bluuebunny/crossref_metadata_2025 huggingface dataset:
The high‐quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae
Authors: Liu Hui , Zhang Jia‐Qi , Zhang Rong‐Rong , Zhao Qin‐Zheng , Su Li‐Yao , Xu Zhi‐Sheng , Cheng Zong‐Ming (Max) , Tan Guo‐Fei , Xiong Ai‐Sheng
Published: January 2024

Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well‐known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high‐quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single‐cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species‐specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high‐quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology.
Rethinking the transfusion pathway in myelodysplastic syndromes: Study protocol for a novel randomized feasibility n‐of‐1 trial of weekly‐interval red cell transfusion in myelodysplastic syndromes
Authors: Mo Allison , Wood Erica , Shortt Jake , Charlton Andrew , Evers Dorothea , Hoeks Marlijn , Pritchard Elizabeth , Daly James , Hodgson Carol , Opat Stephen , Bowen David , Reynolds John , Thi Phung Thao Le , Stanworth Simon J. , McQuilten Zoe
Published: January 2024

Background

Anemia in myelodysplastic syndromes (MDS) is associated with poorer health‐related quality of life (HRQoL) and physical function, and is frequently treated with transfusions. The current common practice of transfusing multiple red blood cells (RBC) units every 2–4 weeks may result in peaks/troughs in hemoglobin (Hb) level, yet maintaining a stable Hb may better improve HRQoL. We describe a study protocol aiming to investigate the feasibility of weekly low‐dose RBC transfusion in MDS patients, including assessing HRQoL and physical function outcomes.

Study Design and Methods

In this n‐of‐1 pilot study, patients receive two treatment arms, with randomly allocated treatment sequence: arm A (patient's usual transfusion schedule) and arm B (weekly transfusion, individualized per patient). To facilitate timely delivery of weekly transfusion, extended‐matched RBCs are provided, with transfusion based upon the previous week's Hb/pre‐transfusion testing results to eliminate delays of awaiting contemporaneous cross‐matching. Primary outcome is the feasibility of delivering weekly transfusion. Secondary outcomes include HRQoL, functional activity measurements, RBC usage, and alloimmunization rates. A qualitative substudy explores patient and staff experiences.

Results

The trial is open in Australia, Netherlands, and UK. The first patient was recruited in 2020. Inter‐country differences in providing RBCs are observed, including patient genotyping versus serological phenotyping to select compatible units.

Discussion

This pilot trial evaluates a novel personalized transfusion approach of weekly matched RBC transfusion and challenges the dogma of current routine pre‐transfusion matching practice. Findings on study feasibility, HRQoL, and physical functional outcomes and the qualitative substudy will inform the design of a larger definitive trial powered for clinical outcomes.
Do winter and summer cohorts of the invasive weed Parthenium hysterophorus differ in seed germination and seedling growth?
Authors: Shrestha A. , Dangol A. , Airi H. , Kharel N. , Thapa L. B. , Devkota A. , Shrestha B. B.
Published: January 2024

The highly invasive weed Parthenium hysterophorus flowers during both hot, humid summers and cold, dry winters in Nepal, yet it remains unknown if there are differences in seed germination and seedling growth during these contrasting seasons. We analysed seed germination and seedling growth of summer and winter cohorts of P. hysterophorus in Kathmandu Valley. Seeds were germinated at low (25/15°C) and high (30/20°C) temperatures, 12/12 h photoperiod and complete dark, and at different levels of water stress. Seedlings were grown in a greenhouse to determine biomass allocation and relative growth rate (RGR). Winter seeds had higher seed biomass than summer seeds, and both seed types germinated under complete dark and 12/12 h photoperiod. Summer seeds germinated at significantly lower rates and percentage than winter seeds at the low temperature, but this difference in germination was not present when summer and winter seeds were incubated at the high temperature. Winter seeds had higher germination (percentage and rate) and took a longer time to reach maximum germination than summer seeds at different levels of water stress. Seedling emergence of both seed types declined with increasing soil depth. Seedling RGRs were nearly equal (summer: 73 mg g−1 day−1, winter: 77 mg g−1 day−1). Biomass allocation to stem and leaves were similar in both cohorts but root biomass allocation was higher in the winter than in the summer cohort. Overall, the maternal environmental effect was moderate on seed germination, and weak on seedling growth. Lack of a pronounced difference in the germination and seedling growth of summer and winter cohorts of P. hysterophorus suggests a wide environmental tolerance of the species, and this could be one of the reasons for the species' ability to invade diverse climatic and geographic regions globally.
Modeling of Optimal Power Generation in Small Hydropower Plants
Authors: Kahraman Gökhan
Published: January 2024

Small hydropower plants (SHPs) have gained international attention as a reliable and versatile renewable energy source. Unfortunately, this energy source is not used efficiently. This is because these systems utilize headwaters with lower water capacity called forebays instead of large water reservoirs like dams. Since this hinders the control of electricity generation, the headwater is either wasted before it can be converted into electricity or it is exhausted very quickly and electricity generation stops after a short time. The aim of this study is to prevent the loss of electricity generation through the efficient use of SHP headwater. For this purpose, a mathematical model was created based on two SHPs operating in tandem. The mathematical model obtained was analyzed, and forebay water level simulation graphs for electricity generation at water flowrates of 2000, 4000, 6000, and 8000 kg/h were obtained. With the help of the obtained graphs, critical wicket gate openings for maximum electricity generation at flowrates of 2000, 4000, 6000, and 8000 kg/h were calculated. The results of this study are applicable to all SHPs. These results are also promising in terms of optimizing the use of a renewable energy source.
Advances in Drilling and Completion Fluid Technologies for Protecting Oil and Gas Reservoirs: Research Progress and Development Trends
Authors: Dindoruk Birol , Zhang Fengyuan
Published: January 2024

The exploration and development of oil and gas reservoirs present significant challenges in achieving objectives such as increased reserves, enhanced production, and improved efficiency. The protection of reservoirs has been internationally recognized as a crucial technology for enabling high output with minimal investment, specifically due to the susceptibility of the drilling and completion phases to severe damage. The resulting harm significantly reduces oil and gas production and may cause drilled wells to become nonproductive, thereby hampering oil and gas field discoveries. Over the past half-century, scholars have extensively researched and developed four generations of temporary plugging-based technologies for oil and gas reservoir protection, including shielding temporary plugging, fine temporary plugging, temporary plugging with physiochemical film, and biomimetic temporary plugging. These advancements have progressively enhanced the effectiveness of reservoir protection. However, the increasing depth and complexity of oil and gas exploration and development have rendered previous technologies inadequate in providing sufficient protection, resulting in amplified risks to drilling safety such as circulation loss, sloughing, obstruction, drill pipe sticking, and blowouts. To overcome these challenges, the development of drilling and completion fluid technologies capable of forming a liquid casing during drilling has emerged as a novel solution for safeguarding oil and gas reservoirs. The successful implementation of this technology on a large scale enables the efficient development of untapped oil and gas resources, marking a breakthrough in reservoir protection. It also identifies future research directions and has practical implications for field technicians and scientific professionals.
Optimizing the Retrofit Design and Operation of Multi-Energy Systems Integrated With Energy Networks
Authors: Dal Cin Enrico , Carraro Gianluca , Lazzaretto Andrea , Tsatsaronis George
Published: January 2024

In the literature, there is a lack of tools able to optimize contextually the design and operation of a multi-energy system in its entirety, encompassing both (i) the number, type, and size of the energy conversion and storage plants supplying the end users of the system with the required energy and (ii) the geometry and capacity of the distribution networks delivering that energy to the users. Moreover, rarely the retrofit design problem is considered, where “retrofit design” refers to the addition of new capacity to components initially available in existing systems. Here, a general method is proposed to simultaneously optimize the retrofit design and operation of a multi-energy system and the associated energy networks. The goal consists of finding the additional capacity to be added to the already available components—energy conversion and storage plants, energy networks—and the new components to be installed in order to comply with given reduction targets in carbon emissions while keeping the life cycle cost of the system at a minimum. A district composed of commercial and residential buildings operating in a microgrid is considered as a case study. Heat can be provided to the end users via a district heating network, while electricity can be either generated on-site or imported from the national power grid. Results of the retrofit design problem show a contextual reduction of 35% in CO2 emission and 20% in life cycle cost with respect to the original system configuration.
Numerical Inspection of Location, Density Ratio, and Turbulent Kinetic Energy of Vortex Generator in Gas Turbine Blade Film Cooling Application
Authors: Halder Nirmal
Published: January 2024

By using a vortex generator, the current numerical study suggests reducing the consequences of a counter-rotating vortex pair. For this study, the delta winglet pair in the common-flow-down configuration is recommended. The investigation of a suitable turbulence model has been studied. The impact of vortex generator placement on the parameters of film cooling efficiency has been studied using numerical simulation. The vortex generator is located before the film hole or upstream, after the film cooling hole or downstream, and both before and after the film cooling hole. The outcome suggests that a vortex generator placed upstream of the circular film cooling hole will function more effectively. The film cooling hole dimension and free stream velocity are used to maintain a Reynolds number of 17000. Additionally, the effects of altering the density ratio (DR), turbulent kinetic energy (TKE), and secondary flow velocity (uj) on cooling effectiveness have been studied. The outcome demonstrates that the decrease in cooling efficiency is caused by an increase in uj and T.K.E. A baseline case is used to compare the outcomes. It has been noted that numerical analysis using commercial code for fluent and the k-omega shear stress transport turbulence model performs better.
A Literature Review on Stewart–Gough Platform Calibrations
Authors: Karmakar Sourabh , Turner Cameron J.
Published: January 2024

Researchers have studied Stewart–Gough platforms, also known as Gough–Stewart platforms or hexapod platforms extensively for their inherent fine control characteristics. Their studies led to the potential deployment opportunities of Stewart–Gough platforms in many critical applications such as medical field, engineering machines, space research, electronic chip manufacturing, automobile manufacturing, etc. Some of these applications need micro- and nano-level movement control in 3D space for the motions to be precise, complicated, and repeatable; a Stewart–Gough platform fulfills these challenges smartly. For this, the platform must be more accurate than the specified application accuracy level and thus proper calibration for a parallel robot is crucial. Forward kinematics-based calibration for these hexapod machines becomes unnecessarily complex and inverse kinematics complete this task with much ease. To experiment with different calibration techniques, various calibration approaches were implemented by using external instruments, constraining one or more motions of the system, and using extra sensors for auto or self-calibration. This survey paid attention to those key methodologies, their outcome, and important details related to inverse kinematic-based parallel robot calibrations. It was observed during this study that the researchers focused on improving the accuracy of the platform position and orientation considering the errors contributed by one source or multiple sources. The error sources considered are mainly kinematic and structural, in some cases, environmental factors also are reviewed; however, those calibrations are done under no-load conditions. This study aims to review the present state of the art in this field and highlight the processes and errors considered for the calibration of Stewart–Gough platforms.
HAXPES reference spectra of UO2 generated with Ga Kα x-ray source
Authors: Dunn Stuart A. , Wood Aaron , Roussel Paul , Spencer Ben F. , Harrison Robert , Kaye Philip , Higginson Matthew A.
Published: January 2024

HAXPES measurements were carried out using a Scienta Omicron HAXPES instrument to provide reference spectra for depleted uranium dioxide. High purity uranium dioxide, as confirmed by trace elemental analysis and x-ray diffraction, was synthesized via the integrated dry route from uranium hexafluoride. The material was fixed on double sided carbon tape for the analysis with charge control measures in place. The expanded energy range, using a Ga Kα x-ray source, presents core level photoelectrons not observed in traditional XPS. In addition, a region associated with the x-ray induced Auger transitions MNN is evident at binding energies only achievable with HAXPES. The reference spectra presented here act as the first in a line of proposed investigations into the comparison of XPS and HAXPES from surface to bulk as well as a fundamental understanding of the electronic structure of uranium materials.
Evaluation of the pumping performance of combinations of Ti–Zr–V–Hf alloy nonevaporable getter coatings with different morphologies, activation protocols controlled at cryogenic temperatures
Authors: Smith Paul , Lodge Sam , Chew Andrew
Published: January 2024

The pumping performance of a range of Ti, V, Zr, and Hf alloy nonevaporable getter (NEG) coatings of order 5 μm thickness and with different modular structures has been investigated. For equal atomic percent Ti–Zr–V–Hf quaternary alloys, dual (columnar layer on the dense layer) coatings gave higher sticking probabilities than columnar and dense morphologies. The same alloy provided the highest sticking probability, followed by the Ti–Zr–V tertiary alloy, and then singular Zr. For a 24 h activation time, single element Zr coatings were shown to require an activation temperature of 300 vs 250 °C for the other alloys. H2 and N2 sticking probabilities increased by a factor of 100 and N2 terminal capacities by a factor of 1000, in the range 150–300 °C. For the dual coated Ti–Zr–V–Hf quaternary alloy at an activation temperature of 140 °C, H2 sticking probabilities increased by a factor of 2 when the activation time increased from 1 to 7 days and that of N2 increased by a factor of 6. The factor of 100 increase in measured sticking probability at LN2 temperature, compared to room temperature, to a value of 0.5 for H2, is transient in nature. Further investigations into this behavior are planned.
Fabrication of blazed gratings by tilted reactive ion beam etching with the side mask for augmented reality applications
Authors: Wang Yunchenxin , Pan Aixi , Zhu Xiaoli , Cui Bo
Published: January 2024

A novel manufacturing method using the side mask and tilted reactive ion beam etching (RIBE) is proposed for the fabrication of blazed gratings. Electron beam lithography was carried out to pattern a groove with a nanoscale line width, and then appropriate mask materials were filled into the SiO2 trench by atomic layer deposition. After being etched by RIBE at specific tilted angles, the required blazed gratings were achieved. In contrast to the typical fabrication process with a patterned mask on top of the surface to be etched, V-shaped nano structures filled into the trenches were used as the side mask. During etching, the surface material located in the shadow of the side mask along incident ion beams was not etched. The depth and blazed angle of blazed gratings are determined by the height of the side mask and the mounting angle of the sample, respectively. In addition, the fabricated blazed gratings can be used as imprinting moulds to duplicate blazed gratings for augmented reality applications. Due to more options for side mask materials, this method is able to provide high repeatability and accurate controllability for fabricating blazed gratings.
Sex Differences in Hydration Biomarkers and Test–Retest Reliability Following Passive Dehydration
Authors: Doherty Colin S. , Fortington Lauren V. , Barley Oliver R.
Published: January 2024

This study investigated (a) differences between males and females for changes in serum, tear, and urine osmolality, hematocrit, and urine specific gravity following acute passive dehydration and (b) assessed the reliability of these biomarkers separately for each sex. Fifteen males (age: 26.3 ± 3.5 years, body mass: 76 ± 7 kg) and 15 females (age: 28.8 ± 6.4 years, body mass: 63 ± 7 kg) completed a sauna protocol twice (5–28 days apart), aiming for 4% body mass loss (BML). Urine, blood, and tear markers were collected pre- and postdehydration, and change scores were calculated. Male BML was significantly greater than that of females in Trial 1 (3.53% ± 0.55% vs. 2.53% ± 0.43%, p < .001) and Trial 2 (3.36% ± 0.66% vs. 2.53% ± 0.44%, p = .01). Despite significant differences in BML, change in hematocrit was the only change marker that displayed a significant difference in Trial 1 (males: 3% ± 1%, females: 2% ± 1%, p = .004) and Trial 2 (males: 3% ± 1%, females: 1% ± 1%, p = .008). Regression analysis showed a significant effect for sex (male) predicting change in hematocrit (β = 0.8, p = .032) and change in serum osmolality (β = −3.3, p = .005) when controlling for BML but not for urinary or tear measures. The intraclass correlation coefficients for females (ICC 2, 1) were highest for change in urine specific gravity (ICC = .62, p = .006) and lowest for change in tear osmolarity (ICC = −.14, p = .689), whereas for males, it was posthematocrit (ICC = .65, p = .003) and post tear osmolarity (ICC = .18, p = .256). Generally, biomarkers showed lower test–retest reliability in males compared with females but, overall, were classified as poor–moderate in both sexes. These findings suggest that the response and reliability of hydration biomarkers are sex specific and highlight the importance of accounting for BML differences.
BadR directly represses the expression of the glycerol utilization operon in the Lyme disease pathogen
Authors: Zhang Jun-Jie , Raghunandanan Sajith , Wang Qian , Priya Raj , Alanazi Fuad , Lou Yongliang , Yang X. Frank
Published: January 2024

Glycerol utilization as a carbohydrate source by
Borreliella burgdorferi
, the Lyme disease spirochete, is critical for its successful colonization and persistence in the tick vector. The expression of the
glpFKD
(
glp
) operon, which encodes proteins for glycerol uptake/utilization, must be tightly regulated during the enzootic cycle of
B. burgdorferi
. Previous studies have established that the second messenger cyclic di-GMP (c-di-GMP) is required for the activation of
glp
expression, while an alternative sigma factor RpoS acts as a negative regulator for
glp
expression. In the present study, we report identification of a
cis
element within the 5´ untranslated region of
glp
that exerts negative regulation of
glp
expression. Further genetic screen of known and predicted DNA-binding proteins encoded in the genome of
B. burgdorferi
uncovered that overexpressing
Borrelia
host adaptation regulator (BadR), a known global regulator, dramatically reduced
glp
expression. Similarly, the
badR
mutant significantly increased
glp
expression. Subsequent electrophoretic mobility shift assay analyses demonstrated that BadR directly binds to this
cis
element, thereby repressing
glp
independent of RpoS-mediated repression. The efficiency of BadR binding was further assessed in the presence of c-di-GMP and various carbohydrates. This finding highlights multi-layered positive and negative regulatory mechanisms employed by
B. burgdorferi
to synchronize
glp
expression throughout its enzootic cycle.

IMPORTANCE

Borreliella burgdorferi
, the Lyme disease pathogen, must modulate its gene expression differentially to adapt successfully to its two disparate hosts. Previous studies have demonstrated that the glycerol uptake and utilization operon,
glpFKD
, plays a crucial role in spirochetal survival within ticks. However, the
glpFKD
expression must be repressed when
B. burgdorferi
transitions to the mammalian host. In this study, we identified a specific
cis
element responsible for the repression of
glpFKD
. We further pinpointed
Borrelia
host adaptation regulator as the direct binding protein to this
cis
element, thereby repressing
glpFKD
expression. This discovery paves the way for a deeper exploration of how zoonotic pathogens sense distinct hosts and switch their carbon source utilization during transmission.
Prefusion stabilization of the Hendra and Langya virus F proteins
Authors: Byrne Patrick O. , Blade Elizabeth G. , Fisher Brian E. , Ambrozak David R. , Ramamohan Ajit R. , Graham Barney S. , Loomis Rebecca J. , McLellan Jason S.
Published: January 2024

Pathogenic henipaviruses such as Nipah virus (NiV) and Hendra virus (HeV) cause respiratory symptoms, with severe cases resulting in encephalitis, seizures, and coma. The work described here shows that the NiV and HeV fusion (F) proteins share common structural features with the F protein from an emerging henipavirus
,
Langya virus (LayV). Sequence alignment alone was sufficient to predict which known prefusion-stabilizing amino acid substitutions from NiV F would stabilize the prefusion conformations of HeV F and LayV F. This work also reveals an unexpected oligomeric interface shared by prefusion HeV F and NiV F. Together, these advances lay a foundation for future antigen design targeting henipavirus F proteins. In this way, Nipah virus can serve as a prototypical pathogen for the development of protective vaccines and monoclonal antibodies to prepare for potential henipavirus outbreaks.
The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time
Authors: Shahid Aniqa , MacLennan Signe , Jones Bradley R. , Sudderuddin Hanwei , Dang Zhong , Cobarrubias Kyle , Duncan Maggie C. , Kinloch Natalie N. , Dapp Michael J. , Archin Nancie M. , Fischl Margaret A. , Ofotokun Igho , Adimora Adaora , Gange Stephen , Aouizerat Bradley , Kuniholm Mark H. , Kassaye Seble , Mullins James I. , Goldstein Harris , Joy Jeffrey B. , Anastos Kathryn , Brumme Zabrina L. ,   the MACS/WIHS combined cohort study (MWCSS), Ofotokun Ighovwerha , Sheth Anandi , Wingood Gina , Brown Todd , Margolick Joseph , Anastos Kathryn , Hanna David , Sharma Anjali , Gustafson Deborah , Wilson Tracey , D’Souza Gypsyamber , Gange Stephen , Topper Elizabeth , Cohen Mardge , French Audrey , Wolinsky Steven , Palella Frank , Stosor Valentina , Aouizerat Bradley , Price Jennifer , Tien Phyllis , Detels Roger , Mimiaga Matthew , Kassaye Seble , Merenstein Daniel , Alcaide Maria , Fischl Margaret , Jones Deborah , Martinson Jeremy , Rinaldo Charles , Kempf Mirjam-Colette , Dionne-Odom Jodie , Konkle-Parker Deborah , Brock James B. , Adimora Adaora , Floris-Moore Michelle
Published: January 2024

Characterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.
DNA transfer between two different species mediated by heterologous cell fusion in
Clostridium
coculture
Authors: Charubin Kamil , Hill John D. , Papoutsakis Eleftherios Terry
Published: January 2024

Investigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of
C. acetobutylicum
and
C. ljungdahlii
undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type
C. acetobutylicum
which acquired the erythromycin resistance (erm) gene from the
C. ljungdahlii
strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid
C. acetobutylicum
/
C. ljungdahlii
cells displaying hybrid DNA-methylation patterns.
Staphylococcus aureus
mutants resistant to the feed-additive monensin show increased virulence and altered purine metabolism
Authors: Warsi Omar M. , Upterworth Lina M. , Breidenstein Annika , Lustig Ulrika , Mikkelsen Kasper , Nagy Tamás , Szatmari Dávid , Ingmer Hanne , Andersson Dan I.
Published: January 2024

This study demonstrates a novel link between ionophore resistance, purine metabolism, and virulence/fitness in the key human and animal pathogen
Staphylococcus aureus
. The results show that mutants with reduced susceptibility to the commonly used ionophore monensin can be readily selected and that the reduced susceptibility observed is associated with an increased expression of the
de novo
purine synthesis pathway. This study increases our understanding of the impact of the use of animal feed additives on both human and veterinary medicine.
Periodontitis aggravates COPD through the activation of γδ T cell and M2 macrophage
Authors: Xiong Kaixin , Ao Keping , Wei Wei , Dong Jiajia , Li Jia , Yang Yutao , Tang Boyu , Li Yan
Published: January 2024

Periodontitis exacerbates chronic obstructive pulmonary disease (COPD) progression. For the first time, the current study identified that the impact of periodontitis on COPD progression was associated with the activation of γδ T cells and M2 macrophages and that M2 polarization of macrophages was affected by γδ T cells activation. The results indicated that targeting at periodontitis treatment and the γδ T-M2 immune mechanism might provide a new practical strategy for COPD prevention or control.
Risk factors for recognized and unrecognized SARS-CoV-2 infection: a seroepidemiologic analysis of the Prospective Urban Rural Epidemiology (PURE) study
Authors: Leong Darryl P. , Loeb Mark , Mony Prem K. , Rangarajan Sumathy , Mushtaha Maha , Miller Matthew S. , Dias Mary , Yegorov Sergey , V Mamatha , Telci Caklili Ozge , Temizhan Ahmet , Szuba Andrzej , Abat Marc Evans M. , Mat-Nasir Nafiza , Diaz Maria Luz , Khansaheb Hamda , Lopez-Jaramillo Patricio , Duong MyLinh , Teo Koon K. , Poirier Paul , Oliveira Gustavo , Avezum Álvaro , Yusuf Salim
Published: January 2024

There are limited data on individual risk factors for SARS-CoV-2 infection (including unrecognized infection). In this seroepidemiologic substudy of an ongoing prospective cohort study of community-dwelling adults, participants were thoroughly characterized pre-pandemic. The SARS-CoV-2 infection was ascertained by serology. Among 8,719 participants from 11 high-, middle-, and low-income countries, 3,009 (35%) were seropositive for SARS-CoV-2. Characteristics independently associated with seropositivity were younger age (odds ratio, OR; 95% confidence interval, CI, per five-year increase: 0.95; 0.91–0.98) and body mass index >25 kg/m
2
(OR, 95% CI: 1.16, 1.01–1.34). Smoking (as compared with never smoking, OR, 95% CI: 0.83, 0.70–0.97) and COVID-19 vaccination (OR, 95% CI: 0.70, 0.60–0.82) were associated with a reduced risk of seropositivity. Among seropositive participants, 83% were unaware of having been infected with SARS-CoV-2. Seropositivity and a lack of awareness of infection were more common in lower-income countries. The COVID-19 vaccination reduces the risk of SARS-CoV-2 infection (including recognized and unrecognized infections). Overweight or obesity is an independent risk factor for SARS-CoV-2 infection. Infection and lack of infection awareness are more common in lower-income countries.

IMPORTANCE

In this large, international study, evidence of SARS-CoV-2 infection was obtained by testing blood specimens from 8,719 community-dwelling adults from 11 countries. The key findings are that (i) the large majority (83%) of community-dwelling adults from several high-, middle-, and low-income countries with blood test evidence of SARS-CoV-2 infection were unaware of this infection—especially in lower-income countries; and (ii) overweight/obesity predisposes to SARS-CoV-2 infection, while COVID-19 vaccination is associated with a reduced risk of SARS-CoV-2 infection. These observations are not attributable to other individual characteristics, highlighting the importance of the COVID-19 vaccination to prevent not only severe infection but possibly any infection. Further research is needed to understand the mechanisms by which overweight/obesity might increase the risk of SARS-CoV-2 infection.
Shewanella
phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family
Authors: Wang Hongmin , Zheng Kaiyang , Wang Min , Ma Keran , Ren Linyi , Guo Ruizhe , Ma Lina , Zhang Hong , Liu Yundan , Xiong Yao , Wu Miaolan , Shao Hongbing , Sung Yeong Yik , Mok Wen Jye , Wong Li Lian , McMinn Andrew , Liang Yantao
Published: January 2024

Shewanella
is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few
Shewanella
phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel
Shewanella
phage, vB_SbaS_Y11, that infects
Shewanella KR11
and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR
AcrVA2
gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to
Pseudomonas
virus H66 and
Pseudomonas
phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named
Ranviridae
.

IMPORTANCE

The Gram-negative
Shewanella
bacterial genus currently includes about 80 species of mostly aquatic
Gammaproteobacteria
, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a
Shewanella
phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR
AcrVA2
gene and belongs to a potential virus family,
Ranviridae
. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of
Shewanella
phage populations.
Klebsiella pneumoniae
DedA family proteins have redundant roles in divalent cation homeostasis and resistance to phagocytosis
Authors: Tiwari Vijay , Sharma Amit , Braga Reygan , Garcia Emily , Appiah Ridhwana , Fleeman Renee , Abuaita Basel H. , Patrauchan Marianna , Doerrler William T.
Published: January 2024

The DedA superfamily is a highly conserved family of membrane proteins. Deletion of
Escherichia coli yqjA
and
yghB
, encoding related DedA family proteins, results in sensitivity to elevated temperature, antibiotics, and alkaline pH. The human pathogen
Klebsiella pneumoniae
possesses genes encoding DedA family proteins with >90% amino acid identity to
E. coli
YqjA and YghB. We hypothesized that the deletion of
K. pneumoniae yqjA
and
yghB
will impact its physiology and may reduce its virulence. The
K. pneumoniae
Δ
yqjA
Δ
yghB
mutant (strain VT101) displayed a growth defect at 42°C and alkaline pH sensitivity, not unlike its
E. coli
counterpart. However, VT101 retained mostly wild-type resistance to antibiotics. We found VT101 was sensitive to the chelating agent EDTA, the anionic detergent SDS, and agents capable of alkalizing the bacterial cytoplasm such as bicarbonate or chloroquine. We could restore growth at alkaline pH and at elevated temperature by addition of 0.5–2 mM Ca
2+
or Mg
2+
to the culture media. VT101 displayed a slower uptake of calcium, which was dependent upon calcium channel activity. VT201, with similar deletions as VT101 but derived from a virulent
K. pneumoniae
strain, was highly susceptible to phagocytosis by alveolar macrophages and displayed a defect in the production of capsule. These findings suggest divalent cation homeostasis and virulence are interlinked by common functions of the DedA family.

IMPORTANCE

Klebsiella pneumoniae
is a dangerous human pathogen. The DedA protein family is found in all bacteria and is a membrane transporter often required for virulence and antibiotic resistance.
K. pneumoniae
possesses homologs of
E. coli
YqjA and YghB, with 60% amino acid identity and redundant functions, which we have previously shown to be required for tolerance to biocides and alkaline pH. A
K. pneumoniae
strain lacking
yqjA
and
yghB
was found to be sensitive to alkaline pH, elevated temperature, and EDTA/SDS and displayed a defect in calcium uptake. Sensitivity to these conditions was reversed by addition of calcium or magnesium to the growth medium. Introduction of Δ
yqjA
and Δ
yghB
mutations into virulent
K. pneumoniae
resulted in the loss of capsule, increased phagocytosis by macrophages, and a partial loss of virulence. These results show that targeting the
Klebsiella
DedA family results in impaired divalent cation transport and, in turn, loss of virulence.
Late Mesozoic subduction-accretion in the southern Qiangtang: Insights from the Sumxi igneous complex of west-central Tibet
Authors: Wang Chao , Ding Lin , Cai Fulong , Zeng Deng , Li Jinxiang , Zhang Liyun , Yue Yahui
Published: January 2024

Knowledge of the evolution of the Bangong-Nujiang Tethyan Ocean is crucial for reconstructing the paleography of the Tethyan Realm, given its significance as a key component of the eastern Tethys. Nonetheless, there has been uncertainty regarding both the timing and the processes involved in the closure of this ocean. This study focused on a 110–106 Ma igneous complex comprising basalts–basaltic andesites, trachyandesites, and granodiorites from the Sumxi area in the western part of the Qiangtang terrane of west-central Tibet. The basalts–basaltic andesites have SiO2 contents of 52.5–58.7 wt% and MgO contents of 2.89–4.63 wt%, and exhibit some arc-like geochemical signatures. However, these rocks also have elevated Nb contents (>10 ppm) and Nb/La ratios (>0.5), as well as enriched Sr-Nd isotopic composition [εNd(t) = −7.40 to −6.00], implying that they are products of a mantle source metasomatized by adakitic melts. The trachyandesites are characterized by intermediate compositions (SiO2 = 63.6–65.2 wt%), high Mg number (40–60), and more enriched εNd(t) values (−8.37 to −7.49). Comparing their geochemical composition to that of mélange rocks, it is postulated that these trachyandesites were formed through the partial melting of a mantle source including mélange matrix rocks within a subduction zone. The granodiorites exhibit adakitic geochemical features (Sr = 830.14–1032.70 ppm, Y = 14.86–15.37 ppm, Sr/Y = 54–68), indicating that they originated from the partial melting of a thickened lower crust in a continental arc setting. Our results, in combination with a synthesis of tectonomagmatism along the Bangong-Nujiang suture zone, provide convincing evidence for subduction of an oceanic plateau and subsequent slab roll-back. The Sumxi igneous complex, with its clear arc affinity, suggests that the Bangong-Nujiang Tethyan Ocean, or at least its western part, remained open until the late Early Cretaceous (ca. 106 Ma).
Hydrologic windows into the crystalline basement and their controls on groundwater flow patterns across the Paradox Basin, western USA
Authors: Person M. , McIntosh J.C. , Kim J.-H. , Noyes C. , Bailey L. , Lingrey S. , Krantz R. , Lucero D. , Reiners P.W. , Ferguson G.
Published: January 2024

Conceptual models of sedimentary basin groundwater flow systems typically assume that the crystalline basement acts as an impermeable boundary and can be neglected. In this study, we use hydrologic models constrained by isotopic and geochemical datasets to argue that the La Sal Mountains, Utah, USA, act as a hydrologic window into the Paradox Basin’s lower aquifer system and underlying crystalline basement. We conducted a sensitivity study in which we varied crystalline basement/laccolith permeability as well as fault zone connectivity along a cross-sectional transect from the La Sal Mountains to Lisbon Valley. When the crystalline basement/laccolith units are set at relatively permeable levels (10–14 m2), simulated tracers that include total dissolved solids, oxygen isotopic composition of pore fluids (δ18O), and groundwater residence times are in closest agreement with field measurements. Model results indicate that pore fluids in the basal aquifer system underlying the Paradox Formation confining unit are a mixture of relatively young meteoric fluids and older Paradox Formation brines. The presence of faults did not significantly modify fluid exchange between the upper and lower aquifer systems. This was due, in part, to underpressuring within the Paradox Formation. Our study concludes that the Paradox Basin represents a regional recharge area for the Colorado Plateau, with groundwater discharge occurring along the Colorado River within the Grand Canyon some 375 km away to the southwest. This is only possible with a permeable crystalline basement. Our findings help explain the genesis of Mississippi Valley-type ore deposits of the US Midcontinent, where the presence of a permeable basement may be useful in addressing issues related to solute mass and energy balance.
Correlating mantle cooling with tectonic transitions on early Earth
Authors: Gunawardana Prasanna M. , Chowdhury Priyadarshi , Morra Gabriele , Cawood Peter A.
Published: January 2024

The dominant tectonic mode operating on early Earth (before ca. 2.5 Ga) remains elusive, with an increasing body of evidence suggesting that non-plate tectonic modes were likely more prevalent at that time. Thus, how plate tectonics evolved after that remains contentious. We performed two-dimensional numerical modeling of mantle convection at temperatures appropriate for the Hadean–Archean eons and show that subduction and rift systems may have spontaneously emerged on Earth from an earlier drip-and-rift–dominated tectonic mode in response to the secular cooling of the mantle. This cooling of the mantle was mediated by repeated events of rifting and dripping that likely occurred over a few hundred million years. As the mantle cooled, its effective viscosity and the thickness and strength of the lithosphere increased, which helped establish rigid plates and initiate plate tectonics on Earth.
Erratum to: Experimental Test of the Acoustic Thermometry Method on a Long Track in the Sea of Japan
Authors: Dolgikh G. I. , Morgunov Yu. N. , Bezotvetnykh V. V. , Burenin A. V. , Golov A. A. , Voitenko E. A. , Razhivin V. V. , Tagiltsev A. A.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050033
Erratum to: Morphology and Sedimentary Cover Structure of Long Segments of the Gakkel Ridge
Authors: Piskarev A. L. , Kaminsky V. D. , Poselov V. A. , Kireev A. A. , Savin V. A. , Smirnov O. E. , Bezumov D. V. , Ovanesian G. I. , Elkina D. V.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050057
Erratum to: Hetero- and Homogeneous States of Hydrocarbon Fluids in the Earth’s Interior: Evidence from the Study of Synthetic Fluid Inclusions
Authors: Balitsky V. S. , Setkova T. V. , Balitskaya L. V. , Golunova M. A. , Bublikova T. M. , Plotnikova I. N. , Aranovich L. Ya.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050124
Erratum to: Age and Tectonic Setting of the Kopri-Type Granitoids at the Junction Zone of the Dzhugdzhur–Stanovoi and Western Stanovoi Superterranes of the Central Asian Fold Belt
Authors: Larin A. M. , Kotov A. B. , Salnikova E. B. , Velikoslavinskii S. D. , Kovach V. P. , Skovitina T. M. , Ivanova A. A. , Plotkina Yu. V. , Zagornaya N. Yu.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X2305015X
Erratum to: Transformation of Malacological Fauna of the Sea of Azov in the Holocene and Its Role in the Formation of Coastal Spit
Authors: Matishov G. G. , Kovalenko E. P. , Titov V. V.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050161
Erratum to: The Unprecedented Duration of the 2020 Ozone Depletion in the Antarctic
Authors: Zuev V. V. , Savelieva E. S. , Pavlinsky A. V. , Sidorovski E. A.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050197
Erratum to: Magma Composition and Formation Conditions of Alkaline-Salic Rocks of the Early Mesozoic Adaatsag Bimodal Association of the Kharkhorin Rift Zone, Central Asia: Data from the Study of Melt Inclusions in Minerals
Authors: Andreeva I. A. , Yarmolyuk V. V. , Borisovsky S. E.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050203
Erratum to: Effect of Sulfur Concentration on Olivine Sulfidation under Lithospheric Mantle PT-parameters
Authors: Bataleva Y. V. , Furman O. V. , Zdrokov E. V. , Borzdov Y. M. , Palyanov Y. N.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050227
Erratum to: Geophysical Effects of the Active Stage of the Stromboli Volcano Eruption on October 9, 2022
Authors: Spivak A. A. , Loktev D. N. , Rybnov Yu. S. , Riabova S. A. , Tikhonova A. V.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1028334X23050264
Robotic surgery in the management of synchronous esophageal and gastric perforation after endoscopic dilation
Authors: Donado Jimenez Maria Jose , Jimenez Maria Carolina , Cubas Robert
Published: January 2024

Upper gastrointestinal perforation is a feared complication of diagnostic and therapeutic endoscopy, with an incidence of perforation between 0.3% and 5%. Even though is rare, the mortality rate can be as high as 40%. Currently, there is no consensus on the best therapeutic strategy and it usually depends on patient stability, the extent of perforation, time to diagnosis, surgeon experience and available resources

We present a case of a patient who presented to our institution to undergo an ambulatory oesophageal dilation. After dilation, the patient developed two full-thickness gastric perforations and a full-thickness oesophageal perforation without haemodynamic instability. All perforations were diagnosed and treated with a combination of intraoperative endoscopy and robotic surgery with excellent outcomes.

We demonstrate that a robotic approach combined with intraoperative diagnostic endoscopy is a safe and feasible treatment option for esophageal and gastric perforations in a stable patient without large extraluminal contamination.
Coaches of youth field sports as delivery agents of injury prevention programmes: how are we training the trainers? A scoping review
Authors: Guilfoyle Lauren , Kenny Ian C , O'Sullivan Kieran , Campbell Mark J , Warrington Giles D , Glynn Liam G , Comyns Tom
Published: January 2024

Objective

To systematically map the coach education (CE) component of injury prevention programmes (IPPs) for youth field sports by identifying and synthesising the design, content and facilitation strategies used to address competency drivers and behaviour change.

Design

Scoping review.

Data sources

PubMed, PsycInfo, EMBASE, CINAHL, SportDiscus and Google Scholar electronic databases were searched using keywords related to IPPs and youth field sports.

Eligibility criteria for selecting studies

Studies of IPPs in youth field sports, that provided ‘train-the-trainer’ education to coaches as designated delivery agents.

Results

20 studies from two field sports (soccer/football; n=17, Rugby Union; n=3) fulfilled the eligibility criteria. Eleven CE interventions occurred in the preseason and 18 occurred at one time-point (single day). Five studies cited use of a behavioural change theory or model in the design of their CE, most frequently the Health Action Process Approach model (n=5); and use of behavioural change techniques varied. Twelve of twenty studies (60%) reported some form of ongoing support to coaches following the CE primary intervention concurrent with IPP implementation.

Conclusion

CE that occurs on 1 day (one time-point) is most popular for preparing coaches as delivery agents of IPPs in youth field sports. While recognising pragmatic barriers, more expansive in-service training, support and feedback may enhance the effective implementation of IPPs.

Trial registration number

https://doi.org/10.17605/OSF.IO/FMHGD