bluuebunny/crossref_metadata_2025_split huggingface dataset:
KED gene expression in early response to wounding stress in tomato plants
Authors: Zhang Xing‐Hai , Vichyavichien Paveena , Nifakos Nicholas , Kaplan Noah , Jin Xiao‐Lu , Wellman Annalise , Spanoudis Alexander , Klingler Marcos 
Published: July 2023

AbstractThe wounding‐responsive KED gene, named for its coding for a lysine (K), glutamic acid (E), and aspartic acid (D)‐rich protein, is widely present among land plants. However, little is known about its regulation or function. In this study, we found that transcription of the tomato (Solanum lycopersicum) KED gene, SlKED, was rapidly and transiently elevated by wounding or ethephon treatment. Compared to the wild‐type plants, the CRISPR/Cas9‐mediated SlKED knockout plants did not exhibit altered expression patterns for genes involved in hormone biosynthesis or stress signaling, suggesting a lack of pleiotropic effect on other stress‐responsive genes. Conversely, jasmonic acid did not appear to directly regulate SlKED expression. Wounded leaves of the KED‐lacking plants exhibited higher binding of Evans blue dye than the wild‐type, indicating a possible role for KED in healing damaged tissues. The SlKED knockout plants showed a similar dietary effect as the wild‐type on the larval growth of tobacco hornworm. But a higher frequency of larval mandible (mouth) movement was recorded during the first 2 minutes of feeding on the wounded KED‐lacking SlKED knockout plants than on the wounded KED‐producing wild‐type plants, probably reflecting an initial differential response by the feeding larvae to the SlKED knockout plants. Our findings suggest that SlKED may be an ethylene‐mediated early responder to mechanical stress in tomato, acting downstream of the wound stress response pathways. Although its possible involvement in response to other biotic and abiotic stresses is still unclear, we propose that SlKED may play a role in plant's rapid, short‐term, early wounding responses, such as in cellular damage healing.
Sanctions and their impacts on medical trade and health outcomes
Authors: Miromanova Anna 
Published: July 2023

AbstractDespite the intention that sanctions, by design, should not harm civilians' welfare, evidence shows that they can negatively affect health outcomes. In this study, I measure the impact of sanctions on international trade in medical supplies and cross‐country mortality rates. I find that sanctions, particularly those imposed by the United States, decrease the volume of medical exports to targeted countries, potentially leading to worse health outcomes. I also discover that sanctions increase mortality rates in the targeted countries, particularly for women with HIV/AIDS infections. Termination of foreign aid, blockades, and partial embargoes have the most damaging effect on mortality.
Long‐term nutrient management effects on organic carbon fractions and carbon sequestration in Typic Haplusterts soils of Central India
Authors: Ramteke Pratik , Gabhane Vijay , Kadu Prakash , Kharche Vilas , Jadhao Shyam , Turkhede Anil , Gajjala Ravindra Chary 
Published: July 2023

AbstractProductivity of agricultural soils, particularly in India's rainfed tropics, has rigorously fallen because of increased losses of soil organic carbon (SOC) during the last decades; consequently, sustaining crop productivity through the maintenance of SOC level is difficult for dryland farmers. Moreover, systematic research on carbon (C) sequestration, SOC pools, their sensitivity to management change and critical C input level for zero change in SOC, especially under cotton–greengram intercropping in Vertisols of semi‐arid climates, is limited. Therefore, we studied cotton–greengram intercropping after 35 years (1987–2022) under continuous application of organics (farmyard manure/gliricidia), chemical fertilizers and substitution of 50% or 100% fertilizer nitrogen (N) through farmyard manure/gliricidia (integrated nutrient management) (INM). The INM treatments recorded significantly higher cotton–greengram system productivity and sustainable yield index. Continuous cropping without an external nutrient source decreased the soil C, while cropping with INM resulted in a positive build‐up of C in both labile and stable pools. On average, about 62% of total organic carbon was stabilized in the passive pool (CLL, Less Labile C + CRC, Recalcitrant C) of SOC. The increment in SOC stock was linearly (y = 0.0767x – 0.2248; R2 = 0.87, p < .001) related to the system productivity. The very labile C, potassium permanganate oxidizable C and microbial biomass C fractions were the most sensitive to nutrient management. A threshold C input of 0.71 Mg C ha−1 year−1 is required to maintain antecedent SOC, which is readily supplied to the soil using the region's current cotton–greengram intercropping system. Thus, this cropping system is quite capable to maintain antecedent SOC. We conclude that, in the context of changing climates, promoting cotton–legume intercropping using locally available farmyard manure/gliricidia as a substitute for 50%‐‐Fertilizer N is a viable strategy for enhancing SOC storage while achieving sustainable productivity in semi‐arid Vertisols of Central India.
Deep learning‐enabled discovery and characterization of HKT genes in Spartina alterniflora
Authors: Yang Maogeng , Chen Shoukun , Huang Zhangping , Gao Shang , Yu Tingxi , Du Tingting , Zhang Hao , Li Xiang , Liu Chun‐Ming , Chen Shihua , Li Huihui 
Published: July 2023

SUMMARYSpartina alterniflora is a halophyte that can survive in high‐salinity environments, and it is phylogenetically close to important cereal crops, such as maize and rice. It is of scientific interest to understand why S. alterniflora can live under such extremely stressful conditions. The molecular mechanism underlying its high‐saline tolerance is still largely unknown. Here we investigated the possibility that high‐affinity K+ transporters (HKTs), which function in salt tolerance and maintenance of ion homeostasis in plants, are responsible for salt tolerance in S. alterniflora. To overcome the imprecision and unstable of the gene screening method caused by the conventional sequence alignment, we used a deep learning method, DeepGOPlus, to automatically extract sequence and protein characteristics from our newly assemble S. alterniflora genome to identify SaHKTs. Results showed that a total of 16 HKT genes were identified. The number of S. alterniflora HKTs (SaHKTs) is larger than that in all other investigated plant species except wheat. Phylogenetically related SaHKT members had similar gene structures, conserved protein domains and cis‐elements. Expression profiling showed that most SaHKT genes are expressed in specific tissues and are differentially expressed under salt stress. Yeast complementation expression analysis showed that type I members SaHKT1;2, SaHKT1;3 and SaHKT1;8 and type II members SaHKT2;1, SaHKT2;3 and SaHKT2;4 had low‐affinity K+ uptake ability and that type II members showed stronger K+ affinity than rice and Arabidopsis HKTs, as well as most SaHKTs showed preference for Na+ transport. We believe the deep learning‐based methods are powerful approaches to uncovering new functional genes, and the SaHKT genes identified are important resources for breeding new varieties of salt‐tolerant crops.
Anterograde trafficking of Toll‐like receptors requires the cargo sorting adaptors TMED‐2 and 7
Authors: Holm Julia E. J. , Soares Sandro G. , Symmons Martyn F. , Huddin Afiqah Saleh , Moncrieffe Martin C. , Gay Nicholas J. 
Published: July 2023

AbstractToll‐Like Receptors (TLRs) play a pivotal role in immunity by recognising conserved structural features of pathogens and initiating the innate immune response. TLR signalling is subject to complex regulation that remains poorly understood. Here we show that two small type I transmembrane receptors, TMED2 and 7, that function as cargo sorting adaptors in the early secretory pathway are required for transport of TLRs from the ER to Golgi. Protein interaction studies reveal that TMED7 interacts with TLR2, TLR4 and TLR5 but not with TLR3 and TLR9. On the other hand, TMED2 interacts with TLR2, TLR4 and TLR3. Dominant negative forms of TMED7 suppress the export of cell surface TLRs from the ER to the Golgi. By contrast TMED2 is required for the ER‐export of both plasma membrane and endosomal TLRs. Together, these findings suggest that association of TMED2 and TMED7 with TLRs facilitates anterograde transport from the ER to the Golgi.
Super‐massive transfusion during liver transplantation
Authors: Lapisatepun Warangkana , Ma Christina , Lapisatepun Worakitti , Agopian Vatche , Wray Christopher , Xia Victor W. 
Published: July 2023

AbstractBackgroundMassive hemorrhage and transfusion during liver transplantation (LT) present great challenges. We aimed to investigate the incidence and risk factors for super‐massive transfusion (SMT) and survival outcome and factors that negatively affect survival in patients who received SMT during LT.Study Design and MethodsWe included adult patients undergoing LT from 2004 to 2019. SMT was defined as transfusion of ≥50 units of red blood cells (RBC) during LT. Independent risk factors were identified by multivariable logistic regression. Ninety‐day survival was recorded and factors that negatively affected survival were analyzed by the Cox survival test.ResultsOf 2772 patients, 158 (5.6%) received SMT during LT. Mean RBC transfusion was 72.6 (±23.4) units with a maximum of 168 units. Four variables (MELD‐Na score, previous upper abdominal surgery, portal vein thrombosis, and remote retransplant) were independent risk factors for SMT (odds ratio 1.800–8.274, 95% CI 1.008–16.685, all p < .005). The 90‐day survival rate in SMT patients was 81.6%. Preoperative pulmonary hypertension and massive postreperfusion transfusion negatively affected 90‐day survival (hazard ratio 2.658–4.633, 95% CI 1.144–10.130, and all p < .05).ConclusionsIn this large retrospective study, we found that SMT occurred in a small percentage of patients and was associated with relatively satisfactory short‐term survival. Identification of preoperative risk factors for SMT and factors that negatively affect survival improve our understanding of this unique LT patient population.
Assessing the Fundamental Movement Skills of Children With Intellectual Disabilities in the Special Olympics Young Athletes Program
Authors: Kavanagh Hayley , Manninen Mika , Meegan Sarah , Issartel Johann 
Published: July 2023

Mastering the ability to move proficiently from a young age is an important contributor to lifelong physical activity participation. This study examined fundamental movement skill (FMS) proficiency in children with intellectual disabilities (n = 96, 60% boys, age 5–12 years) and typically developing children (n = 96, 60% boys, age 5–12 years). Participants were assessed using the Test of Gross Motor Development–3rd edition and balance subtest from the Bruininks–Oseretsky Test of Motor Proficiency 2. The FMS proficiency of typically developing children including mastery/near mastery level (combined variable representing mastery, which is achieving all criteria for the skill, over both trials and near mastery, wherein a participant performs all but one of the components of the skill correctly) was significantly higher than for children with intellectual disabilities. A similar observation was made with multiple linear regression analysis testing the interaction effect of participant group and age/gender on all three FMS subcomponents. The results presented will help establish a baseline of FMS proficiency and guidelines for future intervention for children with intellectual disabilities.
Sports Coaching in an Online Space: What Can We Learn From Endurance Sport Coaches?
Authors: Blanchfield Jamie , McArdle Jean , Haughey Tandy 
Published: July 2023

Within endurance sports (ES), a practice exists in which online remote coaching (RC) is a necessary construct. This study aimed to examine the processes of ES coaches to gain insight into the experiences of coaches engaging in RC before COVID-19 forced others to do the same. To achieve this aim, semistructured interviews were conducted with ES coaches (N = 7; M = 6, F = 1). Transcripts were subject to thematic analysis, with three dimensions (a) remote coach and ES, (b) process of remote coaching, and (c) delivery of training online being identified. An additional 17 higher and 79 lower order themes were found. Results found that to be effective online, ES coaches utilised technology such as instant messaging and online software to increase presence and decrease the perceived distance from athletes. They aimed to create autonomous athletes both by choice and by necessity. The ease of access through technology had a negative and positive impact on work–life balance. A process was developed whereby only technology that served a purpose to further athlete outcomes was used and balanced with subjective feedback. Further research is needed to garner athlete expectations and experiences of RC.
Molecular determinants of avoidance and inhibition of
Pseudomonas aeruginosa
MexB efflux pump
Authors: Gervasoni Silvia , Mehla Jitender , Bergen Charles R. , Leus Inga V. , Margiotta Enrico , Malloci Giuliano , Bosin Andrea , Vargiu Attilio V. , Lomovskaya Olga , Rybenkov Valentin V. , Ruggerone Paolo , Zgurskaya Helen I. 
Published: July 2023

ABSTRACT

Transporters of the resistance-nodulation-cell division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump of
Pseudomonas aeruginosa
is MexAB-OprM, in which the inner membrane transporter MexB is responsible for the recognition and binding of compounds. The high importance of this pump in clinical antibiotic resistance made it a subject of intense investigations and a promising target for the discovery of efflux pump inhibitors. This study is focused on a series of peptidomimetic compounds developed as effective inhibitors of MexAB-OprM. We performed multi-copy molecular dynamics simulations, machine-learning (ML) analyses, and site-directed mutagenesis of MexB to investigate interactions of MexB with representatives of efflux avoiders, substrates, and inhibitors. The analysis of both direct and water-mediated protein-ligand interactions revealed characteristic patterns for each class, highlighting significant differences between them. We found that efflux avoiders poorly interact with the access binding site of MexB, and inhibition engages amino acid residues that are not directly involved in binding and transport of substrates. In agreement, machine-learning models selected different residues predictive of MexB substrates and inhibitors. The differences in interactions were further validated by site-directed mutagenesis. We conclude that the substrate translocation and inhibition pathways of MexB split at the interface (between the main putative binding sites) and at the deep binding pocket and that interactions outside of the hydrophobic patch contribute to the inhibition of MexB. This molecular-level information could help in the rational design of new inhibitors and antibiotics less susceptible to the efflux mechanism.

IMPORTANCE
Multidrug transporters recognize and expel from cells a broad range of ligands including their own inhibitors. The difference between the substrate translocation and inhibition routes remains unclear. In this study, machine learning and computational and experimental approaches were used to understand dynamics of MexB interactions with its ligands. Our results show that some ligands engage a certain combination of polar and charged residues in MexB binding sites to be effectively expelled into the exit funnel, whereas others engage aromatic and hydrophobic residues that slow down or hinder the next step in the transporter cycle. These findings suggest that all MexB ligands fit into this substrate-inhibitor spectrum depending on their physico-chemical structures and properties.
Draft genome sequences of
Pantoea
sp. strains QMID1-QMID4 isolated from the midgut of Japanese honey bee (
Apis cerana japonica
)
Authors: Suzuki Akihiko , Nakajima Nobuyoshi , Sakamoto Yoshiko 
Published: July 2023

ABSTRACT

We report the draft genome sequences of
Pantoea
sp. strains QMID1-QMID4 that were recovered from the midgut of Japanese honey bee (
Apis cerana japonica
). The strains possess the carotenoid biosynthetic gene cluster. The genome information expands our knowledge of their potential use as probiotics and/or prebiotics in honey bees.
Crystalline lens nuclear age prediction as a new biomarker of nucleus degeneration
Authors: Guo Mengjie , Higashita Risa , Lin Chen , Hu Lingxi , Chen Wan , Li Fei , Lai Gilda Wing Ki , Nguyen Anwell , Sakata Rei , Okamoto Keiichiro , Tang Bo , Xu Yanwu , Fu Huazhu , Gao Fei , Aihara Makoto , Zhang Xiulan , Yuan Jin , Lin Shan , Leung Christopher Kai-Shun , Liu Jiang 
Published: July 2023

BackgroundThe crystalline lens is a transparent structure of the eye to focus light on the retina. It becomes muddy, hard and dense with increasing age, which makes the crystalline lens gradually lose its function. We aim to develop a nuclear age predictor to reflect the degeneration of the crystalline lens nucleus.MethodsFirst we trained and internally validated the nuclear age predictor with a deep-learning algorithm, using 12 904 anterior segment optical coherence tomography (AS-OCT) images from four diverse Asian and American cohorts: Zhongshan Ophthalmic Center with Machine0 (ZOM0), Tomey Corporation (TOMEY), University of California San Francisco and the Chinese University of Hong Kong. External testing was done on three independent datasets: Tokyo University (TU), ZOM1 and Shenzhen People’s Hospital (SPH). We also demonstrate the possibility of detecting nuclear cataracts (NCs) from the nuclear age gap.FindingsIn the internal validation dataset, the nuclear age could be predicted with a mean absolute error (MAE) of 2.570 years (95% CI 1.886 to 2.863). Across the three external testing datasets, the algorithm achieved MAEs of 4.261 years (95% CI 3.391 to 5.094) in TU, 3.920 years (95% CI 3.332 to 4.637) in ZOM1-NonCata and 4.380 years (95% CI 3.730 to 5.061) in SPH-NonCata. The MAEs for NC eyes were 8.490 years (95% CI 7.219 to 9.766) in ZOM1-NC and 9.998 years (95% CI 5.673 to 14.642) in SPH-NC. The nuclear age gap outperformed both ophthalmologists in detecting NCs, with areas under the receiver operating characteristic curves of 0.853 years (95% CI 0.787 to 0.917) in ZOM1 and 0.909 years (95% CI 0.828 to 0.978) in SPH.InterpretationThe nuclear age predictor shows good performance, validating the feasibility of using AS-OCT images as an effective screening tool for nucleus degeneration. Our work also demonstrates the potential use of the nuclear age gap to detect NCs.
Excess mortality associated with the COVID-19 pandemic during the 2020 and 2021 waves in Antananarivo, Madagascar
Authors: Rabarison Joelinotahiana Hasina , Rakotondramanga Jean Marius , Ratovoson Rila , Masquelier Bruno , Rasoanomenjanahary Anjaraso Maharavo , Dreyfus Anou , Garchitorena Andres , Rasambainarivo Fidisoa , Razanajatovo Norosoa Harline , Andriamandimby Soa Fy , Metcalf C Jessica , Lacoste Vincent , Heraud Jean-Michel , Dussart Philippe 
Published: July 2023

IntroductionCOVID-19-associated mortality remains difficult to estimate in sub-Saharan Africa because of the lack of comprehensive systems of death registration. Based on death registers referring to the capital city of Madagascar, we sought to estimate the excess mortality during the COVID-19 pandemic and calculate the loss of life expectancy.MethodsDeath records between 2016 and 2021 were used to estimate weekly excess mortality during the pandemic period. To infer its synchrony with circulation of SARS-CoV-2, a cross-wavelet analysis was performed. Life expectancy loss due to the COVID-19 pandemic was calculated by projecting mortality rates using the Lee and Carter model and extrapolating the prepandemic trends (1990–2019). Differences in life expectancy at birth were disaggregated by cause of death.ResultsPeaks of excess mortality in 2020–21 were associated with waves of COVID-19. Estimates of all-cause excess mortality were 38.5 and 64.9 per 100 000 inhabitants in 2020 and 2021, respectively, with excess mortality reaching ≥50% over 6 weeks. In 2021, we quantified a drop of 0.8 and 1.0 years in the life expectancy for men and women, respectively attributable to increased risks of death beyond the age of 60 years.ConclusionWe observed high excess mortality during the pandemic period, in particular around the peaks of SARS-CoV-2 circulation in Antananarivo. Our study highlights the need to implement death registration systems in low-income countries to document true toll of a pandemic.
Parkrun as self-managed cardiac rehabilitation: secondary analysis of a cross-sectional survey of parkrun in the UK
Authors: Haake Steve , Johnson Thomas W , Bourne Jessica , Quirk Helen , Bullas Alice 
Published: July 2023

ObjectivesCardiac rehabilitation following a cardiovascular disease (CVD)-related illness has been shown to reduce the risk of heart attack and hospital admission. The American College of Sports Medicine recommends 3–5 days per week of moderate to vigorous exercise. Despite this, only 38% of those eligible complete rehabilitation programmes. Parkrun organises free, weekly, timed, 5 km running or walking events. The aim of this study was to investigate whether parkrun can support self-managed cardiac rehabilitation.MethodsWe undertook a secondary analysis of a survey of UK parkrunners, comparing responses of those reporting no health conditions (n=53 967) with those with one or more CVD-related conditions (n=404). Thematic analysis was used to analyse 53 open-ended text comments from the latter.ResultsFour hundred and four respondents (0.7% of the total) reported CVD-related conditions with the largest proportions among those walking the event (24% of male participants and 5% of female participants). For those doing <3 days per week of physical activity at registration, 47% increased activity to ≥3 days per week. Among those with CVD-related conditions, participation in parkrun led to perceived improvements in fitness (81% of participants), physical health (80% or participants) and happiness (74% of participants). Two thirds reported improvements to their ability to manage their condition(s) and half to their lifestyle choices. Analysis of 53 open-text comments revealed that those with CVD-related conditions used parkrun to monitor their condition and were motivated by encouragement from the parkrun community. Enjoyment and fun were important for engagement, although some individuals were dispirited by poor performance due to their conditions.ConclusionsIndividuals with CVD-related conditions used parkrun to self-manage their rehabilitation; this applied to those attending parkrun following disease onset as well as those engaged with parkrun prior to their condition. Parkrun, or events with similar characteristics, could support self-managed cardiac rehabilitation.