bluuebunny/crossref_metadata_2025_split huggingface dataset:
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic
Authors: Bonilla H , Quach TC , Tiwari A , Bonilla AE , Miglis M , Yang P , Eggert L , Sharifi H , Horomanski A , Subramanian A , Smirnoff L , Simpson N , Halawi H , Sum-Ping O , Kalinowski A , Patel Z , Shafer R , Geng L. 
Published: August 2022

SummaryBackgroundThe global prevalence of PASC is estimated to be present in 0·43 and based on the WHO estimation of 470 million worldwide COVID-19 infections, corresponds to around 200 million people experiencing long COVID symptoms. Despite this, its clinical features are not well defined.MethodsWe collected retrospective data from 140 patients with PASC in a post-COVID-19 clinic on demographics, risk factors, illness severity (graded as one-mild to five-severe), functional status, and 29 symptoms and principal component symptoms cluster analysis. The Institute of Medicine (IOM) 2015 criteria were used to determine the ME/CFS phenotype.FindingsThe median age was 47 years, 59·0% were female; 49·3% White, 17·2% Hispanic, 14·9% Asian, and 6·7% Black. Only 12·7% required hospitalization. Seventy-two (53·5%) patients had no known comorbid conditions. Forty-five (33·9%) were significantly debilitated. The median duration of symptoms was 285·5 days, and the number of symptoms was 12. The most common symptoms were fatigue (86·5%), post-exertional malaise (82·8%), brain fog (81·2%), unrefreshing sleep (76·7%), and lethargy (74·6%). Forty-three percent fit the criteria for ME/CFS.InterpretationsMost PASC patients evaluated at our clinic had no comorbid condition and were not hospitalized for acute COVID-19. One-third of patients experienced a severe decline in their functional status. About 43% had the ME/CFS subtype.FundingThe study did not received funding.
SARS-CoV-2 Omicron subvariants Spike recognition and neutralization elicited after the third dose of mRNA vaccine
Authors: Tauzin Alexandra , Nicolas Alexandre , Ding Shilei , Benlarbi Mehdi , Medjahed Halima , Chatterjee Debashree , Dionne Katrina , Gong Shang Yu , Gendron-Lepage Gabrielle , Bo Yuxia , Perreault Josée , Goyette Guillaume , Gokool Laurie , Arlotto Pascale , Morrisseau Chantal , Tremblay Cécile , Martel-Laferrière Valérie , De Serres Gaston , Levade Inès , Kaufmann Daniel E. , Côté Marceline , Bazin Renée , Finzi Andrés 
Published: August 2022

SUMMARYSeveral SARS-CoV-2 Omicron subvariants have recently emerged, becoming the dominant circulating strains in many countries. These variants contain a large number of mutations in their Spike glycoprotein, raising concerns about vaccine efficacy. In this study, we evaluate the ability of plasma from a cohort of individuals that received three doses of mRNA vaccine to recognize and neutralize these Omicron subvariant Spikes. We observed that BA.4/5 and BQ.1.1 Spikes are markedly less recognized and neutralized compared to the D614G and the other Omicron subvariant Spikes tested. Also, individuals who have been infected before or after vaccination present better humoral responses than SARS-CoV-2 naïve vaccinated individuals, thus indicating that hybrid immunity generates better humoral responses against these subvariants.
Prevalence and determinants of non-communicable diseases risk factors among reproductive-aged women of Bangladesh: Evidence from Bangladesh Demographic Health Survey 2017-2018
Authors: Chowdhury Saifur Rahman , Islam Md Nazrul , Sheekha Tasbeen Akhtar , Kader Shirmin Bintay , Hossain Ahmed 
Published: August 2022

AbstractIntroductionKnowing the risk factors like hypertension, overweight/obesity, and smoking status among women of reproductive age could allow the development of an effective strategy for reducing the burden of non-noncommunicable diseases (NCD). We sought to determine the prevalence and determinants of NCD risk factors among Bangladeshi women of reproductive age.MethodsThis study utilized the Bangladesh Demographic and Health Survey (BDHS) data from 2017-2018 and analyzed 5,624 women of reproductive age. This nationally representative cross-sectional survey utilized a stratified, two-stage sample of households. Mixed-effects Poisson regression models were fitted to find the adjusted prevalence ratio for smoking, overweight and obesity, and hypertension.ResultsThe average age of 5,624 participants was 31 years (SD=9.07). The prevalence of smoking, overweight/obesity, and hypertension was 9.55%, 31.57%, and 20.27%, respectively. More than one-third of the participants (34.55%) had one NCD risk factor, and 12.51% of participants had two NCD risk factors. Women between 40–49 years had more NCD risk factors than 18–29 years aged women (APR: 2.44; 95% CI: 2.22-2.68). Women with no education (APR: 1.15; 95% CI: 1.00-1.33), married (APR: 2.32; 95% CI: 1.78–3.04), and widowed/divorced (APR: 2.14; 95% CI: 1.59–2.89) were more prevalent in NCD risk factors. Individuals in the Barishal (APR: 1.44; 95% CI: 1.28–1.63) division were living with higher risk factors for NCD. Women who belonged to the richest (APR: 1.82; 95% CI: 1.60–2.07) wealth quintile were more likely to have the risk factors of NCD.ConclusionsThis study revealed that older women, currently married and widowed/divorced women, women from the wealthiest socio-economic group, and women with a lower level of education were more likely to have NCD risk factors. Furthermore, there was a significant relationship between the geographical division and NCD risk factors. To reduce the future prevalence of NCD, it is necessary to implement effective prevention and control programs that target women with a higher risk of having the disease.
Cooperative actin filament nucleation by the Arp2/3 complex and formins maintains the homeostatic cortical array in Arabidopsis epidermal cells
Authors: Xu Liyuan , Cao Lingyan , Li Jiejie , Staiger Christopher J. 
Published: August 2022

AbstractPrecise control over how and where actin filaments are created leads to the construction of unique cytoskeletal arrays within a common cytoplasm. Actin filament nucleators are key players in this activity and include the conserved Actin-Related Protein 2/3 (Arp2/3) complex, that creates dendritic networks of branched filaments, as well as a large family of formins that typically generate long, unbranched filaments and bundles. In some eukaryotic cells, these nucleators compete for a common pool of actin monomers and loss of one favors the activity of the other. To test whether this is a common mechanism, we combined the ability to image single filament dynamics in the homeostatic cortical actin array of living Arabidopsis (Arabidopsis thaliana) epidermal cells with genetic and/or small molecule inhibitor approaches to stably or acutely disrupt nucleator activity. We found that Arp2/3 mutants or acute CK-666 treatment markedly reduced the frequency of side-branched nucleation events as well as overall actin filament abundance. We also confirmed that plant formins contribute to side-branched filament nucleation in vivo. Surprisingly, simultaneous inhibition of both classes of nucleator increased overall actin filament abundance and enhanced the frequency ofde novonucleation events by an unknown mechanism. Collectively, our findings suggest that multiple actin nucleation mechanisms cooperate to generate and maintain the homeostatic cortical array of plant epidermal cells.
Mechanosensitive dynamics of lysosomes along microtubules regulate leader cell emergence in collective cell migration
Authors: Marwaha Rituraj , Rawal Simran , Khuntia Purnati , Banerjee Sanak , Manoj Diya , Jaiswal Manish , Das Tamal 
Published: August 2022

ABSTRACTCollective cell migration during embryonic development, wound healing, and cancer metastasis entails the emergence of leader cells at the migration front. These cells with conspicuous lamellipodial structures provide directional guidance to the collective. Despite their physiological relevance, the mechanisms underlying the emergence of leader cells remain elusive. Here we report that in diverse model systems for wound healing, including cultured epithelial monolayer,Drosophilaembryo, and mouse embryonic skin, leader cells display a peripheral accumulation of lysosomes. This accumulation appears essential for leader cell emergence, involves lysosomal movement along microtubules, and depends on the actomyosin contractility-generated cellular forces. Peripheral lysosomes associate with inactive Rac1 molecules to remove them from the leading periphery, which increases local Rac1-activity, triggering actin polymerization and promoting lamellipodium formation. Taken together, we demonstrate that beyond their catabolic role, lysosomes act as the intracellular platform that links mechanical and biochemical signals to control the emergence of leader cells.
Phages against non-capsulatedKlebsiella pneumoniae: broader host range, slower resistance
Authors: Lourenço Marta , Osbelt Lisa , Passet Virginie , Gravey François , Strowig Till , Rodrigues Carla , Brisse Sylvain 
Published: August 2022

AbstractBackgroundKlebsiella pneumoniae(Kp) is an ecologically generalist bacterium but also an opportunistic pathogen responsible for hospital-acquired infections and a major contributor to the global burden of antimicrobial resistance. In the last decades, few advances have been made in the use of virulent phages as alternative or complement to antibiotics to treat Kp infections. The efficiency of phages relies on their ability to recognize and attach to the bacterial surface structure, and in the case of Kp, capsule (K) is the main surface structure. However, Kp capsule is highly polymorphic and the majority of classically isolated phages are specific for unique K-types, limiting therapy prospects. In this study, we demonstrate the feasibility of an innovative strategy consisting in isolating phages that target capsule-deficient mutant Kp strains, and compare such phages with anti-capsulated cells phages phylogenetically and throughin vitroandin vivoexperiments.MethodsWe isolated 27 phages using 7 capsule-deficient Kp strains as hosts (anti-Kdphages), and 41 phages against 7 wild-type (wt) Kp strains (anti-K phages). We evaluated and compared phenotypically and genotypically their host range, resistance emergence and selected mutations andin-vivoactivity.ResultsIn vitro, anti-Kdphages showed a broader host-range, with most phages being able to infect non-capsulated mutants of multiple sublineages and O-antigen locus types. Besides, the emergence of bacterial subpopulations non-susceptible to anti-Kdphages was slower when compared to anti-K phages and with a different range of genomic differences. One anti-Kdphage (mtp5) was shown to infect non-capsulated Kp strains belonging to 10 of the 12 known O-antigen types. Moreover, this phage was able to replicate in the gut of mice colonised with the wt (capsulated) parent strain.ConclusionsThis work demonstrates the potential value of an anti-Klebsiellaphage isolation strategy that addresses the issue of narrow host-range of anti-K phages. Anti Kd-phages may be active in infection sites where capsule expression is intermittent or repressed, or in combination with anti-K phages, which often induce loss of capsule escape mutants.
Novel genetic modules encoding high-level antibiotic-free protein expression in probiotic lactobacilli
Authors: Dey Sourik , Blanch-Asensio Marc , Kuttae Sanjana Balaji , Sankaran Shrikrishnan 
Published: August 2022

ABSTRACTLactobacilli are ubiquitous in nature, often beneficially associated with animals as commensals and probiotics, and are extensively used in food fermentation. Due to this close-knit association, there is considerable interest to engineer them for healthcare applications in both humans and animals, for which high-performance and versatile genetic parts are greatly desired. For the first time, we describe two genetic modules inLactiplantibacillus plantarumthat achieve high-level gene expression using plasmids that can be retained without antibiotics, bacteriocins or genomic manipulations. These include (i) a promoter, PtlpA, from a phylogenetically distant bacterium,Salmonella typhimurium, that drives up to 5-fold higher level of gene expression compared to previously reported promoters and (ii) multiple toxin-antitoxin systems as a self-contained and easy-to-implement plasmid retention strategy that facilitates the engineering of tunable transient Genetically Modified Organisms. These modules and the fundamental factors underlying their functionality that are described in this work will greatly contribute to expanding the genetic programmability of lactobacilli for healthcare applications.
Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases
Authors: Urquhart Andrew S , Vogan Aaron A , Gardiner Donald M , Idnurm Alexander 
Published: August 2022

AbstractTransposable elements in eukaryotic organisms have historically been considered ‘selfish’, at best conferring indirect benefits to their host organisms. The Starships are a recently discovered feature in fungal genomes that are predicted to confer beneficial traits to their hosts and also have hallmarks of being transposable elements. Here, we provide experimental evidence that Starships are indeed autonomous transposons, using the model Paecilomyces variotii, and identify the HhpA ‘Captain’ tyrosine recombinase as essential for their mobilization into genomic sites with a specific target site consensus sequence. Furthermore, we identify multiple recent horizontal gene transfer of Starships, implying that they frequency jump between species. Fungal genomes have mechanisms to defend against mobile elements, which are frequently detrimental to the host. We discover that Starships are also vulnerable to repeat-induced point mutation defence, thereby having implications on the evolutionary stability of such elements.
A conserved motif suggests a common origin for a group of proteins involved in the cell division of Gram-positive bacteria
Authors: Martinez-Goikoetxea Mikel , Lupas Andrei N. 
Published: August 2022

AbstractDivIVA, GpsB, FilP, and Scy are all involved in bacterial cell division. They have been reported to interact with each other, and although they have been the subject of considerable research interest, not much is known about the molecular basis for their biological activity. Although they show great variability in taxonomic occurrence, phenotypic profile, and molecular properties, we find that they nevertheless share a conserved N-terminal sequence motif, which points to a common evolutionary origin. The motif always occurs N-terminally to a coiled-coil helix that mediates dimerization. We define the motif and coiled coil jointly as a new domain, which we name DivIVA-like. In a large-scale survey of this domain in the protein sequence database, we identify a new family of proteins potentially involved in cell division, whose members, unlike all other DivIVA-like proteins, have between 2 and 8 copies of the domain in tandem. AlphaFold models indicate that the domains in these proteins assemble within a single chain, therefore not mediating dimerization.
Phospholipid tail asymmetry allows cellular adaptation to anoxic environments
Authors: Panconi Luca , Lorenz Chris D , May Robin C , Owen Dylan M , Makarova Maria 
Published: August 2022

AbstractMembrane biophysical properties are critical to cell fitness and depend on unsaturated phospholipid acyl tails. These can only be produced in aerobic environments since eukaryotic desaturases require molecular oxygen. This raises the question of how cells maintain bilayer properties in anoxic environments. Here, we demonstrate the existence of an alternative pathway to regulate membrane fluidity that exploits phospholipid acyl-tail length asymmetry, replacing unsaturated species in the membrane lipidome. We show that the fission yeast, S. japonicus, which can grow in aerobic and anaerobic conditions, is capable of utilizing this strategy whereas its sister species, the well-known model organism S. pombe, cannot. The incorporation of asymmetric-tailed phospholipids might be a general adaptation to hypoxic environmental niches.One-Sentence SummaryIn anoxic environments, saturated asymmetric acyl-tailed phospholipids can replace unsaturated ones to maintain membrane physical properties.
Kinesin-1, -2 and -3 motors use family-specific mechanochemical strategies to effectively compete with dynein during bidirectional transport
Authors: Gicking Allison M. , Ma Tzu-Chen , Feng Qingzhou , Jiang Rui , Badieyan Somayesadat , Cianfrocco Michael A. , Hancock William O. 
Published: August 2022

AbstractBidirectional cargo transport in neurons requires competing activity of motors from the kinesin-1, -2 and -3 superfamilies against cytoplasmic dynein-1. Previous studies demonstrated that when kinesin-1 attached to dynein-dynactin-BicD2 (DDB) complex, the tethered motors move slowly with a slight plus-end bias, suggesting kinesin-1 overpowers DDB but DDB generates a substantial hindering load. Compared to kinesin-1, motors from the kinesin-2 and -3 families display a higher sensitivity to load in single-molecule assays and are thus predicted to be overpowered by dynein complexes in cargo transport. To test this prediction, we used a DNA scaffold to pair DDB with members of the kinesin-1, -2 and -3 families to recreate bidirectional transport in vitro, and tracked the motor pairs using two-channel TIRF microscopy. Unexpectedly, we find that when both kinesin and dynein are engaged and stepping on the microtubule, kinesin-1, -2, and -3 motors are able to effectively withstand hindering loads generated by DDB. Stochastic stepping simulations reveal that kinesin-2 and -3 motors compensate for their faster detachment rates under load with faster reattachment kinetics. The similar performance between the three kinesin transport families highlights how motor kinetics play critical roles in balancing forces between kinesin and dynein, and emphasizes the importance of motor regulation by cargo adaptors, regulatory proteins, and the microtubule track for tuning the speed and directionality of cargo transport in cells.
The sum and the parts: dynamics of multiple and individual metastases during adaptive therapy
Authors: Gallaher Jill , Strobl Maximilian , West Jeffrey , Zhang Jingsong , Gatenby Robert , Robertson-Tessi Mark , Anderson Alexander R. A. 
Published: August 2022

AbstractEvolutionary therapies, such as adaptive therapy, have shown promise in delaying treatment resistance in late-stage cancers. By alternating between drug applications and drug-free vacations, competition between sensitive and resistant cells can be exploited to maximize the time to progression. However, the optimal schedule of this dosing regimen depends on the properties of the tumor, which often are not directly measurable in clinical practice. In this work, we propose that the initial cycle of adaptive therapy can be used as a tool to probe the relevant tumor properties. We present a framework for estimating individual and collective components of a metastatic system through tumor response dynamics, which uses a system of off-lattice agent-based models to represent individual metastatic lesions within independent domains, all of which are subject to the same systemic therapy. We find that the first cycle of adaptive therapy delineates several features of the computational metastatic system: larger metastases have longer cycles; a higher proportion of drug resistant cells slows the cycles; and a faster cell turnover rate speeds up drug response time and slows the regrowth time. The number of metastases does not affect cycle times, as response dynamics are dominated by the largest tumors rather than the aggregate. In addition, the heterogeneity of the system is also a guide for therapeutic approaches: generally, systems with more between-tumor (intertumor) heterogeneity had better success with continuous therapy, while systems with more within-tumor (intratumor) heterogeneity responded better to adaptive therapy. Intertumor heterogeneity was found to correlate more with dynamics from patients with high and low Gleason scores while intratumor heterogeneity was correlated with dynamics from patients with intermediate Gleason scores.
Simulation calculation and experimental study of cathodic protection potential distribution in the tank farm
Authors: Kou Jie , Ren Zhe 
Published: August 2022

Purpose
The corrosion problem of the tank bottom plate is growing more and more obvious as the usage period of the tank increases. The purpose of this study is to explore the specific effects of various factors on the potential distribution of the tank bottom plate and propose reasonable cathodic protection measures for tanks through simulation and indoor tests.

Design/methodology/approach
In this paper, several aspects (such as anode conditions, soil resistivity and so on) impacting the potential distribution of the tank bottom plate are explored by means of indoor tests and MATLAB software simulations, and the related results are presented using Origin software plots.

Findings
The results show that the potential value of the tank bottom plate is positively shifted with the increase of anode well depth and distance and the decrease of output current, and the overall potential distribution uniformity is higher; the anodic well output current has the greatest influence on potential distribution; to set up regional cathodic protection in the multitank area, the anodic well should be arranged in the central position between multiple tanks. Regional cathodic protection potential distribution for multiple anodes is more uniform, but a reasonable number of anodes should be selected, usually 2–3 anodes.

Originality/value
This paper provides solid theoretical and technical support for the future establishment of cathodic protection systems in station yards, as well as the renewal and transformation of cathodic protection systems in old tanks, by investigating the influencing factors on the potential distribution of tank bottom plate and verifying them through indoor experiments.
Relationship of public farmland and timberland REITs with their private equity counterparts and selected asset classes
Authors: Baral Srijana , Mei Bin 
Published: August 2022

PurposeThe purpose of this study is to examine the return sensitivity of public farmland and timberland real estate investment trusts (REITs) to private-equity farmland, timberland and real estate, long-term corporate bonds and large- and small-cap stocks. The study also examines time-dependent contributions of selected asset classes to farmland and timberland REIT volatility.Design/methodology/approachThe authors use a multi-factor asset pricing model under a seemingly unrelated regression framework to evaluate farmland and timberland REIT returns, and a state-space model with the Kalman filter to evaluate the time-dependent contributors of farmland and timberland REIT volatility. The authors first perform orthogonalized regressions to obtain pure independent factors, and then decompose volatility into individual asset components.FindingsSignificant loadings on financial assets are found for both farmland and timberland REITs, suggesting that they are generally driven by some common state variables. Large-cap stocks are found to be the major contributor of farmland and timberland REIT volatility, despite some differing patterns over time.Originality/valueEmpirical analysis of farmland REIT is very scarce. The authors compare the risk-return characteristics of farmland and timberland REITs under a state-space framework with the Kalman filter. This study can improve the understanding of the roles of farmland and timberland REITs in a multi-asset portfolio.