bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation and forecasting of food security based on fuzzy cognitive approach
Authors: Rogachev A F , Antamoshkina E N , Melikhova E V , Pieshenko T V , Belousov I S
Published: October 2020

The analysis of a set of groups of factors that form the food security (FS) of the state and its subjects is carried out, and an analytical review of known mathematical methods, as well as fuzzy models for their assessment is performed. The software tools for fuzzy cognitive modeling of the integral level of PB are justified. The key concepts of ensuring and evaluating FS are generalized and numerical estimates of their mutual influence are obtained based on a fuzzy cognitive approach. Along with the main groups of concepts «Production-Consumption-Stocks-Imports» listed in the national «Food security Doctrine», the constructed cognitive model also provides for accounting for additional ones. One of these factors-concepts is «Ecology», by which the authors understand the linguistic meaning of the integral level of the ecological state of the environment. The constructed cognitive map takes into account 11 basic concepts. It is shown that the advantage of the mathematical apparatus of impulse cognitive modeling, selected for research and implemented on a computer, is the possibility of system forecasting the development trends of the systems under study and the results of management decisions. In addition, it becomes possible to identify non-obvious consequences that are difficult to predict by expert method when the number of factors taken into account increases. The results of the analysis, obtained mainly in linguistic terms, are approximate due to the fuzzy nature of the evaluation scales used and reflect only the main trends in the development of the simulated SES. The results obtained allow us to justify a set of measures for the development and implementation of organizational and economic measures for the implementation of the state policy to ensure food and environmental security of the region.
Logical architecture for green technology applications in Roehren-und Pumpenwerk BAUER GmbH (Austria)
Authors: Roiss O , Melikhov V V , Medvedeva L N
Published: October 2020

The research shows that global climate change and population growth increase the pressure on the planet’s natural resources, especially water and land resources. These statistics reveal the state, dynamics and prospects of agricultural development, the use of agricultural land in the EU and Austria. Data on the use of different types of irrigation by Austrian farmers are provided. The use of Austrian irrigation technology in world agriculture with GPS navigation, irrigation programming function based on data obtained using smart controllers, making it easier for the farmer to predict the future crop yield and consumption of water and energy resources. It is shown that the aspiration of modern companies, such as Roehren-und Pumpenwerk BAUER GmbH (Austria), to use green technologies is responsible behaviour before the future generations of the planet Earth.
Review of modern technologies intellectual decision support in the reclamation of agricultural crops
Authors: Tokarev K E , Lebed N I , Nekrasova T N , Popova O V
Published: October 2020

According to the “Strategy for scientific and technological development of the Russian Federation “and within the framework of the “Digital agriculture” program, in the coming years, one of the priority areas of development is the transition to highly productive agro-aquatic farming. The key vector for the development of scientific and technological progress in the agro-industrial complex is to improve the management of irrigated agriculture, increase productivity on reclaimed land and resource conservation through the development of intelligent decision support systems, digital information technologies and mathematical models of agricultural reproduction. The theoretical and methodological basis of the research is the works of domestic and foreign scientists in the field of information technologies for decision support, mathematical modeling and programming, optimization of technical parameters for the operation of reclamation systems. Relevance of the review of the theory and technologies of crop irrigation management using mathematical models and intelligent technologies at the stage of agricultural digitalization. this is due to the need to create a new generation of reclamation systems that use modern achievements of scientific and technological progress, which will make it possible to practically implement the ideas of highly efficient and environmentally friendly agriculture on irrigated lands.
Aspiration-assisted bioprinting of co-cultured osteogenic spheroids for bone tissue engineering
Authors: Heo Dong Nyoung , Ayan Bugra , Dey Madhuri , Banerjee Dishary , Wee Hwabok , Lewis Gregory S , Ozbolat Ibrahim T
Published: October 2020

Conventional top-down approaches in tissue engineering involving cell seeding on scaffolds have been widely used in bone engineering applications. However, scaffold-based bone tissue constructs have had limited clinical translation due to constrains in supporting scaffolds, minimal flexibility in tuning scaffold degradation, and low achievable cell seeding density as compared with native bone tissue. Here, we demonstrate a pragmatic and scalable bottom-up method, inspired from embryonic developmental biology, to build three-dimensional (3D) scaffold-free constructs using spheroids as building blocks. Human umbilical vein endothelial cells (HUVECs) were introduced to human mesenchymal stem cells (hMSCs) (hMSC/HUVEC) and spheroids were fabricated by an aggregate culture system. Bone tissue was generated by induction of osteogenic differentiation in hMSC/HUVEC spheroids for 10 d, with enhanced osteogenic differentiation and cell viability in the core of the spheroids compared to hMSC-only spheroids. Aspiration-assisted bioprinting (AAB) is a new bioprinting technique which allows precise positioning of spheroids (11% with respect to the spheroid diameter) by employing aspiration to lift individual spheroids and bioprint them onto a hydrogel. AAB facilitated bioprinting of scaffold-free bone tissue constructs using the pre-differentiated hMSC/HUVEC spheroids. These constructs demonstrated negligible changes in their shape for two days after bioprinting owing to the reduced proliferative potential of differentiated stem cells. Bioprinted bone tissues showed interconnectivity with actin-filament formation and high expression of osteogenic and endothelial-specific gene factors. This study thus presents a viable approach for 3D bioprinting of complex-shaped geometries using spheroids as building blocks, which can be used for various applications including but not limited to, tissue engineering, organ-on-a-chip and microfluidic devices, drug screening and, disease modeling.
Wolf effect in the scattering of polychromatic radiation by two spheres having parity-time symmetry
Authors: Vieira R A , Brandão P A
Published: October 2020

It was recently proposed (P A Brandão and S B Cavalcanti 2019 Phys. Rev. A 100 043822) that two small (Dirac) scatterers, one having gain and the other having loss, drastically modifies the spectral density of the scattered radiation field. Here, we extend this previous work by studying the scattering of stochastic radiation by two finite spheres having gain and loss, satisfying the parity-time symmetry condition, and verifying the spectral changes in frequency domain, i.e. the non-Hermitian Wolf effect. Under the Born approximation, we analytically found the specific frequencies where the spectral density of the scattered field vanishes and show that they depend on the gain and loss parameter γ of each material. This is evidence of a non-Hermitian Wolf effect, meaning that the spectrum can be tuned by the gain/loss properties of the system. We have also shown that there is a π/2 phase shift when

γ
≫
1

compared to the Hermitian configuration (γ = 0).
Effects of chirality and stacking on the thermal expansion effects of graphene
Authors: Yang Ning , Li Cheng , Tang Yong
Published: October 2020

Graphene has huge application potential in the field of micro-nano devices, and due to the micro/nano-level application size, the thermal expansion coefficient of graphene has a certain impact on device performance. In this paper, a comprehensive study was carried out by molecular dynamics on the in-plane and through-plane thermal expansion effect of graphene. First of all, the in-plane thermal expansion coefficients of zigzag and armchair graphene were analyzed; they were similar and relatively close to the experiment value in the temperature range of 223–428 K. Secondly, the through-plane thermal expansion effect of double-layered graphene was investigated; the thermal expansion coefficient of through-plane was an order of magnitude larger than that of in-plane. Finally, the influence of graphene stacking on the thermal expansion effect was studied; Order-stacked graphene has a greater thermal expansion effect than that of AB- and ABC-stacked graphene. These discoveries in this article are of great significance to the development and application of graphene-based micro-nano devices.
Mn3GaC inverse perovskite thin films by magnetron sputtering from elemental targets
Authors: Petruhins Andrejs , Ingason Arni Sigurdur , Olafsson Sveinn , Rosen Johanna
Published: October 2020

We have deposited epitaxial thin films of the inverse perovskite Mn3GaC using magnetron sputtering from elemental targets. Two substrates were used, MgO (111) and (100), resulting in corresponding orientation of the Mn3GaC thin films. Both samples displayed magnetic properties consistent with an AFM to FM transition at ∼170 K and a Curie temperature around 265 K, evaluated with vibrating sample magnetometry (in-plane measurements). These two ground states are further supported by first principles calculations. Based on that the two orientations of Mn3GaC display very similar magnetic properties, it can be concluded that shape anisotropy dominates over the material’s easy axis.
Photoluminescent properties of liposome-encapsulated amine-functionalized nanodiamonds
Authors: Douda J , González-Vargas C R , Mota-Díaz I I , Basiuk E V , Hernández-Contreras X A , Fuentes-García J A , Bornacelli J , Torres-Torres C
Published: October 2020

In the present work, amine-functionalized nanodiamonds (NDs) have been encapsulated in liposomes and studied in order to observe the modification of their photoluminescence properties. NDs were functionalized with aromatic amines such as 1-aminopyrene and 2-aminofluorene, and the aliphatic amine 1-octadecylamine. Morphology, structural and optical properties of NDs and amine-modified NDs were analyzed by transmission electron microscopy, atomic force microscopy, scanning electron microscopy, and photoluminescence. The amine-functionalized NDs were successfully encapsulated in lecithin liposomes prepared by the green and conventional methods. The obtained results show significant changes in photoluminescent properties of functionalized NDs, and were more potentialized after liposome encapsulation. Our findings could be applied in the development of new kinds of water-dispersible fluorescent hybrids, liposome-NDs, with the capability of drug encapsulation for use in diagnostics and therapy (theragnostic liposomes). All-optical sensors with possibilities for tailoring their response for other biomedical applications can be also contemplated.
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor
Authors: Cai Lijun , Ren Xuanbai , Fu Xiangzheng , Peng Li , Gao Mingyu , Zeng Xiangxiang
Published: October 2020

Motivation

Enhancers are non-coding DNA fragments with high position variability and free scattering. They play an important role in controlling gene expression. As machine learning has become more widely used in identifying enhancers, a number of bioinformatic tools have been developed. Although several models for identifying enhancers and their strengths have been proposed, their accuracy and efficiency have yet to be improved.

Results

We propose a two-layer predictor called ‘iEnhancer-XG.’ It comprises a one-layer predictor (for identifying enhancers) and a second classifier (for their strength) and uses ‘XGBoost’ as a base classifier and five feature extraction methods, namely, k-Spectrum Profile, Mismatch k-tuple, Subsequence Profile, Position-specific scoring matrix (PSSM) and Pseudo dinucleotide composition (PseDNC). Each method has an independent output. We place the feature vector matrix into the ensemble learning for fusion. This experiment involves the method of ‘SHapley Additive explanations’ to provide interpretability for the previous black box machine learning methods and improve their credibility. The accuracies of the ensemble learning method are 0.811 (first layer) and 0.657 (second layer). The rigorous 10-fold cross-validation confirms that the proposed method is significantly better than existing technologies.

Availability and implementation

The source code and dataset for the enhancer predictions have been uploaded to https://github.com/jimmyrate/ienhancer-xg.

Supplementary information

Supplementary data are available at Bioinformatics online.
Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes
Authors: Hao Nan , Xin Huawei , Shi Xiaowei , Xin Jie , Zhang Haijuan , Guo Shaofen , Wang Zhen , Hao Chunxiang
Published: October 2020

Motivation

Exposure of mouse embryos to atrazine decreased histone tri-methylation at lysine 4 (H3K4me3) and increased expression of alternatively spliced RNA in the third generation. Specificity protein (SP) family motifs were enriched in the promoters of genes encoding differentially expressed alternative transcripts.

Results

H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) of mouse sperm, preimplantation embryo development and male gonad primordial germ cells (PGCs) were analysed to identify the paternal reprogramming-escape H3K4me3 regions (RERs). In total, 251 RERs selected harbour H3K4me3 marks in sperm, with signals occurring in the paternal genome during early development and in male gonad PGCs, and 179 genes had RERs within 1 kb of transcription start sites (TSSs). These genes were significantly enriched in the gene ontology term ‘RNA splicing’, and SP1/SP2/SP3 motifs were enriched in RER-associated H3K4me3 peaks. Overall, the H3K4me3 marks within TSSs of RNA splicing genes survived two rounds of the epigenetic reprogramming process.

Supplementary information

Supplementary data are available at Bioinformatics online.
HPV+ oropharyngeal squamous cell carcinomas from patients with two tumors display synchrony of viral genomes yet discordant mutational profiles and signatures
Authors: Faden Daniel L , Langenbucher Adam , Kuhs Krystle , Lewis James S , Mirabello Lisa , Yeager Meredith , Boland Joseph F , Bass Sara , Steinberg Mia , Cullen Michael , Lawrence Michael S , Ferris Robert L
Published: October 2020

Human papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma (HPV + OPSCC) is increasing in prevalence in the USA, as are cases of patients with multiple HPV + OPSCCs (mHPV + OPSCC). mHPV + OPSCCs present a unique opportunity to examine HPV + OPSCC mutation acquisition and evolution. We performed sequencing of the viral genome, somatic exome and somatic transcriptome from 8 patients each with 2 spatially distinct HPV + OPSCCs, and 37 ‘traditional’ HPV + OPSCCs to first address if paired tumors are caused by the same viral isolate and next, if acquired alterations, and the underlying processes driving mutagenesis, are shared within pairs. All tumor pairs contained viral genomes from the same HPV type 16 sublineage and differed by 0–2 clonal single nucleotide polymorphisms (SNPs), suggesting infection with the same viral isolate. Despite this, there was significant discordance in expression profiles, mutational burden and mutational profiles between tumors in a pair, with only two pairs sharing any overlapping mutations (3/3343 variants). Within tumor pairs there was a striking discrepancy of mutational signatures, exemplified by no paired tumors sharing high APOBEC mutational burden. Here, leveraging mHPV + OPSCCs as a model system to study mutation acquisition in virally mediated tumors, in which the germline, environmental exposures, immune surveillance and tissue/organ type were internally controlled, we demonstrate that despite infection by the same viral isolate, paired mHPV + OPSCCs develop drastically different somatic alterations and even more strikingly, appear to be driven by disparate underlying mutational processes. Thus, despite a common starting point, HPV + OPSCCs evolve through variable mutational processes with resultant stochastic mutational profiles.
Economic Evaluations of New Antibiotics: The High Potential Value of Reducing Healthcare Transmission Through Decolonization
Authors: Toth Damon J A , Samore Matthew H , Nelson Richard E
Published: October 2020

Background

Antibiotics designed to decolonize carriers of drug-resistant organisms could offer substantial population health benefits, particularly if they can help avert outbreaks by interrupting person-to-person transmission chains. However, cost effectiveness of an antibiotic is typically evaluated only according to its benefits to recipients, which can be difficult to demonstrate for carriers of an organism that may not pose an immediate health threat to the carrier.

Methods

We developed a mathematical transmission model to quantify the effects of 2 hypothetical antibiotics targeting carbapenem-resistant Enterobacteriaceae (CRE) among long-term acute care hospital inpatients: one assumed to decrease the death rate of patients with CRE bloodstream infections (BSIs) and the other assumed to decolonize CRE carriers after clinical detection. We quantified the effect of each antibiotic on the number of BSIs and deaths among patients receiving the drug (direct effect) and among all patients (direct and indirect effect) compared to usual care. We applied these results to a cost-effectiveness analysis with effectiveness outcome of life-years gained and assumed costs for antibiotic doses and for CRE BSI.

Results

The decolonizing antibiotic, once indirect effects were included, produced increased relative effectiveness and decreased relative costs compared to both usual care and the BSI treatment antibiotic. In fact, in most scenarios, the decolonizing drug was the dominant treatment strategy (ie, less costly and more effective).

Conclusions

Antibiotics that decolonize carriers of drug-resistant organisms can be highly cost-effective when considering indirect benefits within populations vulnerable to outbreaks. Public health could benefit from finding ways to incentivize development of decolonizing antibiotics in the US, where drugs with unclear direct benefits to recipients would pose difficulties in achieving FDA approval and financial benefit to the developer.
Rural School-Based Mental Health Services: Parent Perceptions of Needs and Barriers
Authors: van Vulpen Kimberly Searcey , Habegar Amy , Simmons Teresa
Published: October 2020

The benefits of school-based mental health services have been supported in prior research and literature. Studies have shown that approximately one in five youths in schools today have diagnosable mental health disorders. However, research has identified that close to 70 percent of those youths do not receive the services they need. This gap in care has a significant impact on the academic, social, and emotional well-being of youths. Parent involvement is essential in bridging services. However, parents often face barriers in accessing mental health care for their child. The aim of this study was to explore parent perceptions of needs and barriers to school-based mental health services. This exploratory study included 607 parent and guardian respondents. Findings showed that parents were overwhelmingly in support of schools being involved in addressing the mental health needs of students. Anxiety, depression, and bullying were the top emotional and behavioral issues that parents recognized as the main challenge for their child. Lack of parent support, understanding that mental health issues even exist in youths, and lack of supportive school programs were identified as key factors that place youths at risk of not receiving the services they need.
Clinical Outcomes of Covid-19 in Patients With Inflammatory Bowel Disease: A Nationwide Cohort Study
Authors: Derikx Lauranne A A P , Lantinga Marten A , de Jong Dirk J , van Dop Willemijn A , Creemers Rob H , Römkens Tessa E H , Jansen Jeroen M , Mahmmod Nofel , West Rachel L , Tan Adriaan C I T L , Bodelier Alexander G L , Gorter Moniek H P , Boekema Paul J , Halet Eric R C , Horjus Carmen S , van Dijk Maarten A , Hirdes Meike M C , Epping Stippel Ludger S M , Jharap Bindia , Lutgens Maurice W M D , Russel Maurice G , Gilissen Lennard P L , Nauta Sjoukje , van Bodegraven Adriaan A , Hoentjen Frank
Published: October 2020

Background and Aims

The COVID-19 risk and disease course in inflammatory bowel disease [IBD] patients remains uncertain. Therefore, we aimed to assess the clinical presentation, disease course, and outcomes of COVID-19 in IBD patients. Second, we determined COVID-19 incidences in IBD patients and compared this with the general population.

Methods

We conducted a multicentre, nationwide IBD cohort study in The Netherlands and identified patients with COVID-19. First, we assessed the COVID-19 disease course and outcomes. Second, we compared COVID-19 incidences between our IBD study cohort and the general Dutch population.

Results

We established an IBD cohort of 34 763 patients. COVID-19 was diagnosed in 100/34 763 patients [0.29%]; 20/100 of these patients [20%] had severe COVID-19 defined as admission to the intensive care unit, mechanical ventilation, and/or death. Hospitalisation occurred in 59/100 [59.0%] patients and 13/100 [13.0%] died. All patients who died had comorbidities and all but one were ≥65 years old. In line, we identified ≥1 comorbidity as an independent risk factor for hospitalisation (odds ratio [OR] 4.20, 95% confidence interval [CI] 1.58–11.17,; p = 0.004). Incidences of COVID-19 between the IBD study cohort and the general population were comparable (287.6 [95% CI 236.6–349.7] versus 333.0 [95% CI 329.3–336.7] per 100000 patients, respectively; p = 0.15).

Conclusions

Of 100 cases with IBD and COVID-19, 20% developed severe COVID-19, 59% were hospitalised and 13% died. A comparable COVID-19 risk was found between the IBD cohort [100/34 763 = 0.29%] and the general Dutch population. The presence of ≥1 comorbidities was an independent risk factor for hospitalisation due to COVID-19.
Atrial fibrillation in heart failure with reduced ejection fraction: a case report of exercise training
Authors: Guimarães Guilherme Veiga , Roque Jean Marcelo , Machado Alexander D T , Fernandes-Silva Miguel Morita , Chizzola Paul Roberto , Bocchi Edimar Alcides
Published: October 2020

Background

Heart failure (HF) and atrial fibrillation (AF) are often concomitant and act in a vicious cycle. Atrial fibrillation is associated with greater functional limitations and increased morbidity and mortality in patients with HF. Moreover, AF associated with HF increases patients' physical inactivity, worsening their clinical condition, and prognosis. Exercise training is safe and has clear benefits in HF. However, these benefits have not been demonstrated when AF is associated with HF.

Case summary

We present the case of a 57-year-old man with permanent AF and HF with reduced ejection fraction, who underwent 12 weeks of exercise training that included cardiopulmonary exercise testing, neuromuscular sympathetic activity (NMSA), and muscle blood flow (MBF) before and after training.

Discussion

Exercise training was shown to have a potential benefit in reducing the activity of the sympathetic nerve and increasing muscle blood flow, as well as increasing VO2peak and decreasing the VE/VCO2 slope in a patient with AF associated with HF with reduced ejection fraction. These results may indicate favourable clinical implications in this group of patients.
The burden of cholesterol accumulation through the lifespan: why pharmacological intervention should start earlier to go further?
Authors: Zambon Alberto , Mello e Silva Alberto , Farnier Michel
Published: October 2020

Among the cardiovascular risk factors, cholesterol-rich atherogenic lipoproteins play a central role in the pathogenesis of atherosclerosis. In middle-aged adults, the size of the total atherosclerotic plaque burden is influenced by both the concentration of circulating atherogenic lipoproteins and the total duration of exposure to these lipoproteins. This review describes the evidence supporting a causal link between lifelong elevations in atherogenic lipoproteins and future risk of atherosclerosis; evidence strengthened by recent epidemiological, genetic, and clinical data. By consequence, adolescence and early adulthood are a crucial time for determining later cardiovascular disease risk. Arguments showing that early optimal lipid control leads to improved outcomes will be presented and suggestions put forward for how those most at risk should be identified and managed.
Ulcerative Colitis Narrative Global Survey Findings: Communication Gaps and Agreements Between Patients and Physicians
Authors: Rubin David T , Hart Ailsa , Panaccione Remo , Armuzzi Alessandro , Suvanto Ulla , Deuring J Jasper , Woolcott John , Cappelleri Joseph C , Steinberg Kathy , Wingate Laura , Schreiber Stefan
Published: October 2020

Background

The Ulcerative Colitis (UC) Narrative global surveys examined patient and physician perspectives on living with UC and tried to identify gaps in optimal care. Questions explored patient-physician interactions, UC management goals, and resources for improving communication.

Methods

Questionnaires were conducted across 10 countries, covering aspects of UC including diagnosis, treatment, and impact on patient quality of life, in addition to standard demographic information. Descriptive statistics were calculated.

Results

Globally, 2100 patients and 1254 physicians were surveyed (from August 2017 to February 2018). Results showed 85% of patients were satisfied with the communication they had with their physician, including discussions relating to symptoms (86%) and medication options (81%). However, 72% of patients wished for more information and support at initial diagnosis, and 48% did not feel comfortable talking to their physician about emotional concerns. Most patients (71%) set UC management goals with their physician. Both patients (63%) and physicians (79%) wished for longer appointments. Although 84% of physicians believed patient advocacy organizations to be important in UC management, more than half (54%) never discussed them with patients.

Conclusions

These survey results highlight overall patient satisfaction with patient-physician communication but emphasize areas for improvement, such as patient desire to have more information earlier in their disease course. There is an unmet need for better information, materials, and support. Physicians need to consider which of the available tools and resources can help patients talk more openly, and accurately, because informed patients are more likely to engage with physicians in a shared decision-making process.
Chern Class Inequalities on Polarized Manifolds and Nef Vector Bundles
Authors: Li Ping , Zheng Fangyang
Published: October 2020

This article is concerned with Chern class and Chern number inequalities on polarized manifolds and nef vector bundles. For a polarized pair $(M,L)$ with $L$ very ample, our 1st main result is a family of sharp Chern class inequalities. Among them the 1st one is a variant of a classical result and the equality case of the 2nd one is a characterization of hypersurfaces. The 2nd main result is a Chern number inequality on it, which includes a reverse Miyaoka–Yau-type inequality. The 3rd main result is that the Chern numbers of a nef vector bundle over a compact Kähler manifold are bounded below by the Euler number. As an application, we classify compact Kähler manifolds with nonnegative bisectional curvature whose Chern numbers are all positive. A conjecture related to the Euler number of compact Kähler manifolds with nonpositive bisectional curvature is proposed, which can be regarded as a complex analogue to the Hopf conjecture.
Utility of Point of Care and Rapid Diagnostics in Humanitarian Emergencies
Authors: Chadwick Stephen , Townes David A , Perrone Lucy A
Published: October 2020

Background

In 2019, there were 70.8 million forcibly displaced people worldwide. Among the top causes of morbidity and mortality were measles, diarrhea, respiratory illness, and malaria. Availability of accurate diagnostics that are of low complexity, affordable, and produce timely results on site without the need for expensive laboratory equipment, extensive training, or distant transport of samples, are essential tools in the response to humanitarian emergencies (HE). Early detection of infectious diseases with epidemic potential and coordinated outbreak response, can result in significant decrease in morbidity and mortality.

Content

This review explores the utility of point of care and rapid diagnostic tests (POCT/RDTs) in HE and presents a review and analysis of the low complexity, availability, and ease of use of these diagnostic modalities that make them helpful tools in these settings, despite the generally lower test performance metrics associated with them over conventional laboratory-based assays. We review the literature to understand how POCT/RDTs have been used in HE response to produce lifesaving information without the need for a robust system for transporting test samples to more sophisticated laboratories, as this is often prohibitive in areas affected by conflict or natural disasters.

We propose that POCT/RDTs be considered essential healthcare tools provided to countries following a HE and suggest that UN agencies and vulnerable countries include effective RDTs in their essential diagnostics as part of their national preparedness and response plans.
Lighting the way: advances in transcriptional regulation and integrative crosstalk of melatonin biosynthetic enzymes in cassava
Authors: Wei Yunxie , Bai Yujing , Cheng Xiao , Reiter Russel J , Yin Xiaojian , Shi Haitao
Published: October 2020

This work highlights the transcriptional regulation and integrative protein complex of melatonin biosynthetic enzymes, and raises the challenges in understanding the precise regulation of plant melatonin biosynthetic enzymes and the underlying crosstalk.
A small secreted protein from Zymoseptoria tritici interacts with a wheat E3 ubiquitin ligase to promote disease
Authors: Karki Sujit Jung , Reilly Aisling , Zhou Binbin , Mascarello Maurizio , Burke James , Doohan Fiona , Douchkov Dimitar , Schweizer Patrick , Feechan Angela
Published: October 2020

Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major threat to wheat production worldwide. The Z. tritici genome encodes many small secreted proteins (ZtSSPs) that are likely to play a key role in the successful colonization of host tissues. However, few of these ZtSSPs have been functionally characterized for their role during infection. In this study, we identified and characterized a small, conserved cysteine-rich secreted effector from Z. tritici which has homologues in other plant pathogens in the Dothideomycetes. ZtSSP2 was expressed throughout Z. tritici infection in wheat, with the highest levels observed early during infection. A yeast two-hybrid assay revealed an interaction between ZtSSP2 and wheat E3 ubiquitin ligase (TaE3UBQ) in yeast, and this was further confirmed in planta using bimolecular fluorescence complementation and co-immunoprecipitation. Down-regulation of this wheat E3 ligase using virus-induced gene silencing increased the susceptibility of wheat to STB. Together, these results suggest that TaE3UBQ is likely to play a role in plant immunity to defend against Z. tritici.
Detailed Studies of IPHAS sources. II. Sab 19, a true planetary nebula and its mimic crossing the Perseus Arm.
Authors: Guerrero M A , Ortiz R , Sabin L , Ramos-Larios G , Alfaro E J
Published: October 2020

The INT Photometric Hα Survey (IPHAS) has provided us with a number of new-emission line sources, among which planetary nebulae (PNe) constitute an important fraction. Here we present a detailed analysis of the IPHAS nebula Sab 19 (IPHASX J055242.8+262116) based on radio, infrared, and optical images and intermediate- and high-dispersion longslit spectra. Sab 19 consists of a roundish 0.10 pc in radius double-shell nebula surrounded by a much larger 2.8 pc in radius external shell with a prominent H-shaped filament. We confirm the nature of the main nebula as a PN whose sub-solar N/O ratio abundances, low ionized mass, peculiar radial velocity, and low-mass central star allow us to catalog it as a type III PN. Apparently, the progenitor star of Sab 19 became a PN when crossing the Perseus Arm during a brief visit of a few Myr. The higher N/O ratio and velocity shift ≃40  km s−1 of the external shell with respect to the main nebula and its large ionized mass suggest that it is not truly associated with Sab 19, but it is rather dominated by a Strömgren zone in the interstellar medium ionized by the PN central star.
Multiwaveband quasi-periodic oscillation in the blazar 3C 454.3
Authors: Sarkar Arkadipta , Gupta Alok C , Chitnis Varsha R , Wiita Paul J
Published: October 2020

We report the detection (>4σ) of a quasi-periodic oscillation (QPO) in the gamma-ray light curve of 3C 454.3 along with a simultaneous marginal QPO detection (>2.4σ) in the optical light curves. Periodic flux modulations were detected in both of these wavebands with a dominant period of ∼47 d. The gamma-ray QPO lasted for over 450 d (from MJD 56800 to 57250), resulting in over nine observed cycles which is among the highest number of periods ever detected in a blazar light curve. The optical light curve was not well sampled for almost half of the gamma-ray QPO span due to the daytime transit of the source, which could explain the lower significance of the optical QPO. Autoregressive Integrated Moving Average (ARIMA) modelling of the light curve revealed a significant, exponentially decaying, trend in the light curve during the QPO, along with the 47 d periodicity. We explore several physical models to explain the origin of this transient quasi-periodic modulation and the overall trend in the observed flux with a month-like period. These scenarios include a binary black hole system, a hotspot orbiting close to the innermost stable circular orbit of the supermassive black hole, and precessing jets. We conclude that the most likely scenario involves a region of enhanced emission moving helically inside a curved jet. The helical motion gives rise to the QPO and the curvature (∼0.05○ pc−1) of the jet is responsible for the observed trend in the light curve.
Cosmological consequences of intrinsic alignments supersample covariance
Authors: Ansarifard Saeed , Movahed S M S
Published: October 2020

We examine cosmological constraints from high-precision weak-lensing surveys including supersample covariance (SSC) due to the finite survey volume. Specifically, we focus on the contribution of beat coupling in the intrinsic alignments as a part of full cosmic shear signal under flat-sky approximation. The SSC-effect grows by going to lower redshift bin and indicates considerable footprint on the intermediate and high multipoles for cumulative signal-to-noise ratio (SNR). The SNR is reduced by $\approx 10{{\ \rm per\ cent}}$ as a consequence of including the intrinsic alignment SSC, for the full cosmic shear signal, depending on the amplitude of intrinsic alignments, the ellipticity dispersion, and the survey redshift ranges, while the contribution of photometric redshift error can be ignored in the cumulative SNR. Using the Fisher-matrix formalism, we find that the impact of large modes beyond the volume of the surveys on the small modes alters the intrinsic alignments. However, corresponding impact on the cosmological parameters’ estimation is marginal compared to that of for gravitational weak lensing, particularly, when all available redshift bins are considered. Our results also demonstrate that including SSC-effect on the intrinsic alignments in the analytical covariance matrix of full cosmic shear leads to increase marginally the confidence interval for σ8 by $\approx 10{{\ \rm per\ cent}}$ for a sample with almost high intrinsic alignment amplitude.
Testing the star formation scaling relations in the clumps of the North American and Pelican nebulae cloud complex
Authors: Das Swagat R , Jose Jessy , Samal Manash R , Zhang Shaobo , Panwar Neelam
Published: October 2020

The processes that regulate star formation within molecular clouds are still not well understood. Various star formation scaling relations have been proposed as an explanation, one of which is to formulate a relation between the star formation rate surface density $\rm \Sigma _{SFR}$ and the underlying gas surface density $\rm \Sigma _{gas}$. In this work, we test various star formation scaling relations, such as the Kennicutt–Schmidt relation, the volumetric star formation relation, the orbital time model, the crossing time model and the multi free-fall time-scale model, towards the North American Nebula and Pelican Nebula and in the cold clumps associated with them. Measuring stellar mass from young stellar objects and gaseous mass from CO measurements, we estimate the mean $\rm \Sigma _{SFR}$, the star formation rate per free-fall time and the star formation efficiency for clumps to be 1.5 $\rm M_{\odot}\, yr^{-1}\, kpc^{-2}$, 0.009 and 2.0 per cent, respectively, while for the whole region covered by both nebulae (which we call the ‘NAN’ complex) the values are 0.6 $\rm M_{\odot}\, yr^{-1}\, kpc^{-2}$, 0.0003 and 1.6 per cent, respectively. For the clumps, we notice that the observed properties are in line with the correlation obtained between $\rm \Sigma _{SFR}$ and $\rm \Sigma _{gas}$, and between $\rm \Sigma _{SFR}$ and $\rm \Sigma _{gas}$ per free-fall time and orbital time for Galactic clouds. At the same time, we do not observe any correlation with $\rm \Sigma _{gas}$ per crossing time and multi free-fall time. Even though we see correlations in the former cases, however, all models agree with each other within a factor of 0.5 dex. It is not possible to discriminate between these models because of the current uncertainties in the input observables. We also test the variation of $\rm \Sigma _{SFR}$ with the dense gas but, because of low statistics, a weak correlation is seen in our analysis.
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations
Authors: Rath Sneha , Sharma Rohit , Gupta Rahul , Ast Tslil , Chan Connie , Durham Timothy J , Goodman Russell P , Grabarek Zenon , Haas Mary E , Hung Wendy H W , Joshi Pallavi R , Jourdain Alexis A , Kim Sharon H , Kotrys Anna V , Lam Stephanie S , McCoy Jason G , Meisel Joshua D , Miranda Maria , Panda Apekshya , Patgiri Anupam , Rogers Robert , Sadre Shayan , Shah Hardik , Skinner Owen S , To Tsz-Leung , Walker Melissa A , Wang Hong , Ward Patrick S , Wengrod Jordan , Yuan Chen-Ching , Calvo Sarah E , Mootha Vamsi K
Published: October 2020

The mammalian mitochondrial proteome is under dual genomic control, with 99% of proteins encoded by the nuclear genome and 13 originating from the mitochondrial DNA (mtDNA). We previously developed MitoCarta, a catalogue of over 1000 genes encoding the mammalian mitochondrial proteome. This catalogue was compiled using a Bayesian integration of multiple sequence features and experimental datasets, notably protein mass spectrometry of mitochondria isolated from fourteen murine tissues. Here, we introduce MitoCarta3.0. Beginning with the MitoCarta2.0 inventory, we performed manual review to remove 100 genes and introduce 78 additional genes, arriving at an updated inventory of 1136 human genes. We now include manually curated annotations of sub-mitochondrial localization (matrix, inner membrane, intermembrane space, outer membrane) as well as assignment to 149 hierarchical ‘MitoPathways’ spanning seven broad functional categories relevant to mitochondria. MitoCarta3.0, including sub-mitochondrial localization and MitoPathway annotations, is freely available at http://www.broadinstitute.org/mitocarta and should serve as a continued community resource for mitochondrial biology and medicine.
Characters from the deciduous dentition and its interest for phylogenetic reconstruction in Hippopotamoidea (Cetartiodactyla: Mammalia)
Authors: Gomes Rodrigues Helder , Lihoreau Fabrice , Orliac Maëva , Boisserie Jean-Renaud
Published: October 2020

Teeth are frequently used in phylogeny in order to better characterize the evolution of extinct mammal species. While most studies have focused on the adult dentition, the consideration of characters from the deciduous dentition could also contribute to reinforce phylogenetic assumptions or disentangle phylogenetic issues. We chose to investigate the characters of the deciduous dentition in cetartiodactyl taxa in relation to the disputed relationships within hippopotamoids, especially the position of Hippopotamidae. We describe the deciduous dentition of 51 species, among a dataset of 70 cetartiodactyls. We noticed that second and third deciduous premolars have a much lower degree of molarization, and are more suitable for coding than fourth deciduous premolars. Thirty-nine resulting characters were thus added to a previously published matrix, and parsimony and maximum-likelihood analyses were performed. Both analyses provided a better resolved topology for most taxa than without these characters, and with better support for most nodes in the parsimony analysis. Moreover, this analysis provides additional characters supporting the hypothesis of an emergence of hippopotamids within bothriodontine anthracotheres from the Palaeogene of Africa. The promising use of characters from the deciduous dentition in phylogeny should allow discussion of the underlying ontogenetic mechanisms at the origin of dental homology.
Benefits of Family Mealtime Across the Growing Years: A Conceptual Model
Authors: Martin-Biggers Jennifer T , Berhaupt-Glickstein Amanda , Worobey John , Byrd-Bredbenner Carol
Published: October 2020

Aspects of the home environment, including family meals, are an understudied, yet critical factor in child health outcomes. A comprehensive literature review, based on the IOM's L.E.A.D. framework (Locate, Evaluate, and Assemble evidence to inform Decisions) was conducted to identify links between family meals (frequency and atmosphere) and health, development, and BMI outcomes and to use these findings to create a conceptual model expressing these links. Key search terms were family, meals, dinner, child(ren), youth, parent(s). A search of PubMed, CINAHL and PsycINFO yielded 68 articles. Evidence demonstrates that across the growing years, greater family meal frequency is associated with increased intake of dietary components related to improved health (i.e., fruits, vegetables, fiber, calcium‐rich foods, vitamins) and decreased intake of components experts recommend consuming in limited amounts (i.e., soft drinks). Increased family meal frequency was inversely related to negative health outcomes, such as depressive symptoms and disturbed eating behaviors. Evidence linking frequency of family meals to obesity risk is not conclusive, however youth in families that served family meals frequently tended to have lower BMIs. The conceptual model created in this study may be used by health promotion and nutrition professionals to visually convey to parents the value of family meals.

Grant Funding Source: United States Department of Agriculture, National Institute of Food and Agriculture, Grant Number 2011‐68001‐30170
Nitro Blue Tetrazolium (NBT) Staining as an Assessment of Thermal Penetration
Authors: Fugett James H. , Bennett Haydon , Shrout Joshua , Coad James
Published: October 2020

Medical devices utilizing hyperthermic tissue injury are increasingly being used in surgical procedures. It is clinically essential to accurately assess the extent of thermal tissue damage these devices have on tissues. Histological stains such as hematoxylin and eosin (H&E) and trichrome staining provide a generic tissue staining, of nucleic acids and proteins. As a result of its generality, the application of these stains in the assessment of tissue injury and viability is similarly limited. In contrast, Nitro Blue Tetrazolium (NBT) staining is requires functional cellular proteins and energy production; as such, this stain has the potential to more accurately establish viability and the extent of tissue injury. Here, we describe a validated methodology for NBT staining to assess the extent of thermal tissue damage/injury using the ex vivo porcine model. Following hyperthermic treatment, the tissues are maintained at room temperature for at least two but not longer than four hours and are then frozen at −80°C. The treatment sites are subsequently dissected and embedded in Optimal Cutting Temperature (OCT) Compound on a liquid nitrogen freezing stage. NBT staining is performed on tissue sections cut between 10–12 microns thick. Histologically, the thermally damaged/injured tissue is quantified by assessing the extent of NBT‐negative (yellow‐tan in color) staining within the treatment zone. In contrast, the thermally unaffected tissue stains NBT‐positive (purple‐blue) due to its preservation of diaphorase protein function and maintenance of energy production. Our results validate NBT staining, as an effective assessment of thermal tissue injury, in several different tissues including muscle, liver, stomach and colon.
Allis Clamp for Cervical Stabilization During Intrauterine Device Insertion: Time for a Change [6G]
Authors: Newbern Kayce , Rone Bryan
Published: October 2020

INTRODUCTION:

Intrauterine devices (IUDs) are a common choice for contraception. A cervical stabilization device is recommended to provide cervical traction and to reduce the uterocervical angle. The device instructions recommend using a single tooth tenaculum. A tenaculum is a traumatic clamp which causes bleeding at the clamp site. We hypothesized that use of an atraumatic Allis clamp would require less hemostatic interventions.

METHODS:

The study was a randomized control trial of 95 IUD insertions. The physicians were randomized to use the Allis clamp or a tenaculum for cervical stabilization. The primary outcome was cervical site bleeding after clamp removal. Other outcomes were the number of interventions required for hemostasis and success of IUD placement. Statistical analyses were performed using the Fisher exact test and Chi-squared test.

RESULTS:

Bleeding was present after clamp removal in 3 (6.3%) insertions using an Allis clamp and 26 (55.3%) insertions using a single tooth tenaculum, P<.0001. Bleeding was absent in 45 (93.8%) insertions using an Allis clamp and 21 (44.7%) insertions using a single tooth tenaculum, P<.0001. There was no difference in the number of interventions required for hemostasis when bleeding occurred after clamp removal. There was no difference in IUD insertion success rates between the two clamps.

CONCLUSION:

The Allis clamp can be successfully used in place of a single tooth tenaculum for cervical stabilization during IUD insertion. The Allis clamp is associated with less bleeding and less need for hemostatic interventions after clamp removal. The Allis clamp is a better device for cervical stabilization during IUD insertion.