bluuebunny/crossref_metadata_2025 huggingface dataset:
Linear optical responses beyond the electric dipole approximation on reflection and transmission: a perturbation treatment
Authors: Zhu X. D.
Published: February 2021

There exist in a material a wide range of linear optical responses to external electromagnetic fields beyond the electric dipole process. These responses reveal more detailed information on properties of the material through their corrections to the zeroth-order dielectric tensor. These corrections introduce small yet distinguishable modifications to reflection and transmission. I here describe a perturbation method for computing these modifications. The method simplifies the computation of optical reflection and transmission that include first-order contributions from processes such as magneto-optic effects, electro-optic effects, surface and ultrathin films, electric quadrupole effects, photoelastic effects, and effects of meta-materials.
Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells
Authors: Parkhitko Andrey A. , Singh Arashdeep , Hsieh Sharon , Hu Yanhui , Binari Richard , Lord Christopher J. , Hannenhalli Sridhar , Ryan Colm J. , Perrimon Norbert
Published: February 2021

TheRB1tumor suppressor is recurrently mutated in a variety of cancers including retinoblastomas, small cell lung cancers, triple-negative breast cancers, prostate cancers, and osteosarcomas. Finding new synthetic lethal (SL) interactions withRB1could lead to new approaches to treating cancers with inactivatedRB1. We identified 95 SL partners ofRB1based on aDrosophilascreen for genetic modifiers of the eye phenotype caused by defects in theRB1ortholog,Rbf1. We validated 38 mammalian orthologs ofRbf1modifiers as RB1 SL partners in human cancer cell lines with defectiveRB1alleles. We further show that for many of theRB1SL genes validated in human cancer cell lines, low activity of the SL gene in human tumors, when concurrent with low levels ofRB1was associated with improved patient survival. We investigated higher order combinatorial gene interactions by creating a novelDrosophilacancer model with co-occurringRbf1,PtenandRasmutations, and found that targeting RB1 SL genes in this background suppressed the dramatic tumor growth and rescued fly survival whilst having minimal effects on wild-type cells. Finally, we found that drugs targeting the identified RB1 interacting genes/pathways, such as UNC3230, PYR-41, TAK-243, isoginkgetin, madrasin, and celastrol also elicit SL in human cancer cell lines. In summary, we identified several high confidence, evolutionarily conserved, novel targets forRB1-deficient cells that may be further adapted for the treatment of human cancer.
Insecticide resistance and genetic structure of Aedes aegypti populations from Rio de Janeiro State, Brazil
Authors: Rahman Rafi Ur , Cosme Luciano Veiga , Costa Monique Melo , Carrara Luana , Lima José Bento Pereira , Martins Ademir Jesus
Published: February 2021

Vector control largely relies on neurotoxic chemicals, and insecticide resistance (IR) directly threatens their effectiveness. In some cases, specific alleles cause IR, and knowledge of the genetic diversity and gene flow among mosquito populations is crucial to track their arrival, rise, and spread. Here we evaluatedAedes aegyptipopulations’ susceptibility status, collected in 2016 from six different municipalities of Rio de Janeiro state (RJ), to temephos, pyriproxyfen, malathion, and deltamethrin. We collected eggs ofAe.aegyptiin Campos dos Goytacazes (Cgy), Itaperuna (Ipn), Iguaba Grande (Igg), Itaboraí (Ibr), Mangaratiba (Mgr), and Vassouras (Vsr). We followed the World Health Organization (WHO) guidelines and investigated the degree of susceptibility/resistance of mosquitoes to these insecticides. We used the Rockefeller strain as a susceptible positive control. We genotyped the V1016I and F1534C knockdown resistance (kdr) alleles using qPCR TaqMan SNP genotyping assay. Besides, with the use ofAe.aegyptiSNP-chip, we performed genomic population analyses by genotyping more than 15,000 biallelic SNPs in mosquitoes from each population. We added previous data from populations from other countries to evaluate the ancestry of RJ populations.

All RJAe.aegyptipopulations were susceptible to pyriproxyfen and malathion and highly resistant to deltamethrin. The resistance ratios for temephos was below 3,0 in Cgy, Ibr, and Igg populations, representing the lowest rates since IR monitoring started in this Brazilian region. We found thekdralleles in high frequencies in all populations, partially justifying the observed resistance to pyrethroid. Population genetics analysis showed thatAe.aegyptirevealed potential higher migration among some RJ localities and low genetic structure for most of them. Future population genetic studies, together with IR data inAe aegyption a broader scale, can help us predict the gene flow within and among the Brazilian States, allowing us to track the dynamics of arrival and changes in the frequency of IR alleles, and providing critical information to improving vector control program.
Ulcerative skin lesions among children in Cameroon: It is not always Yaws
Authors: Ndzomo Ngono Jean-Philippe , Tchatchouang Serges , Noah Tsanga Mireille Victorine , Njih Tabah Earnest , Tchualeu Albert , Asiedu Kingsley , Giacani Lorenzo , Eyangoh Sara , Crucitti Tania
Published: February 2021

Outbreaks of yaws-like ulcerative skin lesions in children are frequently reported in tropical and sub-tropical countries. The origin of these lesions might be primarily traumatic or infectious; in the latter case, Treponema pallidum subspecies pertenue, the yaws agent, and Haemophilus ducreyi, the agent of chancroid, are two of the pathogens commonly associated with the aetiology of skin ulcers. In this work, we investigated the presence of T. p. pertenue and H. ducreyi DNA in skin ulcers in children living in yaws-endemic regions in Cameroon.

Skin lesion swabs were collected from children presenting with yaws-suspected skin lesions during three outbreaks, two of which occurred in 2017 and one in 2019. DNA extracted from the swabs was used to amplify three target genes: the human β2-microglobulin gene to confirm proper sample collection and DNA extraction, the polA gene, highly conserved among all subspecies of T. pallidum, and the hddA gene of H. ducreyi. A fourth target, the tprL gene was used to differentiate T. p. pertenue from the other agents of human treponematoses in polA-positive samples. A total of 112 samples were analysed in this study. One sample, negative for β2-microglobulin, was excluded from further analysis. T. p. pertenue was only detected in the samples collected during the first 2017 outbreak (12/74, 16.2%). In contrast, H. ducreyi DNA could be amplified from samples from all three outbreaks (outbreak 1: 27/74, 36.5%; outbreak 2: 17/24, 70.8%; outbreak 3: 11/13, 84.6%). Our results show that H. ducreyi was more frequently associated to skin lesions in the examined children than T. p. pertenue, but also that yaws is still present in Cameroon. These findings strongly advocate for a continuous effort to determine the aetiology of ulcerative skin lesions during these recurring outbreaks, and to inform the planned mass treatment campaigns to eliminate yaws in Cameroon.
Modeling vehicle ownership with machine learning techniques in the Greater Tamale Area, Ghana
Authors: Abdul Muhsin Zambang Mohammed , Jiang Haobin , Wahab Lukuman
Published: February 2021

Vehicle ownership modeling and prediction is a crucial task in the transportation planning processes which, traditionally, uses statistical models in the modeling process. However, with the advancement in computing power of computers and Artificial Intelligence, Machine Learning (ML) algorithms are becoming an alternative or a complement to the statistical models in modeling the transportation planning processes. Although the application of ML algorithms to the transportation planning processes—like mode choice, and traffic forecasting and demand modeling—have received much attention in research and abound in literature, scanty attention is paid to its application to vehicle ownership modeling especially in the context of small to medium cities in developing countries. Therefore, this study attempts to fill this gap by modeling vehicle ownership in the Greater Tamale Area (GTA), a typically small to medium city in Ghana. Using a cross sectional survey of formal sectors workers, data was collected between June–August 2018. The study applied nine different ML classification algorithms to the dataset using 10-fold cross-validation technique/s and the Cohen-Kappa static/statistic to evaluate the predictive performance of each of the algorithms, and the Permutation Feature Importance to examine the features that contribute significantly to the prediction of vehicle ownership in GTA. The results showed that Linear Support Vector Classification (LinearSVC) classifier performed well in comparison with the other classifiers with regards to the overall predictive ability of the classifiers. In terms of class predictions, K- Nearest Neighbors (KNN) classifier performs well for no-vehicle class whiles Linear Support Vector Classification (LinearSVC) and GaussianNB classifiers performs well for motorcycle ownership. LinearSVC and Logistic Regression classifiers performed well on the car ownership class. Also, the results indicated that travel mode choice, average monthly income, average travel distance to workplace, average monthly expenditure on transport, duration of travel to workplace, occupational rank, age, household size and marital status were significant in predicting vehicle ownership for most of the classifiers. These findings could help policies makers carve out strategies that would reduce vehicle ownership but improve personal mobility.
HDSI: High dimensional selection with interactions algorithm on feature selection and testing
Authors: Jain Rahi , Xu Wei
Published: February 2021

Feature selection on high dimensional data along with the interaction effects is a critical challenge for classical statistical learning techniques. Existing feature selection algorithms such as random LASSO leverages LASSO capability to handle high dimensional data. However, the technique has two main limitations, namely the inability to consider interaction terms and the lack of a statistical test for determining the significance of selected features. This study proposes a High Dimensional Selection with Interactions (HDSI) algorithm, a new feature selection method, which can handle high-dimensional data, incorporate interaction terms, provide the statistical inferences of selected features and leverage the capability of existing classical statistical techniques. The method allows the application of any statistical technique like LASSO and subset selection on multiple bootstrapped samples; each contains randomly selected features. Each bootstrap data incorporates interaction terms for the randomly sampled features. The selected features from each model are pooled and their statistical significance is determined. The selected statistically significant features are used as the final output of the approach, whose final coefficients are estimated using appropriate statistical techniques. The performance of HDSI is evaluated using both simulated data and real studies. In general, HDSI outperforms the commonly used algorithms such as LASSO, subset selection, adaptive LASSO, random LASSO and group LASSO.
The prognostic value of comorbidity for the severity of COVID-19: A systematic review and meta-analysis study
Authors: Fathi Mobina , Vakili Kimia , Sayehmiri Fatemeh , Mohamadkhani Ashraf , Hajiesmaeili Mohammadreza , Rezaei-Tavirani Mostafa , Eilami Owrang
Published: February 2021

Background and objectives

With the increase in the number of COVID-19 infections, the global health apparatus is facing insufficient resources. The main objective of the current study is to provide additional data regarding the clinical characteristics of the patients diagnosed with COVID-19, and in particular to analyze the factors associated with disease severity, lack of improvement, and mortality.

Methods

102 studies were included in the present meta-analysis, all of which were published before September 24, 2020. The studies were found by searching a number of databases, including Scopus, MEDLINE, Web of Science, and Embase. We performed a thorough search from early February until September 24. The selected papers were evaluated and analyzed using Stata software application version 14.

Results

Ultimately, 102 papers were selected for this meta- analysis, covering 121,437 infected patients. The mean age of the patients was 58.42 years. The results indicate a prevalence of 79.26% for fever (95% CI: 74.98–83.26; I2 = 97.35%), 60.70% for cough (95% CI: 56.91–64.43; I2 = 94.98%), 33.21% for fatigue or myalgia (95% CI: 28.86–37.70; I2 = 96.12%), 31.30% for dyspnea (95% CI: 26.14–36.69; I2 = 97.67%), and 10.65% for diarrhea (95% CI: 8.26–13.27; I2 = 94.20%). The prevalence for the most common comorbidities was 28.30% for hypertension (95% CI: 23.66–33.18; I2 = 99.58%), 14.29% for diabetes (95% CI: 11.88–16.87; I2 = 99.10%), 12.30% for cardiovascular diseases (95% CI: 9.59–15.27; I2 = 99.33%), and 5.19% for chronic kidney disease (95% CI: 3.95–6.58; I2 = 96.42%).

Conclusions

We evaluated the prevalence of some of the most important comorbidities in COVID-19 patients, indicating that some underlying disorders, including hypertension, diabetes, cardiovascular diseases, and chronic kidney disease, can be considered as risk factors for patients with COVID-19 infection. Furthermore, the results show that an elderly male with underlying diseases is more likely to have severe COVID-19.
Relationships between fox populations and rabies virus spread in northern Canada
Authors: Nadin-Davis Susan A. , Falardeau Emilie , Flynn Alex , Whitney Hugh , Marshall H. Dawn
Published: February 2021

Rabies spreads in both Arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) throughout the Canadian Arctic but limited wildlife disease surveillance, due to the extensive landmass of the Canadian north and its small widely scattered human population, undermines our knowledge of disease transmission patterns. This study has explored genetic population structure in both the rabies virus and its fox hosts to better understand factors that impact rabies spread. Phylogenetic analysis of 278 samples of the Arctic lineage of rabies virus recovered over 40 years identified four sub-lineages, A1 to A4. The A1 lineage has been restricted to southern regions of the Canadian province of Ontario. The A2 lineage, which predominates in Siberia, has also spread to northern Alaska while the A4 lineage was recovered from southern Alaska only. The A3 sub-lineage, which was also found in northern Alaska, has been responsible for virtually all cases across northern Canada and Greenland, where it further differentiated into 18 groups which have systematically evolved from a common predecessor since 1975. In areas of Arctic and red fox sympatry, viral groups appear to circulate in both hosts, but both mitochondrial DNA control region sequences and 9-locus microsatellite genotypes revealed contrasting phylogeographic patterns for the two fox species. Among 157 Arctic foxes, 33 mitochondrial control region haplotypes were identified but little genetic structure differentiating localities was detected. Among 162 red foxes, 18 control region haplotypes delineated three groups which discriminated among the Churchill region of Manitoba, northern Quebec and Labrador populations, and the coastal Labrador locality of Cartwright. Microsatellite analyses demonstrated some genetic heterogeneity among sampling localities of Arctic foxes but no obvious pattern, while two or three clusters of red foxes suggested some admixture between the Churchill and Quebec-Labrador regions but uniqueness of the Cartwright group. The limited population structure of Arctic foxes is consistent with the rapid spread of rabies virus subtypes throughout the north, while red fox population substructure suggests that disease spread in this host moves most readily down certain independent corridors such as the northeastern coast of Canada and the central interior. Interestingly the evidence suggests that these red fox populations have limited capacity to maintain the virus over the long term, but they may contribute to viral persistence in areas of red and Arctic fox sympatry.
IL-13Rα2 gene expression is a biomarker of adverse outcome in patients with adrenocortical carcinoma
Authors: Kumar Abhinav , Bellayr Ian H. , Singh Hridaya S. , Puri Raj K.
Published: February 2021

Adrenocortical carcinoma (ACC) is a rare but aggressive endocrine malignancy that usually results in a fatal outcome. To allow the better clinical management and reduce mortality, we searched for clinical and molecular markers that are reliable predictor of disease severity and clinical outcome in ACC patients. We determined a correlation between the overexpression ofIL-13Rα2 and the clinical outcome in ACC patients using comprehensive data available in The Cancer Genome Atlas (TCGA) database. The dataset of 79 ACC subjects were divided into groups of low, medium, or high expression ofIL-13Rα2 as determined by RNA-seq. These patients were also stratified by length of survival, overall survival, incidence of a new tumor event, incidence of metastasis, and production of excess hormones. We report a correlation betweenIL-13Rα2 expression and survival of subjects with ACC. High expression ofIL-13Rα2 in ACC tumors was significantly associated with a lower patient survival rate and period of survival compared to low expression (p = 0.0084). In addition, highIL-13Rα2 expression was significantly associated with a higher incidence of new tumor events and excess hormone production compared to low or mediumIL-13Rα2 expression. Within the cohort of patients that produced excess hormone, elevatedIL-13Rα2 expression was significantly associated with a lower survival rate. Additionally,IL-13Rα1 had a potential relationship between transcript level and ACC survival. Our results and promising antitumor activity in preclinical models and trials indicate thatIL-13Rα2 expression is an important prognostic biomarker of ACC disease outcome and a promising target for therapeutic treatment of ACC.
Energy loss associated with in-vitro modeling of mitral annular calcification
Authors: Wiener Philip C. , Darwish Ahmed , Friend Evan , Kadem Lyes , Pressman Gregg S.
Published: February 2021

Introduction

Study aims were to compare hemodynamics and viscous energy dissipation (VED) in 3D printed mitral valves–one replicating a normal valve and the other a valve with severe mitral annular calcification (MAC). Patients with severe MAC develop transmitral gradients, without the commissural fusion typifying rheumatic mitral stenosis (MS), and may have symptoms similar to classical MS. A proposed mechanism relates to VED due to disturbed blood flow through the diseased valve into the ventricle.

Methods

A silicone model of a normal mitral valve (MV) was created using a transesophageal echocardiography dataset. 3D printed calcium phantoms were incorporated into a second valve model to replicate severe MAC. The synthetic MVs were tested in a left heart duplicator under rest and exercise conditions. Fine particles were suspended in a water/glycerol blood analogue for particle image velocimetry calculation of VED.

Results

Catheter mean transmitral gradients were slightly higher in the MAC valve compared to the normal MV, both at rest (3.2 vs. 1.3 mm Hg) and with exercise (5.9 vs. 5.0 mm Hg); Doppler gradients were 2.7 vs. 2.1 mm Hg at rest and 9.9 vs 8.2 mm Hg with exercise. VED was similar between the two valves at rest. During exercise, VED increased to a greater extent for the MAC valve (240%) versus the normal valve (127%).

Conclusion

MAC MS is associated with slightly increased transmitral gradients but markedly increased VED during exercise. These energy losses may contribute to the exercise intolerance and exertional dyspnea present in MAC patients.
Brain morphological and connectivity changes on MRI after stem cell therapy in a rat stroke model
Authors: Son Jeong Pyo , Sung Ji Hee , Kim Dong Hee , Cho Yeon Hee , Kim Suk Jae , Chung Jong-Won , Chang Won Hyuk , Kim Yun-Hee , Kim Eun Hee , Moon Gyeong Joon , Bang Oh Young
Published: February 2021

In animal models of stroke, behavioral assessments could be complemented by a variety of neuroimaging studies to correlate them with recovery and better understand mechanisms of improvement after stem cell therapy. We evaluated morphological and connectivity changes after treatment with human mesenchymal stem cells (hMSCs) in a rat stroke model, through quantitative measurement ofT2-weighted images and diffusion tensor imaging (DTI). Transient middle cerebral artery occlusion rats randomly received PBS (PBS-only), FBS cultured hMSCs (FBS-hMSCs), or stroke patients’ serum cultured hMSCs (SS-hMSCs). Functional improvement was assessed using a modified neurological severity score (mNSS). Quantitative analyses ofT2-weighted ischemic lesion and ventricular volume changes were performed. Brain microstructure/connectivity changes were evaluated in the ischemic recovery area by DTI-derived microstructural indices such as relative fractional anisotropy (rFA), relative axial diffusivity (rAD), and relative radial diffusivity (rRD), and relative fiber density (rFD) analyses. According to mNSS results, the SS-hMSCs group showed the most prominent functional improvement. Infarct lesion volume of the SS-hMSCs group was significantly decreased at 2 weeks when compared to the PBS-only groups, but there were no differences between the FBS-hMSCs and SS-hMSCs groups. Brain atrophy was significantly decreased in the SS-hMSCs group compared to the other groups. In DTI, rFA and rFD values were significantly higher and rRD value was significant lower in the SS-hMSCs group and these microstructure/connectivity changes were correlated withT2-weighted morphological changes.T2-weighted volume alterations (ischemic lesion and brain atrophy), and DTI microstructural indices and rFD changes, were well matched with the results of behavioral assessment. These quantitative MRI measurements could be potential outcome predictors of functional recovery after treatment with stem cells for stroke.
Statistical learning of unbalanced exclusive-or temporal sequences in humans
Authors: Lazartigues Laura , Mathy Fabien , Lavigne Frédéric
Published: February 2021

A pervasive issue in statistical learning has been to determine the parameters of regularity extraction. Our hypothesis was that the extraction of transitional probabilities can prevail over frequency if the task involves prediction. Participants were exposed to four repeated sequences of three stimuli (XYZ) with each stimulus corresponding to the position of a red dot on a touch screen that participants were required to touch sequentially. The temporal and spatial structure of the positions corresponded to a serial version of the exclusive-or (XOR) that allowed testing of the respective effect of frequency and first- and second-order transitional probabilities. The XOR allowed the first-order transitional probability to vary while being not completely related to frequency and to vary while the second-order transitional probability was fixed (p(Z|X, Y) = 1). The findings show that first-order transitional probability prevails over frequency to predict the second stimulus from the first and that it also influences the prediction of the third item despite the presence of second-order transitional probability that could have offered a certain prediction of the third item. These results are particularly informative in light of statistical learning models.
Caesarean section and severe upper and lower respiratory tract infections during infancy: Evidence from two UK cohorts
Authors: Alterman Neora , Kurinczuk Jennifer J. , Quigley Maria A.
Published: February 2021

Background

Several studies have reported that birth by caesarean section is associated with increased risk of lower respiratory tract infections in the child, but it is unclear whether this applies to any caesarean section or specifically to planned caesareans. Furthermore, although infections of the upper respiratory tract are very common during childhood, there is a scarcity of studies examining whether caesarean is also a risk factor for this site of infection.

Methods

We obtained data from two UK cohorts: the Millennium Cohort Study (MCS) and linked administrative datasets of the population of Wales through the Secure Anonymised Information Linkage (SAIL) databank. The study focused on term-born singleton infants and included 15,580 infants born 2000–2002 (MCS) and 392,145 infants born 2002–2016 (SAIL). We used information about mode of birth (vaginal delivery, assisted vaginal delivery, planned caesarean and emergency caesarean) from maternal report in the MCS and from hospital birth records in SAIL. Unplanned hospital admission for lower respiratory tract infection (LRTI) was ascertained from maternal report in the MCS and from hospital record ICD codes in SAIL. Information about admissions for upper respiratory tract infection (URTI) was available from SAIL only. Cox regression was used to estimate hazard ratios for each outcome and cohort separately while accounting for a wide range of confounders. Gestational age at birth was further examined as a potential added, indirect risk of planned caesarean birth due to the early delivery.

Findings

The rate of hospital admission for LRTI was 4.6 per 100 child years in the MCS and 5.9 per 100 child years in SAIL. Emergency caesarean was not associated with LRTI admission during infancy in either cohort. In the MCS, planned caesarean was associated with a hazard ratio of 1.39 (95% CI 1.03, 1.87) which further increased to 1.65 (95% CI 1.24, 2.19) when gestational age was not adjusted for. In SAIL, the adjusted hazard ratio was 1.10 (95% CI 1.05, 1.15), which increased to 1.17 (95% CI 1.12, 1.22) when gestational age was not adjusted for. The rate of hospital admission for URTI was 5.9 per 100 child years in SAIL. Following adjustments, emergency caesarean was found to have a hazard ratio of 1.09 (95% CI 1.05, 1.14) for hospital admission for URTI. Planned caesarean was associated with a hazard ratio of 1.11 (95% CI 1.06, 1.16) which increased to 1.17 (95% CI 1.12, 1.22) when gestational age was not adjusted for.

Conclusions

The risk of severe LRTIs during infancy is moderately elevated in infants born by planned caesarean compared to those born vaginally. Infants born by any type of caesarean may also be at a small increased risk of severe URTIs. The estimated effect sizes are stronger if including the indirect effect arising from planning the caesarean birth for an earlier gestation than would have occurred spontaneously. Further studies are needed to confirm these results.
Comparison of diagnostic performance between convolutional neural networks and human endoscopists for diagnosis of colorectal polyp: A systematic review and meta-analysis
Authors: Xu Yixin , Ding Wei , Wang Yibo , Tan Yulin , Xi Cheng , Ye Nianyuan , Wu Dapeng , Xu Xuezhong
Published: February 2021

Prospective randomized trials and observational studies have revealed that early detection, classification, and removal of neoplastic colorectal polyp (CP) significantly improve the prevention of colorectal cancer (CRC). The current effectiveness of the diagnostic performance of colonoscopy remains unsatisfactory with unstable accuracy. The convolutional neural networks (CNN) system based on artificial intelligence (AI) technology has demonstrated its potential to help endoscopists in increasing diagnostic accuracy. Nonetheless, several limitations of the CNN system and controversies exist on whether it provides a better diagnostic performance compared to human endoscopists. Therefore, this study sought to address this issue. Online databases (PubMed, Web of Science, Cochrane Library, and EMBASE) were used to search for studies conducted up to April 2020. Besides, the quality assessment of diagnostic accuracy scale-2 (QUADAS-2) was used to evaluate the quality of the enrolled studies. Moreover, publication bias was determined using the Deeks’ funnel plot. In total, 13 studies were enrolled for this meta-analysis (ranged between 2016 and 2020). Consequently, the CNN system had a satisfactory diagnostic performance in the field of CP detection (sensitivity: 0.848 [95% CI: 0.692–0.932]; specificity: 0.965 [95% CI: 0.946–0.977]; and AUC: 0.98 [95% CI: 0.96–0.99]) and CP classification (sensitivity: 0.943 [95% CI: 0.927–0.955]; specificity: 0.894 [95% CI: 0.631–0.977]; and AUC: 0.95 [95% CI: 0.93–0.97]). In comparison with human endoscopists, the CNN system was comparable to the expert but significantly better than the non-expert in the field of CP classification (CNN vs. expert: RDOR: 1.03, P = 0.9654; non-expert vs. expert: RDOR: 0.29, P = 0.0559; non-expert vs. CNN: 0.18, P = 0.0342). Therefore, the CNN system exhibited a satisfactory diagnostic performance for CP and could be used as a potential clinical diagnostic tool during colonoscopy.
Distribution and diversity of mosquitoes and Oropouche-like virus infection rates in an Amazonian rural settlement
Authors: Pereira-Silva Jordam William , Ríos-Velásquez Claudia María , Lima Gervilane Ribeiro de , Marialva dos Santos Eric Fabrício , Belchior Heliana Christy Matos , Luz Sergio Luiz Bessa , Naveca Felipe Gomes , Pessoa Felipe Arley Costa
Published: February 2021

Mosquito diversity and disease transmission are influenced by landscape modifications, i.e., vectors and pathogens previously found only in forests are now found close to human environments due to anthropic changes. This study determined the diversity and distribution of mosquitoes in forest environments in order to analyze the potential vectors of Amazonian forest arboviruses. Mosquitoes were collected by 1) vertical stratification from forest canopy and ground areas using Hooper Pugedo (HP) light traps and human attraction and 2) horizontal stratification using HP light traps in peridomicile, forest edge, and forest environments near the Rio Pardo rural settlement, Amazonas, Brazil. A total of 3,750 mosquitoes were collected, representing 46 species. 3,139 individuals representing 46 species were sampled by vertical stratification. Both the Shannon-Weaver diversity index (H’) and equitability (J’) were higher in the canopy than on the ground. 611 individuals representing 13 species were sampled by horizontal stratification. H’ decreased in the following order: forest edge > forest > peridomicile, and J’ was greater at the forest edge and smaller in the peridomicile environment. Moreover, H’ was higher for the human attraction collection method than the HP traps. A total of 671 pools were analyzed by RT-qPCR; three species were positive for Oropouche-like viruses (Ochlerotatus serratus,Psorophora cingulata, andHaemagogus tropicalis) and the minimum infection rate was 0.8%. The composition of mosquito species did not differ significantly between anthropic and forest environments in Rio Pardo. Some mosquito species, due to their abundance, dispersion in the three environments, and record of natural infection, were hypothesized to participate in the arbovirus transmission cycle in this Amazonian rural settlement.
Mask usage, social distancing, racial, and gender correlates of COVID-19 vaccine intentions among adults in the US
Authors: Latkin Carl A. , Dayton Lauren , Yi Grace , Colon Brian , Kong Xiangrong
Published: February 2021

Vaccine hesitancy could become a significant impediment to addressing the COVID-19 pandemic. The current study examined the prevalence of COVID-19 vaccine hesitancy and factors associated with vaccine intentions. A national panel survey by the National Opinion Research Center (NORC) was designed to be representative of the US household population. Sampled respondents were invited to complete the survey between May 14 and 18, 2020 in English or Spanish. 1,056 respondents completed the survey—942 via the web and 114 via telephone. The dependent variable was assessed by the item “If a vaccine against the coronavirus becomes available, do you plan to get vaccinated, or not?” Approximately half (53.6%) reported intending to be vaccinated, 16.7% did not intend, and 29.7% were unsure. In the adjusted stepwise multinominal logistic regression, Black and Hispanic respondents were significantly less likely to report intending to be vaccinated as were respondents who were females, younger, and those who were more politically conservative. Compared to those who reported positive vaccine intentions, respondents with negative vaccine intentions were significantly less likely to report that they engaged in the COVID-19 prevention behaviors of wearing masks (aOR = 0.53, CI = 0.37–0.76) and social distancing (aOR = 0.22, CI = 0.12–0.42). In a sub-analysis of reasons not to be vaccinated, significant race/ethnic differences were observed. This national survey indicated a modest level of COVID-19 vaccine intention. These data suggest that public health campaigns for vaccine uptake should assess in greater detail the vaccine concerns of Blacks, Hispanics, and women to tailor programs.
Patient journey through cases of depression from claims database using machine learning algorithms
Authors: Kitanishi Yoshitake , Fujiwara Masakazu , Binkowitz Bruce
Published: February 2021

Health insurance and acute hospital-based claims have recently become available as real-world data after marketing in Japan and, thus, classification and prediction using the machine learning approach can be applied to them. However, the methodology used for the analysis of real-world data has been hitherto under debate and research on visualizing the patient journey is still inconclusive. So far, to classify diseases based on medical histories and patient demographic background and to predict the patient prognosis for each disease, the correlation structure of real-world data has been estimated by machine learning. Therefore, we applied association analysis to real-world data to consider a combination of disease events as the patient journey for depression diagnoses. However, association analysis makes it difficult to interpret multiple outcome measures simultaneously and comprehensively. To address this issue, we applied the Topological Data Analysis (TDA) Mapper to sequentially interpret multiple indices, thus obtaining a visual classification of the diseases commonly associated with depression. Under this approach, the visual and continuous classification of related diseases may contribute to precision medicine research and can help pharmaceutical companies provide appropriate personalized medical care.
Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations
Authors: Yousefi-Mashouf Navid , Mehrabani-Yeganeh Hassan , Nejati-Javaremi Ardeshir , Bailey Ernest , Petersen Jessica L.
Published: February 2021

The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calculation of pairwise FST. Both Persian breeds were discriminated from the Thoroughbred. Pairwise FST between the two Persian samples (0.013) was significantly greater than zero and several fold less than those found between the Thoroughbred and Kurdish (0.052) or Thoroughbred and Persian Arabian (0.057). Cluster analysis assuming three genetic clusters assigned the Kurdish horse and Thoroughbred to distinct clusters (0.942 in cluster 2 and 0.953 in cluster 3 respectively); the Persian Arabian was not in a distinct cluster (0.519 in cluster 1), demonstrating shared ancestry or recent admixture with the Kurdish breed. Diversity as quantified by expected heterozygosity was the highest in the Kurdish horse (0.342), followed by the Persian Arabian (0.328) and the Thoroughbred (0.326). Analysis of Molecular Variance showed that 4.47% of the genetic variation was present among populations (P<0.001). Population-specific inbreeding indices (FIS) were not significantly different from zero in any of the populations. Analysis of individual inbreeding based on runs of homozygosity using a larger SNP set suggested greater diversity in both the Kurdish and Persian Arabian than in the Thoroughbred. These results have implications for developing conservation strategies to achieve sound breeding goals while maintaining genetic diversity.
An integrated clinical and genetic model for predicting risk of severe COVID-19: A population-based case–control study
Authors: Dite Gillian S. , Murphy Nicholas M. , Allman Richard
Published: February 2021

Up to 30% of people who test positive to SARS-CoV-2 will develop severe COVID-19 and require hospitalisation. Age, gender, and comorbidities are known to be risk factors for severe COVID-19 but are generally considered independently without accurate knowledge of the magnitude of their effect on risk, potentially resulting in incorrect risk estimation. There is an urgent need for accurate prediction of the risk of severe COVID-19 for use in workplaces and healthcare settings, and for individual risk management. Clinical risk factors and a panel of 64 single-nucleotide polymorphisms were identified from published data. We used logistic regression to develop a model for severe COVID-19 in 1,582 UK Biobank participants aged 50 years and over who tested positive for the SARS-CoV-2 virus: 1,018 with severe disease and 564 without severe disease. Model discrimination was assessed using the area under the receiver operating characteristic curve (AUC). A model incorporating the SNP score and clinical risk factors (AUC = 0.786; 95% confidence interval = 0.763 to 0.808) had 111% better discrimination of disease severity than a model with just age and gender (AUC = 0.635; 95% confidence interval = 0.607 to 0.662). The effects of age and gender are attenuated by the other risk factors, suggesting that it is those risk factors–not age and gender–that confer risk of severe disease. In the whole UK Biobank, most are at low or only slightly elevated risk, but one-third are at two-fold or more increased risk. We have developed a model that enables accurate prediction of severe COVID-19. Continuing to rely on age and gender alone (or only clinical factors) to determine risk of severe COVID-19 will unnecessarily classify healthy older people as being at high risk and will fail to accurately quantify the increased risk for younger people with comorbidities.
Type IV pilus retraction enables sustained bacteremia and plays a key role in the outcome of meningococcal sepsis in a humanized mouse model
Authors: Barnier Jean-Philippe , Euphrasie Daniel , Join-Lambert Olivier , Audry Mathilde , Schonherr-Hellec Sophia , Schmitt Taliah , Bourdoulous Sandrine , Coureuil Mathieu , Nassif Xavier , El Behi Mohamed
Published: February 2021

Neisseria meningitidis (the meningococcus) remains a major cause of bacterial meningitis and fatal sepsis. This commensal bacterium of the human nasopharynx can cause invasive diseases when it leaves its niche and reaches the bloodstream. Blood-borne meningococci have the ability to adhere to human endothelial cells and rapidly colonize microvessels. This crucial step enables dissemination into tissues and promotes deregulated inflammation and coagulation, leading to extensive necrotic purpura in the most severe cases. Adhesion to blood vessels relies on type IV pili (TFP). These long filamentous structures are highly dynamic as they can rapidly elongate and retract by the antagonistic action of two ATPases, PilF and PilT. However, the consequences of TFP dynamics on the pathophysiology and the outcome of meningococcal sepsis in vivo have been poorly studied. Here, we show that human graft microvessels are replicative niches for meningococci, that seed the bloodstream and promote sustained bacteremia and lethality in a humanized mouse model. Intriguingly, although pilus-retraction deficient N. meningitidis strain (ΔpilT) efficiently colonizes human graft tissue, this mutant did not promote sustained bacteremia nor induce mouse lethality. This effect was not due to a decreased inflammatory response, nor defects in bacterial clearance by the innate immune system. Rather, TFP-retraction was necessary to promote the release of TFP-dependent contacts between bacteria and, in turn, the detachment from colonized microvessels. The resulting sustained bacteremia was directly correlated with lethality. Altogether, these results demonstrate that pilus retraction plays a key role in the occurrence and outcome of meningococcal sepsis by supporting sustained bacteremia. These findings open new perspectives on the role of circulating bacteria in the pathological alterations leading to lethal sepsis.
Hausdorffen dimentsioa talde profinituetan
Authors: De las Heras Iker , Zozaya Andoni
Published: February 2021

Hausdorffen dimentsioa eta kutxa-dimentsioa geometria fraktalaren esparruko oinarrizko kontzeptuak dira. Horiek ohiko dimentsio topologikoaren ideia orokortzen dute; izan ere, objektu geometriko arrunten dimentsioari ohiko balio bera ematen dieten bitartean, intuitiboki hain dimentsio argia ez duten zenbait multzo patologikori dimentsio ez oso bat esleitzen diote. Bestalde, azken hamarkadetan, Hausdorffen dimentsioaren kontzeptuak aplikazio emankor eta interesgarriak eman ditu oinarri zenbakigarriko talde profinituen testuinguruan, talde horiei espazio metriko egitura eman baitakieke. Artikulu honetan, alde batetik, Hausdorffen dimentsioaren eta kutxa-dimentsioaren teoriaren sarrera orokor bat egingo dugu. Beste alde batetik, Hausdorffen dimentsioak talde profinituetan eman dituen zenbait emaitza esanguratsu azalduko dira, arreta bi alor konkretutara bideratuz: Hausdorffen espektroa eta talde R-analitikoak.
Epigenetika helburu duten sendagaiak
Authors: Martínez Peula Oihane , Rivero Calera Guadalupe
Published: February 2021

Epigenetika hitzak DNA-sekuentzia aldatu gabe aktibitate genetikoan gertatzen den edozein aldaketari egiten dio erreferentzia. Faktore ez-genetikoek (hala nola, infekzioak eta farmakoak) aldaketa epigenetikoak eragin ditzakete, gure genoma osotik zein gene adieraziko diren eta zein ez erabakiz. Hortaz, epigenetika genetikaren eta inguruko faktoreen eta esperientzien arteko lokailua da. Garai erabakigarrietan (garapen fetalean, haurtzaro goiztiarrean eta nerabetasunean) eraginez, faktore ez-genetikoek gure epigenoma ezarriko lukete, deskribatu izan diren 3 mekanismoren bidez: DNAren metilazioa, histonen itzulpen osteko aldaketak eta RNA ez-kodetzaileen eragina. Azken hamarkadetan, epigenetikaren inguruko ikerketa ugari egin dira; gehien aztertu den mekanismo epigenetikoa itzulpen osteko histonen azetilazioa izan da. Azetilazio-asaldurak hainbat gaixotasunen garapenarekin erlazionatu dira. Horren adibiderik aipagarriena minbizia izan da. Horretan oinarrituz, histonen deazetilasen inhibitzaileak (HDACi) minbiziaren kontrako tratamendu gisa postulatu ziren. Gaur egun, lau HDACi daude onartuta minbizi-mota ezberdinen aurkako tratamendurako, eta 20 baino gehiago fase klinikoan ebaluatzen ari dira. HDACi-ek minbizian duten eraginkortasunak beste gaixotasun batzuetan aztertzeko aukera eman du. Gaixotasun neuroendeka- tzaile eta psikiatrikoen konplexutasuna eta tratamendu eraginkorren falta dela eta, HDACi-ak terapia potentzial interesgarri bihurtu dira. HDACi-ek eragile neurobabesle gisa joka dezaketenez, Huntingtonen eta Parkinsonen gaixotasunetan duten eraginkortasuna aztertzen ari da. Asaldura bipolarrean eta eskizofrenian ere aurrera doa HDACi-en ikerketa.
Challenges and Practices of Research Data Management at Kepustakaan LIPI Kawasan Bandung
Authors:   Lembaga Ilmu Pengetahuan Indonesia, Kamaludin Kamaludin
Published: February 2021

In the past 10 years, an international agenda around Research Data Management (RDM) emerged as a practice that can occur at various stages in the research cycle. RDM is a description of organizational activities, storage, preservation and sharing of data collected for research. This study aims to determine the challenges and practices of RDM at Kepustakaan LIPI Kawasan Bandung PDDI-LIPI in the management of video files as authentic research data from the results of research activities. The method used was a descriptive research method. From the research results, it was known that Kepustakaan LIPI Kawasan Bandung-PDDI-LIPI as a multimedia library had compiled a research plan for the period 2019 to 2023, after joining the PDDI-LIPI, research planning was augmented with research data management (primary data). But in the planning, training activities that support the implementation of RDM had not been made. Research data collection had been done, there was research data in the form of video files total 4.517 titles stored on Network-Attached Storage, it was found photos and audio that had not been collected properly. Processing and analyzing research data had been done, but only research data was packaged in video files, while photos and audio had not been done. Publishing and sharing of research data had been done. Preservation of research data in the video file format was managed and stored in the Digital Asset Management application. Researchers who need research data in the video file, for re-using data, they could visit Kepustakaan LIPI Kawasan Bandung-PDDI-LIPI. Considering that training is very important, it is advisable to make plans for employee participation in RDM training. It is recommended that all research data including photos and audio to be collected properly. Making a website as a means of publishing and sharing, also re-using research data is recommended to be made immediately.
Innovation in Library Services Post COVID-19 Pandemic
Authors:   Lembaga Ilmu Pengetahuan Indonesia, Bakti Ludya Arica ,   Lembaga Ilmu Pengetahuan Indonesia, Prasetyadi Abdurrakhman ,   Lembaga Ilmu Pengetahuan Indonesia, Nugroho Dwiyanto Wahyu Ari ,   Lembaga Ilmu Pengetahuan Indonesia, Trianggoro Cahyo ,   Lembaga Ilmu Pengetahuan Indonesia, Rosiyan Nur Rizzal ,   Lembaga Ilmu Pengetahuan Indonesia, Subagyo Hendro
Published: February 2021

Covid-19 pandemic which hit various parts of the world has bring changes in living arrangements including library, documentation, and information. Thus, library organizations need to adapt in response addressing service demands in new normal era. This study analyzed the use of social networking services in the library post COVID-19 based on Zoom webinar. The analysis results revealed that most participants (97%) declare the importance of changing the role of libraries and librarians post COVID-19. In addition, as many as 88% of participants stated that innovation in creating new products by librarians is urgent to meet the users need post COVID-19. Changing the paradigm of librarians is also needed according to (94%) participants, by changing the mindset and working patterns of traditional librarians (providing services) into a creator of information and advancing skills set in digital literacy. The findings of this study are expected to help stakeholders improve library service.