bluuebunny/crossref_metadata_2025 huggingface dataset:
Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale
Authors: Zhang Zhengdong , Liu Zhentao , Meng Yafei , Chen Zhen , Han Jiayu , Wei Yimin , Shen Tie , Yi Yin , Xie Xiaoyao
Published: June 2020

Background

A precise map of the metabolic fluxome, the closest surrogate to the physiological phenotype, is becoming progressively more important in the metabolic engineering of photosynthetic organisms for biofuel and biomass production. For photosynthetic organisms, the state-of-the-art method for this purpose is instationary 13C fluxomics, which has arisen as a sibling of transcriptomics or proteomics. Instationary 13C data processing requires solving high-dimensional nonlinear differential equations and leads to large computational and time costs when its scope is expanded to a genome-scale metabolic network.

Result

Here, we present a parallelized method to model instationary 13C labeling data. The elementary metabolite unit (EMU) framework is reorganized to allow treating individual mass isotopomers and breaking up of their networks into strongly connected components (SCCs). A variable domain parallel algorithm is introduced to process ordinary differential equations in a parallel way. 15-fold acceleration is achieved for constant-step-size modeling and ~ fivefold acceleration for adaptive-step-size modeling.

Conclusion

This algorithm is universally applicable to isotope granules such as EMUs and cumomers and can substantially accelerate instationary 13C fluxomics modeling. It thus has great potential to be widely adopted in any instationary 13C fluxomics modeling.
The impact of community-wide, mass drug administration on aggregation of soil-transmitted helminth infection in human host populations
Authors: Werkman Marleen , Wright James E. , Truscott James E. , Oswald William E. , Halliday Katherine E. , Papaiakovou Marina , Farrell Sam H. , Pullan Rachel L. , Anderson Roy M.
Published: June 2020

Background

Soil-transmitted helminths (STH) are intestinal parasites estimated to infect over 1.5 billion people. Current treatment programmes are aimed at morbidity control through school-based deworming programmes (targeting school-aged children, SAC) and treating women of reproductive age (WRA), as these two groups are believed to record the highest morbidity. More recently, however, the potential for interrupting transmission by treating entire communities has been receiving greater emphasis and the feasibility of such programmes are now under investigation in randomised clinical trials through the Bill & Melinda Gates Foundation funded DeWorm3 studies. Helminth parasites are known to be highly aggregated within human populations, with a small minority of individuals harbouring most worms. Empirical evidence from the TUMIKIA project in Kenya suggests that aggregation may increase significantly after anthelminthic treatment.

Methods

A stochastic, age-structured, individual-based simulation model of parasite transmission is employed to better understand the factors that might induce this pattern. A simple probabilistic model based on compounded negative binomial distributions caused by age-dependencies in both treatment coverage and exposure to infection is also employed to further this understanding.

Results

Both approaches confirm helminth aggregation is likely to increase post-mass drug administration as measured by a decrease in the value of the negative binomial aggregation parameter,k. Simple analytical models of distribution compounding describe the observed patterns well.

Conclusions

The helminth aggregation that was observed in the field was replicated with our stochastic individual-based model. Further work is required to generalise the probabilistic model to take account of the respective sensitivities of different diagnostics on the presence or absence of infection.
Environmental and biotic factors affecting freshwater snail intermediate hosts in the Ethiopian Rift Valley region
Authors: Olkeba Beekam Kebede , Boets Pieter , Mereta Seid Tiku , Yeshigeta Mesfin , Akessa Geremew Muleta , Ambelu Argaw , Goethals Peter L. M.
Published: June 2020

Background

Knowledge of the distribution and habitat preference of freshwater snail intermediate hosts can provide information to initiate and set-up effective snail control programmes. However, there is limited research conducted on the factors driving the occurrence and abundance of freshwater snail intermediate hosts in the Ethiopian Rift Valley. Hence, in this study, we investigated how environmental and biotic factors influence the occurrence and abundance of the snail intermediate hosts in Ethiopian Rift Valley region.

Methods

Data on freshwater snails, physico-chemical water quality parameters, physical characteristics of habitat, predators and competitors, and anthropogenic activity variables were collected from 174 sampling sites during the wet season of 2017 and 2018. Generalized linear models were used to identify the main environmental and biotic factors affecting the occurrence and abundance of the snail species.

Results

It was found thatBulinus globosus(31.7%) was the most abundant snail species followed byLymnaea natalensis(21.6%),Lymnaea truncatula(15.1%) andBiomphalaria pfeifferi(14.6%). Generalized linear models indicated that physico-chemical parameters (water temperature, turbidity, chlorophyll-a, dissolved oxygen, chemical oxygen demand, alkalinity, calcium, magnesium, nitrate and ammonia), physical habitat characteristics (water depth, canopy cover, macrophyte cover and substrate type) and biotic factors (abundance of predators and competitors) were found to be the main variables determining the occurrence and abundance of snail species in the Ethiopian Rift Valley region. In terms of anthropogenic activities, human settlement, farming, bathing and swimming, clothes washing, grazing, drainage of land, car washing, boating, fishing and silviculture were also important variables determining the occurrence and abundance of snail species in the region.

Conclusions

The findings reported herein suggest that integrated snail control strategies should be considered to control snailsviaprotection of water bodies from disturbance by anthropogenic activities. In this way, it is possible to reduce the concentration of organic matter and dissolved ions in aquatic ecosystems which are conducive for the presence of snails.
Young blood plasma reduces Alzheimer’s disease-like brain pathologies and ameliorates cognitive impairment in 3×Tg-AD mice
Authors: Zhao Ying , Qian Ran , Zhang Jin , Liu Fei , Iqbal Khalid , Dai Chun-Ling , Gong Cheng-Xin
Published: June 2020

Background

Recent studies indicated that circulatory factors in blood plasma from young animals can reactivate neurogenesis, restore synaptic plasticity, and improve cognitive function in aged animals. Here, we investigated if young plasma could have a possible therapeutic effect for treatment of Alzheimer’s disease (AD)-like pathologies and cognitive impairment in triple-transgenic AD (3×Tg-AD) mice.

Methods

We intravenously injected plasma from 2- to 3-month-old C57BL/6 J wild-type mice into 16–17-month-old 3×Tg-AD mice twice a week for 8 weeks. The behavioral tests including open field, novel object recognition, Morris water maze, and reversal Morris water maze were conducted after 4-week plasma injections. The effect of young plasma on tau and Aβ pathologies and on the levels of synaptic proteins and neuroinflammation were assessed by Western blots and immunohistochemical staining.

Results

Young plasma treatment improved short-term memory in the novel object recognition test and enhanced the spatial learning and memory in Morris water maze test and reversal Morris water maze test. Biochemical studies revealed that young plasma treatment reduced both tau and Aβ pathologies, as well as neuroinflammation in the mouse brain. However, we did not detect any significant changes in levels of synaptic proteins or the dentate gyrus neurogenesis in the mouse brain after the treatment with young plasma.

Conclusions

These data indicate that young blood plasma not only ameliorates tau and Aβ pathologies but also enhances the cognitive function in 3×Tg-AD mice. These findings suggest that transfusion with young blood plasma could be a potentially effective treatment for AD.
Hypoxia-challenged MSC-derived exosomes deliver miR-210 to attenuate post-infarction cardiac apoptosis
Authors: Cheng Hao , Chang Shufu , Xu Rende , Chen Lu , Song Xiaoyue , Wu Jian , Qian Juying , Zou Yunzeng , Ma Jianying
Published: June 2020

Background

Myocardial infarction (MI) is a major cause of death worldwide. Although percutaneous coronary intervention and coronary artery bypass grafting can prolong life, cardiac damage persists. In particular, cardiomyocytes have no regenerative capacity. Mesenchymal stem cells (MSCs) are attractive candidates for the treatment of MI. The manner by which MSCs exert a beneficial effect upon injured cells is a source of continued study.

Methods

After the isolation and identification of exosomes from MSCs, the expression of miR-210 was determined by microarray chip. Subsequently, gain- and loss-function approaches were conducted to detect the role of exosomes and exosomal-miR-210 in cell proliferation and apoptosis of cardiomyocytes, as well as the MI in vivo. Dual-Luciferase Report Gene System was used to demonstrate the target gene of miR-210.

Results

We tested the hypothesis that MSC-derived exosomes transfer specific miRNA to protect cardiomyocytes from apoptotic cell death. Interestingly, direct cardiac injection of MSC exosomes reduced infarct size and improved heart function after coronary ligation. In vitro, the MSC exosomes enhanced cardiomyocyte survival to hypoxia. Confirmation of exosome uptake in myocytes was confirmed. Dual-luciferase reporter assay implicated miR-210 as a mediator of the therapeutic effect and AIFM3 as a downstream target. Treatment with miR-210 overexpressing MSC exosomes improved myocyte protection to both in vitro and in vivo stress. Furthermore, the endogenous and exogenous miR-210 had the same therapeutic effects.

Conclusion

These results demonstrated that the beneficial effects offered by MSC-exosomes transplantation after MI are at least partially because of excreted exosome containing mainly miR-210.

Graphical abstract
Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors
Authors: Li Xuanyi , Xu Yinqiu , Yao Hequan , Lin Kejiang
Published: June 2020

With the rise of artificial intelligence (AI) in drug discovery, de novo molecular generation provides new ways to explore chemical space. However, because de novo molecular generation methods rely on abundant known molecules, generated molecules may have a problem of novelty. Novelty is important in highly competitive areas of medicinal chemistry, such as the discovery of kinase inhibitors. In this study, de novo molecular generation based on recurrent neural networks was applied to discover a new chemical space of kinase inhibitors. During the application, the practicality was evaluated, and new inspiration was found. With the successful discovery of one potent Pim1 inhibitor and two lead compounds that inhibit CDK4, AI-based molecular generation shows potentials in drug discovery and development.
Mucormycosis in intensive care unit: surgery is a major prognostic factor in patients with hematological malignancy
Authors: Claustre Johanna , Larcher Romaric , Jouve Thomas , Truche Anne-Sophie , Nseir Saad , Cadiet Julien , Zerbib Yoann , Lautrette Alexandre , Constantin Jean-Michel , Charles Pierre-Emmanuel , Daubin Cedric , Coudroy Remi , Dellamonica Jean , Argaud Laurent , Phelouzat Pierre , Contou Damien , Pocquet Juliette , Voiriot Guillaume , Navellou Jean-Christophe , Lavagne Pierre , Durand Michel , Cornet Muriel , Schwebel Carole , Terzi Nicolas
Published: June 2020

Background

Mucormycosis is an invasive fungal infection, with an increasing incidence especially in patients with hematological malignancies. Its prognosis is poor because of its high invasive power and its intrinsic low susceptibility to antifungal agents. We aimed to describe the epidemiology of mucormycosis in intensive care units (ICU) and evaluate the outcomes. We performed a retrospective multi-center study in 16 French ICUs between 2008 and 2017. We compared the patients who survived in ICU and the patients who did not to identify factors associated with ICU survival. Then, we focused on the subgroup of patients with hematological malignancies.

Results

Mucormycosis was diagnosed in 74 patients during the study period. Among them, 60 patients (81%) were immunocompromised: 41 had hematological malignancies, 9 were solid organ transplant recipients, 31 received long-term steroids, 11 had diabetes, 24 had malnutrition. Only 21 patients survived to ICU stay (28.4%) with a median survival of 22 days (Q1–Q3 = 9–106) and a survival rate at day 28 and day 90, respectively, of 35.1% and 26.4%. Survivors were significantly younger (p = 0.001), with less frequently hematological malignancies (p = 0.02), and less malnutrition (p = 0.05). Median survival in patients with hematological malignancies (n = 41) was 15 days (Q1–Q3 = 5–23.5 days). In this subgroup, curative surgery was a major factor associated with survival in multivariate analysis (odds ratio = 0.71, [0.45–0.97], p < 0.001).

Conclusion

Overall prognosis of mucormycosis in ICU remains poor, especially in patients with hematological malignancies. In this subgroup of patients, a therapeutic strategy including curative surgery was the main factor associated with survival.
Robust image hashing with compressed sensing and ordinal measures
Authors: Tang Zhenjun , Zhang Hanyun , Lu Shenglian , Yao Heng , Zhang Xianquan
Published: June 2020

Image hashing is an efficient technology for processing digital images and has been successfully used in image copy detection, image retrieval, image authentication, image quality assessment, and so on. In this paper, we design a new image hashing with compressed sensing (CS) and ordinal measures. This hashing method uses a visual attention model called Itti model and Canny operator to construct an image representation, and exploits CS to extract compact features from the representation. Finally, the CS-based compact features are quantized via ordinal measures. L2 norm is used to judge similarity of hashes produced by the proposed hashing method. Experiments about robustness validation, discrimination test, block size discussion, selection of visual attention model, selection of quantization scheme, and effectiveness of the use of ordinal measures are conducted to verify performances of the proposed hashing method. Comparisons with some state-of-the-art algorithms are also carried out. The results illustrate that the proposed hashing method outperforms some compared algorithms in classification according to ROC (receiver operating characteristic) graph.
Racial/ethnic differences in the prevalence and incidence of metabolic syndrome in high-income countries: a protocol for a systematic review
Authors: Adjei Nicholas Kofi , Samkange-Zeeb Florence , Kebede Mihiretu , Saleem Maham , Heise Thomas L. , Zeeb Hajo
Published: June 2020

Background

Metabolic syndrome is a constellation of various cardiovascular and type 2 diabetes risk factors, such as abdominal obesity, atherogenic dyslipidemia, high blood pressure, and high blood glucose, but its prevalence varies widely by geographical region, sex, and race/ethnicity. The objective of this study is to examine the prevalence and incidence of metabolic syndrome among adults of different racial/ethnic origins in high-income countries.

Methods

We designed and registered a study protocol for a systematic review of descriptive epidemiological data. Observational studies (e.g., cross sectional and cohort studies) reporting morbidity data of metabolic syndrome and conducted in a wide range of adult people (e.g., different racial/ethnic origins, including migrants) will be included. The primary outcome will be the prevalence and incidence of metabolic syndrome. Secondary outcomes will be the prevalence and incidence of individual components of metabolic syndrome (e.g., abdominal obesity, dyslipidemia, high blood pressure, and high blood glucose). Literature searches will be conducted in several electronic databases (from inception onwards), including MEDLINE, Web of Science Core Collection (Science Citation Index and Social Science Citation Index), CINAHL, and Cochrane Library. Two investigators will independently screen all reference titles, abstracts, and full-text articles. The methodological quality (or potential bias) of selected studies will be appraised using an appropriate tool. Our results will be described narratively. Random-effects meta-analysis will be conducted, if feasible and appropriate. Additional analyses will be conducted to explore the potential sources of heterogeneity.

Conclusion

This systematic review will identify, evaluate, and integrate prevalence and incidence data of metabolic syndrome, with focus on racial/ethnic differences in high-income countries. We anticipate our findings may guide policy formulation and identify knowledge gaps in the literature that future research should address.

Systematic review registration

PROSPERO, CRD42020157189
Prevalence and determinants of alcohol use among adults living with HIV/AIDS in Ethiopia: a systematic review protocol
Authors: Mekuriaw Birhanie , Belayneh Zelalem , Molla Alemayehu , Mehare Tsegaye
Published: June 2020

Background

Alcohol use is a challenging problem which attributes to more than 5% of the overall global burden of disease. It is more common among persons with HIV infection than the general population. Although there are separate studies regarding people with HIV/AIDS in Ethiopia, their results are highly variable and discrepant. The objectives of this study will be to evaluate the prevalence of alcohol use and to identify its associated factors among people with HIV/AIDS in Ethiopia.

Methods

A systematic search of electronic databases (from inception onwards) of PubMed/MEDLINE, Embase, PsycINFO, and Cochrane Library will be conducted. Moreover, grey literatures will be searched from different sources (such as Google Scholar, OpenGrey, and World Health Organization websites). Reference lists of the selected articles will also be searched manually. Observational studies (cross-sectional, case-control, cohort) reporting the prevalence of alcohol use and/or its associated factors among adults with HIV/AIDS in Ethiopia will be included. The primary outcomes will be the prevalence of alcohol use among HIV/AIDS population. Secondary outcomes will be the determinants of alcohol use described in the included studies. Two reviewers will independently screen all citations and full-text articles and extract data. The studies’ methodological quality (or bias) will be appraised using an appropriate tool. If feasible, we will conduct a random effects meta-analysis of observational data. Heterogeneity of primary studies will be assessed using the I2 test. Prevalence estimates will be stratified according to gender, age, and geographical location. Small-study effects (publication bias) also will be examined.

Discussion

Our systematic review and meta-analysis will prevail the pooled prevalence of alcohol use and its determinants among people with HIV/AIDS in Ethiopia. The finding of this study will be helpful to design appropriate preventive and interventional strategies for alcohol use among people with HIV/AIDS. This can have direct or indirect policy responses and clinical implications.

Systematic review registration

PROSPERO CRD42019132524
Adult attachment style and maternal-infant bonding: the indirect path of parenting stress
Authors: Nordahl Dag , Rognmo Kamilla , Bohne Agnes , Landsem Inger Pauline , Moe Vibeke , Wang Catharina Elisabeth Arfwedson , Høifødt Ragnhild Sørensen
Published: June 2020

Background

The quality of maternal-infant bonding is related to important child outcomes. The literature has assumed that the ability to form relationships is a relatively stable trait, and research studies have suggested that a mother’s attachment style in close adult relationships is related to mother-infant bonding. The transition to parenthood is also often stressful, and the adult attachment style may relate to parenting stress in the first year after birth. Such stress could possibly have a negative relationship with the mother-infant bond. In the present study, we examined the associations between maternal adult attachment styles and the quality of mother-infant bonding and whether this relationship is mediated by parenting stress.

Methods

The present study sample comprised 168 women (mean age 31.0 years, SD 4.23 years). Between weeks 31 and 41 of gestation, the anxious and avoidant adult attachment dimensions were measured with the Experiences in Close Relationships questionnaire (ECR). Between 5 and 15 weeks after birth mother-infant bonding and parenting stress were measured with the Maternal Postnatal Attachment Scale (MPAS) and the Parenting Stress Index-Parent Domain (PSI-PD), respectively.

Results

Both attachment-related avoidance and attachment-related anxiety correlated significantly and negatively with mother-infant bonding. However, a regression analysis showed that only attachment-related avoidance was a significant predictor of mother-infant bonding when controlling for demographic variables and maternal mental health history. The relationship between the adult attachment style and bonding was mediated by parenting stress. Higher scores on attachment avoidance and anxiety were related to increased stress, which was related to decreased quality of bonding. The overall parent domain and the subscale of competence in the parent-related stress dimension mediated between attachment avoidance and bonding, and the overall parent domain and the subscales of competence and role restriction mediated between attachment anxiety and bonding. There was no direct relationship between the adult attachment style and mother-infant bonding when parenting stress was included as a mediator.

Conclusions

This study illustrates that maternal adult attachment style relates to mother-infant bonding. This relationship was mediated by parenting stress. The results may have implications for the early identification of mothers at risk of having bonding difficulties.
Development and Validation of a Clinical Polygenic Risk Score to Predict Breast Cancer Risk
Authors: Hughes Elisha , Tshiaba Placede , Gallagher Shannon , Wagner Susanne , Judkins Thaddeus , Roa Benjamin , Rosenthal Eric , Domchek Susan , Garber Judy , Lancaster Johnathan , Weitzel Jeffrey , Kurian Allison W. , Lanchbury Jerry S. , Gutin Alexander , Robson Mark
Published: June 2020

PURPOSE

Women with a family history of breast cancer are frequently referred for hereditary cancer genetic testing, yet < 10% are found to have pathogenic variants in known breast cancer susceptibility genes. Large-scale genotyping studies have identified common variants (primarily single-nucleotide polymorphisms [SNPs]) with individually modest breast cancer risk that, in aggregate, account for considerable breast cancer susceptibility. Here, we describe the development and empirical validation of an SNP-based polygenic breast cancer risk score.

METHODS

A panel of 94 SNPs was examined for association with breast cancer in women of European ancestry undergoing hereditary cancer genetic testing and negative for pathogenic variants in breast cancer susceptibility genes. Candidate polygenic risk scores (PRSs) as predictors of personal breast cancer history were developed through multivariable logistic regression models adjusted for age, cancer history, and ancestry. An optimized PRS was validated in 2 independent cohorts (n = 13,174; n = 141,160).

RESULTS

Within the training cohort (n = 24,259), 4,291 women (18%) had a personal history of breast cancer and 8,725 women (36%) reported breast cancer in a first-degree relative. The optimized PRS included 86 variants and was highly predictive of breast cancer status in both validation cohorts ( P = 6.4 × 10−66; P < 10−325). The odds ratio (OR) per unit standard deviation was consistent between validations (OR, 1.45 [95% CI, 1.39 to 1.52]; OR 1.47 [95% CI, 1.45 to 1.49]). In a direct comparison, the 86-SNP PRS outperformed a previously described PRS of 77 SNPs.

CONCLUSION

The validation and implementation of a PRS for women without pathogenic variants in known breast cancer susceptibility genes offers potential for risk stratification to guide surveillance recommendations.
Landscape of Genomic Alterations inIDHWild-Type Glioblastoma Identifies PI3K as a Favorable Prognostic Factor
Authors: Yan Yuanqing , Takayasu Takeshi , Hines Gabriella , Dono Antonio , Hsu Sigmund H. , Zhu Jay-Jiguang , Riascos-Castaneda Roy F. , Kamali Arash , Bhattacharjee Meenakshi B. , Blanco Angel I. , Tandon Nitin , Kim Dong H. , Ballester Leomar Y. , Esquenazi and Yoshua
Published: June 2020

PURPOSE

IDH wild-type (WT) glioblastoma (GBM) is an aggressive tumor with poor survival despite current therapies. The aim of this study was to characterize its genomic profile and determine whether a particular molecular signature is associated with improved survival outcomes.

PATIENTS AND METHODS

Tumor samples from 232 patients with IDH-WT GBM were sequenced, and the landscape of genomic alterations was fully delineated. Genomics data from The Cancer Genome Atlas (TCGA) cohort were analyzed for confirmation. Association of alterations with survival was evaluated in both univariable and multivariable approaches.

RESULTS

The genomic landscape of IDH-WT GBM revealed a high frequency of CDKN2A/B loss, TERT promoter mutations, PTEN loss, EGFR alteration, and TP53 mutations. Novel variants or gene mutations, such as ARID1B and MLL2, were identified. To better understand synergistic effects and facilitate decision making for precision medicine, we identified 11 pairs of gene alterations that tended to co-occur or were mutually exclusive, which were confirmed in the TCGA cohort. Survival analysis showed that genomic alterations in TP53 were associated with worse overall survival (OS). However, alterations in PI3K class I genes were associated with significantly better OS (univariable analysis: P = .002; multivariable analysis: hazard ratio [HR], 0.5785; P = .00162) and longer progression-free survival (univariable analysis: P = .0043; multivariable analysis: HR, 0.6228; P = .00913).

CONCLUSION

Genomic alterations in PI3K class I are a favorable prognostic factor in IDH-WT GBM. This new prognostic biomarker may facilitate risk stratification of patients, assist in clinical trial enrollment, and provide potential therapeutic targets
From Point Zero to the Future
Authors: Silvestre Helena
Published: June 2020

This text seeks to describe the territories of the favelas as a fertile ground for the birth of organizational forms that can strengthen struggles toward an emancipated society, in which life is free. It aims to trace the trajectory of resistance in those territories, the occupations, and evictions that shaped and continue shaping them. It highlights the feminized bodies in struggle against forced evictions of communities or carrying out occupations for housing: the conflictual recuperation of parts of the territory to construct commons that nourish our resistance. This effort is necessary because we cannot look at Indigenous women—in defense of forests—or Black women—defending immaterial ancestral territories—without recognizing that the women of the favelas are the daughters of those other women, continuing their resistance and resignifying it in places that are close to us and our everyday lives.
Evidence of two types of balance between stem cell mitosis and enterocyte nucleus growth in the Drosophila midgut
Authors: Tamamouna Vasilia , Panagi Myrofora , Theophanous Andria , Demosthenous Maria , Michail Maria , Papadopoulou Markella , Teloni Savvas , Pitsouli Chrysoula , Apidianakis Yiorgos
Published: June 2020

Systemic and stem cell niche-emanating cytokines and growth factors can promote regeneration, through mitosis. High mitosis, however, predisposes for all types of cancer and, thus, a trade-off exists between regeneration capacity and tissue homeostasis. Here, we study the role of tissue-intrinsic regenerative signaling in stem cell mitosis of adult Drosophila midgut of different genetic backgrounds. We provide evidence of two naturally occurring types of balance between mitosis and enterocyte nucleus growth: one based mostly on stem cell mitosis producing new cells and the other based mostly on the degree of young enterocyte nucleus size increase. Mitosis promotes intestinal host defense to infection, but predisposes for dysplasia in the form of stem cell-like clusters. Enterocyte nucleus growth also promotes host defense, without the drawback of promoting dysplasia. Through quantitative genetics, we identified eiger as an autocrine and paracrine inducer of stem cell mitosis. eiger expression in immature epithelial cells tilts the balance towards mitosis and dysplasia via a positive-feedback loop of highly mitotic stem cells sustaining more small nucleus enterocytes, which in turn supply more Eiger.
Drogas e medicamentos investigados para o tratamento do COVID-19
Authors: Neto Ulisses Estevam Alves , Pires Andressa Cavalcanti
Published: June 2020

Objetivo: determinar drogas e medicamentos sugeridos para o tratamento do covid-19. Métodos: nesta pesquisa, foram utilizados os estudos que estavam definidos como ainda não recrutando e em fase de recrutamento, disponíveis no site Clinical Trials, em que foram inseridos os meios de intervenção, por meio de drogas e medicamentos. Resultados: com os filtros aplicados, os estudos em que ainda não estavam recrutando somaram um total de 131, e nos estudos que estavam em fase de recrutamento, existiam 126 análises. Conclusão: de acordo com a busca ativa, tanto nos estudos ainda não recrutando, quanto nos que estavam em recrutamento, a hidroxicloroquina é o medicamento que está sendo mais investigado.
One-year test-retest reliability of ten vision tests in Canadian athletes
Authors: Aloosh Mehdi , Leclerc Suzanne , Long Stephanie , Zhong Guowei , Brophy James M. , Schuster Tibor , Steele Russell , Shrier Ian
Published: June 2020

Background: Vision tests are used in concussion management and baseline testing. Concussions, however, often occur months after baseline testing and reliability studies generally examine intervals limited to days or one week. Our objective was to determine the one-year test-retest reliability of these tests.

Methods: We assessed one-year test-retest reliability of ten vision tests in elite Canadian athletes followed by the Institut National du Sport du Quebec. We included athletes who completed two baseline (preseason) annual evaluations by one clinician within 365±30 days. We excluded athletes with any concussion or vision training in between the annual evaluations or presented with any factor that is believed to affect the tests (e.g. migraines). Data were collected from clinical charts. We evaluated test-retest reliability using Intraclass Correlation Coefficient (ICC) and 95% limits of agreement (LoA).

Results: We examined nine female and seven male athletes with a mean age of 22.7 (SD 4.5) years. Among the vision tests, we observed excellent test-retest reliability in Positive Fusional Vergence at 30cm (ICC=0.93) but this dropped to 0.55 when an outlier was excluded in a sensitivity analysis. There was good to moderate reliability in Negative Fusional Vergence at 30cm (ICC=0.78), Phoria at 30cm (ICC=0.68), Near Point of Convergence break (ICC=0.65) and Saccade (ICC=0.56). The ICC for Positive Fusional Vergence at 3m (ICC=0.56) also decreased to 0.21 after removing one outlier. We found poor reliability in Near Point of Convergence (ICC=0.47), Gross Stereoscopic Acuity (ICC=0.03) and Negative Fusional Vergence at 3m (ICC=0.0). ICC for Phoria at 3m was not appropriate because scores were identical in 14/16 athletes. 95% LoA of the majority of tests were ±40% to ±90%.

Conclusions: Five tests had good to moderate one-year test-retest reliability. The remaining tests had poor reliability. The tests would therefore be useful only if concussion has a moderate-large effect on scores.
A non-fluorescent HaloTag blocker for improved measurement and visualization of protein synthesis in living cells
Authors: Cohen Laurie D. , Boulos Ayub , Ziv Noam E.
Published: June 2020

Background: HaloTag is a modified bacterial enzyme that binds rapidly and irreversibly to an array of synthetic ligands, including chemical dyes. When expressed in live cells in conjunction with a protein of interest, HaloTag can be used to study protein trafficking, synthesis, and degradation. For instance, sequential HaloTag labeling with spectrally separable dyes can be used to separate preexisting protein pools from proteins newly synthesized following experimental manipulations or the passage of time. Unfortunately, incomplete labeling by the first dye, or labeling by residual, trapped dye pools can confound interpretation.

Methods: Labeling specificity of newly synthesized proteins could be improved by blocking residual binding sites. To that end, we synthesized a non-fluorescent, cell permeable blocker (1-chloro-6-(2-propoxyethoxy)hexane; CPXH), essentially the HaloTag ligand backbone without the reactive amine used to attach fluorescent groups.

Results: High-content imaging was used to quantify the ability of CPXH to block HaloTag ligand binding in live HEK cells expressing a fusion protein of mTurquoise2 and HaloTag. Full saturation was observed at CPXH concentrations of 5-10 µM at 30 min. No overt effects on cell viability were observed at any concentration or treatment duration. The ability of CPXH to improve the reliability of newly synthesized protein detection was then demonstrated in live cortical neurons expressing the mTurquoise2-HaloTag fusion protein, in both single and dual labeling time lapse experiments. Practically no labeling was observed after blocking HaloTag binding sites with CPXH when protein synthesis was suppressed with cycloheximide, confirming the identification of newly synthesized protein copies as such, while providing estimates of protein synthesis suppression in these experiments.

Conclusions: CPXH is a reliable (and inexpensive) non-fluorescent ligand for improving assessment of protein-of-interest metabolism in live cells using HaloTag technology.
Information and communication the concept of accounting theory
Authors: Akat'eva Marina
Published: June 2020

The monograph is devoted to theoretical and methodological aspects of information and communication of the concept of accounting theory — meaningful and professionally appraised by the author, including historical context. It considers the fundamental provisions of the concept formed in the respective paradigms, principles and postulates, presents the modern understanding of information and communication components of the accounting system of the economic entity, including civil-legal framework, practical issues of organization, planning, coordination and control of generated accounting information.
Intended for scientific workers and specialists of accounting and economic profile, other specialists, and graduate and undergraduate students.
Promotion Optimization for Multiple Items in Supermarkets
Authors: Cohen Maxime C. , Kalas Jeremy J. , Perakis Georgia
Published: June 2020

Promotions are a critical decision for supermarket managers, who must decide the price promotions for a large number of items. Retailers often use promotions to boost the sales of the different items by leveraging the cross-item effects. We formulate the promotion optimization problem for multiple items as a nonlinear integer program. Our formulation includes several business rules as constraints. Our demand models can be estimated from data and capture the postpromotion dip effect and cross-item effects (substitution and complementarity). Because demand functions are typically nonlinear, the exact formulation is intractable. To address this issue, we propose a general class of integer programming approximations. For demand models with additive cross-item effects, we prove that it is sufficient to account for unilateral and pairwise contributions and derive parametric bounds on the performance of the approximation. We also show that the unconstrained problem can be solved efficiently via a linear program when items are substitutable and the price set has two values. For more general cases, we develop efficient rounding schemes to obtain an integer solution. We conclude by testing our method on realistic instances and convey the potential practical impact for retailers.

This paper was accepted by Yinyu Ye, optimization.
Using Markov Chains to Determine Expected Propagation Time for Probabilistic Zero Forcing
Authors: Chan Yu , Curl Emelie , Geneson Jesse , Hogben Leslie , Liu Kevin , Odegard Isaac , Ross Michael
Published: June 2020

Zero forcing is a coloring game played on a graph where each vertex is initially colored blue or white and the goal is to color all the vertices blue by repeated use of a (deterministic) color change rule starting with as few blue vertices as possible. Probabilistic zero forcing yields a discrete dynamical system governed by a Markov chain. Since in a connected graph any one vertex can eventually color the entire graph blue using probabilistic zero forcing, the expected time to do this is studied. Given a Markov transition matrix for a probabilistic zero forcing process, an exact formula is established for expected propagation time. Markov chains are applied to determine bounds on expected propagation time for various families of graphs.
Does Cozen's phenomenon warrant surgical intervention?
Authors: Papamerkouriou Yvonne-Mary , Tsoumpos Pantelis , Tagaris George , Christodoulou George
Published: June 2020

Purpose

Proximal tibial metaphyseal fractures can be complicated by a late valgus deformity, referred to as Cozen's phenomenon. We studied children with such fractures to determine whether the child's age at the time of injury influenced the development of Cozen's as well as the occurrence of elongation. In addition, we explored whether the deformity resolved at long-term follow-up.

Methods

We conducted a retrospective study of 33 patients (six months to 14 years old). Mean follow-up was 8.8 years (3 to 25). We measured angulation of the fractured limb post-treatment, at maximum deformity and final follow-up, as well as elongation and compared them with the uninjured limb.

Results

Three of the fractures were treated surgically whereas the rest, nonoperatively. In all, 15 out of 33 fractures developed late valgus deformity between eight and 19 months (mean time 12.5 months). A total of 24 fractures developed elongation. We found no association of either of these with age. Angulation increased to a statistically significant level, from post-treatment to maximum deformity, and then decreased at final follow-up, leaving no statistically significant difference from the initial measurement. The difference in valgus between fractured and uninjured limb increased to a statistically significant level from post-treatment to maximum deformity and then decreased, leaving an excess from the initial measurement.

Conclusion

In almost half the patients, late valgus deformity developed within two years post-fracture and corrected to the initial post-treatment angles. Patients should be warned of this possibility and reassured of its natural resolution.

Level of evidence

IV
Clubfoot deformity in the Solomon Islands: Melanesian versus Polynesian ethnicity, a retrospective cohort study
Authors: Todd Maya Rani Louise Chandra , Kodovaru Stephen Sikaveke , Antoniou Georgia , Cundy Peter J.
Published: June 2020

Purpose

Congenital talipes equinovarus (CTEV) has a high incidence in the South Pacific, with New Zealand Maori and Polynesian rates of up to seven per 1000 live births, at least five times higher than the Caucasian population. A genetic component is suggested to explain this, however, there is little information regarding the difference of incidence between Polynesian and Melanesian ethnicity in the South Pacific. Our aim was to investigate the effects of ethnicity on the incidence of CTEV in the Solomon Islands, specifically comparing Melanesian and Polynesian ethnicity.

Methods

Between 2011 and 2017, data was collected in the Solomon Islands from over 40 clinics upon introduction of the Ponseti programme for treatment of CTEV. Records were kept using the validated Global Clubfoot Initiative data form. Ethnicity was documented, including family history.

Results

In total, 138 children presented during this period, with 215 affected feet reviewed and treated. In all, 74% of children had solely Melanesian parents and 6% Polynesian. Using the general population ethnic breakdown of 95.3% Melanesian and 3.1% Polynesian, the odds of CTEV in children of Melanesian parents were 0.41 times lower compared with the odds in children of Polynesian parents.

Conclusion

The results indicate that in the Solomon Islands, CTEV in Melanesian children was less than half as likely to occur in Polynesian children. Our findings also support the theories of minimal Polynesian genetic material persisting in the Solomon Islands and a different genetic risk of CTEV between Polynesians and Melanesians.

Level of Evidence

III
Expert knowledge and policymaking: a multi-disciplinary research agenda
Authors: Christensen Johan
Published: June 2020

The role of experts and expert knowledge in policymaking has attracted growing public and academic attention. Scholarship on the topic has, however, remained deeply fragmented. It is discussed in separate silos of the literature – such as evidence-based policymaking, epistemic communities, and ideas and politics – and this has hindered sustained empirical study. This article argues that to stimulate more systematic research on the role that experts play in policymaking and develop a theoretical understanding of it, we need to foster dialogue across these literatures. To facilitate this, the article critically reviews how the role of expert knowledge in policymaking is conceptualised and explained in existing literatures, and offers suggestions about how to create common ground for future research by reframing research around the question of the influence of experts, and examining more closely the administrative underpinnings of expert influence.
Fabric defect detection using a hybrid particle swarm optimization-gravitational search algorithm and a Gabor filter
Authors: So Yongguk , Kim Jongchol , Hwang Hyok
Published: June 2020

Recently, fabric defect inspection techniques have received attention in textile production procedures, since demands for various textile fabrics are growing. However, visual inspection for fabric defect detection is a very difficult problem because of the complexity of the fabric pattern and various defects. In this paper, we propose a method to detect the defects in fabric surfaces using the hybrid Particle Swarm Optimization-Gravitational Search Algorithm (PSO-GSA) and ellipse Gabor filter (EGF). In the proposed method, the hybrid PSO-GSA been employed to optimize the parameters of the EGF. Gabor filter parameters for the texture of the nondefective fabric images adjusted via the hybrid PSO-GSA with good convergence and solution characteristics. The defective fabric image is convoluted with the selected optimal Gabor filter, and we generate binary images by thresholding processing. The proposed method uses only one optimal filter, so fabric defect inspection is faster and more cost effective. Experimental results show that the proposed method is robust and achieves accurate detection of fabric defects.
Nonuniqueness of the quasinormal mode expansion of electromagnetic Lorentz dispersive materials
Authors: Gras A. , Lalanne P. , Duruflé M.
Published: June 2020

Any optical structure possesses resonance modes, and its response to an excitation can be decomposed onto the quasinormal and numerical modes of a discretized Maxwell operator. In this paper, we consider a dielectric permittivity that is an N-pole Lorentz function of the frequency. Even for discretized operators, the literature proposes different formulas for the coefficients of the quasinormal-mode expansion, and this comes as a surprise. We propose a general formalism, based on auxiliary fields, which explains why and evidences that there is, in fact, an infinity of mathematically sound possible expansion coefficients. The nonuniqueness is due to a choice of the linearization of Maxwell’s equations with respect to frequency and of the choice of the form of the source term. Numerical results validate the different formulas and compare their accuracy.
High harmonic generation in armchair carbon nanotubes
Authors: Zurrón-Cifuentes Óscar , Boyero-García Roberto , Hernández-García Carlos , Plaja Luis
Published: June 2020

We study high-order harmonic generation (HHG) in armchair-type single-wall carbon nanotubes (SWNTs) driven by ultrashort, mid-infrared laser pulses. For a SWNT with chiral indices (n, n), we demonstrate that HHG is dominated by bands |m| = n − 1 and that the cut-off frequency saturates with intensity, as it occurs in the case of single layer graphene. As a consequence, HHG in SWNTs can be described effectively as a one-dimensional periodic system, whose high-frequency emission can be modified through the proper control of the structural parameters. Additionally, we show that the HHG mechanism in nanotubes has some similarities to that previously reported in single layer graphene. However, as a main difference, the electron-hole pair excitation in SWNTs is connected to the non-adiabatic crossing through the first van Hove singularity of the |m| = n − 1 bands, instead of the crossing through the Dirac point that takes place in graphene.
Characterization of nanoporous Al2O3 films at terahertz frequencies
Authors: Zhai Min , Locquet A. , Jung Mi , Woo Deokha , Citrin D. S.
Published: June 2020

Terahertz birefringence in nanoporous

A
l

2

O

3

films grown on Al substrates is characterized nondestructively by polarization-resolved terahertz spectroscopy. Sparse deconvolution is used to find the film thicknesses from the data, showing good agreement with the values measured directly by destructive cross-sectional field-emission scanning electron microscopy.
Highly sensitive multi-stage terahertz parametric detector
Authors: Sakai Hikaru , Kawase Kodo , Murate Kosuke
Published: June 2020

In this Letter, we developed a high-sensitivity multi-stage terahertz (THz)-wave parametric detection system that operates at room temperature. This detection system has high sensitivity over a wide wavelength range through upconversion of a THz wave to near-infrared light. The broadband noise associated with parametric generation limited the detection sensitivity in the previous setup; however, in the multi-stage configuration using multiple

L
i
N
b
O

3

crystals, the THz parametric detection sensitivity was improved by spatially eliminating the broadband noise using an iris between the former and latter stages. With this improvement, the minimum detectable sensitivity at 1.05 THz approached 130 zJ (

z
J

=

10

−
21

J

), which is equivalent to 90 photons or less. Furthermore, by combining this detector with an injection-seeded THz-wave parametric generator, which is a high-power, tunable THz-wave source, the THz-wave measurement system achieved a maximum dynamic range of 125 dB.
All-optical non-linear activation function for neuromorphic photonic computing using semiconductor Fano lasers
Authors: Rasmussen Thorsten S. , Yu Yi , Mork Jesper
Published: June 2020

We predict that semiconductor Fano lasers can be used to realize an all-optical non-linear activation function for neuromorphic photonic computing. By exploiting optical control of a Fano mirror, the laser can generate optical pulses with low threshold energy, gigahertz repetition rates, and orders of magnitude suppression between the on- and off-states. Analytical estimates of the switching threshold energy, extinction ratio, and refractory period agree well with numerical results.