Miracle-dz/UniFAR-FTUs huggingface dataset:
Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

Crustaceans of the order Notostraca (Branchiopoda) are distributed worldwide and are known for the remarkable morphological stasis between their extant and Permian fossil species. Moreover, these crustaceans show relevant ecological traits and a wide range of reproductive strategies. However, genomic studies on notostracans are fairly limited. Here, we present the genome sequences of two notostracan taxa, Lepidurus arcticus and Lepidurus apus lubbocki. Taking advantage of the small genome sizes (~0.11 pg) of these taxa, genomes were sequenced for one individual per species with one run on the Illumina HiSeq X platform. We finally assembled 73.2 Mbp (L. arcticus) and 90.3 Mbp (L. apus lubbocki) long genomes. Assemblies cover up to 84% of the estimated genome size, with a gene completeness >97% for both genomes. In total, 13%–16% of the assembled genomes consist of repeats, and based on read mapping, L. apus lubbocki shows a significantly lower transposable element content than L. arcticus. The analysis of 2,376 orthologous genes indicates an ~7% divergence between the two Lepidurus taxa, with a nucleotide substitution rate significantly lower than that of Daphnia taxa. Ka/Ks analysis suggests purifying selection in both branchiopod lineages, raising the question of whether the low substitution rate of Lepidurus is correlated with morphological conservation or is linked to specific biological traits. Our analysis demonstrates that, in these organisms, it is possible to obtain high‐quality draft genomes from single individuals with a relatively low sequencing effort. This result makes Lepidurus and Notostraca interesting models for genomic studies at taxonomic, ecological and evolutionary levels.
The Anticancer Properties of Cordycepin and Their Underlying Mechanisms

Cordyceps is a genus of ascomycete fungi that has been used for traditional herbal remedies. It contains various bioactive ingredients including cordycepin. Cordycepin, also known as 3-deoxyadenosine, is a major compound and has been suggested to have anticancer potential. The treatment of various cancer cells with cordycepin in effectively induces cell death and retards their cancerous properties. However, the underlying mechanism is not fully understood. Recent evidence has shed light on the molecular pathways involving cysteine-aspartic proteases (caspases), mitogen-activated protein kinases (MAPKs), and glycogen synthase kinase 3 beta (GSK-3β). Furthermore, the pathways are mediated by putative receptors, such as adenosine receptors (ADORAs), death receptors (DRs), and the epidermal growth factor receptor (EGFR). This review provides the molecular mechanisms by which cordycepin functions as a singular or combinational anticancer therapeutic agent.
Differences in the toxicity of cerium dioxide nanomaterials after inhalation can be explained by lung deposition, animal species and nanoforms

Abstract Considerable differences in pulmonary responses have been observed in animals exposed to cerium dioxide nanoparticles via inhalation. These differences in pulmonary toxicity might be explained by differences in lung deposition, species susceptibility or physicochemical characteristics of the tested cerium dioxide nanoforms (i.e. same chemical substance, different size, shape, surface area or surface chemistry). In order to distinguish the relative importance of these different influencing factors, we performed a detailed analysis of the data from several inhalation studies with different exposure durations, species and nanoforms, namely published data on NM211 and NM212 (JRC repository), NanoAmor (commercially available) and our published and unpublished data on PROM (industry provided). Data were analyzed by comparing the observed pulmonary responses at similar external and internal dose levels. Our analyses confirm that rats are more sensitive to developing pulmonary inflammation compared to mice. The observed differences in responses do not result purely from differences in the delivered and retained doses (expressed in particle mass as well as surface area). In addition, the different nanoforms assessed showed differences in toxic potency likely due to differences in their physicochemical parameters. Primary particle and aggregate/agglomerate size distributions have a substantial impact on the deposited dose and consequently on the pulmonary response. However, in our evaluation size could not fully explain the difference observed in the analyzed studies indicating that the pulmonary response also depends on other physicochemical characteristics of the particles. It remains to be determined to what extent these findings can be generalized to other poorly soluble nanomaterials.
Improved generalization bounds for robust learning

We consider a model of robust learning in an adversarial environment. The learner gets uncorrupted training data with access to possible corruptions that may be affected by the adversary during testing. The learner's goal is to build a robust classifier that would be tested on future adversarial examples. We use a zero-sum game between the learner and the adversary as our game theoretic framework. The adversary is limited to $k$ possible corruptions for each input. Our model is closely related to the adversarial examples model of Schmidt et al. (2018); Madry et al. (2017). Our main results consist of generalization bounds for the binary and multi-class classification, as well as the real-valued case (regression). For the binary classification setting, we both tighten the generalization bound of Feige, Mansour, and Schapire (2015), and also are able to handle an infinite hypothesis class $H$. The sample complexity is improved from $O(\frac{1}{\epsilon^4}\log(\frac{|H|}{\delta}))$ to $O(\frac{1}{\epsilon^2}(k\log(k)VC(H)+\log\frac{1}{\delta}))$. Additionally, we extend the algorithm and generalization bound from the binary to the multiclass and real-valued cases. Along the way, we obtain results on fat-shattering dimension and Rademacher complexity of $k$-fold maxima over function classes; these may be of independent interest. For binary classification, the algorithm of Feige et al. (2015) uses a regret minimization algorithm and an ERM oracle as a blackbox; we adapt it for the multi-class and regression settings. The algorithm provides us with near-optimal policies for the players on a given training sample.
Effect of national HIV testing recommendations and local interventions on HIV testing practices in a Swiss university hospital: a retrospective analysis between 2012 and 2015

Objectives Despite HIV testing recommendations published by the Federal Office of Public Health (FOPH) since 2007, many individuals living with HIV are diagnosed late in Switzerland. The aim of this study is to examine the effect of the 2013 FOPH HIV testing recommendations on HIV testing rates. Setting Ten clinical services at Lausanne University Hospital, Lausanne, Switzerland. Participants Patients attending between 1 January 2012 and 31 December 2015. Design Retrospective analysis using two existing hospital databases. HIV testing rates calculated as the percentage of tests performed (from the Immunology Service database) per number of patients seen (from the central hospital database). Primary and secondary outcome measures The primary outcome was testing rate change following the 2013 FOPH testing recommendations, comparing testing rates 2 years before and 2 years after their publication. Secondary outcomes were demographic factors of patients tested or not tested for HIV. Results 147 884 patients were seen during the study period of whom 9653 (6.5%) were tested for HIV, with 34 new HIV diagnoses. Mean testing rate increased from 5.6% to 7.8% after the recommendations (p=0.001). Testing rate increases were most marked in services involved in clinical trials on HIV testing, whose staff had attended training seminars on testing indications and practice. Testing rates were lower among older (aged >50 years), female and Swiss patients compared with younger, male and non-Swiss patients, both globally (p=0.001) and in specific clinical services. Conclusions This simple two-database tool demonstrates clinical services in which HIV testing practice can be optimised. Improved testing rates in services involved in clinical trials on testing suggest that local engagement complements the effect of national recommendations. While, overall, HIV testing rates increased significantly over time, testing rates were lower among patients with similar demographic profiles to individuals diagnosed late in Switzerland.
Beyond diagnosis: the relevance of social interactions for participation in inclusive preschool settings

ABSTRACT Purpose: This study aims to explore the role of three specific factors within the child–environment interaction process – engagement, independence and social interactions – in influencing development and learning of children with disabilities in inclusive preschool settings. The main question is whether children can be categorised in homogenous groups based on engagement, independence and social interactions (proximal variables within a biopsychosocial framework of human development). The study also examined whether children with the same diagnosis would group together or separately, when trying to identify clusters of engagement, independence and social interactions, and additionally whether such clusters vary as a function of individual child characteristics, and/or as a function of structural and process characteristics of preschool environment. Methods: Data was taken from an intervention study conducted in mainstream preschools in Portugal. A person-centered cluster analysis was conducted to explore group membership of children with various diagnoses, based on their engagement, independence and social interaction profiles. Results: Results show that children clustered based on similarity of engagement, independence and social interaction patterns, rather than on diagnosis. Besides, it was found that quality of peer interaction was the only predictor of cluster membership. Conclusion: These findings support the argument that participation profiles may be more informative for intervention purposes than diagnostic categories, and that preschool process quality, namely peer interaction, is crucial for children’s participation.
Network analysis of symptoms in a Parkinson patient using experience sampling data: An n = 1 study

Around 50% of Parkinson's disease patients experience motor fluctuations after long‐term treatment with levodopa. These fluctuations may be accompanied by mood fluctuations. Routine cross‐sectional assessments cannot capture the extent of these motor and mood fluctuations and their possible associations. Experience sampling techniques that use frequently repeated measurements of symptoms over time are able to capture such fluctuations. Based on such data, longitudinal associations between symptoms can be studied using network analysis.
Elosulfase alfa for the treatment of mucopolysacchoridosis IVA

Mucopolysacchariodosis IVA is a lysosomal storage disorder characterized by deficiency of the enzyme N-acetylgalactosamine-6-sulfatase leading to accumulation of glycosaminoglycans. Mucopolysacchariodosis IVA affects many organs, especially the skeletal system. The disease is progressive, leads to serious cardiopulmonary problems and is severely debilitating. Enzyme replacement therapy with elosulfase alfa is the only approved treatment for this rare genetic condition. The results from a Phase III clinical trial demonstrated that elosulfase alfa at dose 2.0 mg/kg weekly given intravenously improved the walking distance in 6 min. The results of the 3-min stair climb test and respiratory function test did not show statistically significant improvement over the placebo. However, the composite end point analysis combining changes from baseline in walking distance in 6 min, 3-min stair climb test and respiratory function showed that at dose 2.0 mg/kg weekly, subjects performed better than the placebo, indicating that the effects of treatment are clinically meaningful. Serious side effects are uncommon and infusion-associated reactions are manageable.
Ergodic Capacity of Triple-Hop All-Optical Amplify-and-Forward Relaying over Free-Space Optical Channels

In this paper, we propose a comprehensive research over triple hop all-optical relaying free-space optical (FSO) systems in the presence of all main noise sources including background, thermal and amplified spontaneous emission (ASE) noise and by considering the effect of the optical degree-of- freedom (DoF). Using full CSI relaying, we derive the exact expressions for the noise variance at the destination. Then, in order to simplify the analytical expressions of full CSI relaying, we also propose and investigate the validity of different approximations over noise variance at the destination. Finally, we evaluate the the performance of considered triple-hop all-optical relaying FSO system in term of ergodic capacity.
Finding Solutions to Generative Adversarial Privacy

We present heuristics for solving the maximin problem induced by the generative adversarial privacy setting for linear and convolutional neural network (CNN) adversaries. In the linear adversary setting, we present a greedy algorithm for approximating the optimal solution for the privatizer, which performs better as the number of instances increases. We also provide an analysis of the algorithm to show that it not only removes the features most correlated with the private label first, but also preserves the prediction accuracy of public labels that are sufficiently independent of the features that are relevant to the private label. In the CNN adversary setting, we present a method of hiding selected information from the adversary while preserving the others through alternately optimizing the goals of the privatizer and the adversary using neural network backpropagation. We experimentally show that our method succeeds on a fixed adversary.
Tobacco Smoking and Psychotic-Like Experiences in a General Population Sample.

OBJECTIVE Recent findings suggest an association between tobacco and psychosis, but whether this association is mediated by confounding factors is unknown. Psychosis-like experiences (PLEs) are a subclinical expression of psychosis. To disentangle the association of tobacco with PLEs, we examined data from a large US population-based, nationally representative sample. METHODS Analysis was conducted on Wave 2 of the National Epidemiologic Survey of Alcohol and Related Conditions (N = 34,653 adults, conducted from 2004 to 2005). Participants were assessed with the Alcohol Use Disorder and Associated Disabilities Interview Schedule-IV. Twenty-two PLEs previously described as observed indicators of psychosis were used. Participants were stratified according to their smoking status (never/former/current) for 5 different types of tobacco. RESULTS There was a significant association (ie, with 95% CIs for which the lower value was ≥ 1) between smoking status and 14 of the 22 assessed PLEs. These associations remained significant after adjustment for sociodemographic variables (including urbanicity or ethnicity), lifetime drug use disorder, and past-year cannabis use. While 26.33% of nonsmokers reported at least 1 PLE, this prevalence was slightly higher in former smokers (27.48%) and rose as high as 39.09% in current smokers (for current smokers vs lifetime abstainers, adjusted OR = 1.33; 95% CI, 1.23-1.45). All 22 PLEs had higher prevalence in smokers than in former smokers or lifetime abstainers. A total of 8.56% of smokers reported at least 5 PLEs, compared to 3.42% in lifetime abstainers (aOR = 1.56; 95% CI, 1.32-1.84). CONCLUSIONS In a large population-based, nationally representative sample, smoking status was associated with various PLEs. This association was not explained only by other known risk factors of PLEs or schizophrenia. There is a need to identify the potential neurobiological mechanisms by which smoking and PLEs are associated, for patients and from a public health perspective.
Characterization of antimicrobial resistance mechanisms in carbapenem-resistant Pseudomonas aeruginosa carrying IMP variants recovered from a Mexican Hospital

Purpose Pseudomonas aeruginosa infections in hospitals constitute an important problem due to the increasing multidrug resistance (MDR) and carbapenems resistance. The knowledge of resistance mechanisms in Pseudomonas strains is an important issue for an adequate antimicrobial treatment. Therefore, the objective was to investigate other antimicrobial resistance mechanisms in MDR P. aeruginosa strains carrying blaIMP, make a partial plasmids characterization, and determine if modifications in oprD gene affect the expression of the OprD protein. Methodology Susceptibility testing was performed by Kirby Baüer and by Minimum Inhibitory Concentration (presence/absence of efflux pump inhibitor); molecular typing by Pulsed-field gel electrophoresis (PFGE), resistance genotyping and integrons by PCR and sequencing; OprD expression by Western blot; plasmid characterization by MOB Typing Technique, molecular size by PFGE-S1; and blaIMP location by Southern blot. Results Among the 59 studied P. aeruginosa isolates, 41 multidrug resistance and carbapenems resistance isolates were detected and classified in 38 different PFGE patterns. Thirteen strains carried blaIMP; 16 blaGES and four carried both genes. This study centered on the 17 strains har-boring blaIMP. New variants of β-lactamases were identified (blaGES-32, blaIMP-56, blaIMP-62) inside of new arrangements of class 1 integrons. The presence of blaIMP gene was detected in two plasmids in the same strain. The participation of the OprD protein and efflux pumps in the resistance to carbapenems and quinolones is shown. No expression of the porin OprD due to stop codon or IS in the gene was found. Conclusions This study shows the participation of different resistance mechanisms, which are reflected in the levels of MIC to carbapenems. This is the first report of the presence of three new variants of β-lactamases inside of new arrangements of class 1 integrons, as well as the presence of two plasmids carrying blaIMP in the same P. aeruginosa strain isolated in a Mexican hospital.
Gait Type Analysis Using Dynamic Bayesian Networks

This paper focuses on gait abnormality type identification—specifically, recognizing antalgic gait. Through experimentation, we demonstrate that detecting an individual’s gait type is a viable biometric that can be used along with other common biometrics for applications such as forensics. To classify gait, the gait data is represented by coordinates that reflect the body joint coordinates obtained using a Microsoft Kinect v2 system. Features such as cadence, stride length, and other various joint angles are extracted from the input data. Using approaches such as the dynamic Bayesian network, the obtained features are used to model as well as perform gait type classification. The proposed approach is compared with other classification techniques and experimental results reveal that it is capable of obtaining a 88.68% recognition rate. The results illustrate the potential of using a dynamic Bayesian network for gait abnormality classification.
Micronutrient Intake and Risk of Hematological Malignancies in Adults: A Systematic Review and Meta-analysis of Cohort Studies

Abstract There has been accumulating evidence that several micronutrients may play a protective role in the risk of solid cancers. However, their role in hematological malignancies remains to be elucidated; this meta-analysis aims to evaluate the associations between micronutrient intake as well as supplementation and risk of hematological cancer in adults. Eligible cohort studies (examining intake of vitamin A, vitamin C, vitamin D, vitamin E, lycopene, folate, iron, carotenoids, beta-carotene, selenium, pyridoxine) were sought in PubMed up to July 31, 2016. Random-effects models were used for the calculation of pooled relative risks (RR) with their 95% confidence intervals (CI). Twelve cohort studies were deemed eligible. Null associations were noted regarding supplemented vitamin A (pooled relative risk [RR] = 0.92, 95% confidence interval [CI]: 0.80–1.07), supplemented vitamin C (pooled RR = 1.00, 95%CI: 0.90–1.12), total vitamin D (pooled RR = 1.05, 95%CI: 0.91–1.20), supplemented vitamin E (pooled RR = 0.98, 95%CI: 0.88–1.10), and dietary lycopene intake (pooled RR = 1.00, 95%CI: 0.86–1.16) and the risk of non-Hodgkin lymphoma. No summary estimates are provided for other hematological malignancies due to the limited number of studies. Future prospective trials should be conducted for a better understanding of this field; especially regarding Hodgkin lymphoma, leukemia and plasma cell neoplasms, on which data are scarce.
Anti-inflammatory effects of Kaempferol on Helicobacter pylori-induced inflammation

ABSTRACT Inflammation induced by Helicobacter pylori infection related to gastric carcinogenesis. In this study, we have investigated the anti-inflammatory effect and its mechanism of kaempferol in the inflammatory response caused by H. pylori infection in vitro. We found that kaempferol reduced the expression of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-8) and production of IL-8 in AGS cells. In addition, kaempferol suppressed translocation of cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA) of H. pylori to AGS cells. It was due to decreased transcription of type IV secretion system (T4SS) components involved in CagA injection and secretion system subunit protein A (SecA) of type V secretion system (T5SS) involved in VacA secretion by kaempferol. In conclusion, kaempferol shows the anti-inflammatory effect by suppressing the translocation of CagA and VacA proteins and leading to the down-regulation of pro-inflammatory cytokines. Abbreviations: CagA: cytotoxin-associated gene A; VacA: vacuolating cytotoxin A; T4SS: type IV secretion systems; SecA: secretion system subunit protein A; T5SS: type V secretion system; Graphical Abstract Kaempferol has an anti-inflammatory effect on H. pylori infection by suppressing the translocation of CagA and VacA proteins.
Women’s knowledge about risk factors of breast cancer in a Brazilian community

ABSTRACT Knowledge about risk factors for breast cancer was identified as an important variable that affects women’s avoidance behavior and their screening performance. The present study assessed women’s knowledge about risk factors and associated socio-economic variables. Data from 417 women aged 20–86 years were obtained in Caicó, Rio Grande do Norte, Brazil. In agreement with the recognition of 26 potential risk factors and prevention behaviors, two groups with good (N = 203) and poor (N = 214) knowledge were formed, respectively. Having a close relative with cancer remained the unique significant variable in the adjusted model. Women without any close relative with cancer, were 1.54 (95% confidence interval [CI] 1.036–2.288) times as likely to have poor knowledge, compared to women who had a close relative with cancer (p = 0.033). Other socio-economic variables, including income, employment status and educational level had no significant association with knowledge (p = 0.450, p = 0.914, p = 0.639, respectively). Of 417 women, 302 (72.42%), 339 (81.29%), and 309 (74.10%), respectively, did not identify “physical inactivity,” “overweight after menopause,” and “no breastfeeding of children” as risk factors. Knowledge could help to avoid risk factors and motivate prevention behavior. Information about risk factors should be disseminated in health campaigns.