bluuebunny/crossref_metadata_2025 huggingface dataset:
The berry health tool chest – an evidence map and interactive resource
Authors: Kay Kristine L , Strauch Renee C , Granillo Cheryl D , Bame Megan W , Xiong Jia , Mast Aubrey C , Burton-Freeman Britt , Kay Colin D , Lila Mary Ann
Published: February 2021

Berry consumption is linked to diverse health benefits, but numerous questions remain regarding mechanism of action, dose efficacy, and optimal duration and frequency of intake. Addressing these outstanding questions requires an organized assessment of current research, to inform future study designs and fill critical knowledge gaps. Tools that organize such information will also facilitate consumer messaging, targeted nutritional health initiatives, and dietary intake guidelines. This review aimed to describe the development and utility of the “Berry Health Tool Chest,” an evidence map summarizing trial design features of studies characterizing the impact of berry consumption upon human health biomarkers. A systematic search strategy identified relevant high-quality human feeding studies, whose study design parameters were collected and compiled into an evidence map that is freely available as an interactive online interface enabling tabulated data to be interrogated, filtered, and exported. Of the 231 included studies, approximately 70% were of less than 3 months’ duration and/or fewer than 50 participants, illustrating research gaps that could potentially inform the design of future studies.
Mass Media and the Colonial Informant: Messaoud Djebari and the French Empire, 1880–1901
Authors: Asseraf Arthur
Published: February 2021

The nineteenth century saw an explosion of mass media as well as an expansion of colonial states. These two processes mutually influenced each other, and at the intersection lay a thin layer of individuals who could gain inordinate power to influence global information flows. This article follows the career of one such individual, Messaoud Djebari, an Algerian man who generated several controversies by fabricating information first in Tunisia in 1881, and then across West Africa and France in 1892–5. Djebari’s case suggests that some men trained to act as colonial intermediaries could end up playing important roles in shaping the circulation of information well beyond their territory of origin. Colonial informants were defined less by their role within a given colonial territory than by an ability to portray themselves as conduits to valuable information inaccessible to Europeans, irrespective of the location. Beyond the colonial context, this calls our attention to a particular practice of information manipulation characteristic of this age: the art of making oneself into a conduit by passing off one’s opinions as somebody else’s information.
Bacterial diketopiperazines stimulate diatom growth and lipid accumulation
Authors: Sittmann John , Bae Munhyung , Mevers Emily , Li Muzi , Quinn Andrew , Sriram Ganesh , Clardy Jon , Liu Zhongchi
Published: February 2021

Diatoms are photosynthetic microalgae that fix a significant fraction of the world’s carbon. Because of their photosynthetic efficiency and high-lipid content, diatoms are priority candidates for biofuel production. Here, we report that sporulating Bacillus thuringiensis and other members of the Bacillus cereus group, when in co-culture with the marine diatom Phaeodactylum tricornutum, significantly increase diatom cell count. Bioassay-guided purification of the mother cell lysate of B. thuringiensis led to the identification of two diketopiperazines (DKPs) that stimulate both P. tricornutum growth and increase its lipid content. These findings may be exploited to enhance P. tricornutum growth and microalgae-based biofuel production. As increasing numbers of DKPs are isolated from marine microbes, the work gives potential clues to bacterial-produced growth factors for marine microalgae.
OsmiR396/growth regulating factor modulate rice grain size through direct regulation of embryo-specific miR408
Authors: Yang Xiaofang , Zhao Xiaoling , Dai Zhengyan , Ma Feilong , Miao Xuexia , Shi Zhenying
Published: February 2021

microRNAs (miRNAs) are promising targets for crop improvement of complex agricultural traits. Coordinated activity between/among different miRNAs may fine-tune specific developmental processes in diverse organisms. Grain size is a main factor determining rice (Oryza sativa L.) crop yield, but the network of miRNAs influencing this trait remains uncharacterized. Here we show that sequestering OsmiR396 through target mimicry (MIM396) can substantially increase grain size in several japonica and indica rice subspecies and in plants with excessive tillers and a high panicle density. Thus, OsmiR396 has a major role related to the regulation of rice grain size. The grain shape of Growth Regulating Factor8 (OsGRF8)-overexpressing transgenic plants was most similar to that of MIM396 plants, suggesting OsGRF8 is a major mediator of OsmiR396 in grain size regulation. A miRNA microarray analysis revealed changes to the expression of many miRNAs, including OsmiR408, in the MIM396 plants. Analyses of gene expression patterns and functions indicated OsmiR408 is an embryo-specific miRNA that positively regulates grain size. Silencing OsmiR408 expression (miR408KO) using CRISPR technology resulted in small grains. Moreover, we revealed the direct regulatory effects of OsGRF8 on OsMIR408 expression. A genetic analysis further showed that the large-grain phenotype of MIM396 plants could be complemented by miR408KO. Also, several hormone signaling pathways might be involved in the OsmiR396/GRF-meditated grain size regulation. Our findings suggest that genetic regulatory networks comprising various miRNAs, such as OsmiR396 and OsmiR408, may be crucial for controlling rice grain size. Furthermore, the OsmiR396/GRF module may be important for breeding new high-yielding rice varieties.
Analysis of formin functions during cytokinesis using specific inhibitor SMIFH2
Authors: Zhang Laining , Smertenko Tetyana , Fahy Deirdre , Koteyeva Nuria , Moroz Natalia , Kuchařová Anna , Novák Dominik , Manoilov Eduard , Smertenko Petro , Galva Charitha , Šamaj Jozef , Kostyukova Alla S. , Sedbrook John C. , Smertenko Andrei
Published: February 2021

The phragmoplast separates daughter cells during cytokinesis by constructing the cell plate, which depends on interaction between cytoskeleton and membrane compartments. Proteins responsible for these interactions remain unknown, but formins can link cytoskeleton with membranes and several members of formin protein family localize to the cell plate. Progress in functional characterization of formins in cytokinesis is hindered by functional redundancies within the large formin gene family. We addressed this limitation by employing Small Molecular Inhibitor of Formin Homology 2 (SMIFH2), a small-molecule inhibitor of formins. Treatment of tobacco (Nicotiana tabacum) tissue culture cells with SMIFH2 perturbed localization of actin at the cell plate; slowed down both microtubule polymerization and phragmoplast expansion; diminished association of dynamin-related proteins with the cell plate independently of actin and microtubules; and caused cell plate swelling. Another impact of SMIFH2 was shortening of the END BINDING1b (EB1b) and EB1c comets on the growing microtubule plus ends in N. tabacum tissue culture cells and Arabidopsis thaliana cotyledon epidermis cells. The shape of the EB1 comets in the SMIFH2-treated cells resembled that of the knockdown mutant of plant Xenopus Microtubule-Associated protein of 215 kDa (XMAP215) homolog MICROTUBULE ORGANIZATION 1/GEMINI 1 (MOR1/GEM1). This outcome suggests that formins promote elongation of tubulin flares on the growing plus ends. Formins AtFH1 (A. thaliana Formin Homology 1) and AtFH8 can also interact with EB1. Besides cytokinesis, formins function in the mitotic spindle assembly and metaphase to anaphase transition. Our data suggest that during cytokinesis formins function in: (1) promoting microtubule polymerization; (2) nucleating F-actin at the cell plate; (3) retaining dynamin-related proteins at the cell plate; and (4) remodeling of the cell plate membrane.
Herbal Topical Analgesic for Pain Management: Perspectives from Cancer Patients
Authors: Liou Kevin T , Chen Connie , Emard Nicholas , Lynch Kathleen A , Hou Yen Nien , Mao Jun J
Published: February 2021

Objective

Herbs and natural products are increasingly used by cancer patients for pain management, but few studies have examined their integration within conventional cancer care. This study describes the characteristics, experiences, and perspectives of cancer patients who were prescribed an herbal topical analgesic for pain management.

Design and Setting

Program evaluation of a pilot herbal dispensary at a National Cancer Institute–designated comprehensive cancer center.

Subjects

Cancer patients who were prescribed the Tibetree Pain-Relieving Plaster (PRP) by an integrative medicine physician.

Methods

Sociodemographic and clinical characteristics of patients were abstracted from medical records. Semistructured phone interviews were conducted 1–2 weeks after PRP prescription to evaluate patient experiences with using PRP for pain. Interviews were analyzed through thematic content analysis.

Results

From February 2019 to February 2020, 50 patients were prescribed PRP. Median age (range) was 63 years (21–86), 37 patients (74%) were female, 14 (28%) were non-White, and 38 (76%) were using oral analgesics. During interviews, the majority of patients reported that the PRP improved pain and health-related outcomes, was convenient to use, and addressed pain management needs that were not fulfilled by oral analgesics. However, a few patients described adverse experiences with PRP, including skin irritation.

Conclusions

Understanding patient experiences and perspectives is a critical step toward evidence-based integration of herbs and natural products into cancer pain management. Findings from this program evaluation will inform the design of a randomized clinical trial on the efficacy and safety of PRP for pain in patients with cancer.
Time evolution of lepton number carried by Majorana neutrinos
Authors: Adam Apriadi Salim , Benoit Nicholas J , Kawamura Yuta , Matsuo Yamato , Morozumi Takuya , Shimizu Yusuke , Tokunaga Yuya , Toyota Naoya
Published: February 2021

We revisit the time evolution of the lepton family number for an SU(2) doublet consisting of a neutrino and a charged lepton. The lepton family number is defined through the weak basis of the SU(2) doublet, where the charged lepton mass matrix is real and diagonal. The lepton family number carried by the neutrino is defined by the left-handed current of the neutrino family. For this work we assume that the neutrinos have Majorana mass. This Majorana mass term is switched on at time $t=0$ and the lepton family number evolves. Since the operator in the flavor eigenstate is continuously connected to that of the mass eigenstate, the creation and annihilation operators for the two eigenstates are related to each other. We compute the time evolution of all lepton family numbers by choosing a specific initial flavor eigenstate for a neutrino. The evolution is studied for relativistic and non-relativistic neutrinos. The non-relativistic region is of particular interest for the cosmic neutrino background predicted from Big Bang models. In that region we find that the lepton family numbers are sensitive to the Majorana and Dirac phases, the absolute mass, and the mass hierarchy of neutrinos.
Public perspectives of social prescribing
Authors: Khan Koser , Ward Fiona , Halliday Emma , Holt Vivien
Published: February 2021

Background

There is a strong national drive within the UK government and National Health Service for social prescribing. Previous research studies have mainly focused on service user perspectives and evaluating their experiences. There is limited evidence on how the general public perceive and understand what social prescribing is and how these views could influence service planning and delivery. This paper seeks to understand perceptions of social prescribing within the wider community.

Methods

Semi-structured focus groups were conducted with 37 members of the public in four areas in north-west England. We explored public awareness and understanding of social prescribing.

Results

Limited knowledge of the term social prescribing was found amongst participants as well as limited involvement in community discussions of the topic. Concerns were raised about the short-term nature of activities and the need for adequate resourcing to support continuity of service provision. The social prescribing link worker was considered to be important in supporting engagement with services and it was preferred this role was undertaken by people with local knowledge.

Conclusions

The findings provide evidence of public perspectives on social prescribing and highlight how wider community perceptions can supplement service user feedback to support social prescribing service planning, commissioning and delivery.
Is irrigation driven by the price of internationally traded agricultural products?
Authors: Cheptea Angela , Laroche Dupraz Catherine
Published: February 2021

A recent trend of literature investigates how international trade compensates or accentuates the differences in countries’ endowments in water resources and whether trade regulation should be used to improve the use of water resources at the global level. We develop a simple model establishing a positive link between the demand for irrigation water of agricultural producers and the international price of irrigated crops. Unlike previous works that focus on the cost and scarcity of water resources, we emphasize the role of international trade in the allocation of water resources in agriculture. We test our model empirically using data on 243 irrigated crops exported by 183 countries, and find that countries’ irrigation behavior is strongly linked to the global price of crops. The export price effect is stronger when countries are net exporters of irrigated crops and weaker for cereals that constitute a pillar of most countries’ domestic food security.
A Problem Shared? The Role of the Public in the Legitimation of Policy: A Case Study of Gendered Welfare Change in the United Kingdom
Authors: Richards-Gray Laura
Published: February 2021

This article argues that shared problematizations—shared political and public ways of thinking—legitimize policies and their outcomes. To support this argument, it examines the legitimation of gendered welfare reform in the recent U.K. context. Drawing on focus groups with the public, it provides evidence that the public’s problematization of welfare, specifically that reform was necessary to “make work pay” and “restore fairness”, aligned with that of politicians. It argues that the assumptions and silences underpinning this shared problematization, especially silences relating to the value and necessity of care, have allowed for welfare policies that have disadvantaged women.
Hotchpot and the insolvent trading trustee: Commissioner of Taxation v Lane [2020] FCAFC 184
Authors: Walpole Samuel
Published: February 2021

For forty years, the insolvency of trading trustees in Australia has produced uncertainty. In 2019, the High Court of Australia resolved the central controversy, holding that the proceeds of the exercise of the insolvent trading trustee’s right of exoneration could only be distributed to trust creditors and that the statutory priorities regime applied. The Full Federal Court’s recent decision in Commissioner of Taxation v Lane addresses several of the remaining questions. This note focuses on the Full Court’s conclusion that the hotchpot principle applied to the distribution of the non-trust assets of an insolvent trading trustee with both trust and non-trust creditors.
Organic nitrogen nutrition: LHT1.2 protein from hybrid aspen (Populus tremula L. x tremuloides Michx) is a functional amino acid transporter and a homolog of Arabidopsis LHT1
Authors: Gratz Regina , Ahmad Iftikhar , Svennerstam Henrik , Jämtgård Sandra , Love Jonathan , Holmlund Mattias , Ivanov Rumen , Ganeteg Ulrika
Published: February 2021

The contribution of amino acids (AAs) to soil nitrogen (N) fluxes is higher than previously thought. The fact that AA uptake is pivotal for N nutrition in boreal ecosystems highlights plant AA transporters as key components of the N cycle. At the same time, very little is known about AA transport and respective transporters in trees. Tree genomes may contain 13 or more genes encoding the lysine histidine transporter (LHT) family proteins, and this complicates the study of their significance for tree N-use efficiency. With the strategy of obtaining a tool to study N-use efficiency, our aim was to identify and characterize a relevant AA transporter in hybrid aspen (Populus tremula L. x tremuloides Michx.). We identified PtrLHT1.2, the closest homolog of Arabidopsis thaliana (L.) Heynh AtLHT1, which is expressed in leaves, stems and roots. Complementation of a yeast AA uptake mutant verified the function of PtrLHT1.2 as an AA transporter. Furthermore, PtrLHT1.2 was able to fully complement the phenotypes of the Arabidopsis AA uptake mutant lht1 aap5, including early leaf senescence-like phenotype, reduced growth, decreased plant N levels and reduced root AA uptake. Amino acid uptake studies finally showed that PtrLHT1.2 is a high affinity transporter for neutral and acidic AAs. Thus, we identified a functional AtLHT1 homolog in hybrid aspen, which harbors the potential to enhance overall plant N levels and hence increase biomass production. This finding provides a valuable tool for N nutrition studies in trees and opens new avenues to optimizing tree N-use efficiency.
Research priorities for control of zoonoses in South Africa
Authors: Simpson Greg , Quesada Fabiola , Chatterjee Pranab , Kakkar Manish , Chersich Matthew F , Thys Séverine
Published: February 2021

Background

Zoonoses pose major threats to the health of humans, domestic animals and wildlife, as seen in the COVID-19 pandemic. Zoonoses are the commonest source of emerging human infections and inter-species transmission is facilitated by anthropogenic factors such as encroachment and destruction of wilderness areas, wildlife trafficking and climate change. South Africa was selected for a ‘One Health’ study to identify research priorities for control of zoonoses due to its complex disease burden and an overstretched health system.

Methods

A multidisciplinary group of 18 experts identified priority zoonotic diseases, knowledge gaps and proposed research priorities for the next 5 y. Each priority was scored using predefined criteria by another group of five experts and then weighted by a reference group (n=28) and the 18 experts.

Results

Seventeen diseases were mentioned with the top five being rabies (14/18), TB (13/18), brucellosis (11/18), Rift Valley fever (9/11) and cysticercosis (6/18). In total, 97 specific research priorities were listed, with the majority on basic epidemiological research (n=57), such as measuring the burden of various zoonoses (n=24), followed by 20 on development of new interventions. The highest research priority score was for improving existing interventions (0.77/1.0), followed by health policy and systems research (0.72/1.0).

Conclusion

Future zoonotic research should improve understanding of zoonotic burden and risk factors and new interventions in public health. People with limited rural services, immunocompromised, in informal settlements and high-risk occupations, should be the highest research priority.
Epidemiological Characterization of Lettuce Drop (Sclerotinia spp.) and Biophysical Features of the Host Identify Soft Stem as a Susceptibility Factor
Authors: Mamo Bullo Erena , Eriksen Renée L. , Adhikari Neil D. , Hayes Ryan J. , Mou Beiquan , Simko Ivan
Published: February 2021

The soilborne fungus Sclerotinia minor was not known to produce sclerotia in the stems of infected and uncollapsed Lactuca standing intact until our observation in a greenhouse in 2017. We investigated lettuce–environment–S. minor interactions in two tolerant and four susceptible Lactuca genotypes to determine putative risk factors and targets for disease control. Symptomatological, pathophysiological, developmental, basal stem biophysical, and microclimate responses (27 variables) of the genotypes were determined under field or greenhouse conditions. Distinct patterns of infection responses were observed between modern cultivars and their primitive or wild relatives. Modern cultivars were susceptible to rapid basal stem and root degradations by S. minor. Oilseed lettuce PI 251246 and wild Lactuca serriola 11-G99 were resilient to degradations and significantly deterred mycelium emergence and symptom development but sclerotia formed to a significantly higher height in their stems. Photosynthetic efficiency declined rapidly within 1 day postinoculation (dpi) in susceptible plants but remained intact approximately 5 to 6 dpi in the tolerant 11-G99. Stomatal conductance spiked rapidly in 11-G99 plants within 1 to 3 dpi, coinciding with the emergence of fungal mycelia at the crown. A strong negative correlation detected between basal stem degradation severity or collapse, and stem mechanical strength indicated that stem strength-mediated genetic factors determine the outcome of Sclerotinia infections. Soft stem is a prominent lettuce drop susceptibility factor that could be targeted in resistance breeding and provides the prelude for the analysis of the biological basis of plant architecture-mediated resistance to Sclerotinia spp. in lettuce and other hosts.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Glaucoma patient screening from online retinal fundus images via Artificial Intelligence
Authors: Franco Pablo , Coronado-Gutierrez David , Lopez Carlos , Burgos-Artizzu Xavier P.
Published: February 2021

Objectives

To design and evaluate a novel automated glaucoma classifier from retinal fundus images.

Methods

We designed a novel Artificial Intelligence (AI) automated tool to detect glaucoma from retinal fundus images. We then downloaded publicly available retinal fundus image datasets containing healthy patients and images with verified glaucoma labels. Two thirds of the images were used to train the classifier. The remaining third of the images was used to create several cross-validation evaluation sets with a realistic glaucoma prevalence, to evaluate the classifier’s performance in a screening scenario.

Results

10,658 retinal fundus images from seven different sources were found and downloaded. They were randomly divided into 7,106 for training and 3,551 for validation. Glaucoma prevalence was 24%. Using the validation set, we created 50 random sets of 1,000 images with a 5% glaucoma prevalence. On these sets, the classifier reached a detection rate of 84.1% (CI 95=+-1.1%) and 95.8% (CI 95=+-0.2%) specificity.

Conclusions

A novel glaucoma classifier from retinal fundus images showed promising results as screening tool on a large cohort of patients. A large clinical study is needed to confirm these results.
Climate Change and Child Health - Assessment of Parents’ Perspective and Relevance
Authors: Lagally Lena , Schorlemmer Julia , Schoierer Julia , Edlinger Maximilian , Bose-O’Reilly Stephan
Published: February 2021

Background

Ongoing climate change has several indirect and direct health consequences. Children are among the most vulnerable group to suffer from these health impacts. Parents as caregivers play a particularly important role in protecting them adequately.

Objectives

The aim of the study was to investigate how parents perceive the health consequences of climate change. Of particular interest were their information status and already used communication channels, to make them more addressable. In addition, their risk perception and relevance estimation of the health consequences of climate change for their children were investigated.

Methods

Parents were able to participate anonymously in the study from March to June 2020 by means of an online questionnaire. The study sample consisted of 292 parents living in Germany (age: M = 42.02; SD = 7.73; sex: ♀ = 190; ♂ = 54) with at least one child aged 0 to 18 years. Open-ended questions and closed-ended questions with Likert scales were used. Data were analyzed descriptively. Correlations and regression analysis were performed.

Findings

About 75% of the respondents knew at least one health consequence of climate change. Heat related illnesses were named as the most important health consequences (74.1%). Parents obtain most of their information from the Internet (73.3%). The increase of air pollutants is estimated as the most relevant risk for the health of their children. Relevance estimation affects risk perception.

Conclusion

Parents are aware of the importance of being informed about the health consequences of climate change. Therefore, knowledge about the health consequences in relation to the relevance assessment must be communicated clearly and sufficiently. Information channels already used should be improved and further multipliers identified.
Molecular diagnosis of causality in T cell mediated severe cutaneous adverse drug reactions
Authors: Teo Ying X , Haw Wei Y , Vallejo Andres F , McGuire Carolann , Woo Jeongmin , Friedmann Peter S , Polak Marta E , Ardern-Jones Michael R
Published: February 2021

Background

One of the most severe forms of T cell mediated cutaneous adverse drug reactions is ‘drug reaction with eosinophilia and systemic symptoms’ (DRESS), hence subsequent avoidance of the causal drug is imperative. However, attribution of drug culpability in DRESS is challenging and standard skin allergy tests are not recommended due to for patient safety reasons. We sought to identify potential biomarkers for development of a diagnostic test.

Methods

Peripheral blood mononuclear cells (PBMCs) from a ‘discovery’ cohort (n=5) challenged to drug or control were analysed for transcriptomic profile. A signature panel of genes was then tested in a validation cohort (n=6), and compared to tolerant controls and other inflammatory conditions which can clinically mimic DRESS. A scoring system to identify presence of drug hypersensitivity was developed based on gene expression alterations of this panel.

Results

Whole transcriptome analysis identified 4 major gene clusters including those regulating T cell activation via NFAT and cytokine receptor activity. 22 differentially expressed gene transcripts were identified as a DRESS signature including Type 1 interferon pathways and Th2 activation. The DRESS transcriptomic panel identified antibiotic-DRESS cases in a validation cohort but was not altered in other inflammatory conditions. Machine learning or differential expression selection of a biomarker panel showed high sensitivity and specificity (100% and 85.7-100% respectively) for identification of the culprit drug in DRESS.

Conclusion

Transcriptomic analysis of DRESS revealed important insights into the key activated pathways and identified a transcriptional signature which shows potential as a test with high sensitivity for drug culpability attribution.
The rise of SARS-CoV-2 variant B.1.1.7 in Israel intensifies the role of surveillance and vaccination in elderly
Authors: Munitz A , Yechezkel M , Dickstein Y , Yamin D. , Gerlic M
Published: February 2021

Since the emergence of the SARS-CoV-2 pandemic various generic variants have been described. Of specific interest is a new variant, which was observed in England during December 2020 and is now termed B.1.1.7. This variant is now associated with increased infectivity and therefore its spread within the community is of great importance. The Israeli government established three noteworthy programs namely, mass PCR testing, focused protection of the elderly and more recently an unparalleled prioritized vaccination program. In this study we analyzed primary data of >300,000 RT-PCR samples collected throughout December 6th 2020 until February 10th 2021 in the general community and nursing homes. We identified that within a period of six weeks, the B.1.1.7 variant was capable of out competing the wildtype SARS-CoV-2 strain to become the main strain. Furthermore, we show that the transmission of B.1.1.7 in the 60+ population reached a near complete halt, due to an ongoing surveillance testing program in nursing homes and the vaccination program of Israel. Thus, proactive protection programs such as routine surveillance and monitoring of populations at risk combined with prioritized vaccination, is achievable and will result in a reduction of severe illness and subsequent death.
Evaluation of sampling frequency and normalization of SARS-CoV-2 wastewater concentrations for capturing COVID-19 burdens in the community
Authors: Feng Shuchen , Roguet Adélaïde , McClary-Gutierrez Jill S. , Newton Ryan J. , Kloczko Nathan , Meiman Jonathan G. , McLellan Sandra L.
Published: February 2021

Wastewater surveillance for SARS-CoV-2 provides an approach for assessing the infection burden across a city. For these data to be useful for public health, measurement variability and the relationship to case data need to be established. We measured SARS-CoV-2 RNA concentrations in the influent of twelve wastewater treatment plants from August 2020 to January 2021. Replicate samples demonstrated that N1 gene target concentrations varied by ±21% between technical replicate filters and by ±14% between duplicate assays. COVID-19 cases were correlated significantly (rho≥0.70) to wastewater SARS-CoV-2 RNA concentrations for seven plants, including large and small cities. SARS-CoV-2 data normalized to flow improved correlations to reported COVID-19 cases for some plants, but normalizing to a spiked recovery control (BCoV) or a fecal marker (PMMoV or HF183) generally reduced correlations. High frequency sampling demonstrated that a minimum of two samples collected per week was needed to maintain accuracy in trend analysis. We found a significantly different ratio of COVID-19 cases to SARS-CoV-2 loads in one of three large communities, suggesting a higher rate of undiagnosed cases. These data demonstrate that SARS-CoV-2 wastewater surveillance can provide a useful community-wide metric to assess the course of the COVID-19 pandemic.
Diagnostic Performance of Pooled RT-PCR Testing for SARS-CoV-2 Detection
Authors: Ricarte Diadem , Gador Aubrey , Mendiola Leomill , Gonzales Ian Christian
Published: February 2021

Background

With the high number of COVID-19 cases, a need to optimize testing strategy must be regarded to obtain timely diagnosis for early containment measures. With this, several studies have employed pooled RT-PCR testing for SARS-CoV-2 as this could potentially conserve laboratory resources while has the capacity to test several individuals. However, this was recommended to firstly validate the method as different laboratory reagents and equipment vary with its diagnostic performance.

Objective

The aim of this study was to determine the diagnostic performance of pooled SARS-CoV-2 nasopharyngeal/oropharyngeal swabbed samples using RT-PCR technique.

Methods

A records review of two-staged pooled RT-PCR testing data from August 10, 26, 30 and September 5, 2020 was utilized from Northern Mindanao Medical Center COVID-19 Satellite Laboratory (formerly CHDNM TB Regional Center). For the first stage, using known samples, a total of 30 pools were made for each of the pooling size, 5- and 10-pooled, on both pooling phase, pre- and post-RNA extraction. One positive individual was used to represent each of the Cycle threshold values given (<24, 25-28, 29-32, 33-36, and 37-40) while the rest of the samples were negative. For the second stage, 54 pools of five from 270 random unknown samples were used to validate the results. Target gene performance of N gene and RdRp was also determined.

Key Results

Results show that 5-pooled sample has higher sensitivity (SN), specificity (SP), positive predictive value (PPV), and negative predictive value (NPV) of 100% (95% confidence interval (CI) 88.97-100), 66.95% (95% CI, 60.75-72.6), 28.18% (95% CI, 20.62-37.22), and 100% (95% CI, 97.66-100) compared to 10-pooled sample that has 87.1% (95% CI, 71.15-94.87), 56.9% (50.57-63.02), 20.77% (95% CI, 14.68-28.53) and 97.14% (95% CI, 92.88-98.88). Further, these Ct values were only from the N gene, emphasizing its higher diagnostic performance as well to detect SARS-CoV-2 compared to RdRp as only a few samples were detected, thus, no analysis was made.

Conclusion

This study found out that 5-pooled sample has better diagnostic performance compared to 10-pooled samples. Specifically, all positive individual samples were detected in 5-pooled samples in pre-RNA extraction phase which these results are evident and consistent on both known and unknown samples. N gene was found out to detect more SARS-CoV-2 samples compared to RdRp.
Over 100 years of Rift Valley Fever: a patchwork of data on pathogen spread and spillover
Authors: Bron Gebbiena M. , Strimbu Kathryn , Cecilia Hélène , Lerch Anita , Moore Sean , Tran Quan , Perkins T. Alex , ten Bosch Quirine A.
Published: February 2021

During the past 100 years, Rift Valley fever virus (RVFV), a mosquito-borne virus, has caused potentially lethal disease in livestock, and has been associated with significant economic losses and trade bans. Spillover to humans occurs and can be fatal. Here, we combined data on RVF disease in humans (22 countries) and animals (37 countries) from 1931 to 2020 with seroprevalence studies from 1950 to 2020 (N=226) from publicly available databases and publications to draw a more complete picture of past and current RVFV epidemiology. RVFV has spread from its original focus in Kenya throughout Africa and into the Arabian Peninsula. Throughout the study period, seroprevalence increased in both humans and animals, suggesting potentially increased RVFV exposure. In 24 countries animals or humans tested positive for RVFV antibodies even though outbreaks had never been reported there, suggesting RVFV transmission may well go unnoticed. Among ruminants, sheep were most likely to be exposed during RVF outbreaks, but not during periods of cryptic spread. We discuss critical data gaps and highlight the need for detailed study descriptions, and long-term studies using a one health approach to further convert the patchwork of data to the tale of RFV epidemiology.
Transcript analysis for variant classification resolution in a child with primary ciliary dyskinesia
Authors: Ing Alexander , Wlodaver Alissa , Kirschmann Dawn , Toledo Erica , McCabe Christopher , Kadri Sabah , McIntyre Mary Kate , Salazar Joanne , Firestein Kristina , Charrow Joel , Sanders Victoria , Laguna Theresa , Yap Kai Lee
Published: February 2021

Transcriptional analysis can be utilized to reconcile variants of uncertain significance, particularly those predicted to impact splicing. Laboratory analysis of the predicted mRNA transcript may allow inference of the in vivo impact of the variant and aid prediction of its clinical significance. We present a patient with classical features of primary ciliary dyskinesia (PCD) who was identified to have compound heterozygous variants in the DNAH11 gene (c.10691 + 2T > C, c.13523_13543dup21) via trio whole-exome sequencing in 2013. These variants were originally classified as Mutation and Likely Mutation. However, these variants were downgraded to variants of uncertain significance (VUSs) during reanalysis in 2016 because of uncertainty that they caused a loss of function of the gene. c.10691 + 2T > C is predicted to abrogate the canonical splice site and lead to the skipping of exon 65, but the adjoining of exon 64 and exon 66 in the DNAH11 transcript preserves the reading frame of the resultant protein. c.13523_13543dup21 is located in the last exon of the DNAH11 coding sequence, upstream of the canonical stop codon, which suggests a reduced likelihood to trigger nonsense-mediated decay (NMD). Transcriptional analysis was performed to characterize the impact of the variants, resulting in reclassification of c.10691 + 2T > C to Likely Pathogenic by providing evidence that it results in a deleterious effect and subsequent downstream reclassification of c.13523_13543dup21 to Likely Pathogenic as well. Our case illustrates the potential impact of transcriptional analysis on variant resolution, supporting its usage on variants that exert an unpredictable effect on splicing.
The anisotropy in the optical constants of quartz crystals for soft X-rays
Authors: Andrle A. , Hönicke P. , Vinson J. , Quintanilha R. , Saadeh Q. , Heidenreich S. , Scholze F. , Soltwisch V.
Published: February 2021

The refractive index of a y-cut SiO2 crystal surface is reconstructed from orientation-dependent soft X-ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L
2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near-edge regions.
Generating the atomic pair distribution function without instrument or emission profile contributions
Authors: Coelho Alan A. , Chater Philip A. , Evans Michael J.
Published: February 2021

A method for generating the atomic pair distribution function (PDF) from powder diffraction data by the removal of instrument contributions, such as Kα2 from laboratory instruments or peak asymmetry from neutron time-of-flight data, has been implemented in the computer programs TOPAS and TOPAS-Academic. The resulting PDF is sharper, making it easier to identify structural parameters. The method fits peaks to the reciprocal-space diffraction pattern data whilst maximizing the intensity of a background function. The fit to the raw data is made `perfect' by including a peak at each data point of the diffraction pattern. Peak shapes are not changed during refinement and the process is a slight modification of the deconvolution procedure of Coelho [J. Appl. Cryst. (2018), 51, 112–123]. Fitting to the raw data and subsequently using the calculated pattern as an estimation of the underlying signal reduces the effects of division by small numbers during atomic scattering factor and polarization corrections. If the peak shape is sufficiently accurate then the fitting process should also be able to determine the background if the background intensity is maximized; the resulting calculated pattern minus background should then comprise coherent scattering from the sample. Importantly, the background is not allowed complete freedom; instead, it comprises a scan of an empty capillary sample holder with a maximum of two additional parameters to vary its shape. Since this coherent scattering is a calculated pattern, it can be easily recalculated without instrumental aberrations such as capillary sample aberration or Kα2 from laboratory emission profiles. Additionally, data reduction anomalies such as incorrect integration of data from two-dimensional detectors, resulting in peak position errors, can be easily corrected. Multiplicative corrections such as polarization and atomic scattering factors are also performed. Once corrected, the pattern can be scaled to produce the total scattering structure factor F(Q) and from there the sine transform is applied to obtain the pair distribution function G(r).
Expression of virulence factors under different environmental conditions in Aggregatibacter actinomycetemcomitans
Authors: Fujita Ayumi , Oogai Yuichi , Kawada‐Matsuo Miki , Nakata Masanobu , Noguchi Kazuyuki , Komatsuzawa Hitoshi
Published: February 2021

Aggregatibacter actinomycetemcomitans is a facultative anaerobic Gram‐negative bacterium associated with periodontal diseases, especially aggressive periodontitis. The virulence factors of this pathogen, including adhesins, exotoxins, and endotoxin, have been extensively studied. However, little is known about their gene expression mode in the host. Herein, we investigated whether culture conditions reflecting in vivo environments, including serum and saliva, alter expression levels of virulence genes in the strain HK1651, a JP2 clone. Under aerobic conditions, addition of calf serum (CS) into a general medium induced high expression of two outer membrane proteins (omp100 and omp64). The high expression of omp100 and omp64 was also induced by an iron‐limited medium. RNA‐seq analysis showed that the gene expressions of several factors involved in iron acquisition were increased in the CS‐containing medium. When HK1651 was grown on agar plates, genes encoding many virulence factors, including the Omps, cytolethal distending toxin, and leukotoxin, were differentially expressed. Then, we investigated their expression in five other A. actinomycetemcomitans strains grown in general and CS‐containing media. The expression pattern of virulence factors varied among strains. Compared with the other five strains, HK1561 showed high expression of omp29 regardless of the CS addition, while the gene expression of leukotoxin in HK1651 was higher only in the medium without CS. HK1651 showed reduced biofilm in both CS‐ and saliva‐containing media. Coaggregation with Fusobacterium nucleatum was remarkably enhanced using HK1651 grown in the CS‐containing medium. Our results indicate that the expression of virulence factors is altered by adaptation to different conditions during infection.
Cascading effects of N fertilization activate biologically driven mechanisms promoting P availability in a semi‐arid grassland ecosystem
Authors: Cui Haiying , Sun Wei , Delgado‐Baquerizo Manuel , Song Wenzheng , Ma Jian‐Ying , Wang Keying , Ling Xiaoli
Published: February 2021

Nitrogen (N) fertilization due to N deposition, N in manure from grazing livestock and direct input to soil by humans are impacting our terrestrial ecosystems globally. However, to date, our understanding of how artificial gradients of N fertilization indirectly affect phosphorus (P) availability by altering the rates and interrelationships of multiple structural and functional attributes of terrestrial ecosystems is still limited.

Here, we conducted a 3‐year field experiment to evaluate the direct and indirect effects of multiple level of N addition on a wide range of ecosystem structural and functional attributes associated with >20 plant, soil and microbial variables in a semi‐arid grassland.

We found that N fertilization can have multiple cascading effects on ecosystem structures and functions. These cascading events ultimately result in the activation of multiple biologically driven mechanisms to promote P availability (e.g. increased soil organic P mineralization, plant phosphorus resorption, enzymatic and genetic processes of phosphatase). The increasing phosphatase production and its functional gene expression, and decreasing plant and microbial biomass might imply important shifts in the carbon‐use strategies of plants and microbes allocating more resources to high‐C consuming enzymatic and genetic processes and less in plant and microbial biomass. Nitrogen addition decreases fungal community biomass which suggests the decoupling of key symbiotic plant–fungal relationships for nutrient acquirement.

Overall, our study advances our understanding of how and why N fertilization simultaneously influences multiple structural and functional attributes, ultimately accelerating phosphorus cycle in terrestrial ecosystems.
The Female Condition: Gender and Deformity in High‐Medieval Miracle Narratives
Authors: Bailey Anne E
Published: February 2021

This article explores the intersection of medicine, religion and gender within the context of miracle narratives compiled in England and France in the High Middle Ages. Women in miracle accounts have much to tell us about medieval ideas of gendered sickness and health, yet this is an area which has received little scholarly attention. Focusing on stories of female deformity and disfigurement, it is argued that sickness has a feminising effect on women's bodies in these sources, but proposed that symptoms of excess femininity were not always seen as the spiritual hindrance that might be expected.
Supplemental minimal‐activity PET/CT to validate ambiguous findings with less than 1 mSv: Proof of concept
Authors: Gühne Falk , Drescher Robert , Seifert Philipp , Freesmeyer Martin
Published: February 2021

Short‐term follow‐up examinations could verify ambiguous findings in PET/CT diagnostics, but are often avoided due to radiation and financial burdens. We demonstrate the feasibility of a focused, minimal‐activity PET protocol as a supplemental examination for uncertain findings after standard PET/CT. After changing conditions, e.g. patient positioning, preparation and bypassing an interval as well as a targeted tracer change, an additional examination with less than 1 mSv of additional radiation exposure was performed. Lowered administered activity of radiopharmaceuticals could be compensated by prolonged acquisition time, which was made possible by the limitation to a single body region. A sufficient visual and quantitative image quality of scans could be achieved. In all cases, the ambiguous finding could be clarified, so further diagnostic procedures or unnecessary interventions were avoided.
Relationship between the Extent of Igneous Rocks and Deep Structures as Determined by Gravitational and Magnetic Data in the South China Sea
Authors: YANG Min , WANG Wanyin , ZHANG Gongcheng , MA Jie
Published: February 2021

The distribution of oil and gas resources in the South China Sea and adjacent areas is closely related to the structural pattern that helped to define the controlling effect of deep processes on oil‐bearing basins. Igneous rocks can record important information from deep processes. Deep structures such as faults, basin uplift and depression, Cenozoic basement and magnetic basement are all the results of energy exchange within the earth. The study of the relationship between igneous rocks and deep structures is of great significance for the study of the South China Sea. By using the minimum curvature potential field separation technique and the correlation analysis technique of gravitational and magnetic anomalies, the fusion of gravitational and magnetic data reflecting igneous rocks can be obtained, through which the igneous rocks with high susceptibility/high density or high susceptibility/low density can be identified. In this study area, igneous rocks do not develop in the Yinggehai basin, Qiongdongnan basin, Zengmu basin and Brunei‐Sabah basin, whilst igneous rocks with high susceptibility/high density or high susceptibility/low density are widely‐developed in other basins. In undeveloped igneous areas, faults are also undeveloped, the Cenozoic thickness is greater, the magnetic basement depth is greater and the Cenozoic thickness is highly positively correlated with the magnetic basement depth. In igneously developed regions, the distribution pattern of the Qiongtai block is mainly controlled by primary faults, while the distribution of the Zhongxisha block, Xunta block and Yongshu‐Taiping block is mainly controlled by secondary faults, the Cenozoic thickness having a low correlation with the depth of the magnetic basement.