bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractSince 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

AbstractWastewater 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

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

AbstractDuring 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.
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

AbstractAggregatibacter 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

Abstract

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

AbstractThis 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

SummaryShort‐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

AbstractThe 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.
Hybrid approach with laparoscopic wall‐inversion surgery and single‐incision intragastric surgery for intraluminal gastrointestinal stromal tumor: A case report
Authors: Kusunoki Chikako , Hamakawa Takuya , Nishikawa Kazuhiro , Sato Hiromichi , Imamura Sayumi , Miyahara Satoru , Sakano Yu , Miyazaki Hazuki , Seto Hiroto , Ueda Ryuta , Toshiyama Reishi , Miyo Masaaki , Takahashi Yusuke , Sakai Kenji , Miyake Masakazu , Miyamoto Atsushi , Kato Takeshi , Mori Kiyoshi , Hirao Motohiro 
Published: February 2021

AbstractLaparoscopic wedge resection (LWR) for intraluminal gastrointestinal stromal tumor (GIST) leads to excessive resection of normal gastric wall. We report a case of GIST around the cardia successfully treated with full‐thickness partial resection using a hybrid approach of laparoscopic surgery and single‐incision intragastric surgery (SIIGS). A 69‐year‐old woman had a 5 cm intraluminal GIST at the posterior wall around the cardia. Submucosal injection of glycerin and indigo carmine was performed with transoral endoscopy. Circumferential seromuscular incision followed by placement of seromuscular sutures to invert the lesion into the stomach was performed under laparoscopy. By SIIGS, resection of the inverted mucosa and retrieval of the tumor were completed. A hybrid approach consisting of laparoscopic wall‐inversion surgery and SIIGS was useful for intraluminal GIST and may expand the indications for laparoscopic wall‐inversion surgery by removing size limitations.
Using the faecal immunochemical test in patients with rectal bleeding: evidence from the NICE FIT study
Authors: Hicks Georgina , D’Souza Nigel , Georgiou Delisle Theo , Chen Michelle , Benton Sally C. , Abulafi Muti ,   the NICE FIT steering group
Published: February 2021

AbstractAimThe aim of this work was to investigate whether the faecal immunochemical test (FIT) could safely rule out colorectal cancer (CRC) in patients with rectal bleeding (RB).MethodThis was a multicentre, double‐blinded diagnostic accuracy study in 50 National Health Service hospitals. Patients referred from primary care with suspected CRC on an urgent 2‐week‐wait pathway were asked to perform a FIT prior to colonoscopy. The primary outcome measure was the sensitivity of the FIT for CRC in patients with RB versus nonrectal bleeding symptoms (NRB). The secondary outcome measures included the diagnostic accuracy of the FIT for CRC and other serious bowel disease.ResultsOf 9822 patients included in the study, 3143 (32.0%) were referred with RB. CRC was present in 4.7% of patients with RB versus 2.7% of patients with NRB (p < 0.05). Faecal haemoglobin (f‐Hb) was detectable (>2 µg/g) in 44.1% of patients with RB and 33.9% with NRB (p < 0.05). In RB patients, CRC was present in 10.4% when f‐Hb was >2 µg/g compared with 0.1% when f‐Hb was not detected. Flexible sigmoidoscopy in this group would further reduce the risk of CRC to 0.03%. The sensitivity of the FIT for CRC in RB versus NRB groups was 98.6% (95% CI 95.2%–99.8%) vs 95.6% (91.5%–98.1%) for f‐Hb >2 µg/g and 96.6% (92.2%–98.9%) vs 86.3 (80.4%–90.9%) for f‐Hb >10 µg/g.ConclusionFaecal haemoglobin is not always detectable in patients with RB; 56% of patients had undetectable f‐Hb (<2 µg/g) and CRC was present in 0.1%. The high sensitivity of the FIT can be used to rule out CRC in patients with RB and triage them more appropriately for investigation.
Time‐varying impact of global, region‐, and country‐specific uncertainties on the volatility of international trade
Authors: Gül Selçuk , Gupta Rangan 
Published: February 2021

AbstractWe use a dynamic factor model with time‐varying parameters and stochastic volatility to decompose the variance of exports and imports over time for 22 Organization for Economic Co‐operation and Development countries spanning the quarterly period of 1960:01–2016:04 into contributions from country‐ and region‐specific uncertainties and uncertainty common to all countries. We find that, while idiosyncratic uncertainty has a dominant role in explaining the volatility of international trade, global, country‐, and region‐specific uncertainties drive around 40% of the volatility of real exports and imports, with the impact of the latter three uncertainties rising in explanatory power during episodes of crises. Our results have important policy implications.
Global distribution and conservation of avian diet specialization
Authors: Morelli Federico , Benedetti Yanina , Hanson Jeffrey O. , Fuller Richard A. 
Published: February 2021

AbstractEcologically specialist species are more prone to extinction than generalist species, yet the global distribution and conservation of ecological specialism is poorly understood. Here, we show that the global distribution of avian dietary specialization is roughly congruent with overall bird species richness for resident and breeding species, as well as for non‐breeding species. However, some areas harbour a higher number of diet specialist birds than expected given overall species richness (e.g. the Amazon, Gabon and Cameroon in Central Africa, extensive parts of Indonesia and some parts of northern Eurasia, Baltic cost and Mediterranean areas for resident and breeding birds, and tropical zone and south part of subtropical zone in South America for non‐breeding birds). These areas represent hotspots of avian specialization that need to carefully be considered in conservation strategies. We found that overall, 49.6% of resident and breeding species and 45.5% of non‐breeding diet specialist species are adequately represented by the global protected area system, but that this percentage is lower for the most threatened species. Policies that modify conservation planning approaches to include measures of specialization alongside other more traditional metrics of biodiversity could improve the protection of biodiversity in the face of rapidly accelerating anthropogenic threats.
Bimonthly viral monitoring for late‐onset cytomegalovirus infection in kidney transplant recipients
Authors: Melgarejo Ivy , Jorgensen Dana , Hariharan Sundaram , Puttarajappa Chethan M. 
Published: February 2021

AbstractKidney transplant recipients with high‐risk cytomegalovirus (CMV) serostatus (seropositive donor to seronegative recipient) are at risk for late‐onset CMV after cessation of antiviral prophylaxis. We report findings from a strategy of bimonthly (every 2 weeks) CMV screening for late‐onset CMV. This is a single‐center retrospective cohort study of 70 high‐risk CMV kidney transplant recipients transplanted between June 2016 and September 2018. Patients were monitored at 6–12 months post‐transplantation for late‐onset CMV using bimonthly CMV nucleic acid testing (NAT). Adherence to screening and its correlation with CMV‐related hospitalizations were assessed. Failure to prevent CMV‐related hospitalization was classified into three categories (non‐adherence to CMV testing, rapid CMV progression, and health system failure). Twenty‐one (30%) patients developed CMV DNAemia, of whom 10 (14%) required hospitalization. Reasons for CMV‐related hospitalization despite screening were (i) screening non‐adherence (50%), (ii) rapid progression (40%), and (iii) health system failure (10%). Adherence to screening was associated with lower viral counts at diagnosis (r = ‐.44, p = .049) and a trend towards lower risk of CMV‐related hospitalization (OR: 0.97 per 1% increase in adherence; 95% CI: 0.94–1.00; p = .06). Bimonthly monitoring for late‐onset CMV allows for early CMV detection and may lower CMV‐related hospitalization.