bluuebunny/crossref_metadata_2025 huggingface dataset:
Social network characteristics and alcohol use by ethnic origin: An ego-based network study on peer similarity, social relationships, and co-existing drinking habits among young Swedes
Authors: Gustafsson Nina-Katri , Rydgren Jens , Rostila Mikael , Miething Alexander
Published: April 2021

The study explores how social network determinants relate to the prevalence and frequency of alcohol use among peer dyads. It is studied how similar alcohol habits co-exist among persons (egos) and their peers (alters) when socio-demographic similarity (e.g., in ethnic origin), network composition and other socio-cultural aspects were considered. Data was ego-based responses derived from a Swedish national survey with a cohort of 23-year olds. The analytical sample included 7987 ego-alter pairs, which corresponds to 2071 individuals (egos). A so-called dyadic design was applied i.e., all components of the analysis refer to ego-alter pairs (dyads). Multilevel multinomial-models were used to analyse similarity in alcohol habits in relation to ego-alter similarity in ethnic background, religious beliefs, age, sex, risk-taking, educational level, closure in network, duration, and type of relationship, as well as interactions between ethnicity and central network characteristics. Ego-alter similarity in terms of ethnic origin, age and sex was associated with ego-alter similarity in alcohol use. That both ego and alters were non-religious and were members of closed networks also had an impact on similarity in alcohol habits. It was concluded that network similarity might be an explanation for the co-existence of alcohol use among members of peer networks.
Fatigue, induced via repetitive upper-limb motor tasks, influences trunk and shoulder kinematics during an upper limb reaching task in a virtual reality environment
Authors: Dupuis Frédérique , Sole Gisela , Wassinger Craig , Bielmann Mathieu , Bouyer Laurent J. , Roy Jean-Sébastien
Published: April 2021

Background

Efficient shoulder movement depends on the ability of central nervous system to integrate sensory information and to create an appropriate motor command. Various daily encountered factors can potentially compromise the execution of the command, such as fatigue. This study explored how fatigue influences shoulder movements during upper limb reaching.

Methods

Forty healthy participants were randomly assigned to one of two groups: Control or Fatigue Group. All participants completed an upper limb reaching task at baseline and post-experimental, during which they reached four targets located at 90° of shoulder abduction, 90° external rotation at 90° abduction, 120° scaption, and 120° flexion in a virtual reality environment. Following the baseline phase, the Fatigue Group completed a shoulder fatigue protocol, while Controls took a 10-minute break. Thereafter, the reaching task was repeated. Upper limb kinematic (joint angles and excursions) and spatiotemporal (speed and accuracy) data were collected during the reaching task. Electromyographic activity of the anterior and middle deltoids were also collected to characterize fatigue. Two-way repeated-measures ANOVA were performed to determine the effects of Time, Group and of the interaction between these factors.

Results

The Fatigue group showed decreased mean median power frequency and increased electromyographic amplitudes of the anterior deltoid (p < 0.05) following the fatigue protocol. Less glenohumeral elevation, increased trunk flexion and rotation and sternoclavicular elevation were also observed in the Fatigue group (Group x Time interaction, p < 0.05). The Control group improved their movement speed and accuracy in post-experimental phase, while the Fatigue group showed a decrease of movement speed and no accuracy improvement (Group x Time interaction, p < 0.05).

Conclusion

In a fatigued state, changes in movement strategy were observed during the reaching task, including increased trunk and sternoclavicular movements and less glenohumeral movement. Performance was altered as shown by the lack of accuracy improvement over time and a decrease in movement speed in the Fatigue group.
The impact and cost-effectiveness of introducing the 10-valent pneumococcal conjugate vaccine into the paediatric immunisation programme in Iceland—A population-based time series analysis
Authors: Eythorsson Elias , Ásgeirsdóttir Tinna L. , Erlendsdóttir Helga , Hrafnkelsson Birgir , Kristinsson Karl G. , Haraldsson Ásgeir
Published: April 2021

Introduction

Streptococcus pneumoniae is a cause of infections that range in severity from acute otitis media (AOM) to pneumonia and invasive pneumococcal disease (IPD). The 10-valent pneumococcal conjugate vaccine (PHiD-CV10) was introduced into the Icelandic paediatric immunisation programme in 2011. The aim was to estimate the population impact and cost-effectiveness of PHiD-CV10 introduction.

Methods

Data on primary care visits from 2005–2015 and hospitalisations from 2005–2017 were obtained from population-based registries. A Bayesian time series analysis with synthetic controls was employed to estimate the number of cases of AOM, pneumonia and IPD that would have occurred between 2013–2017, had PHiD-CV10 not been introduced. Prevented cases were calculated by subtracting the observed number of cases from this estimate. The cost of the programme was calculated accounting for cost-savings due to prevented cases.

Results

The introduction of PHiD-CV10 prevented 13,767 (95% credible interval [CI] 2,511–29,410) visits for AOM from 2013–2015, and prevented 1,814 (95%CI -523-4,512) hospitalisations for pneumonia and 53 (95%CI -17-177) admissions for IPD from 2013–2017. Visits for AOM decreased both among young children and among children 4–19 years of age, with rate ratios between 0.72–0.89. Decreases were observed in both pneumonia hospitalisations (rate ratios between 0.67–0.92) and IPD (rate ratios between 0.27–0.94). The total cost of implementing PHiD-CV10 in Iceland was -7,463,176 United States Dollars (USD) (95%CI -16,159,551–582,135) with 2.1 USD (95%CI 0.2–4.7) saved for every 1 USD spent.

Conclusions

The introduction of PHiD-CV10 was associated with large decreases in visits and hospitalisations for infections commonly caused by pneumococcus and was cost-saving during the first five years of the immunisation programme.
Real world effectiveness of standard of care triple therapy versus two-drug combinations for treatment of people living with HIV
Authors: Teira Ramón , Diaz-Cuervo Helena , Aragão Filipa , Marguet Sophie , de la Fuente Belén , Muñoz Maria Jose , Abdulghani Nadia , Ribera Esteban , Domingo Pere , Deig Elisabeth , Peraire Joaquim , Roca Bernardino , Montero Marta , Galindo Maria José , Romero Alberto , Espinosa Nuria , Lozano Fernando , Merino María Dolores , Martínez Elisa , Geijo Paloma , Estrada Vicente , García Josefina , Sepúlveda M. Antonia , Berenguer Juan
Published: April 2021

Background

Since 1996, the standard of care (SOC) therapy for HIV treatment has consisted of a backbone of two nucleoside analogue reverse transcriptase inhibitors (NRTI) paired with a third agent. Use of two-drug combinations (2DC) has been considered for selected patients to avoid toxicities associated with the use of NRTIs. This study aimed to compare the real-world outcomes of integrase strand transfer inhibitor (INSTI)-containing triple therapy (TT) to dolutegravir- (DTG) and/or boosted protease inhibitor (bPI)-based 2DC in a large Spanish cohort of HIV patients.

Methods

A retrospective analysis was performed using data from the VACH cohort, a prospective multicentre Spanish cohort of adult HIV patients. All treatment experienced patients initiating a TT of an INSTI combined with two NRTIs or a 2DC-containing DTG and/or a bPI between 01/01/2012 and 01/06/2017 were included. The unit of analysis was patient-regimens. The overall sample analysis was complemented with two sub-analyses. The first sub-analysis focused on patients treated with a backbone plus DTG compared to those treated with DTG+ one other antiretroviral. The second sub-analysis focused on patients with HIV RNA<50 copies/mL at baseline, irrespective of the regimen used. The following endpoints were assessed: time to discontinuation for any reason, time to switch due to virologic failure, and time to switch due to toxicity (reasons for discontinuation according to clinician report in the database). Time-to-event analyses were conducted using Kaplan–Meier survival curves and Cox regression models.

Results

Overall 7,481 patients were included in the analysis, contributing to 9,243 patient-regimens. Patient characteristics at baseline differed among groups, with the 2DC group being significantly older and having a higher proportion of women, a longer time on ART and a higher number of previous virologic failures. Median (95% Confidence Interval [C.I.]) time to switch was 2.5 years (2.3, 2.7) in 2DC group versus 2.9 years (2.7, 3.0) in TT. Adjusted hazard ratios (95% C.I.) for discontinuation due to any reason, virologic failure and toxicity in the 2DC vs TT group were 1.29 (1.15; 1.44), 2.06 (1.54; 2.77) and 1.18 (0.94; 1.48), respectively. Results were consistent in the two sub-analyses.

Conclusion

In this analysis, time to discontinuation and probability of remaining free of virologic failure were significantly higher in patients on INSTI-based TT compared to DTG- and/or bPI-containing 2DC, with no differences in toxicity.
The first 90: Progress in HIV detection in Zhejiang Province, 2008–2018
Authors: Chen Lin , Luo Mingyu , Xu Yun , Xia Yan , Zhou Xin , Chen Wanjun , Wang Hui , Jiang Tingting , Chen Weiyong , Luo Yan , Ma Qiaoqin , Jiang Jianmin , Pan Xiaohong
Published: April 2021

To analyze the results of HIV screening and the HIV-positive rate based on different HIV detection strategies in Zhejiang Province, China. Data were downloaded from the AIDS Prevention and Control Information System on May 1, 2019. HIV screening, prevalence, and incidence data were analyzed from 2008 to 2018. The incidence of HIV was calculated from the results of BED testing. SPSS software (ver. 19.0) was used for the analysis. The number of people screened for HIV increased by 229.7% from 2008 to 2018, while the incidence of HIV increased from 1.14‱ (2010) to 1.67‱ (2018), peak by 2015 (2.28‱). The proportion of people screened for HIV in medical institutions increased from 62.0% in 2008 to 67.1% in 2018, while of all positive tests, 47.9% were conducted at medical institutions in 2008, which increased to 63.2% in 2018. VCT and STD clinic attendees, who had only 4.5% of all those undergoing HIV tests, accounted for 23.7% of all HIV positive in 2018. The rate of HIV-positive people and incidence of HIV both increased in Zhejiang Province between 2008 and 2015. The most effective strategy for detecting HIV new cases is screening visitors to VCT and STD clinics.
Spatial patterns of pulmonary tuberculosis (TB) cases in Zimbabwe from 2015 to 2018
Authors: Gwitira Isaiah , Karumazondo Norbert , Shekede Munyaradzi Davis , Sandy Charles , Siziba Nicolas , Chirenda Joconiah
Published: April 2021

Introduction

Accurate mapping of spatial heterogeneity in tuberculosis (TB) cases is critical for achieving high impact control as well as guide resource allocation in most developing countries. The main aim of this study was to explore the spatial patterns of TB occurrence at district level in Zimbabwe from 2015 to 2018 using GIS and spatial statistics as a preamble to identifying areas with elevated risk for prioritisation of control and intervention measures.

Methods

In this study Getis-Ord Gi* statistics together with SaTscan were used to characterise TB hotspots and clusters in Zimbabwe at district level from 2015 to 2018. GIS software was used to map and visualise the results of cluster analysis.

Results

Results show that TB occurrence exhibits spatial heterogeneity across the country. The TB hotspots were detected in the central, western and southern part of the country. These areas are characterised by artisanal mining activities as well as high poverty levels.

Conclusions and recommendations

Results of this study are useful to guide TB control programs and design effective strategies which are important in achieving the United Nations Sustainable Development goals (UNSDGs).
Specimen-specific drift of densities defines distinct subclasses of extracellular vesicles from human whole saliva
Authors: Yamamoto Satoshi , Okamura Kohji , Fujii Risa , Kawano Takamasa , Ueda Koji , Yajima Yasutomo , Shiba Kiyotaka
Published: April 2021

Extracellular vesicles (EVs) in body fluids constitute heterogenous populations, which mirror their diverse parental cells as well as distinct EV-generation pathways. Various methodologies have been proposed to differentiate EVs in order to deepen the current understanding of EV biology. Equilibrium density-gradient centrifugation has often been used to separate EVs based on their buoyant densities; however, the standard conditions used for the method do not necessarily allow all EVs to move to their equilibrium density positions, which complicates the categorization of EVs. Here, by prolonging ultracentrifugation time to 96 h and fractionating EVs both by floating up or spinning down directions, we allowed 111 EV-associated protein markers from the whole saliva of three healthy volunteers to attain equilibrium. Interestingly, the determined buoyant densities of the markers drifted in a specimen-specific manner, and drift patterns differentiated EVs into at least two subclasses. One class carried classical exosomal markers, such as CD63 and CD81, and the other was characterized by the molecules involved in membrane remodeling or vesicle trafficking. Distinct patterns of density drift may represent the differences in generation pathways of EVs.
Targeting Candida albicans in dual-species biofilms with antifungal treatment reduces Staphylococcus aureus and MRSA in vitro
Authors: Luo Yu , McAuley Daniel F. , Fulton Catherine R. , Sá Pessoa Joana , McMullan Ronan , Lundy Fionnuala T.
Published: April 2021

Polymicrobial biofilms consisting of fungi and bacteria are frequently formed on endotracheal tubes and may contribute to development of ventilator associated pneumonia (VAP) in critically ill patients. This study aimed to determine the role of early Candida albicans biofilms in supporting dual-species (dual-kingdom) biofilm formation with respiratory pathogens in vitro, and investigated the effect of targeted antifungal treatment on bacterial cells within the biofilms. Dual-species biofilm formation between C. albicans and three respiratory pathogens commonly associated with VAP (Pseudomonas aeruginosa, Escherichia coli and Staphylococcus aureus) was studied using quantitative PCR. It was shown that early C. albicans biofilms enhanced the numbers of E. coli and S. aureus (including methicillin resistant S. aureus; MRSA) but not P. aeruginosa within dual-species biofilms. Transwell assays demonstrated that contact with C. albicans was required for the increased bacterial cell numbers observed. Total Internal Reflection Fluorescence microscopy showed that both wild type and hyphal-deficient C. albicans provided a scaffold for initial bacterial adhesion in dual species biofilms. qPCR results suggested that further maturation of the dual-species biofilm significantly increased bacterial cell numbers, except in the case of E.coli with hyphal-deficient C. albicans (Ca_gcn5Δ/Δ). A targeted preventative approach with liposomal amphotericin (AmBisome®) resulted in significantly decreased numbers of S. aureus in dual-species biofilms, as determined by propidium monoazide-modified qPCR. Similar results were observed when dual-species biofilms consisting of clinical isolates of C. albicans and MRSA were treated with liposomal amphotericin. However, reductions in E. coli numbers were not observed following liposomal amphotericin treatment. We conclude that early C. albicans biofilms have a key supporting role in dual-species biofilms by enhancing bacterial cell numbers during biofilm maturation. In the setting of increasing antibiotic resistance, an important and unexpected consequence of antifungal treatment of dual-species biofilms, is the additional benefit of decreased growth of multi-drug resistant bacteria such as MRSA, which could represent a novel future preventive strategy.
A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses
Authors: Fu Yuan , Thomas Ann , Gasior Dagmara , Harper John , Gay Alan , Jones Charlotte , Hegarty Matthew , Asp Torben , Fradera-Sola Albert , Armstead Ian , Fernandez-Fuentes Narcis
Published: April 2021

Ryegrasses(Loliumspp.) and fescues (Festucaspp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their traits. We have compared patterns of differentially expressed genes (DEGs) in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of a festulolium (predominantly Italian ryegrass) and meadow fescue with the onset of water stress, focussing on overall patterns of DEGs and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation) and, as the medium dried, at 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated comparing the EWC sampling points from RNAseq data using a combination of analysis methods. For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. GO terms shared by all four genotypes were often enriched by both up- and down-regulated DEGs in the leaf, whereas generally, only by either up- or down-regulated DEGs in the root. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5–15% of the DEGs enriching common GO terms were shared by all 4 genotypes, suggesting considerable variation in DEGs between related genotypes in enacting similar biological processes.
Phytophthora infestans RXLR effector AVR1 disturbs the growth of Physcomitrium patens without affecting Sec5 localization
Authors: Overdijk Elysa J. R. , Putker Vera , Smits Joep , Tang Han , Bouwmeester Klaas , Govers Francine , Ketelaar Tijs
Published: April 2021

Plant pathogens often exploit a whole range of effectors to facilitate infection. The RXLR effector AVR1 produced by the oomycete plant pathogen Phytophthora infestans suppresses host defense by targeting Sec5. Sec5 is a subunit of the exocyst, a protein complex that is important for mediating polarized exocytosis during plant development and defense against pathogens. The mechanism by which AVR1 manipulates Sec5 functioning is unknown. In this study, we analyzed the effect of AVR1 on Sec5 localization and functioning in the moss Physcomitrium patens. P. patens has four Sec5 homologs. Two (PpSec5b and PpSec5d) were found to interact with AVR1 in yeast-two-hybrid assays while none of the four showed a positive interaction with AVR1ΔT, a truncated version of AVR1. In P. patens lines carrying β-estradiol inducible AVR1 or AVR1ΔT transgenes, expression of AVR1 or AVR1ΔT caused defects in the development of caulonemal protonema cells and abnormal morphology of chloronema cells. Similar phenotypes were observed in Sec5- or Sec6-silenced P. patens lines, suggesting that both AVR1 and AVR1ΔT affect exocyst functioning in P. patens. With respect to Sec5 localization we found no differences between β-estradiol-treated and untreated transgenic AVR1 lines. Sec5 localizes at the plasma membrane in growing caulonema cells, also during pathogen attack, and its subcellular localization is the same, with or without AVR1 in the vicinity.
Post-COVID-19 syndrome among symptomatic COVID-19 patients: A prospective cohort study in a tertiary care center of Bangladesh
Authors: Mahmud Reaz , Rahman Md. Mujibur , Rassel Mohammad Aftab , Monayem Farhana Binte , Sayeed S. K. Jakaria Been , Islam Md. Shahidul , Islam Mohammed Monirul
Published: April 2021

Background

Post-coronavirus disease (COVID-19) syndrome includes persistence of symptoms beyond viral clearance and fresh development of symptoms or exaggeration of chronic diseases within a month after initial clinical and virological cure of the disease with a viral etiology. We aimed to determine the incidence, association, and risk factors associated with development of the post-COVID-19 syndrome.

Methods

We conducted a prospective cohort study at Dhaka Medical College Hospital between June 01, 2020 and August 10, 2020. All the enrolled patients were followed up for a month after clinical improvement, which was defined according the World Health Organization and Bangladesh guidelines as normal body temperature for successive 3 days, significant improvement in respiratory symptoms (respiratory rate <25/breath/minute with no dyspnea), and oxygen saturation >93% without assisted oxygen inhalation.

Findings

Among the 400 recruited patients, 355 patients were analyzed. In total, 46% patients developed post-COVID-19 symptoms, with post-viral fatigue being the most prevalent symptom in 70% cases. The post-COVID-19 syndrome was associated with female gender (relative risk [RR]: 1.2, 95% confidence interval [CI]: 1.02–1.48, p = 0.03), those who required a prolonged time for clinical improvement (p<0.001), and those showing COVID-19 positivity after 14 days (RR: 1.09, 95% CI: 1.00–1.19, p<0.001) of initial positivity. Patients with severe COVID-19 at presentation developed post-COVID-19 syndrome (p = 0.02). Patients with fever (RR: 1.5, 95% CI: 1.05–2.27, p = 0.03), cough (RR: 1.36, 95% CI: 1.02–1.81, p = 0.04), respiratory distress (RR: 1.3, 95% CI: 1.4–1.56, p = 0.001), and lethargy (RR: 1.2, 95% CI: 1.06–1.35, p = 0.003) as the presenting features were associated with the development of the more susceptible to develop post COVID-19 syndrome than the others. Logistic regression analysis revealed female sex, respiratory distress, lethargy, and long duration of the disease as risk factors.

Conclusion

Female sex, respiratory distress, lethargy, and long disease duration are critical risk factors for the development of post-COVID-19 syndrome.
Microbiome profiling of uncinate tissue and nasal polyps in patients with chronic rhinosinusitis using swab and tissue biopsy
Authors: Cho Sung-Woo , Kim Dong-Young , Choi Sungmi , Won Sungho , Kang Hye-Ryun , Yi Hana
Published: April 2021

Chronic rhinosinusitis (CRS) is characterized according to the presence or absence of nasal polyps (NPs) and displays nasal microbiota dysbiosis. However, optimal sampling methods of the nasal microbiome in CRS have not been identified. We aimed to assess the microbial composition in patients with CRS, comparing different sampling methods (swab and tissue biopsy), tissue types (uncinate tissue and NP), and disease subtypes. Samples were obtained by swabbing the middle meatus and taking a biopsy of uncinate tissue (UT) in patients with CRS with (CRSwNP, N = 8) or without NP (CRSsNP, N = 6) and controls (N = 8). NPs were also harvested in CRSwNP. DNAs were extracted from fifty-two samples and analyzed by 16S rRNA gene amplicon sequencing. As a result, a great interpersonal variance was observed in nasal swabs, while UT samples presented distinct microbiome with low inter-personal differences. Moreover, the UT microbiomes were further differentiated into three clusters which are associated with disease status (control, CRSsNP, and CRSwNP). Compared to UT, NP revealed a unique microbiome profile with significantly less bacterial diversity. Prevotella was the genus whose abundance was negatively correlated with disease severity in NP. In conclusion, tissue samples are better specimens than nasal swabs for assessing the microbiomes of CRS patients. Several bacteria in UT and NP tissues revealed an association with clinical severity of CRSwNP.
Electrical signalling on Bt and non-Bt cotton plants under stress by Aphis gossypii
Authors: Pachú Jéssica K. S. , Macedo Francynes C. O. , Malaquias José B. , Ramalho Francisco S. , Oliveira Ricardo F. , Franco Flávia Pereira , Godoy Wesley A. C.
Published: April 2021

Plants have developed various mechanisms to respond specifically to each biotrophic attack. It has been shown that the electrical signals emitted by plants are associated with herbivory stress responses and can lead to the activation of multiple defences. Bt cotton is a genetically modified pest-resistant plant that produces an insecticide from Bacillus thuringiensis (Bt) to control Lepidopteran species. Surprisingly, there is no study–yet, that characterizes the signalling mechanisms in transgenic cotton plants attacked by non-target insects, such as aphids. In this study, we characterized the production of electrical signals on Bt and non-Bt cotton plants infested with Aphis gossypii and, in addition, we characterized the dispersal behaviour of aphids to correlate this behaviour to plant signalling responses. Electrical signalling of the plants was recorded with an extracellular measurement technique. Impressively, our results showed that both Bt and non-Bt cotton varieties, when attacked by A. gossypii, emitted potential variation-type electrical signals and clearly showed the presence of distinct responses regarding their perception and the behaviour of aphids, with evidence of delay, in terms of signal amount, and almost twice the amount of Cry1F protein was observed on Bt cotton plants at the highest density of insects/plant. We present in our article some hypotheses that are based on plant physiology and insect behaviour to explain the responses found on Bt cotton plants under aphid stress.
The lockdown effect: A counterfactual for Sweden
Authors: Born Benjamin , Dietrich Alexander M. , Müller Gernot J.
Published: April 2021

While most countries imposed a lockdown in response to the first wave of COVID-19 infections, Sweden did not. To quantify the lockdown effect, we approximate a counterfactual lockdown scenario for Sweden through the outcome in a synthetic control unit. We find, first, that a 9-week lockdown in the first half of 2020 would have reduced infections and deaths by about 75% and 38%, respectively. Second, the lockdown effect starts to materialize with a delay of 3–4 weeks only. Third, the actual adjustment of mobility patterns in Sweden suggests there has been substantial voluntary social restraint, although the adjustment was less strong than under the lockdown scenario. Lastly, we find that a lockdown would not have caused much additional output loss.
Genome-wide identification and expression analysis of late embryogenesis abundant protein-encoding genes in rye (Secale cereale L.)
Authors: Ding Mengyue , Wang Lijian , Zhan Weimin , Sun Guanghua , Jia Xiaolin , Chen Shizhan , Ding Wusi , Yang Jianping
Published: April 2021

Late embryogenesis abundant (LEA) proteins are members of a large and highly diverse family that play critical roles in protecting cells from abiotic stresses and maintaining plant growth and development. However, the identification and biological function of genes of Secale cereale LEA (ScLEA) have been rarely reported. In this study, we identified 112 ScLEA genes, which can be divided into eight groups and are evenly distributed on all rye chromosomes. Structure analysis revealed that members of the same group tend to be highly conserved. We identified 12 pairs of tandem duplication genes and 19 pairs of segmental duplication genes, which may be an expansion way of LEA gene family. Expression profiling analysis revealed obvious temporal and spatial specificity of ScLEA gene expression, with the highest expression levels observed in grains. According to the qRT-PCR analysis, selected ScLEA genes were regulated by various abiotic stresses, especially PEG treatment, decreased temperature, and blue light. Taken together, our results provide a reference for further functional analysis and potential utilization of the ScLEA genes in improving stress tolerance of crops.
Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights
Authors: Aguilar-Ordoñez Israel , Pérez-Villatoro Fernando , García-Ortiz Humberto , Barajas-Olmos Francisco , Ballesteros-Villascán Judith , González-Buenfil Ram , Fresno Cristobal , Garcíarrubio Alejandro , Fernández-López Juan Carlos , Tovar Hugo , Hernández-Lemus Enrique , Orozco Lorena , Soberón Xavier , Morett Enrique
Published: April 2021

There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average Native American ancestry. On average, each individual has 3.26 million Single Nucleotide Variants and short indels, that together comprise a catalog of 9,737,152 variants, 44,118 of which are novel. We report 497 common Single Nucleotide Variants (with allele frequency > 5%) mapped to drug responses and 316,577 in enhancer or promoter elements; interestingly we found some of these enhancer variants in PPARG, a nuclear receptor involved in highly prevalent health problems in Mexican population, such as obesity, diabetes, and insulin resistance. By detecting signals of positive selection we report 24 enriched key pathways under selection, most of them related to immune mechanisms. No missense variants in ACE2, the receptor responsible for the entry of the SARS CoV-2 virus, were found in any individual. Population genomics and phylogenetic analyses demonstrated stratification in a Northern-Central-Southern axis, with major substructure in the Central region. The Seri, a northern group with the most genetic divergence in our study, showed a distinctive genomic context with the most novel variants, and the most population specific genotypes. Genome-wide analysis showed that the average haplotype blocks are longer in Native Mexicans than in other world populations. With this dataset we describe previously undetected population level variation in Native Mexicans, helping to reduce the gap in genomic data representation of such groups.
Occupational and environmental asbestos exposure and the risk of lung cancer in Korea: A case-control study in South Chungcheong Province of Korea
Authors: Huh Da-An , Kang Min-Sung , Lee Jiyun , Choi Ji Yoon , Moon Kyong Whan , Lee Yong-Jin
Published: April 2021

Despite the use of large amounts of asbestos in the 1990s, few studies have been conducted in Korea on occupational and environmental asbestos exposure and lung cancer risk. The main aim of this study was to estimate the risk of lung cancer development caused by occupational and environmental asbestos exposures in residents of South Chungcheong Province, where about half of the asbestos mines in Korea operated. We conducted a case-control study, for which the information on asbestos exposure history and demographic characteristics was provided by the Environmental Health Center for asbestos of Soonchunhyang University Cheonan Hospital. After adjusting for all covariates, the odds ratios for lung cancer tended to increase with higher exposure probability for both occupational as well as environmental asbestos. The relative risk of occupational asbestos exposure was higher than that of environmental exposure; the interaction of co-exposure was not statistically significant. The estimated means of the latency period were significantly shorter in participants who were engaged in the production of asbestos-containing products and in those who lived near asbestos industries as compared to other groups.
Global biochemical analysis of plasma, serum and whole blood collected using various anticoagulant additives
Authors: Kennedy Adam D. , Ford Lisa , Wittmann Bryan , Conner Jesse , Wulff Jacob , Mitchell Matthew , Evans Anne M. , Toal Douglas R.
Published: April 2021

Introduction

Analysis of blood for the evaluation of clinically relevant biomarkers requires precise collection and sample handling by phlebotomists and laboratory staff. An important consideration for the clinical application of metabolomics are the different anticoagulants utilized for sample collection. Most studies that have characterized differences in metabolite levels in various blood collection tubes have focused on single analytes. We define analyte levels on a global metabolomics platform following blood sampling using five different, but commonly used, clinical laboratory blood collection tubes (i.e., plasma anticoagulated with either EDTA, lithium heparin or sodium citrate, along with no additive (serum), and EDTA anticoagulated whole blood).

Methods

Using an untargeted metabolomics platform we analyzed five sample types after all had been collected and stored at -80°C. The biochemical composition was determined and differences between the samples established using matched-pair t-tests.

Results

We identified 1,117 biochemicals across all samples and detected a mean of 1,036 in the sample groups. Compared to the levels of metabolites in EDTA plasma, the number of biochemicals present at statistically significant different levels (p<0.05) ranged from 452 (serum) to 917 (whole blood). Several metabolites linked to screening assays for rare diseases including acylcarnitines, bilirubin and heme metabolites, nucleosides, and redox balance metabolites varied significantly across the sample collection types.

Conclusions

Our study highlights the widespread effects and importance of using consistent additives for assessing small molecule levels in clinical metabolomics. The biochemistry that occurs during the blood collection process creates a reproducible signal that can identify specimens collected with different anticoagulants in metabolomic studies.

Impact statement

In this manuscript, normal/healthy donors had peripheral blood collected using multiple anticoagulants as well as serum during a fasted blood draw. Global metabolomics is a new technology being utilized to draw clinical conclusions and we interrogated the effects of different anticoagulants on the levels of biochemicals from each of the donors. Characterizing the effects of the anticoagulants on biochemical levels will help researchers leverage the information using global metabolomics in order to make conclusions regarding important disease biomarkers.
Vancomycin-resistant enterococci and coagulase-negative staphylococci prevalence among patients attending at Felege Hiwot Comprehensive Specialized Hospital, Bahir Dar, Ethiopia
Authors: Ashagrie Degu , Genet Chalachew , Abera Bayeh
Published: April 2021

Background

Vancomycin resistant enterococci (VRE) and vancomycin resistance coagulase negative staphylococci (VRCoNS) are common pathogens causing difficult to treat health care associated infections (HAI). Hence, the World Health Organization listed VRE as one of the high priority pathogens for new antibiotic discovery and antimicrobial resistance surveillance. Despite this, data on the prevalence of VRE and VRCoNS in Ethiopia is scarce. Thus, the present study determined prevalence of VRE and VRCoNS among patients attending Felege-Hiwot comprehensive specialized hospital, Ethiopia.

Methods

A hospital based cross-sectional study was conducted on 384 patients selected conveniently from February to March 2020. Data on demographic and clinical variables were collected using a structured questionnaire by face-to-face interview. Simultaneously urine, venous blood and wound swab were collected and processed following standard bacteriological technique. Antimicrobial susceptibility test was performed by minimum inhibitory concentration method using E-test for vancomycin and Kirby-Bauer disc diffusion method for other classes of antibiotics. Data was entered and analyzed using SPSS version 23. Logistic regression was performed to identify factors associated with VRE infection. P. value < 0.05 was considered as statistically significant.

Results

The prevalence of enterococci and CoNS were 6.8% and 12% respectively. The prevalence of VRE was 34.61% (9/26), while all CoNS (46 isolates) were susceptible to vancomycin. The majority (66.7%) of VRE was isolated from blood samples. Furthermore all VRE (100%), 58.8% of vancomycin susceptible enterococci and 45.7% of CoNS were multidrug resistant (MDR). Having educational level of secondary school and below (AOR = 12.80, CI = 1.149–142.5), previous exposure to catheterization (AOR = 56.0, CI = 4.331–724.0) and previous antibiotic use practice (AOR = 26.25, CI = 3.041–226.2) were a significant associated explanatory factor for VRE infection.

Conclusions

The prevalence of vancomycin resistance enterococci, which is also multidrug resistant, was significantly high. Though no vancomycin resistance CoNS detected, the MDR level of CoNS was high. Thus to limit enterococci and CoNS infections and MDR development, focused infection prevention measures should be implemented.
Long-term outcome of prolonged critical illness: A multicentered study in North Brisbane, Australia
Authors: Laupland Kevin B. , Ramanan Mahesh , Shekar Kiran , Edwards Felicity , Clement Pierre , Tabah Alexis
Published: April 2021

Background

Although critical illness is usually of high acuity and short duration, some patients require prolonged management in intensive care units (ICU) and suffer long-term morbidity and mortality.

Objective

To describe the long-term survival and examine determinants of death among patients with prolonged ICU admission.

Methods

A retrospective cohort of adult Queensland residents admitted to ICUs for 14 days or longer in North Brisbane, Australia was assembled. Comorbid illnesses were classified using the Charlson definitions and all cause case fatality established using statewide vital statistics.

Results

During the study a total of 28,742 adult Queensland residents had first admissions to participating ICUs of which 1,157 (4.0%) had prolonged admissions for two weeks or longer. Patients with prolonged admissions included 645 (55.8%), 243 (21.0%), and 269 (23.3%) with ICU lengths of stay lasting 14–20, 21–27, and ≥28 days, respectively. Although the severity of illness at admission did not vary, pre-existing comorbid illnesses including myocardial infarction, congestive heart failure, kidney disease, and peptic ulcer disease were more frequent whereas cancer, cerebrovascular accidents, and plegia were less frequently observed among patients with increasing ICU lengths of stay lasting 14–20, 21–27, and ≥28 days. The ICU, hospital, 90-day, and one-year all cause case-fatality rates were 12.7%, 18.5%, 20.2%, and 24.9%, respectively, and were not different according to duration of ICU stay. The median duration of observation was 1,037 (interquartile range, 214–1888) days. Although comorbidity, age, and admitting diagnosis were significant, neither ICU duration of stay nor severity of illness at admission were associated with overall survival outcome in a multivariable Cox regression model.

Conclusions

Most patients with prolonged stays in our ICUs are alive at one year post-admission. Older age and previous comorbidities, but not severity of illness or duration of ICU stay, are associated with adverse long-term mortality outcome.
Zaraa Uul: An archaeological record of Pleistocene-Holocene palaeoecology in the Gobi Desert
Authors: Janz Lisa , Rosen Arlene M. , Bukhchuluun Dashzeveg , Odsuren Davaakhuu
Published: April 2021

Environmentally-based archaeological research at Zaraa Uul, including zooarchaeology, phytolith analysis, and radiocarbon dating, is the first of its kind in Mongolia and presents critical new insight on the relationship between periods of occupational intensity and climatic amelioration from the earliest anatomically modern humans to the adoption of pastoralism. The palaeoenvironmental and faunal record of Zaraa Uul show that Early-Middle Holocene hydrology and species distributions were distinct from all other periods of human occupation. Holocene hunter-gatherers inhabited an ecosystem characterized by extensive marshes, riparian shrub and arboreal vegetation along the hill slopes and drainages. The exploitation of species associated with riparian and wetland settings supports the hypothesis of, but suggests an earlier timing for, oasis-based logistical foraging during the Early-Middle Holocene of arid Northeast Asia. The onset of wetter conditions at 8500 cal BP agrees with other regional studies, but multiple lines of evidence present the first integrated field- and laboratory-based record of human-environment relationships in arid East Asia during the Holocene Climatic Optimum. We compare it to Late Pleistocene climatic amelioration, and highlight specific responses of the hydrological, vegetative and faunal communities to climate change in arid Northeast Asia.
Aetiology of acute diarrhoea in children in Shanghai, 2015–2018
Authors: Chang Hailing , Guo Jiayin , Wei Zhongqiu , Huang Zheng , Wang Chuning , Qiu Yue , Xu Xuebin , Zeng Mei
Published: April 2021

Diarrhoea remains a major cause of childhood morbidity and mortality worldwide. This study aimed to monitor the aetiology of acute diarrhoea in children in Shanghai. Paediatric outpatients with acute diarrhoea were enrolled in the study from Jan 2015 to Dec 2018. Faecal samples were collected for testing. Enteric bacteria were identified and typed by culture and serotyping, respectively. Enteric viruses were identified by real-time PCR. Enteric pathogens were identified in 1572 (58.4%) of the 2692 enrolled children with acute diarrhoea. Viruses were detected more frequently than bacteria (41.3% versus 25.0%). Nontyphoidal Salmonella spp. (NTS) was the most common (10.3%) bacteria isolated, followed by enteropathogenic Escherichia coli (EPEC) (6.5%), enteroaggregative Escherichia coli (EAEC) (6.2%), Campylobacter spp. (3.6%), enterotoxigenic Escherichia coli (ETEC) (1.1%), Shigella spp. (0.2%), and enterohemorrhagic Escherichia coli (EHEC) (0.1%). Rotavirus was the most common (16.0%) virus detected, followed by norovirus (15.5%), adenovirus (7.2%), sapovirus (3.0%) and astrovirus (2.7%). Rotavirus, norovirus and NTS were the major pathogens responsible for diarrhoea in Shanghainese children. Improving uptake of the rotavirus vaccine and strengthening foodborne-pathogen prevention will aid in reducing the burden of diarrhoeal disease in children in Shanghai.
Acute toxicity and ecological risk assessment of 4,4’-dihydroxybenzophenone, 2,4,4’-trihydroxybenzophenone and 4-MBC in ultraviolet (UV)-filters
Authors: Han Jing , Qin Ze-Tian , Zhang Jing , Wang Wen-Qiang , Wu Jing-Ya , Lu Yong-Ze , Sun Li-Wei
Published: April 2021

Ultraviolet (UV) filters are used in cosmetics, personal care products and packaging materials to provide sun protection for human skin and other substances. Little is known about these substances, but they continue to be released into the environment. The acute toxicity of 4,4’-dihydroxybenzophenone, 2,4,4’-trihydroxybenzophenone and 4-MBC to Chlorella vulgaris and Daphnia magna were analyzed in this study. The 96 h-EC50 values of 4,4’-dihydroxybenzophenone, 2,4,4’-trihydroxybenzophenone and 4-MBC on C. vulgaris were 183.60, 3.50 and 0.16874 mg/L, respectively. The 48 h-LC50 of 4,4’-dihydroxybenzophenone, 2,4,4’-trihydroxybenzophenone and 4-MBC on D. magna were 12.50, 3.74 and 0.54445 mg/L, respectively. The toxicity of a mixture of 4,4’-dihydroxybenzophenone and 4-MBC showed addictive effect on C. vulgaris, while the toxicity of mixtures of 4,4’-dihydroxybenzophenone and 2,4,4’-trihydroxybenzophenone, 2,4,4’-trihydroxybenzophenone and 4-MBC as well as 4,4’-dihydroxybenzophenone, 2,4,4’-trihydroxybenzophenone and 4-MBC all showed antagonistic effect on C. vulgaris. The induced no-effect concentrations of 4,4’-dihydroxybenzophenone, 2,4,4’-trihydroxybenzophenone and 4-MBC by the assessment factor (AF) method were 0.0125, 0.00350 and 0.000169 mg/L, respectively.
Effectiveness and safety of rivaroxaban versus warfarin in Taiwanese patients with end-stage renal disease and nonvalvular atrial fibrillation: A real-world nationwide cohort study
Authors: Lin Yi-Cheng , Chen Bi-Li , Shih Chun-Ming , Lin Feng-Yen , Chen Chih-Wei , Hsu Chien-Yi , Kao Yung-Ta , Bi Wei-Fung , Chen Li-Ying , Chien Li-Nien , Fang Te-Chao , Huang Chun-Yao
Published: April 2021

Background

The optimal anticoagulant for end-stage renal disease patients for stroke prophylaxis is unknown. The efficacy and safety of warfarin in this population are debatable. In addition, real-world evidence of direct oral anticoagulants in patients with end-stage renal disease is limited. The aim of this study was to evaluate the clinical outcomes of rivaroxaban compared with warfarin in Taiwanese patients with end-stage renal disease with nonvalvular atrial fibrillation in a real-world setting.

Methods and results

This was a retrospective population-based cohort study conducted using Taiwan’s National Health Insurance Research Database. Patients with nonvalvular atrial fibrillation and end-stage renal disease who started on rivaroxaban or warfarin between February 2013 and September 2017 were eligible to participate in the study. The inverse probability of treatment weighting approach was used to balance baseline characteristics. Bleeding and thromboembolic outcomes were compared using competing risk analyses. The study population consisted of 3358 patients (173 and 3185 patients on rivaroxaban and warfarin, respectively). In the rivaroxaban group, 50.8%, 38.7%, and 10.4% of the patients received 10, 15, and 20 mg of the drug, respectively. The cumulative incidence of major bleeding was similar between the two groups; however, the gastrointestinal bleeding rate was lower in the rivaroxaban group (adjusted subdistribution hazard ratio [SHR]: 0.56, 95% confidence interval [CI]: 0.34–0.91) than in the warfarin group. Furthermore, the composite risk of ischemic stroke or systemic embolism was significantly lower in the rivaroxaban group (adjusted SHR: 0.36, 95% CI: 0.17–0.79). Similar findings were observed for patients who received 10 mg of rivaroxaban.

Conclusions

In Taiwanese patients with end-stage renal disease and nonvalvular atrial fibrillation, rivaroxaban may be associated with a similar risk of major bleeding but a lower risk of thromboembolism compared with warfarin. The potential benefit of 10 mg of rivaroxaban in this population requires further investigation.