Miracle-dz/UniFAR-FTUs huggingface dataset:
GII.4 norovirus recombinant causes gastroenteritis epidemic in Eastern Australia, winter 2017

In Victoria, Australia, 160 gastroenteritis outbreaks were norovirus positive for the period January‐September 2017. A distinctive peak in norovirus outbreaks was seen May‐August, with 118 positive outbreaks occurring in the peak period. The peak was primarily due to the emergence of a GII. P4_NewOrleans_2009/GII. 4_Sydney_2012 recombinant that had genetically changed sufficiently to escape herd immunity. This recombinant was also identified elsewhere in Australia, with highly similar sequences identified in Queensland during the same time period. The recombinant GII. P4_NewOrleans_2009/GII. 4_Sydney_2012 has not been reported to cause norovirus epidemics outside Australia, suggesting regional factors play a role in determining norovirus genotype incidence.
Stage-specific IFN-induced and IFN gene expression reveal convergence of type I and type II IFN and highlight their role in both acute and chronic stage of pathogenic SIV infection

Interferons (IFNs) play a major role in controlling viral infections including HIV/SIV infections. Persistent up-regulation of interferon stimulated genes (ISGs) is associated with chronic immune activation and progression in SIV/HIV infections, but the respective contribution of different IFNs is unclear. We analyzed the expression of IFN genes and ISGs in tissues of SIV infected macaques to understand the respective roles of type I and type II IFNs. Both IFN types were induced in lymph nodes during early stage of primary infection and to some extent in rectal biopsies but not in PBMCs. Induction of Type II IFN expression persisted during the chronic phase, in contrast to undetectable induction of type I IFN expression. Global gene expression analysis with a major focus on ISGs revealed that at both acute and chronic infection phases most differentially expressed ISGs were inducible by both type I and type II IFNs and displayed the highest increases, indicating strong convergence and synergy between type I and type II IFNs. The analysis of functional signatures of ISG expression revealed temporal changes in IFN expression patterns identifying phase-specific ISGs. These results suggest that IFN-γ strongly contribute to shape ISG upregulation in addition to type I IFN.
Communication Avoiding Gaussian elimination

We present CALU, a Communication Avoiding algorithm for the LU factorization of dense matrices distributed in a two-dimensional cyclic layout. The algorithm is based on a new pivoting strategy, which is stable in practice. The new algorithm is optimal (up to polylogarithmic factors) in the amount of communication it performs. Our experiments show that CALU leads to a reduction in the parallel time, in particular when the latency time is an important factor of the overall time. The factorization of a block-column, a subroutine of CALU, outperforms the corresponding routine PDGETF2 from ScaLAPACK up to a factor of 4.37 on an IBM POWER 5 system and up to a factor of 5.58 on a Cray XT4 system. On square matrices of order 104, CALU outperforms the corresponding routine PDGETRF from ScaLAPACK by a factor of 1.24 on IBM POWER 5 and by a factor of 1.31 on Cray XT4.
“It’s natural and healthy, but I don’t want to see it”: Using Entertainment-Education to Improve Attitudes Toward Breastfeeding in Public

ABSTRACT While it has been well established that breastfeeding provides the best nourishment for children, few women achieve the recommended breastfeeding duration. Negative media messages have been identified as one explanation for the lack of individual and public support for breastfeeding. This study explored the influence of media on the knowledge and attitudes of a nearly childless population to ascertain if and how entertainment media can positively impact perceptions of breastfeeding. Using cultivation and parasocial interaction, this research measured entertainment television’s effect on breastfeeding attitudes using randomized-group experiments involving 375 students. Overall, participants generally held positive attitudes but were uncomfortable seeing breastfeeding. Moreover, results indicate that viewing a prime-time television clip that depicted public breastfeeding not only significantly lessened the extent to which participants believed that breastfeeding was a private activity but also improved attitudes and support for breastfeeding in public. This study concludes that more pro-breastfeeding media messages in entertainment media could help create a climate conducive to breastfeeding success.
Outcome of Subclassification of Indeterminate (Thy-3) Thyroid Cytology into Thy-3a and Thy-3f

Objectives: The British Thy system is a widely used classification system for reporting thyroid fine-needle aspiration (FNA) cytology. The Royal College of Pathologists in 2009 recommended the subdivision of the Thy-3 (indeterminate) category into Thy-3a (atypia) and Thy-3f (follicular neoplasm). Our objective was to examine the malignancy rates of Thy-3a and Thy-3f cases at our institution and to investigate whether the risk of malignancy in Thy-3a cases is reduced by FNA on a different occasion showing benign cytology. Methods: This is a retrospective study of 748 thyroid nodules undergoing 1,032 FNAs, with indeterminate (Thy-3) cytology subdivided into Thy-3a and Thy-3f. Cases were correlated with final histology in surgical cases. Incidental carcinomas occurring outside the biopsied nodule were discounted. Results: A total of 109 nodules had a final cytological diagnosis of Thy-3a, of which 67 underwent surgery, with an incidence of malignancy of 13.4% (9/67); 90 nodules had a final cytological diagnosis of Thy-3f, of which 84 underwent surgery, with an incidence of malignancy of 17.9% (15/84). The difference in malignancy rates was not significant (p = 0.51). The incidence of malignancy in nodules with benign and Thy-3a cytology on separate occasions was not significantly different from cases with a single Thy-3a cytology. Conclusions: Thyroid nodules with Thy-3a cytology have a slightly lower risk of malignancy than Thy-3f cases. However, the difference is not significant and does not appear to be reduced by FNA on a separate occasion showing benign cytology. Management decisions for patients with Thy-3a cytology should be taken carefully to avoid missing cancers.
WIBECAM: Device Free Human Activity Recognition Through WiFi Beacon-Enabled Camera

This paper presents WIBECAM, a Human Activity Recognition system which does not require neither user instrumentation, nor specialized infrastructure, nor active operation - it passively leverages Beacon frames periodically emitted by a single off-the-shelf Wi-Fi access point. As many other recent proposals, WIBECAM also exploits the different multipath conditions (and their temporal variations) induced by human activity. In most of the previously proposed systems, the classification is based on the characterization of the signal strength variations, caused by the human activity. WIBECAM's main distinguishing aspect is that it 'watches' the channel in the frequency domain where spectral metrics, calculated on the raw signal samples of the received Beacon frames, are like 'snapshots' of the channel taken in a regular and periodical way. The classification process uses properly selected features that measure the changes of consecutive 'snapshots'. WIBECAM adapts to any Wi-Fi access point (and may comply even with legacy 802.11b-only ones), as it does not exploit neither OFDM and CSI extracted from the receiver, nor MIMO/multiple antennas. WIBECAM has been built into USRP software radios. Its classification accuracy has been preliminarily assessed for four different activities in two different environments; the resulting confusion matrices show very promising performance.
Description of the male of Coronatella paulinae (Crustacea, Branchiopoda, Chydoridae) with an identification key for the genus based on the male morphology

Cladoceran males are not very frequent in natural populations, since they are only produced in stress situations. Thus, only a few species have had the male morphology described. Nevertheless, whenever data concerning the morphology of males is available, they are used as a tool to resolve taxonomic problems. In this study, the morphology of Coronatella paulinae Sousa, Elmoor-Loureiro and Santos, 2015 (Cladocera: Chydoridae) was described and compared to other species within the genus. Coronatella paulinae shares the diagnostic morphological traits typically attributed to the genus: (1) gonopores opening ventrally, subapically to the postabdominal claw; (2) marginal setulae arranged in groups on the postanal margin; (3) Inner Distal Lobe (IDL) armed with three setae, of which one is the male seta. The absence of lateral aesthetascs on male antennules might also be an important diagnostic character for the genus, since they are present in other Aloninae groups. Coronatella paulinae males present a unique combination of morphological traits on the postabdomen, which distinguish them from other Coronatella Dybowsky and Grochowski, 1894 species, such as a marked postanal angle and an almost straight basal spine, longer than the mid-length of the postabdominal claw.
Nutrition knowledge, outcome expectations, self-efficacy, and eating behaviors by calcium intake level in Korean female college students

BACKGROUND/OBJECTIVES Calcium is important but deficient in diets of young adult women. This study aimed to examine if cognitive factors and eating behaviors differ according to calcium intake based on the Social Cognitive Theory. SUBJECTS/METHODS Subjects were female college students in Seoul, Korea. Three hundred students completed the questionnaire regarding calcium intake, nutrition knowledge, outcome expectations, self-efficacy and eating behaviors. Data on 240 students were analyzed using t-test or χ2-test. Subjects were categorized into two groups, high calcium intake (HC, ≥ 650 mg/day) and low calcium intake (LC, < 650 mg/day), according to recommended intakes of calcium for women aged 19-29 years. RESULTS The LC group constituted 77.9% of total subjects. Nutrition knowledge was not different according to calcium intake. Three out of 12 outcome expectations items were significantly different between the HC and LC groups. Subjects in the HC group agreed more strongly with the practical benefits of consuming calcium-rich foods, including 'taste' (P < 0.01) and 'going well with other snacks' (P < 0.05), compared to those in the LC group. Negative expectations of 'indigestion' were stronger in the LC group than HC group (P < 0.001). Among self-efficacy items, perceived ability of 'eating dairy foods for snacks' (P < 0.001), 'eating dairy foods every day' (P < 0.01), and 'eating calcium-rich side dishes at meals' (P < 0.05) differed significantly between the HC and LC groups. Eating behaviors including more frequent consumption of dairy foods, fruits or fruit juice (P < 0.001), anchovy, seaweeds, green vegetables, protein-rich foods (P < 0.05), and less frequent consumption of sweets or soft drinks (P < 0.01) were significantly related to calcium intake. CONCLUSIONS This study found that outcome expectations, self-efficacy in consuming calcium-rich foods, and eating behaviors are important in explaining calcium intake. Nutrition education needs to address practical benefits, reduce negative expectations of calcium-rich foods, increase self-efficacy, and modify eating behaviors contributing to calcium intake.
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

Understanding the aspects of the cell functionality that account for disease or drug action mechanisms is a main challenge for precision medicine. Here we propose a new method that models cell signaling using biological knowledge on signal transduction. The method recodes individual gene expression values (and/or gene mutations) into accurate measurements of changes in the activity of signaling circuits, which ultimately constitute high-throughput estimations of cell functionalities caused by gene activity within the pathway. Moreover, such estimations can be obtained either at cohort-level, in case/control comparisons, or personalized for individual patients. The accuracy of the method is demonstrated in an extensive analysis involving 5640 patients from 12 different cancer types. Circuit activity measurements not only have a high diagnostic value but also can be related to relevant disease outcomes such as survival, and can be used to assess therapeutic interventions.
Retinoic acid signaling promotes the cytoskeletal rearrangement of embryonic epicardial cells

All‐trans‐retinoic acid (RA), a vitamin A metabolite, is an important signaling molecule required for the proper development of the heart. The epicardium is the main source of RA in the embryonic heart, yet the car‐diogenic functions of epicardial‐produced RA are not fully understood. Here, we investigated the roles of RA signaling in the embryonic epicardium using in vivo and in vitro models of excess or deficiency of RA. Our results suggested that RA signaling facilitates the cytoskeletal rearrangement required for the epicardial‐to‐mesenchymal transition of epicardial cells. In vivo treatment with an inhibitor of RA synthesis delayed the migration of epicardial‐derived precursor cells (EPDCs) into the myocardium; the opposite was seen in the case of dehydrogenase/reductase superfamily (DHRS)3‐deficient embryos, a mouse model of RA excess. Analysis of the behavior of epicardial cells exposed to RA receptor agonists or inhibitors of RA synthesis in vitro revealed that appropriate levels of RA are important in orchestrating the platelet‐derived growth factor‐induced loss of epithelial character, cytoskeletal remodeling, and migration, necessary for the infiltration of the myocardium by EPDCs. To understand the molecular mechanisms by which RA regulates epicardial cytoskeletal rearrangement, we used a whole transcriptome profiling approach, which in combination with pull‐down and inhibition assays, demonstrated that the Ras homolog gene family, member A (RhoA) pathway is required for the morphologic changes induced by RA in epi‐cardial cells. Collectively, these data demonstrate that RA regulates the cytoskeletal rearrangement of epicardial cells via a signaling cascade that involves the RhoA pathway. —Wang, S. , Yu, J., Jones, J. W. , Pierzchalski, K. , Kane, M. A. , Trainor, P. A. , Xavier‐Neto, J., Moise, A. R. Retinoic acid signaling promotes the cytoskeletal rearrangement of embryonic epicardial cells. FASEB J. 32, 3765–3781 (2018). www.fasebj. org
Control of phytoplankton growth by iron supply and irradiance in the subantarctic Southern Ocean: Experimental results from the SAZ Project

The influence of irradiance and iron (Fe) supply on phytoplankton processes was investigated, north (47S, 142E) and south (54S, 142E) of the Subantarctic Front in austral autumn (March 1998). At both sites, resident cells exhibited nutrient stress (Fv/ Fm 0.3). Shipboard perturbation experiments examined two light (mean in situ and elevated) and two Fe (nominally 0.5 and 3 nM) treatments under silicic acid-replete conditions. Mean in situ light levels (derived from incident irradiances, mixed layer depths (MLDs), wind stress, and a published vertical mixing model) differed at the two sites, 25% of incident irradiance I 0 at 47S and 9% I 0 at 54S because of MLDs of 40 (47S) and 90 m (54S), when these stations were occupied. The greater MLD at 54S is reflected by tenfold higher cellular chlorophyll a levels in the resident phytoplankton. In the 47S experiment, chlorophyll a levels increased to 1 gL 1 only in the high-Fe treatments, regardless of irradiance levels, suggesting Fe limitation. This trend was also noted for cell abundances, silica production, and carbon fixation rates. In contrast, in the 54S experiment there were increases in chlorophyll a (to 2 gL 1 ), cell abundances, silica production, and carbon fixation only in the high-light treatments to which Fe had been added, suggesting that Fe and irradiance limit algal growth rates. Irradiance by altering algal Fe quotas is a key determinant of algal growth rate at 54S (when silicic acid levels are nonlimiting); however, because of the integral nature of Fe/light colimitation and the restricted nature of the current data set, it was not possible to ascertain the relative contributions of Fe and irradiance to the control of phytoplankton growth. On the basis of a climatology of summer mean MLD for subantarctic (SA) waters south of Australia the 47 and 54S sites appear to represent minimum and maximum MLDs, where Fe and Fe/ irradiance, respectively, may limit/colimit algal growth. The implications for changes in the factors limiting algal growth with season in SA waters are discussed.
Spiritual Criminology: The Case of Jewish Criminology

Throughout the ages and in most cultures, spiritual and religious thinking have dealt extensively with offending (person against person and person against the Divine), the response to offending, and rehabilitation of offenders. Although modern criminology has generally overlooked that body of knowledge and experience, the study of spirituality and its relation to criminology is currently growing. Frequently, though, it is conducted from the secular scientific perspective, thus reducing spiritual knowledge into what is already known. Our aim here is to present a complementary perspective; that is, spiritual criminology that emerges from the spiritual perspective. Following a description of the state-of-the-art in criminological research concerning spirituality and its impact upon individuals, we focus on Jewish criminology as an illustrative case study, and present a spiritual Jewish view on good and evil, including factors that lead to criminality, the issue of free choice, the aim of punishment and societal response, crime desistance, rehabilitation, and prevention. The proposed establishment of spiritual criminology can be further developed by including parallel schools of spirituality, to create an integrated field in criminology.
An intelligent guide for virtual environments

In T. H. White's famous retelli ng of the Arthurian legend, the aged wizard Merlyn is tutor to the young boy Wart, who will grow up to be King Arthur. Through his magic, Merlyn changes Wart into different creatures and transports him to alien environments so he can learn about worlds other than his own. In this paper, we introduce Merlyn as an autonomous intelli gent agent, whose purpose is to be a guide and companion to children in their explorations of virtual worlds. Merlyn has an integrated personality and variable moods, so he will be a companion rather than a tool for the child's use. We discuss how Merlyn operates in “annotated environments,” where the perceived world is reflected in data structures directly accessible to a broad variety of agents. Merlyn becomes more knowledgeable about such worlds as he travels with the child, and he can use these annotations to guide his choice of interactions. Annotations also allow Merlyn to “endow” the child with environment-specific capabiliti es to guide the child's experiential learning. Merlyn is also capable of monitoring the child's interests and abiliti es, and tailoring his personality and actions to them. With Merlyn as a companion, a child can be guided into strategically-chosen learning activities while having a friendly, entertaining experience in the virtual environment.
A comprehensive investigation of sperm DNA damage and oxidative stress injury in infertile patients with subclinical, normozoospermic, and astheno/oligozoospermic clinical varicocoele

One of the main pathogeneses of varicocoele and infertility is oxidative stress (OS), nevertheless, the oxidative damaged DNA in infertile patients with varicocoele remains poorly clarified. The objective of this study was to comprehensively investigate whether sperm DNA damage and OS injury were related with different issues of varicocoele. According to the varicocoele practice guidelines, surgical treatment was not indicated in the infertile patients with subclinical (SubVc, n = 15) and normozoospermic clinical varicocoele (NCVc, n = 22), the infertile astheno/oligozoospermic patients with clinical varicocoele (AOCVc, n = 51) would receive microsurgerical varicocoelectomy. Normozoospermic healthy donors with proven fertility (n = 25) were recruited as controls. Thiobarbituric acid and sperm chromatin structure assay (SCSA) methods were preformed to analyze seminal lipid peroxidation product malondialdehyde (MDA) and sperm DNA fragmentation index (DFI). We found that AOCVc and NCVc, except SubVc, could significantly elevate sperm DFI and seminal MDA levels. Varicocoelectomy could substantially improve semen parameters, and reduce sperm DFI and seminal MDA levels in the AOCVc patients. However, the non‐operative NCVc patients would possibly suffer a severe deterioration of semen parameters accompanied by aberrantly higher levels of sperm DFI and seminal MDA, whereas no differences occurred in the non‐operative SubVc patients. Sperm DFI level in the pregnant group was much lower compared to the non‐pregnant group (AOCVc, p < 0.01; NCVc, p < 0.05) with the best cutoff value of 19.73%, while no differences in seminal MDA (p > 0.05) could be observed. Finally, a strong positive correlation was found between sperm DFI and seminal MDA (Rs = 0.504, p < 0.01), and they were also closely correlated with crucial semen parameters except normal morphology. Therefore, sperm DNA damage in clinical varicocoele, but not in SubVc, might be associated with the role of seminal reactive oxygen species (ROS) in mediating such damage. Varicocoelectomy could be beneficial for reducing OS injury and sperm DFI, and males with low sperm fragmented‐DNA level had more opportunities to become pregnant.
Immunology of Chronic Obstructive Pulmonary Disease and Sulfur Mustard Induced Airway Injuries: Implications for Immunotherapeutic Interventions.

BACKGROUND Sulfur mustard (SM)-induced airway injuries and chronic obstructive pulmonary disease (COPD) are characterized by chronic inflammation of the respiratory tract and share some similarities regarding the cellular and molecular mechanisms orchestrating airway destruction. Since available data regarding the immunobiology of COPD is much more known compared with SM-mediated injuries, and considering the similarities in the immunopathogenesis of these diseases, comparison of the immunopathogenesis of COPD and SM-induced respiratory complications can help designing new therapeutic approaches for treatment of SM-induced injuries. METHODS A multi-database search was performed to identify articles dealing with the role of immune system function in the pathogenesis of COPD and mustard mustard-induced respiratory complications. RESULTS This review outlines the role of different components of the immune system in the pathogenesis of COPD and mustard-induced respiratory complications, and suggests therapeutic implication for improving the management of the latter condition as the most common chronic complication of sulfur mustard exposure. CONCLUSION Although COPD and mustard lung are overlapping phenotypes and have shared pathophysiologic features, there are certain differences between these two diseases that necessitate further scrutiny. Combination therapies to counterbalance inflammation, oxidative stress and immune imbalance hold promise for the management of SM-induced respiratory complications but the success of such combined treatments need to be confirmed in proof-ofconcept trials.