a slight advantage across all data sets compared to all other methods evaluated in this work.
Evaluation of the Feasibility of a Two-Week Course of Aquatic Therapy and Thalassotherapy in a Mild Post-Stroke Population

Strokes are a leading cause of disability in developed countries. Patients with disabilities need rehabilitation to improve their physical functioning, mental status, and quality of life. Currently, no high-quality evidence can be found attesting the benefits of any of the interventions that are nowadays used. Water-based exercise may improve the physical conditions and quality of life of people in the post-stroke phase. The objective of this study is to test whether aquatic therapy in an enriched environment at the seaside (a thalassotherapy center) could play a role in this condition. A quasi-experimental prospective study consisting of a specific program assessed 62 patients with a mild–moderate disability pre- and post-2 weeks of intensive treatment. They followed a thalassotherapy regimen including aquatic therapy in a sea water pool at 32–34 °C for 45 min daily five times a week. The outcomes measured were the Berg Balance scale, the Timed Up and Go test, the 10-meter walking test, the 6-min walking test, the Pain Visual Analogue Scale, the WHO Well-being index, EuroQoL VAS and EuroQoL 5D. We observed a significant improvement in all outcomes measured (p < 0.001, except mobility EuroQoL p < 0.05), except in the other four dimensions of the EuroQoL 5D and 10-metre walking test (NS). Conclusion: A two-week intensive course of aquatic therapy and thalassotherapy may be beneficial in the short term by reducing pain and improving the functional status and overall well-being of post-stroke patients.
Risk factors associated with carbapenem-resistant Klebsiella pneumoniae bloodstream infections in a tertiary-care hospital in India

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Exposure to COVID‐19 pandemic stress: Associations with depression and anxiety in emerging adults in the United States

Stressful events due to the coronavirus disease‐2019 (COVID‐19) pandemic are likely to have profound effects on mental health, and validated methods for assessing these experiences and associations with psychopathology are needed. We developed the Pandemic Stress Questionnaire (PSQ) and tested its psychometric properties, characterized experiences in emerging adults, and examined associations with internalizing symptoms.
Targeting PAK4 Inhibits Ras-Mediated Signaling and Multiple Oncogenic Pathways in High-Risk Rhabdomyosarcoma

These data demonstrate a novel oncogenic role for PAK4 in rhabdomyosarcoma and show that targeting PAK4 activity is a promising viable therapeutic option for advanced rhabdomyosarcoma. Rhabdomyosarcoma (RMS) is the most prevalent pediatric soft-tissue sarcoma. Multimodal treatment, including surgery and traditional chemotherapy with radiotherapy, has contributed to improvements in overall survival rates. However, patients with recurrent or metastatic disease have 5-year survival rates of less than 30%. One reason for the lack of therapeutic advancement is identification and targeting of critical signaling nodes. p21-activated kinases (PAK) are a family of serine/threonine kinases downstream of multiple critical tumorigenic receptor tyrosine kinase receptors and oncogenic regulators, including IGFR and RAS signaling, that significantly contribute to aggressive malignant phenotypes. Here, we report that RMS cell lines and tumors exhibit enhanced PAK4 expression levels and activity, which are further activated by growth factors involved in RMS development. Molecular perturbation of PAK4 in multiple RMS models in vitro and in vivo resulted in inhibition of RMS development and progression. Fusion-positive and -negative RMS models were sensitive to two PAK4 small-molecule inhibitors, PF-3758309 and KPT-9274, which elicited significant antitumor and antimetastatic potential in several primary and metastatic in vivo models, including a relapsed RMS patient-derived xenograft model. Transcriptomic analysis of PAK4-targeted tumors revealed inhibition of the RAS-GTPase, Hedgehog, and Notch pathways, along with evidence of activation of antitumor immune response signatures. This PAK4-targeting gene signature showed prognostic significance for patients with sarcoma. Overall, our results show for the first time that PAK4 is a novel and viable therapeutic target for the treatment of high-risk RMS. Significance: These data demonstrate a novel oncogenic role for PAK4 in rhabdomyosarcoma and show that targeting PAK4 activity is a promising viable therapeutic option for advanced rhabdomyosarcoma.
Sleep pattern in the US and 16 European countries during the COVID-19 outbreak using crowdsourced smartphone data

Abstract Background To stop the spread of the new coronavirus disease in 2019 (COVID-19), many countries had completely locked down. This lockdown restricted the everyday life of the affected residents and changed their mobility pattern, but its effects on sleep pattern were largely unknown. Methods Here, utilizing one of the largest crowdsourced database (Sleep as Android), we analyzed the sleep pattern of 25 217 users with 1 352 513 sleep records between 1 January and 29 April 2020 in the US and 16 European countries (Germany, UK, Spain, France, Italy, The Netherlands, Belgium, Hungary, Denmark, Finland, Norway, Czech, Sweden, Austria, Poland and Switzerland) with more than 100 records in all days of 2020. Results During the COVID-19 pandemic, the sleeping pattern before and after the country-level lockdown largely differed. The subjects increased their sleep duration by an average of 11.3 to 18.6 min on weekday nights, except Denmark (4.9 min) and Finland (7.1 min). In addition, subjects form all 16 European countries delayed their sleep onset from 10.7 min (Sweden) to 29.6 min (Austria). Conclusion During the COVID-19 pandemic, residents in the US and 16 European countries delayed their bedtime and slept longer than usual.
Sustained Attention in Developmental Language Disorder and Its Relation to Working Memory and Language

Purpose Based on evidence of deficits in domain-general cognitive abilities associated with developmental language disorder (DLD), the current study examined sustained attention performance in children with DLD compared to children with typical language development (TLD) and the interrelations between visual–spatial sustained attention, visual–spatial working memory, and language abilities across groups. Method Participants included 67 children at 7 years of age: 25 children with DLD (13 girls and 12 boys) and 42 children with TLD (23 girls and 19 boys). We assessed children's visual–spatial sustained attention, visual–spatial working memory, and language ability on a test of narrative language. Result Children with DLD scored significantly below their peers on a measure of visual–spatial sustained attention. Significant intercorrelations were observed between sustained attention, working memory, and language ability within the DLD group, but no correlations were observed between these measures in the TLD group. Conclusion Children with DLD have domain-general deficits in sustained attention, and correlational results have implications for whether and how language abilities are supported by domain-general cognition in both typical and disordered development.
Biological network analysis with deep learning

Abstract Recent advancements in experimental high-throughput technologies have expanded the availability and quantity of molecular data in biology. Given the importance of interactions in biological processes, such as the interactions between proteins or the bonds within a chemical compound, this data is often represented in the form of a biological network. The rise of this data has created a need for new computational tools to analyze networks. One major trend in the field is to use deep learning for this goal and, more specifically, to use methods that work with networks, the so-called graph neural networks (GNNs). In this article, we describe biological networks and review the principles and underlying algorithms of GNNs. We then discuss domains in bioinformatics in which graph neural networks are frequently being applied at the moment, such as protein function prediction, protein–protein interaction prediction and in silico drug discovery and development. Finally, we highlight application areas such as gene regulatory networks and disease diagnosis where deep learning is emerging as a new tool to answer classic questions like gene interaction prediction and automatic disease prediction from data.
Pilot study for the evaluation of safety profile of a potential inhibitor of SARS-CoV-2 endocytosis

Background and aim of the work: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current pandemics of coronavirus disease. This virus is able to attack the cells of the airway epithelium by binding to the transmembrane angiotensin I converting enzyme 2 (ACE2). We developed an oral spray that could inhibit the SARS-CoV-2 endocytosis. The spray contains hydroxytyrosol for its anti-viral, anti-inflammatory and anti-oxidant properties, and α-cyclodextrin for its ability to deplete sphingolipids, that form the lipid rafts where ACE2 localizes. The aim of the present pilot multi-centric open non-controlled observational study was to evaluate the safety profile of the “Endovir Stop” spray. Methods: An MTT test was performed to evaluate cytotoxicity of the spray in two human cell lines. An oxygen radical absorbance capacity assay was performed to evaluate the antioxidant capacity of the spray. The spray was also tested on 87 healthy subjects on a voluntary basis. Results: The MTT test revealed that the spray is not cytotoxic. The ORAC assay showed a good antioxidant capacity for the spray. Endovir Stop tested on healthy volunteers showed the total absence of side effects and drug interactions during the treatment. Conclusions: We demonstrated that Endovir Stop spray is safe. The next step would be the administration of the efficacy of the spray by testing it to a wider range of people and see whether there is a reduced infection rate of SARS-CoV-2 in the treated subjects than in the non-treated individuals. (www.actabiomedica.it)
Surgical resection of synchronous liver metastases in gastric cancer patients. A propensity score-matched study

Abstract Background The aim of the study was to determine the value of synchronous liver resection in patients with oligo-metastatic gastric cancer and the prognostic factors in these patients. Patients and methods We compared the results of 21 gastric patients with liver metastases and synchronous liver resection (LMR) to 21 propensity score-matched patients with gastric cancer and liver metastases in whom liver resection was not performed (LM0) and to a propensity score-matched control group of 21 patients without liver metastases and stage III and IV resectable gastric cancer (CG). Results The overall 5-year survival of LMR, LM0 and CG were 14.3%, 0%, and 19%, respectively (p = 0.002). Five-year survival was 47.5% for well-differentiated tumour compared to 0% in patients with moderate or poor tumour differentiation (p = 0.006). In addition, patients with R0 resection and TNM stage N0–1 had a significantly better survival compared to patients with TNM N stage N2–3 (5-year survival: 60% for N0–1 vs. 7.7% for N2–3; p = 0.007). Conclusions The results presented in the study support synchronous liver resections in gastric patients and provide additional criteria for patient selection.
Situation strength as a basis for interactions in psychological models.

One of the most important methods that psychological scientists use to understand behavior and cognition is theorizing. Increasingly, theorizing is used to support not only additive hypotheses, but also multiplicative ones. And yet, authors often struggle to provide adequate theoretical justifications for multiplicative hypotheses. In the late 1960s and early 1970s, W. Mischel averred that, in "strong" situations, behavior is relatively uniform regardless of one's personality characteristics. In "weak" situations, that is, those that lack clear behavioral expectations, behavior is not constrained by the situation and is free to covary with personality. This is the situational strength interaction, and although this reasoning has been applied to personality-behavior models, we show that it can be used to justify many interaction models in psychology more generally. In some cases, such reasoning may serve to bolster the more traditional interaction arguments. In other cases, it shows that the traditional interaction arguments must be incorrect. In this tutorial, we describe a generalized situation strength phenomenon, called the restricted variance interaction, that can be used to pinpoint the nature, direction, and even the magnitude of many interaction hypotheses in the psychological sciences. We illustrate the value and application of restricted variance reasoning using examples from the workplace mistreatment literature and then extrapolate to several other areas of psychology. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
Study of the Motivation of Spanish Amateur Runners Based on Training Patterns and Gender

The objectives of the present study are to analyze the different training patterns of the amateur runners, according to their gender, and to find out a correlation between the training pattern and the motivation. The sample was composed of 457 amateur runners. For the collection of data, a two-part questionnaire was used. The first part consisted of questions about sporting and healthy patterns and the second part consisted of the Perception of Success Questionnaire (POSQ), adapted to Spanish. The obtained results indicated that their motives for starting to practice running and to continue their involvement are health and fun. The training pattern is as follows: they practise one to three days per week, running from three to five hours overall plus additional stretching and high intensity training. They participated in less than one running event per month. Most of them did not belong to an athletic club, did not have a coach, were not federated and have more than four years’ experience of running. What concerns the gender differences, the men trained more than the women, and they did it with relatives and friends; women preferred to do it with friends or by themselves with the assistance of a coach. Age and running hours per week were the best variables to predict the task goal orientation, especially for men. For women, training hours per week predicted the goal orientation but to the ego. This finding could be especially helpful for coaches. A high number of training hours for men was linked with a task goal orientation, and on the other hand, for women it meant an ego goal orientation. The consequences of their behaviours were likely to be markedly different.
TaDrAp1 and TaDrAp2, Partner Genes of a Transcription Repressor, Coordinate Plant Development and Drought Tolerance in Spelt and Bread Wheat

Down-regulator associated protein, DrAp1, acts as a negative cofactor (NC2α) in a transcription repressor complex together with another subunit, down-regulator Dr1 (NC2β). In binding to promotors and regulating the initiation of transcription of various genes, DrAp1 plays a key role in plant transition to flowering and ultimately in seed production. TaDrAp1 and TaDrAp2 genes were identified, and their expression and genetic polymorphism were studied using bioinformatics, qPCR analyses, a 40K Single nucleotide polymorphism (SNP) microarray, and Amplifluor-like SNP genotyping in cultivars of bread wheat (Triticum aestivum L.) and breeding lines developed from a cross between spelt (T. spelta L.) and bread wheat. TaDrAp1 was highly expressed under non-stressed conditions, and at flowering, TaDrAp1 expression was negatively correlated with yield capacity. TaDrAp2 showed a consistently low level of mRNA production. Drought caused changes in the expression of both TaDrAp1 and TaDrAp2 genes in opposite directions, effectively increasing expression in lower yielding cultivars. The microarray 40K SNP assay and Amplifluor-like SNP marker, revealed clear scores and allele discriminations for TaDrAp1 and TaDrAp2 and TaRht-B1 genes. Alleles of two particular homeologs, TaDrAp1-B4 and TaDrAp2-B1, co-segregated with grain yield in nine selected breeding lines. This indicated an important regulatory role for both TaDrAp1 and TaDrAp2 genes in plant growth, ontogenesis, and drought tolerance in bread and spelt wheat.
Psychometric Assessment of the European Health Literacy Survey Questionnaire (HLS-EU-Q16) for Arabic/French-Speaking Migrants in Southern Europe

Improving health literacy (HL) is critical for addressing health inequalities. Low literacy rates are believed to be more prevalent in ethnic minorities, which may have an impact on people’s health. For measures to be implemented in this regard, HL must be evaluated to obtain specific indicators. Our aim, therefore, was to develop a version of the European Health Literacy Survey Questionnaire (HLS-EU-Q16), which is recommended to be used with vulnerable populations, suited to Arabic/French-speaking migrants who reside in south-eastern Spain, and to explore its psychometric properties for assessing health literacy in this population. A cross-sectional survey was carried out in a convenient sample of 205 migrants. The structural validity was calculated by a confirmatory factorial analysis (CFA), which suggested appropriate adjustment indicators, and which indicated that the three-dimensional model is adequately adjusted to the data obtained in the study. The coefficient omega showed high internal consistency in the three HL dimensions (health care, disease prevention, and health promotion). Concurrent validity presented a significant correlation with the Newest Vital Sign test (r = 0.390; p < 0.001). The multigroup CFA showed that the heterogeneity of the sample used was not a problem for establishing the structural validity of the scale. The Arabic/French version showed good construct validity.
Neural generators involved in visual cue processing in children with attention‐deficit/hyperactivity disorder (ADHD)

Event‐related potentials (ERP) studies report alterations in the ongoing visuo‐attentional processes in children with attention‐deficit/hyperactivity disorder (ADHD). We hypothesized that the neural generators progressively recruited after a cue stimulus imply executive‐related areas well before engagement in executive processing in children with ADHD compared to typically developed children (TDC). We computed source localization (swLORETA) of the ERP and ERSP evoked by the Cue stimulus during a visual Cue‐Go/Nogo paradigm in 15 ADHD compared to 16 TDC. A significant difference in N200/P200 amplitude over the right centro‐frontal regions was observed between ADHD and TDC, supported by a stronger contribution of the left visuo‐motor coordination area, premotor cortex, and prefrontal cortex in ADHD. In addition, we recorded a greater beta power spectrum in ADHD during the 80–230 ms interval, which was explained by increased activity in occipito‐parieto‐central areas and lower activity in the left supramarginal gyrus and prefrontal areas in ADHD. Successive analysis of the ERP generators (0–500 ms with successive periods of 50 ms) revealed significant differences beginning at 50 ms, with higher activity in the ventral anterior cingulate cortex, premotor cortex, and fusiform gyrus, and ending at 400–500 ms with higher activity of the dorsolateral prefrontal cortex and lower activity of the posterior cingulate cortex in ADHD compared to TDC. The areas contributing to ERP in ADHD and TDC differ from the early steps of visuo‐attentional processing and reveal an overinvestment of the executive networks interfering with the activity of the dorsal attention network in children with ADHD.