bluuebunny/crossref_metadata_2025 huggingface dataset:
Seed microbiota revealed by a large‐scale meta‐analysis including 50 plant species
Authors: Simonin Marie , Briand Martial , Chesneau Guillaume , Rochefort Aude , Marais Coralie , Sarniguet Alain , Barret Matthieu
Published: February 2022

Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing to its role for plant health and productivity.

Here, we performed a meta‐analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat.

Seed microbiota are diverse and extremely variable, with taxa richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e. flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples.

Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa.

The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.
Intracellular reactive oxygen species trafficking participates in seed dormancy alleviation in Arabidopsis seeds
Authors: Jurdak Rana , Rodrigues Guilherme de Almeida Garcia , Chaumont Nicole , Schivre Geoffrey , Bourbousse Clara , Barneche Fredy , Bou Dagher Kharrat Magda , Bailly Christophe
Published: February 2022

Reactive oxygen species (ROS) release seed dormancy through an unknown mechanism. We used different seed dormancy‐breaking treatments to decipher the dynamics and localization of ROS production during seed germination.

We studied the involvement of ROS in the breaking of Arabidopsis seed dormancy by cold stratification, gibberellic acid (GA3) and light. We characterized the effects of these treatments on abscisic acid and gibberellins biosynthesis and signalling pathways. ROS, mitochondrial redox status and peroxisomes were visualized and/or quantified during seed imbibition. Finally, we performed a cytogenetic characterization of the nuclei from the embryonic axes during seed germination.

We show that mitochondria participate in the early ROS production during seed imbibition and that a possible involvement of peroxisomes in later stages should still be analysed. At the time of radicle protrusion, ROS accumulated within the nucleus, which correlated with nuclear expansion and chromatin decompaction.

Taken together, our results provide evidence of the role of ROS trafficking between organelles and of the nuclear redox status in the regulation of seed germination by dormancy.
UNUSUAL DEPOSITION ON BRONZE AGE AND IRON AGE SETTLEMENTS AND HILLFORTS IN THE UPPER AND MIDDLE THAMES VALLEY
Authors: Davies Alex
Published: February 2022

Contexts producing unusual deposits have long been recognized on later prehistoric settlements. These can include complete or shattered pots; complete animal and/or human skeletons, skulls or articulating segments; or unusually large quantities of material culture. Interpretation has tended to follow theoretical fashions, but the intentions and meanings behind these strange deposits are still poorly understood. This paper approaches the subject through a macro‐scale analysis, looking at 230 sites in one region over c.1550 years, from the Middle Bronze to the Middle Iron Ages. This regional, diachronic study has found patterns in settlement deposition that are specific to certain periods. Sometimes, these recurring patterns appear to be immediately functional practices, although in most instances recurrent depositional themes have been argued to have specific ritual intent and to be relatable to wider aspects of social organization and the archaeological record. This study also suggests that hillforts witnessed increased levels of deposition of a range of different material. The analysis provides new perspectives on this important aspect of later prehistoric archaeology.
Protective effect of γ‐glutamylcysteine against UVB radiation in NIH‐3T3 cells
Authors: Lu Shuai , Liu Jie , Zhang Xiaoxue , Zhou Jinyi , Liu Huimin , Liang Juanjuan , Jiang Longwei , Hu Jianhua , Zhang Yan , Ma Lihua , Luo Lan , Jia Shaochang , Yin Zhimin
Published: February 2022

Background

Ultraviolet (UV) radiation‐induced oxidative stress is the main cause of photodamage to the skin. Glutathione (GSH) serves important physiological functions, including scavenging oxygen‐free radicals and maintaining intracellular redox balance. γ‐glutamylcysteine (γ‐GC), as an immediate precursor of GSH and harboring antioxidant and anti‐inflammatory properties, represents an unexplored option for skin photodamage treatment.

Purpose

The purpose of this study was to investigate whether γ‐GC can reduce UVB‐induced NIH‐3T3 cell damage.

Methods

The experimental groups were as follows: control, UVB radiation, UVB radiation after pretreatment with γ‐GC. Cell counting kit‐8 (CCK‐8) assays were used to measure cell proliferation, flow cytometry, and immunoblotting to detect the apoptosis rate and apoptosis‐associated proteins. The levels of Reactive Oxygen Species (ROS), Superoxide Dismutase (SOD), and GSH/GSSG (oxidized GSH) were measured to assess oxidative stress. Immunoblotting and immunofluorescence were used to detect DNA damage. The members of the MAPK signaling pathways were detected by immunoblotting.

Results

UVB irradiation significantly reduced cell viability and destroyed the oxidative defense system. Pretreatment with γ‐GC reduced UVB‐induced cytotoxicity, restored the oxidation defense system, and inhibited activation of the MAPK pathway. It also reduced the apoptosis rate, downregulated the levels of cleaved caspase 3 and cleaved PARP. Furthermore, pretreatment with γ‐GC reduced the accumulation of γH2AX after UVB radiation exposure, indicating that γ‐GC could protect cells from DNA damage.

Conclusion

γ‐GC protected NIH‐3T3 from damage caused by UVB irradiation. The photoprotective effect of γ‐GC is mediated via strengthening the endogenous antioxidant defense system, which prevents DNA damage and inhibits the activation of the MAPK pathway.
Strongly unbalanced gender attractiveness in a dioecious mass flowering tropical tree pollinated by stingless bees
Authors: Calaça P. , de Freitas L. D. , Schlindwein C.
Published: February 2022

In dioecious, bee‐pollinated tree species, male and female flowers offer different resources. It is unclear how this unbalanced quantity and quality of floral resources affects flower visits and pollen transfer to female flowers. We asked, what characteristics of flowering and dynamics of resource production by trees favour flights of bees between male and female trees.

We quantified the floral resources produced by individual flowers and entire trees of Myracrodruon urundeuva (Anacardiaceae), measured pollen flow to female flowers, fruit set of naturally pollinated flowers and determined the effective pollinators.

Crown volume of male trees was four‐fold, flower number 15‐fold and nectar volume 60 times higher than in female trees. While ~70% of male flowers opened in the morning, ~70% of female flowers opened in the afternoon. Fruit set was 27%. Stingless bee species were the main pollinators, while honeybees were common only on male flowers.

Strongly unbalanced production of floral resources, high potential lifespan of female flowers and anticipated opening of male flowers favour pollinator movement and pollen deposition on female flowers, albeit low (0.003% of pollen that reached stigmas), but sufficient to produce thousands of fruits per tree. Besides being an astonishing pollen and nectar source for numerous social bee species, only a few of them were effective pollinators. Our quantitative approach to floral resource production of each gender provides new insights, such as the proportion of resources allocated to each gender and the corresponding behaviour of flower visitors, for understanding the reproductive strategy of dioecious tropical mass‐flowering trees.
Characterization of Fusarium asiaticum and F. graminearum isolates from gramineous weeds in the proximity of rice fields in Korea
Authors: Ahn Seojin , Kim Minjoo , Lim Jae Yun , Choi Gyung Ja , Seo Jeong‐Ah
Published: February 2022

Fusarium graminearum species complexes (FGSCs), such as Fusarium asiaticum and F. graminearum, are important pathogens that cause Fusarium head blight (FHB) in several cereal crops worldwide. In this study, we collected 342 gramineous weed samples in the proximity of rice fields from May to June 2018 in Korea. Among the 500 Fusarium isolates from the weed samples, 13 species of Fusarium were identified, and F. asiaticum (41.2%), F. avenaceum (18.0%), F. acuminatum (16.4%) and F. graminearum (14.8%) were the most frequently isolated. The trichothecene genotype analysis showed that 206 F. asiaticum strains consisted of the nivalenol (NIV) genotype (n = 195, 94.7%) and 3‐acetyldeoxynivalenol (3ADON) genotype (n = 11, 5.3%), whereas 74 F. graminearum strains consisted of the 15‐acetyldeoxynivalenol (15ADON) genotype (n = 58, 78.4%) and 3ADON genotype (n = 16, 21.6%). Geographical differences were observed in the FGSC and trichothecene genotype compositions, which appeared host‐dependent between the southern provinces and mid‐eastern provinces. The aggressiveness assessment of FHB showed that the 3ADON chemotype was most aggressive followed by the 15ADON and NIV chemotypes in wheat, while the NIV chemotype was most aggressive followed by the 3ADON and 15ADON chemotypes in rice. The F. asiaticum strains grew slowly and produced fewer conidia and perithecia than the F. graminearum strains, regardless of their chemotypes. The results of this study suggest that F. asiaticum with the NIV chemotype has a host preference for rice, and FHB‐causing pathogens can be harboured in gramineous weeds, which play a role in the dispersal of FHB pathogens to rice and other cereal crops.
Forbs included in conservation seed mixes exhibit variable blooming detection rates and cost‐effectiveness: implications for pollinator habitat design
Authors: Simanonok Stacy C. , Otto Clint R. V. , Iovanna Rich
Published: February 2022

Although forb‐rich plantings for pollinator habitat are becoming more common, natural resource managers lack insight on the cost‐effectiveness of forbs seeded in private land conservation programs. Additional information on the possible benefits of including more forb species in a mix may help guide the design of future pollinator habitat. We examined the detection of blooming forbs from seed mixes, colonization of non‐seeded blooming forbs, and bee utilization of forbs on private lands enrolled in United States Department of Agriculture (USDA) conservation programs. By obtaining the original seed mixes used on conservation program lands and sampling forbs and bees, we provide a first‐hand evaluation of the cost‐effectiveness of USDA conservation plantings in a field setting. We identified seeded forbs with the highest blooming detection rates and the most common colonizing forbs across 27 sites, the majority of which were considered young conservation plantings. We additionally designated 16 forbs as the most cost‐effective due to their higher‐than‐average blooming detection rate and lower‐than‐average seed cost. We found a positive association between seed mix richness and number of blooming, seeded forbs detected and found a negative association with blooming, non‐native colonizing forbs, which highlights potential benefits of increasing forb richness in seed mixes. However, we did not observe an association between seed mix richness and wild bee or honey bee counts. Examining the cost‐effectiveness of seeded forbs on USDA conservation enrollments and subsequent bee utilization can inform land managers in designing seed mixes for pollinator habitat.
Lifting Scheme for Streamflow Data in River Networks
Authors: Park Seoncheol , Oh Hee-Seok
Published: February 2022

This paper presents a new multiscale method for analysing water pollutant data located in river networks. The main idea of the proposed method is to adapt the conventional lifting scheme, reflecting the characteristics of streamflow data in the river network domain. Due to the complexity of the data domain structure, it is difficult to apply the lifting scheme to the streamflow data directly. To solve this problem, we propose a new lifting scheme algorithm for streamflow data that incorporates flow-adaptive neighbourhood selection, flow proportional weight generation and flow-length adaptive removal point selection. A nondecimated version of the proposed lifting scheme is also provided. The simulation study demonstrates that the proposed method successfully performs a multiscale analysis of streamflow data. Furthermore, we provide a real data analysis of water pollutant data observed on the Geum-River basin compared to the existing smoothing method.
Contrasting intensity of aragonite dissolution and dolomite cementation in glacial versus interglacial intervals of a subtropical carbonate succession
Authors: Reuning Lars , Deik Hanaa , Petrick Benjamin , Auer Gerald , Takayanagi Hideko , Iryu Yasufumi , Courtillat Margot , Bassetti Maria‐Angela
Published: February 2022

Aragonite and high‐Mg calcite are abundant in modern, neritic carbonate systems but almost absent in their fossil counterparts. Dissolution of these metastable mineral phases commonly leaves no visible trace in the sedimentary record, compromising the derivation of palaeoenvironmental information from the rock record. The upper 25 m of Integrated Ocean Drilling Program (IODP) Site U1460 on the outer ramp of the western Australian Shelf were investigated to study shallow burial (tens of metres) marine diagenesis in organic‐carbon poor sediments using microscopic, total organic carbon, biomarkers and mineralogical analysis in combination with porewater geochemistry. Aragonite dissolution is negligible at the seafloor but intensifies ca 5 m below, even though bulk porewaters are supersaturated for aragonite. This apparent contradiction likely results from dissolution in undersaturated microenvironments. Aragonite dissolution below 5 to 6 m is on average more intense in interglacial compared to glacial intervals. The presence of disseminated framboidal pyrite and porewater results indicate that minor sulphate reduction is active at IODP Site U1460. Sulphate reduction is probably limited by the low organic matter content (ca 0.2%). It is well‐known from the literature that incipient sulphate reduction can lead to a drop in pH and consequently to carbonate dissolution. It is therefore assumed that the slightly higher concentration of organic matter in the interglacial intervals allowed increased aragonite dissolution during sulphate reduction compared to glacial beds. Low amounts of dolomite cement (<15%) start to form at the same depth (5 to 6 m) as aragonite dissolution intensifies. Dolomite formation and aragonite dissolution also show covariance on a metre‐scale below 5 to 6 m, indicating that a low carbonate saturation state might enhance dolomite formation. This mechanism provides an indirect link between dolomite formation, aragonite dissolution and orbital cycles. The outcome of this study, therefore, contributes to a better understanding of differential diagenesis in marine carbonates.
Orofacial conditions and oral health behavior of young athletes: A comparison of amateur and competitive sports
Authors: Merle Cordula Leonie , Richter Lisa , Challakh Nadia , Haak Rainer , Schmalz Gerhard , Needleman Ian , Wolfarth Bernd , Ziebolz Dirk , Wüstenfeld Jan
Published: February 2022

Purpose

This retrospective cross‐sectional study aimed to evaluate oral health status (dental, periodontal, and functional) and oral health behavior in young German athletes including the comparison of competitive (CA) and amateur sports (AA).

Methods

Data of CA (German national teams, perspective, and youth squads) and AA aged between 18 and 30 years with an available oral examination in 2019 were included. Clinical examination: caries experience (DMF‐T), non‐carious wear (erosion, BEWE), partially erupted wisdom teeth, gingival inflammation (PBI), plaque index, periodontal screening (PSI), and temporomandibular dysfunction (TMD) screening. Questionnaires: oral health behavior and periodontal symptoms.

Results

88 CA (w = 51%, 20.6 ± 3.5 years) of endurance sports and 57 AA (w = 51%, 22.2 ± 2.1 years) were included. DMF‐T was comparable (CA: 2.7 ± 2.2, AA: 2.3 ± 2.2; p = 0.275) with more D‐T in CA (0.6 ± 1.0) than AA (0.3 ± 0.7; p = 0.046; caries prevalence: CA: 34%, AA: 19%; p = 0.06). Both groups had low severity of erosion (BEWE about 3.5). CA had more positive TMD screenings (43% vs. 25%; p = 0.014). In both groups, all athletes showed signs of gingival inflammation, but on average of low severity (PBI <1). More CA needed complex periodontal treatment than AA (maximum PSI = 3 in 40% vs. 12%; p < 0.001). Oral health behavior was comparable (daily tooth brushing; regular dental check‐ups in >70%).

Conclusions

Young German athletes (CA and AA) generally showed signs of gingival inflammation and needed to improve their oral health behavior. CA showed slightly increased oral findings (more D‐T, periodontal and TMD screening findings) than AA, but similar oral health behavior. This may imply an increased dental care need in competitive sports.
The personal is social: Four sociological approaches to nonsuicidal self‐injury
Authors: Steggals Peter , Lawler Steph , Graham Ruth
Published: February 2022

Sociological interest in nonsuicidal self‐injury is over 20 years old, and the last decade shows a marked increase in journal articles and research monographs. Here, we survey and critically evaluate this growing sociology of self‐injury, providing a short history of its development, and describing the focus of four contrasting approaches used in exploring a sociology of such a private practice: institutional interactions; processes of social construal and construction; the social in the lived experience of subjects; and the role of social relations and communication. We argue that these approaches in the sociology of self‐injury more generally represent four broader social theoretical perspectives on how the personal is always‐already social. Understanding this connection between the empirical search for the social in self‐injury, and theoretical conceptualizations of the social in the personal, is key to opening up the future of the sociology of self‐injury, and appreciating what it has to offer sociology more generally. The more we understand what is social in self‐injury, the more we will understand how the personal is always‐already social; and the greater the theoretical investment in our methodological apparatus, the more we will be able to detect and comprehend the social dimension of this intensely personal practice.
Self and political efficacy and the justifiability of political violence and the role of state terror: A cross‐national analysis
Authors: Julkif Nabil “Bill”
Published: February 2022

Objective

This article looks at whether political and self‐efficacy predict the justifiability of political violence and terrorism.

Methods

Utilizing the World Values Survey sample of 41,178 respondents from 31 countries, this article uses a mixed effect logistic regression with country‐level random intercepts to answer the research question and test the hypothesis.

Results

Self‐efficacy predicts less support for political violence or justifiability of terrorism, and less political efficacy predicts less support for terrorism while not influencing political violence in a significant manner. The interaction between self‐efficacy and economic insecurity was significant with high economic security and low self‐efficacy predicting more justifiability of terrorism.

Conclusions

Support is found for Saab et al. (2016) “gun and the olive branch” thesis. Specifically, being politically efficacious and finding conventional political activism efficacious does not reduce support for political violence. However, finding conventional activism efficacious makes one less likely to find terrorism justifiable. Support is also found for the prosocial effect of self‐efficacy (Rottweiler and Gill 2020).
Low-frequency acoustic radiation from a flanged circular pipe at an inclined angle
Authors: Su Jialin , Yang Dong , Morgans Aimee S.
Published: February 2022

The generic problem of low-frequency acoustic radiation through quiescent air from a circular pipe that is inclined with respect to its exit flange is studied in this work. The exit flange is taken to extend as an infinite plane away from the pipe opening. The analysis implements a hybrid method that combines modal expansions with the boundary element method. The reflection coefficient and pipe end correction for Helmholtz numbers (based on the pipe radius) less than 2.5 are calculated for various inclination angles up to 75°. Calculations are validated using simulations from the finite-element solver of the commercial software package COMSOL. The reflection coefficient and end correction predictions agree closely with the validation simulations yet differ notably from the results available in the literature. The solution obtained from the hybrid method is subsequently used to analyse the acoustic field at the pipe exit and in the downstream space. The key aspects of the governing physics pertaining to practical engineering applications at low frequencies are captured in a low-order approximation, which significantly reduces the degrees of freedom of the problem and provides generally good estimates of the reflection coefficient and end correction, as well as the downstream acoustic field.
From cohorts to molecules: Adverse impacts of endocrine disrupting mixtures
Authors: Caporale Nicolò , Leemans Michelle , Birgersson Lina , Germain Pierre-Luc , Cheroni Cristina , Borbély Gábor , Engdahl Elin , Lindh Christian , Bressan Raul Bardini , Cavallo Francesca , Chorev Nadav Even , D’Agostino Giuseppe Alessandro , Pollard Steven M. , Rigoli Marco Tullio , Tenderini Erika , Tobon Alejandro Lopez , Trattaro Sebastiano , Troglio Flavia , Zanella Matteo , Bergman Åke , Damdimopoulou Pauliina , Jönsson Maria , Kiess Wieland , Kitraki Efthymia , Kiviranta Hannu , Nånberg Eewa , Öberg Mattias , Rantakokko Panu , Rudén Christina , Söder Olle , Bornehag Carl-Gustaf , Demeneix Barbara , Fini Jean-Baptiste , Gennings Chris , Rüegg Joëlle , Sturve Joachim , Testa Giuseppe
Published: February 2022

Convergent evidence associates exposure to endocrine disrupting chemicals (EDCs) with major human diseases, even at regulation-compliant concentrations. This might be because humans are exposed to EDC mixtures, whereas chemical regulation is based on a risk assessment of individual compounds. Here, we developed a mixture-centered risk assessment strategy that integrates epidemiological and experimental evidence. We identified that exposure to an EDC mixture in early pregnancy is associated with language delay in offspring. At human-relevant concentrations, this mixture disrupted hormone-regulated and disease-relevant regulatory networks in human brain organoids and in the model organisms
Xenopus leavis
and
Danio rerio
, as well as behavioral responses. Reinterrogating epidemiological data, we found that up to 54% of the children had prenatal exposures above experimentally derived levels of concern, reaching, for the upper decile compared with the lowest decile of exposure, a 3.3 times higher risk of language delay.
Reducing adverse impacts of Amazon hydropower expansion
Authors: Flecker Alexander S. , Shi Qinru , Almeida Rafael M. , Angarita Héctor , Gomes-Selman Jonathan M. , García-Villacorta Roosevelt , Sethi Suresh A. , Thomas Steven A. , Poff N. LeRoy , Forsberg Bruce R. , Heilpern Sebastian A. , Hamilton Stephen K. , Abad Jorge D. , Anderson Elizabeth P. , Barros Nathan , Bernal Isabel Carolina , Bernstein Richard , Cañas Carlos M. , Dangles Olivier , Encalada Andrea C. , Fleischmann Ayan S. , Goulding Michael , Higgins Jonathan , Jézéquel Céline , Larson Erin I. , McIntyre Peter B. , Melack John M. , Montoya Mariana , Oberdorff Thierry , Paiva Rodrigo , Perez Guillaume , Rappazzo Brendan H. , Steinschneider Scott , Torres Sandra , Varese Mariana , Walter M. Todd , Wu Xiaojian , Xue Yexiang , Zapata-Ríos Xavier E. , Gomes Carla P.
Published: February 2022

Proposed hydropower dams at more than 350 sites throughout the Amazon require strategic evaluation of trade-offs between the numerous ecosystem services provided by Earth’s largest and most biodiverse river basin. These services are spatially variable, hence collective impacts of newly built dams depend strongly on their configuration. We use multiobjective optimization to identify portfolios of sites that simultaneously minimize impacts on river flow, river connectivity, sediment transport, fish diversity, and greenhouse gas emissions while achieving energy production goals. We find that uncoordinated, dam-by-dam hydropower expansion has resulted in forgone ecosystem service benefits. Minimizing further damage from hydropower development requires considering diverse environmental impacts across the entire basin, as well as cooperation among Amazonian nations. Our findings offer a transferable model for the evaluation of hydropower expansion in transboundary basins.
Complete Genome Sequence of
Luteitalea
sp. Strain TBR-22
Authors: Yamamoto Kyosuke , Yoneda Yasuko , Makino Ayaka , Tanaka Yasuhiro , Meng Xian-Ying , Hashimoto Junko , Shin-ya Kazuo , Satoh Noriyuki , Fujie Manabu , Toyama Tadashi , Mori Kazuhiro , Ike Michihiko , Morikawa Masaaki , Kamagata Yoichi , Tamaki Hideyuki
Published: February 2022

We report a complete genome sequence of a novel bacterial isolate, strain TBR-22, belonging to the class
Vicinamibacteria
of the phylum
Acidobacteria
, which was isolated from duckweed fronds. The genome expands our knowledge of the lifestyle of this abundant but rarely characterized phylum.
Draft Genome Sequence of an Unusual Ectomycorrhizal Fungus, Pseudotulostoma volvatum
Authors: Koch Rachel A. , Bach Christopher E. , Pirro Stacy , Aime M. Catherine
Published: February 2022

Here, we report the draft genome sequence of
Pseudotulostoma volvatum
, an unusual ectomycorrhizal fungus in the “mold” order Eurotiales (Ascomycota, Pezizomycotina). The assembled genome is 60.4 Mbp and contains an estimated 5,492 genes. Compared with closely related species, the
P. volvatum
genome is depauperate in secondary metabolite gene clusters.
Genome Sequence of Xanthomonas campestris Strain FDWSRU 18048, an Emerging Pathogen of Nonnative, Invasive Garlic Mustard (
Alliaria petiolata
)
Authors: Tancos Matthew A. , Dubrow Zoë E. , Carpenter Sara C. D. , Bogdanove Adam J.
Published: February 2022

Xanthomonas campestris
infections of nonnative, invasive garlic mustard populations have been recently reported in the eastern United States. Here, we report the genome sequence of the pathogenic
X. campestris
strain FDWSRU 18048. The genome is 4,978,509 bp and closely related to the genome of
X. campestris
pv. incanae strain CFBP2527.
Assembly and Annotation of Escherichia coli Bacteriophage U115
Authors: An William , Emsbo Camilla , Frey Emma , Hu Vicky , Jones Ashley , Latif Nipa , Perrilli Makayla , Reillo Krystalia , Schwarz Joshua C. , Strasner Sydney , Theroux Austin , Vargas Luz D. , Turner Paul E. , Burmeister Alita R.
Published: February 2022

Here, we present the annotated genome sequence of
Escherichia coli
bacteriophage U115, a T4-like bacteriophage. Phage U115 has a genome length of 166,986 bp and has 286 predicted genes.
Complete Genome Sequence of Stenotrophomonas maltophilia 1800, a New Bacterial Strain with Potential for Bioremediation of Oil-Contaminated Environments
Authors: Semai Annela , Plewniak Frédéric , Lledo Joanna , Annonay Gwenolah , Vandecasteele Céline , Lopez-Roques Céline , Bertin Philippe N.
Published: February 2022

Stenotrophomonas maltophilia
strain 1800 was isolated from the effluent of an industrial oil refinery in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and assembled using Unicycler. It is composed of one chromosome of 4.83 Mb.
Complete Genome Sequence of
Acidianus
sp. Strain HS-5, Isolated from the Unzen Hot Spring in Japan
Authors: Omokawa Hiromi , Kurosawa Norio , Sakai Hiroyuki D.
Published: February 2022

The genus
Acidianus
is composed of facultatively aerobic archaea growing on elemental sulfur as an energy source. Here, we report the 2.58-Mb complete genome sequence of
Acidianus
sp. strain HS-5, which was isolated from a sulfur hot spring located in Unzen, Japan.
Prediction model to predict type 1 retinopathy of prematurity using gestational age and birth weight (PW-ROP)
Authors: Iu Lawrence Pui Leung , Yip Wilson Wai Kuen , Lok Julie Ying Ching , Fan Michelle Ching Yim , Lai Connie Hong Yee , Ho Mary , Young Alvin Lerrmann
Published: February 2022

Purpose

To develop a prediction model for type 1 retinopathy of prematurity (ROP) from an Asian population.

Methods

This retrospective cohort study included 1043 premature infants who had ROP screening in a tertiary hospital in Hong Kong from year 2006 to 2018. The ROP prediction model was developed by multivariate logistic regression analyses on type 1 ROP. The cut-off value and the corresponding sensitivity and specificity were determined by receiver operating characteristic curve analysis. A validation group of 353 infants collected from another tertiary hospital in another region of Hong Kong from year 2014 to 2017 was used for external validation.

Results

There were 1043 infants in the study group. The median gestational age (GA) was 30 weeks and 1 day and median birth weight (BW) was 1286 g. The prediction model required only GA and BW as parameters (prematurity-birth weight ROP (PW-ROP)). The area under curve value was 0.902. The sensitivity and specificity were 87.4% and 79.3%, respectively. Type 1 ROP developed in 0.9%, 17.4% and 50% of infants with PW-ROP scores<0, between 0 and <300, and ≥300 respectively (p<0.001). On external validation, our prediction model correctly predicted 95.8% of type 1 ROP (sensitivity=95.8%, specificity=74.8%) in the validation group.

Conclusion

The PW-ROP model is a simple model which could predict type 1 ROP with high sensitivity and specificity. Incorporating this model to ROP examination would help identify infants at risk for ROP treatment.
Postcholecystectomy diarrhoea rate and predictive factors: a systematic review of the literature
Authors: Farrugia Alexia , Attard Joseph Anthony , Khan Saboor , Williams Nigel , Arasaradnam Ramesh
Published: February 2022

Objectives

Cholecystectomy is one of the most common surgical procedures performed worldwide to treat gallstone-related disease. Postcholecystectomy diarrhoea (PCD) is a well-reported phenomenon, however, the actual rate, predictive factors and mechanism of action have not been well determined. A systematic review was undertaken to determine the rate and predictive factors associated with diarrhoea in the postcholecystectomy setting.

Methods

The review was conducted according to the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocol. Databases searched included Medline, Embase, Pubmed, Cochrane and Google Scholar up to 29 September 2020. The inclusion criteria consisted of cohort studies or randomised trials which investigated the rate of PCD and predictive factors. Case reports, case series, conference abstracts and expert opinion pieces were excluded as were other systematic reviews as all the original articles from those reviews were included in this review. Papers that did not include PCD as a separate entity were excluded. Bias assessment was performed using the Newcastle-Ottawa Scale for cohort studies and the Cochrane risk of bias tool for randomised controlled trials as appropriate. Data were extracted by two authors (AF and JAA) and an overall rate of PCD was calculated. Predictive factors were also extracted and compared between studies.

Results

1204 papers were obtained and 21 were found to contain relevant information about PCD, including the number of patients developing diarrhoea, method of symptom assessment and time of onset postcholecystectomy. A pooled total of 3476 patients were included across the identified studies with 462 (13.3%) patients developing PCD. Possible predictive factors varied across all studies, with characteristics such as gender, age and weight of patients postulated as being predictive of PCD, with no agreement across studies.

Discussion

PCD is therefore relatively common (13.3%). This has important implications for patient consent. Patients ought to be investigated early for bile acid diarrhoea in suspected PCD. More studies are required to determine the possible predictive factors for PCD. Limitations of the study included that most studies were not powered for calculation of PCD, and assessment methods between studies varied.

PROSPERO registration number

CRD42019140444.
Use of a deep learning and random forest approach to track changes in the predictive nature of socioeconomic drivers of under-5 mortality rates in sub-Saharan Africa
Authors: Nasejje Justine B , Mbuvha Rendani , Mwambi Henry
Published: February 2022

Objectives

We used machine learning algorithms to track how the ranks of importance and the survival outcome of four socioeconomic determinants (place of residence, mother’s level of education, wealth index and sex of the child) of under-5 mortality rate (U5MR) in sub-Saharan Africa have evolved.

Settings

This work consists of multiple cross-sectional studies. We analysed data from the Demographic Health Surveys (DHS) collected from four countries; Uganda, Zimbabwe, Chad and Ghana, each randomly selected from the four subregions of sub-Saharan Africa.

Participants

Each country has multiple DHS datasets and a total of 11 datasets were selected for analysis. A total of n=85 688 children were drawn from the eleven datasets.

Primary and secondary outcomes

The primary outcome variable is U5MR; the secondary outcomes were to obtain the ranks of importance of the four socioeconomic factors over time and to compare the two machine learning models, the random survival forest (RSF) and the deep survival neural network (DeepSurv) in predicting U5MR.

Results

Mother’s education level ranked first in five datasets. Wealth index ranked first in three, place of residence ranked first in two and sex of the child ranked last in most of the datasets. The four factors showed a favourable survival outcome over time, confirming that past interventions targeting these factors are yielding positive results. The DeepSurv model has a higher predictive performance with mean concordance indexes (between 67% and 80%), above 50% compared with the RSF model.

Conclusions

The study reveals that children under the age of 5 in sub-Saharan Africa have favourable survival outcomes associated with the four socioeconomic factors over time. It also shows that deep survival neural network models are efficient in predicting U5MR and should, therefore, be used in the big data era to draft evidence-based policies to achieve the third sustainable development goal.
Identification of the optimal treatment strategy for complex appendicitis in the paediatric population: a protocol for a multicentre prospective cohort study (CAPP study)
Authors: van Amstel Paul , Bakx Roel , van der Lee Johanna H , van der Weide Marijke C , Eekelen Rik van , Derikx Joep P M , van Heurn Ernest L W , Gorter Ramon R
Published: February 2022

Introduction

In daily practice large heterogeneity in the treatment of children with complex appendicitis exists. Complex appendicitis can be divided into two subtypes; complex appendicitis with and without appendiceal mass and/or abscess. As complex appendicitis is associated with high morbidity and costs, identification of the optimal treatment strategy is essential. In this article, we present the study protocol for the CAPP (Complex Appendicitis in the Pediatric Population) study.

Methods and analysis

This nation-wide, multi-centre, comparative, non-randomised prospective cohort study includes all children <18 years old with a preoperative suspicion of complex appendicitis, which is based on imaging confirmed acute appendicitis and predefined criteria regarding the severity of appendicitis. Eligible patients are recruited in more than 30 hospitals. Open appendectomy will be compared with laparoscopic appendectomy for children without appendiceal mass and/or abscess and initial non-operative treatment (ie, intravenous antibiotics with or without percutaneous drainage) to direct appendectomy for children with appendiceal mass and/or abscess. Based on historical data supplied by the participating hospitals and an inclusion period of 2 years and 9 months, a sample size of 1308 patients is aimed. Primary outcome is the proportion of patients experiencing any complication at 3 months follow-up. Reported complications will be assessed by an independent adjudication committee. Secondary outcomes include, but are not limited to, quality of life, and (in)direct costs. To adjust for baseline differences and selection bias, outcomes will be compared after propensity score analysis (inverse probability weighting and stratification).

Ethics and dissemination

The Medical Ethics Review Committee of the Amsterdam UMC, location AMC, declared that the Medical Research involving Human Subjects Act (WMO) did not apply to this study. Therefore, no official approval was required by national law. Study results will be presented in peer-reviewed scientific journals and at (inter)national conferences.

Trial registration numbers

NCT04755179; NL9371.
Physical and verbal abuse amid COVID-19: a nationwide cross-sectional survey in Japan
Authors: Bhandari Divya , Ozaki Akihiko , Suzuki Tomoya , Kotera Yasuhiro , Shrestha Sunil , Horiuchi Sayaka , Miyachi Takashi , Tabuchi Takahiro
Published: February 2022

Objectives

The detrimental impacts of abuse on victims’ well-being are well documented globally, including Japan. The ongoing COVID-19 pandemic may increase the incidence of abuse in the community, creating an additional burden amid the crisis. However, the incidence of abuse in Japan during COVID-19 remains to be evaluated. Accordingly, our study aimed to assess the incidence of physical and verbal abuse among the general population in Japan and to identify the associated factors of abuse during COVID-19.

Design and setting

We used the data obtained from a nationwide, cross-sectional internet survey conducted in Japan between August and September 2020. Sampling weights were used to calculate national estimates, and multivariable logistic regression was performed to identify the associated factors for physical and verbal abuse.

Results

Out of the total 25 482 participants, 965 (3.8 %) reported experiencing physical abuse and 1941 (7.6%) verbal abuse from April 2020 to September 2020. The incidence of physical and verbal abuse was higher among female participants. Participants who lived in areas where the ‘state of emergency’ was enforced were more likely to suffer from physical abuse. Similarly, vulnerable participants such as those below age 18, with low income, bad family relationships, and disabled people were more likely to experience both physical and verbal abuse. Participants suffering from COVID-19-related symptoms, who had poor health status and widows/divorcees were more likely to be verbally abused. Furthermore, those who did not follow preventive behaviours such as wearing masks in public places, abusing drugs and drinking alcohol in high amounts were also more likely to experience abuse.

Conclusion

The impact of abuse was found disproportionately greater in more vulnerable groups of the population. Pandemic has reinforced the existing social inequalities, which need to be addressed timely to prevent precarious repercussions.
Risk stratification of women with gestational diabetes mellitus using mutually exclusive categories based on the International Association of Diabetes and Pregnancy Study Groups criteria for the development of postpartum dysglycaemia: a retrospective cohort study
Authors: Dai Fei , Mani Hemaavathi , Nurul Syaza Razali , Tan Kok Hian
Published: February 2022

Objectives

Women with gestational diabetes mellitus (GDM) are more predisposed to develop postpartum diabetes mellitus (DM). This study aimed to estimate the relative risk (RR) of postpartum dysglycaemia (prediabetes and DM) using mutually exclusive categories according to the International Association of Diabetes and Pregnancy Study Groups (IADPSG) criteria cut-off points in patients with GDM, so as to establish a risk-stratification method for developing GDM management strategies.

Design, setting and participants

In this retrospective cohort study, 942 women who had been diagnosed with GDM (IADPSG criteria) at 24–28 weeks of gestation from November 2016 to April 2018 underwent a 75 g oral glucose tolerance test (OGTT) at 6–12 weeks postpartum in a tertiary hospital of Singapore. Seven mutually exclusive categories (three one timepoint positive categories (fasting, 1 hour and 2 hours), three two timepoint positive categories (fasting+1 hour, fasting+2 hours and 1 hour+2 hours) and one three timepoint positive category (fasting+1 hour+2 hours)) were derived from the three timepoint antenatal OGTT according to the IADPSG criteria. To calculate the RRs of postpartum dysglyceamia of each mutually exclusive group, logistic regression was applied.

Results

924 mothers with GDM, whose mean age was 32.7±4.7 years, were mainly composed of Chinese (45.4%), Malay (21.7%) and Indian (14.3%) ethnicity. The total prevalence of postnatal dysglycaemia was 16.7% at 6–12 weeks postpartum. Stratifying subjects into seven mutually exclusive categories, the RRs of the one-time, two-time and three-time positive groups of the antenatal OGTT test were 1.0 (Ref.), 2.0 (95% CI=1.3 to 3.1; p=0.001) and 6.7 (95% CI=4.1 to 10.9; p<0.001), respectively, which could be used to categorise patients with GDM into low-risk, intermediate-risk and high-risk group.

Conclusions

Mutually exclusive categories could be useful for risk stratification and early management of patients with prenatal GDM. It is plausible and can be easily translated into clinical practice.
Diagnostic features, management and prognosis of type 2 myocardial infarction compared to type 1 myocardial infarction: a systematic review and meta-analysis
Authors: White Kyle , Kinarivala Mansey , Scott Ian
Published: February 2022

Importance

Distinguishing type 2 (T2MI) from type 1 myocardial infarction (T1MI) in clinical practice can be difficult, and the management and prognosis for T2MI remain uncertain.

Objective

To compare precipitating factors, risk factors, investigations, management and outcomes for T2MI and T1MI.

Data sources

Medline and Embase databases as well as reference list of recent articles were searched January 2009 to December 2020 for term ‘type 2 myocardial infarction’.

Study selection

Studies were included if they used a universal definition of MI and reported quantitative data on at least one variable of interest.

Data extraction and synthesis

Data were pooled using random-effect meta-analysis. Risk of bias was assessed using Newcastle-Ottawa quality assessment tool. Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines were followed. All review stages were conducted by two reviewers.

Main outcomes and measures

Risk factors, presenting symptoms, cardiac investigations such as troponin and angiogram, management and outcomes such as mortality.

Results

40 cohort studies comprising 98 930 patients with T1MI and 13 803 patients with T2MI were included. Compared with T1MI, patients with T2MI were: more likely to have pre-existing chronic kidney disease (OR 1.87; 95% CI 1.53 to 2.28) and chronic heart failure (OR 2.35; 95% CI 1.82 to 3.03), less likely to present with typical cardiac symptoms of chest pain (OR 0.19; 95% CI 0.13 to 0.26) and more likely to present with dyspnoea (OR 2.64; 95% CI 1.86 to 3.74); more likely to demonstrate non-specific ST-T wave changes on ECG (OR 2.62; 95% CI 1.81 to 3.79) and less likely to show ST elevation (OR 0.22; 95% CI 0.17 to 0.28); less likely to undergo coronary angiography (OR 0.09; 95% CI 0.06 to 0.12) and percutaneous coronary intervention (OR 0.06; 95% CI 0.04 to 0.10) or receive cardioprotective medications, such as statins (OR 0.25; 95% CI 0.16 to 0.38) and beta-blockers (OR 0.45; 95% CI 0.33 to 0.63). T2MI had greater risk of all cause 1-year mortality (OR 3.11; 95% CI 1.91 to 5.08), with no differences in short-term mortality (OR 1.34; 95% CI 0.63 to 2.85).

Conclusion and relevance

This review has identified clinical, management and survival differences between T2MI and T1MI with greater precision and scope than previously reported. Differential use of coronary revascularisation and cardioprotective medications highlight ongoing uncertainty of their utility in T2MI compared with T1MI.
Vaccine hesitancy from parents and healthcare providers perspectives in Hadhramout Governorate, Yemen: a mixed-method study protocol
Authors: Sutan Rosnah , Batarfi Suha Ali , Ismail Halim , Bin-Ghouth Abdulla Salem
Published: February 2022

Introduction

Although immunisation prevents the death of millions of infants and children each year, the vaccination coverage of routine childhood vaccination does not reach its target. The reasons for low vaccination uptake can be related to both demand and supply side determinants. The prevalence of vaccine hesitancy is increasing globally. However, data on vaccine hesitancy in low-income Arabic countries are scarce. To investigate this issue in Yemen, an Arabic low-income country, we aim to examine the link between vaccine hesitancy and the immunisation status of children living in Costal Hadhramout, Yemen, from the perspective of their parents and healthcare providers.

Methods and analysis

We will use a mixed-method research design. The study will be conducted in Costal Hadhramout in three phases. Phase 1 will involve a situational analysis using secondary data from records of the national expanded immunisation programme in Costal Hadhramout to examine the trend for previous years. Phase 2 will be a quantitative study aimed at assessing the prevalence of vaccination status of children aged <2 years and the determinants of parental vaccine hesitancy perception through a validated questionnaire. Lastly, phase 3 will be a qualitative study that explores vaccine hesitancy in Yemen using in-depth interviews and focus group discussions with parents and healthcare providers, respectively.

Ethics and dissemination

The study has been approved by the Research Committee of the Faculty of Medicine, University Kebangsaan Malaysia. The findings will be disseminated via publication in peer-reviewed academic journals, academic conferences and public presentations.