bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots
Authors: Liu Li , Heidecker Michel , Depuydt Thomas , Manosalva Perez Nicolas , Crespi Martin , Blein Thomas , Vandepoele Klaas
Published: June 2023

Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of 8 annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis (Arabidopsis thaliana). For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation (ChIP) data were used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 15,686 interactions. We found that properties characterizing lincRNA expression, conservation, and regulation differ between plants and animals. Experimental validation confirmed the role of 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs, regulated by these TFs, showing strong root cell type-specific expression or chromatin accessibility, which are linked with genome-wide association studies genetic associations related to root system development and growth. The multilevel genome-wide characterization covering chromatin state information, promoter conservation, and chromatin immunoprecipitation-based TF binding, for all detectable lincRNAs across 769 expression samples, permits rapidly defining the biological context and relevance of Arabidopsis lincRNAs through regulatory networks.
The functions of a 5′ tRNA-Ala-derived fragment in gene expression
Authors: Li Yuanyuan , Gao Junping , Wang Ying , Cai Jun , Wu Dousheng , Wang Long , Pu Wenxuan , Yu Feng , Zhu Sirui
Published: June 2023

Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5′ tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.
Evaporation-driven internal hydraulic redistribution alleviates root drought stress: Mechanisms and modeling
Authors: Liu Yang , Nadezhdina Nadezhda , Hu Wei , Clothier Brent , Duan Jie , Li Ximeng , Xi Benye
Published: June 2023

Many tree species have developed extensive root systems that allow them to survive in arid environments by obtaining water from a large soil volume. These root systems can transport and redistribute soil water during drought by hydraulic redistribution (HR). A recent study revealed the phenomenon of evaporation-driven hydraulic redistribution (EDHR), which is driven by evaporative demand (transpiration). In this study, we confirmed the occurrence of EDHR in Chinese white poplar (Populus tomentosa) through root sap flow measurements. We utilized microcomputed tomography technology to reconstruct the xylem network of woody lateral roots and proposed conceptual models to verify EDHR from a physical perspective. Our results indicated that EDHR is driven by the internal water potential gradient within the plant xylem network, which requires 3 conditions: high evaporative demand, soil water potential gradient, and special xylem structure of the root junction. The simulations demonstrated that during periods of extreme drought, EDHR could replenish water to dry roots and improve root water potential up to 38.9% to 41.6%. This highlights the crucial eco-physiological importance of EDHR in drought tolerance. Our proposed models provide insights into the complex structure of root junctions and their impact on water movement, thus enhancing our understanding of the relationship between xylem structure and plant hydraulics.
Discordance between patient- and physician-reported disease activity in adult idiopathic inflammatory myopathy
Authors: Keret Shiri , Saygin Didem , Moghadam-Kia Siamak , Ren Dianxu , Oddis Chester V , Aggarwal Rohit
Published: June 2023

Objectives

Patient-reported global disease activity (patient-global) is a myositis core set measure. Understanding the drivers of patient-global is important in patient assessment, and disagreements between physician and patient perception of disease activity may negatively impact shared decision making. We examined the determinants of patient-global and discordance between patient-global and physician-reported global disease activity (physician-global) in idiopathic inflammatory myopathies (IIMs).

Methods

Adults with IIM were enrolled in a prospective observational cross-sectional study. The following myositis outcome measures were collected: patient-global, physician-global, extramuscular and muscle disease activity, manual muscle testing, HAQ, creatine kinase, fatigue, pain, Patient-Reported Outcomes Measurement Information System physical function, 36-item Short Form, sit to stand, timed up and go, 6-minute walk and Actigraph steps/min/day count. A linear regression model was used to determine the contribution of each measure to patient-global. Discordance was defined as ≥3 points difference between patient-global and physician-global.

Results

Fifty patients [60% females; mean age 51.6 years (s.d. 14.9)] with probable/definite IIM (EULAR/ACR classification criteria for IIM) were enrolled. Physical function and fatigue measures contributed to patient-global the most, followed by measures of pain, physical activity, quality of life and muscle disease, while physician-global was primarily driven by muscle disease activity. Patient-global was discordant with physician-global in 30% of the patients, of which patient-global was higher than physician-global in 66%. Pain, fatigue and physical activity contributed more to patient-global than physician-global.

Conclusion

Fatigue, pain and physical activity are important driving factors of the differences observed in the patient vs physician assessment of myositis disease activity. Understanding the gap between patient and physician perspectives may help provide better patient-centred care.
Studying the health benefits of improved housing in rural Tanzania: challenges and progress
Authors: Mshamu Salum , Halifa Salma , Meta Judith , Mmbando Arnold , Lindsay Steven W , Okumu Fredros , Wood Hannah Sloan , Wood Otis Sloan , Bøjstrup Thomas Chevalier , Day Nicholas P J , Knudsen Jakob , Deen Jacqueline , Pell Christopher , von Seidlein Lorenz
Published: June 2023

Millions of affordable healthy homes are needed for the rapidly expanding population of sub-Saharan Africa. This enormous challenge is an opportunity to address pervasive health issues linked to housing, where diseases that most impact children—malaria, diarrhoea and respiratory tract infections—are often acquired. A pilot project in northern Tanzania demonstrated the potential of novel house designs to reduce infectious disease transmission in homes. To conduct a randomized controlled trial of one novel-design house, the research team moved to the southeast of the country. This article describes the challenges experienced during the construction and initial evaluation of the novel house.
Care delivery options for infusion therapy services
Authors: Woods Janet
Published: June 2023

Patients have various options to consider when determining the optimal location for receiving outpatient infusion therapy and specialty treatments. Understanding the benefits and challenges of each site of care will enable nurses to help patients make informed decisions.
Group A Streptococcal infections on the rise
Authors: Schweon Steven J.
Published: June 2023

Increasing cases of invasive group A Streptococcal (GAS) disease have been reported in Europe and the US, particularly after the relaxation of lockdowns and mitigation strategies related to the COVID-19 pandemic. This article provides an overview of GAS infection, with updates on testing, treatment, and patient education.
The Associations Between Workplace Noise, Ototoxic Chemicals, and Tinnitus
Authors: Lewkowski Kate , Heyworth Jane S. , Williams Warwick , Goulios Helen , McCausland Kahlia , Gray Corie , Fritschi Lin
Published: June 2023

Objective:

To investigate the occupational risk factors associated with tinnitus in the Australian working population.

Design:

The research was conducted using data collected from the Australian Workplace Exposure Survey-Hearing, a national cross-sectional study of 4970 workers conducted in 2016 to 2017. Workers were asked if they experienced tinnitus and if they answered affirmatively, they were asked about the frequency and length of the presentations. Based on their answers, each worker was categorized as having no tinnitus or any tinnitus, with an additional group of workers with any tinnitus subcategorized as having constant tinnitus. Exposure assessment was conducted using an automated expert assessment method. Exposures included daily noise (LAeq,8h), hand-arm vibration (A(8)), impulse noise, smoking status, styrene, trichloroethylene, toluene, n-hexane, p-xylene, ethylbenzene, lead, and carbon monoxide. Univariate and multivariate logistic regression models were used to examine the associations between workplace exposures and tinnitus.

Results:

Workers with an estimated noise exposure above the workplace limit (LAeq,8h > 85 dBA) had 1.73 (95% confidence interval [CI]: 1.42 to 2.11) increased odds of any tinnitus and 2.15 (95% CI: 1.60 to 2.89) odds of constant tinnitus. The odds of workers having any tinnitus increased with increasing noise exposure levels in a dose–response relationship that strengthened when considering only those with constant tinnitus. In the fully adjusted model, statistically significant associations were seen for lead exposure with both any and constant tinnitus, toluene exposure with constant tinnitus, and carbon monoxide exposure with any tinnitus.

Conclusions:

These results suggest that, in addition to workplace noise, occupational exposures to lead, toluene, and carbon monoxide are associated with tinnitus.
EXPANSILE GAS KINETICS FOR PNEUMATIC RETINOPEXY
Authors: Teh Boon Lin , Toh Steven , Williamson Tom H. , Obara Boguslaw , Guillemaut Jean-Yves , Steel David H.
Published: June 2023

Purpose:

To study the behavior of expansile intravitreal gases and air used in treating rhegmatogenous retinal detachment.

Methods:

A validated mathematical model of gas expansion and absorption in human eyes was used to simulate the effect of varying volumes of pure air, SF6, C2F6, and C3F8 injected into the vitreous cavity. Variation in axial length was accounted for by using three different vitreous cavity volumes to represent hypermetropic, emmetropic, and myopic eyes.

Results:

The time course of varying volumes of pure air and fluorinated gases injected into the vitreous cavity was tabulated, with calculated parameters including volume of gas, percentage gas fills, and corresponding retinal contact angles at different time points.

Conclusion:

We produced a comprehensive compilation of expansive gas kinetics aiming to facilitate surgeon selection of the most suitable choice of gas and volume to use, tailored to an individual patient's clinical need.
Bacteriophage Therapy of Multidrug-resistant Achromobacter in an 11-Year-old Boy With Cystic Fibrosis Assessed by Metagenome Analysis
Authors: Bradley John S. , Hajama Hamza , Akong Kathryn , Jordan Mary , Stout Dayna , Rowe Ryan S. , Conrad Douglas J. , Hingtgen Sara , Segall Anca M.
Published: June 2023

Background:

Cystic fibrosis (CF) is a genetic disease associated with lung disease characterized by chronic pulmonary infection, increasingly caused by multiple drug-resistant pathogens after repeated antibiotic exposure, limiting antibiotic treatment options. Bacteriophages can provide a pathogen-specific bactericidal treatment used with antibiotics to improve microbiologic and clinical outcomes in CF.

Methods:

Achromobacter species isolates from sputum of a chronically infected person with CF, were assessed for susceptibility to bacteriophages: 2 highly active, purified bacteriophages were administered intravenously every 8 hours, in conjunction with a 14-day piperacillin/tazobactam course for CF exacerbation. Sputum and blood were collected for metagenome analysis during treatment, with sputum analysis at 1-month follow-up. Assessments of clinical status, pulmonary status and laboratory evaluation for safety were conducted.

Results:

Bacteriophage administration was well-tolerated, with no associated clinical or laboratory adverse events. Metagenome analysis documented an 86% decrease in the relative proportion of Achromobacter DNA sequence reads in sputum and a 92% decrease in blood, compared with other bacterial DNA reads, comparing pretreatment and posttreatment samples. Bacteriophage DNA reads were detected in sputum after intravenous administration during treatment, and at 1-month follow-up. Reversal of antibiotic resistance to multiple antibiotics occurred in some isolates during treatment. Stabilization of lung function was documented at 1-month follow-up.

Conclusions:

Bacteriophage/antibiotic treatment decreased the host pulmonary bacterial burden for Achromobacter assessed by metagenome analysis of sputum and blood, with ongoing bacteriophage replication documented in sputum at 1-month follow-up. Prospective controlled studies are needed to define the dose, route of administration and duration of bacteriophage therapy for both acute and chronic infection in CF.
Determining specified intraocular lens powers when silicone oil is to be used in the vitreous chamber
Authors: Atchison David A. , Cooke David L.
Published: June 2023

Purpose:

To apply a theoretical approach to determining how specified intraocular lens (IOL) powers should change when vitreous oil substitution is combined with IOL implantation.

Setting:

University laboratory, private Ophthalmological practice.

Design:

Theoretical raytracing.

Methods:

Raytracing was done backwards from the retina with equi-convex 20 diopters (D) and 25 D IOLs, of refractive index 1.5332, to the object side of the anterior IOL surface. The 1.336 vitreous index was replaced with a high index 1.405 silicone oil. Raytracing was repeated with increase in specified power, that power as if 1.336 index was still surrounding the IOL, so that the object reduced vergence on the anterior side of the lens matched that of the original IOL power. This was done for a range of lens shapes from plano-convex (front surface flat), through equi-convex, to plano-convex (back surface flat), and for a range of axial lengths. The true power, the power with 1.336 index on the object side and silicone oil on the image side, was also determined.

Results:

Replacing vitreous by silicone oil increases the necessary specified IOL power. This increase varies from approximately 14% for flat back surfaces, to 40% for equi-convex lenses, to 80% for flat front surface IOLs. True powers increase by about 15% across the range of IOL shapes. In terms of percentages, effects of changing the original IOL power and the axial length are small.

Conclusions:

When silicone oil is to remain in an eye after cataract surgery, biconvex IOLs require much higher specified powers than convex-plano IOLs.
Relationship between chronotype and pain threshold in a sample of young healthy adults
Authors: Zerbini Giulia , Göller Peter Justus , Lembke Katharina , Kunz Miriam , Reicherts Philipp
Published: June 2023

Introduction:

Chronotype indicates the biological preference for timing of activity and sleep. Being a late chronotype (ie, having a tendency for late sleep times) is associated with several mental and physical health problems. Previous studies found that late chronotypes are also more susceptible to chronic pain, but the relationship between chronotype and pain sensitivity remains unclear.

Objectives:

The aim of this study was to investigate the relationship between chronotype and heat pain threshold (as an indicator of pain sensitivity) in a sample of young healthy adults.

Methods:

We analyzed data from 316 young healthy adults participating in 4 different studies run at the Medical Faculty of the University of Augsburg. In all studies, chronotype and other sleep variables (eg, sleep duration) were assessed using the micro Munich ChronoType Questionnaire. Heat pain threshold was assessed with the method of adjustment.

Results:

Chronotype was not significantly associated with the heat pain threshold. Entering the other sleep variables in separate regression models did also not significantly explain variance in heat pain threshold.

Conclusion:

Our null findings are in contrast with previous notions that late chronotypes might be more sensitive to pain and more susceptible to chronic pain. Given the scarcity of the literature on this topic, more studies are needed to clarify the relationship between chronotype and pain sensitivity in different age populations, while also considering distinct pain modalities or other types of pain tests.
Genetic drift vs natural selection affecting the evolution of spectral and functional traits of two key macrophytes: Phragmites australis and Nuphar lutea
Authors: Castellani Maria Beatrice , Dalla Vecchia Alice , Bolpagni Rossano , Natale Roberto , Piaser Erika , Lastrucci Lorenzo , Coppi Andrea , Villa Paolo
Published: June 2023

Both genetic and phenotypic intraspecific diversity play a crucial role in the ecological and evolutionary dynamics of organisms. Several studies have compared phenotypic divergence (Pst) and differentiation of neutral loci (Fst) to infer the relative roles of genetic drift and natural selection in population differentiation (Pst - Fst comparison). For the first time, we assessed and compared the genetic variation and differentiation at the leaf trait level in two key macrophytes, Phragmites australis and Nuphar lutea. To this aim, we quantified and described the genetic structure and phenotypic diversity of both species in five lake systems in north-central Italy. We then investigated the relative roles of genetic drift and natural selection on leaf trait differentiation (Pst - Fst), assuming that Fst reflects divergence caused only by genetic drift while Pst also incorporates the effects of selective dynamics on the phenotype. In terms of genetic structure, the results for P. australis were in line with those observed for other Italian and European conspecific populations. Conversely, N. lutea showed a more complex genetic structure than expected at the site level, likely due to the combined effect of genetic isolation and its mixed mating system. Both species exhibited high variability in leaf functional traits within and among sites, highlighting a high degree of phenotypic plasticity. Pst - Fst comparisons showed a general tendency towards directional selection in P. australis and a more complex pattern in N. lutea. Indeed, the drivers of phenotypic differentiation in N. lutea showed a variable mix of stabilizing and directional selection or neutral divergence at most sites. The prevalence of vegetative over generative reproduction leads P. australis populations to be dominated by a few clones that are well adapted to local conditions, including phenotypes that respond plastically to the environment. In contrast, in N. lutea the interaction of a mixed mating system and geographical isolation among distant sites tends to reduce the effect of outbreeding depression and provides the genetic basis for adaptive capacity. The first joint analysis of the genetic structure of these two key macrophytes allowed a better understanding of the relative roles of genetic drift and natural selection in the diversification of phenotypic traits within habitats dominated by P. australis and N. lutea.
Geographic distribution of terpenoid chemotypes inTanacetum vulgaremediates tansy aphid occurrence and abundance
Authors: Rahimova Humay , Neuhaus-Harr Annika , Clancy Mary V. , Guo Yuan , Junker Robert R. , Ojeda-Prieto Lina , Petrén Hampus , Senft Matthias , Zytynska Sharon E. , Weisser Wolfgang W. , Heinen Robin , Schnitzler Jörg-Peter
Published: June 2023

Aim

Intraspecific variations of specialized metabolites in plants, such as terpenoids, are used to determine chemotypes. Tansy (Tanacetum vulgareL.) exhibits diverse terpenoid profiles, that affect insect communities. However, it is not fully known whether patterns of their chemical composition and associated insects vary on a large scale. Here, we investigated the geographic distribution of mono- and sesquiterpenoid chemotypes in tansy leaves and the effects of these chemotypes on colonization by insect communities across Germany.

Methods

We sampled tansy leaves from 26 sites along a north-south and west-east transect in Germany. Leaves from ten plants with and five plants without aphids was collected from each site. Hexane-extracted metabolites from leaf tissues were analysed by gas chromatography-mass spectrometry (GC-MS). Plant morphological traits, aphid occurrence and abundance, and occurrence of ants were recorded. The effect of plant chemotype, plant morphological parameters, and site parameters such as temperature and precipitation on insect occurrences were analysed.

Results

Plants clustered into four monoterpenoid and four sesquiterpenoid chemotype classes. Monoterpene classes differed in their latitudinal distribution, whereas sesquiterpenes were more evenly distributed across the transect. Aphid and ant occurrence were influenced by monoterpenoids and specific traits. Plants of monoterpenoid class 1 were colonized byMetopeurum fuscovirideand ants significantly more often than expected by chance compared to plants from monoterpenoid class 4. Aphid abundance was negatively affected by host plant height, and increasing average annual temperature positively influenced the occurrence of ants.

Conclusion

We found significant geographic differences in the chemodiversity of tansy and show that monoterpenoids affect aphid and ant occurrence, while host plant height can influence aphid abundance. We show that geographic variation in plant chemistry and morphology influences insect communities’ assemblage on tansy plants.
InGene: Finding influential genes from embeddings of nonlinear dimension reduction techniques
Authors: Goswami Chitrita , Bhattacharya Namrata , Sengupta Debarka
Published: June 2023

We introduceInGene, the first of its kind, fast and scalable non-linear, unsupervised method for analyzing single-cell RNA sequencing data (scRNA-seq). While non-linear dimensionality reduction techniques such as t-SNE and UMAP are effective at visualizing cellular sub-populations in low-dimensional space, they do not identify the specific genes that influence the transformation.InGeneaddresses this issue by assigning an importance score to each expressed gene based on its contribution to the construction of the low-dimensional map.InGenecan provide insight into the cellular heterogeneity of scRNA-seq data and accurately identify genes associated with cell-type populations or diseases, as demonstrated in our analysis of scRNA-seq datasets.
N-6-methyladenosine (m6A) Promotes the Nuclear Retention of mRNAs with Intact 5′ Splice Site Motifs
Authors: Lee Eliza S. , Smith Harrison. W. , Wang Yifan E. , Ihn Sean S. J. , Scalize de Olivera Leticia , Kejiou Nevraj S. , Liang Yijing L. , Nabeel-Shah Syed , Jomphe Robert Y. , Pu Shuye , Greenblatt Jack F. , Palazzo Alexander F.
Published: June 2023

In humans, misprocessed mRNAs containing intact 5′ Splice Site (5′SS) motifs are nuclear retained and targeted for decay by ZFC3H1, a component of the Poly(A) Exosome Targeting complex, and U1-70K, a component of the U1 snRNP. InS. pombe, the ZFC3H1 homolog, Red1, binds to the YTH-domain containing protein Mmi1 to target certain RNA transcripts to nuclear foci for nuclear retention and decay. Here we show that YTHDC1 and YTHDC2, two YTH domain-containing proteins that bind toN-6-methyladenosine (m6A) modified RNAs, interact with ZFC3H1 and U1-70K, and are required for the nuclear retention of mRNAs with intact 5′SS motifs. Disruption of m6A deposition inhibits both the nuclear retention of these transcripts and their accumulation in YTHDC1-enriched foci that are adjacent to nuclear speckles. Endogenous RNAs with intact 5′SS motifs, such as intronic polyadenylated transcripts, tend to be m6A-modified at low levels. Thus, m6A modification acts in a conserved quality control mechanism that targets misprocessed mRNAs for nuclear retention and decay.
Isoxanthohumol improves obesity and glucose metabolism via inhibiting intestinal lipid absorption with a bloom ofAkkermansia muciniphilain mice
Authors: Watanabe Yoshiyuki , Fujisaka Shiho , Morinaga Yoshitomo , Watanabe Shiro , Nawaz Allah , Hatta Hideki , Kado Tomonobu , Nishimura Ayumi , Bilal Muhammad , Aslam Muhammad Rahil , Honda Keiko , Nakagawa Yoshimi , Softic Samir , Hirabayashi Kenichi , Nakagawa Takashi , Nagai Yoshinori , Tobe Kazuyuki
Published: June 2023

Aims

Dysbiosis is an important factor that leads to metabolic disorders by disrupting energy balance and insulin sensitivity. A decrease inAkkermansia muciniphilais a phenotype of obesity-induced dysbiosis. Although interventions to increaseA. muciniphilaare expected to improve glucose metabolism, the underlying mechanism has not been fully understood.

Methods

Isoxanthohumol (IX), a prenylated flavonoid found in beer hops was administered to high fat diet-fed mice. We analyzed glucose metabolism, gene expression profiles and histology of liver, epididymal adipose tissue and colon. Lipase activity, fecal lipid profiles and plasma metabolomic analysis were assessed. Fecal 16s rRNA sequencing was obtained and selected bacterial species were used for in vitro studies. Fecal microbiota transplantation and monocolonization were conducted to antibiotic-treated or germ-free (GF) mice.

Results

The administration of IX lowered weight gain, decreased steatohepatitis and improved glucose metabolism. Mechanistically, IX inhibited pancreatic lipase activity and lipid absorption by decreasing the expression of the fatty acid transporter CD36 in the small intestine, which was confirmed by increased lipid excretion in feces. IX administration improved the gut barrier function and reduced metabolic endotoxemia. In contrast, the effects of IX were nullified by antibiotics. As revealed using 16S rRNA sequencing, the microbial community structure changed with a significant increase in the abundance ofA. muciniphilain the IX-treated group. An anaerobic chamber study showed that IX selectively promoted the growth ofA. muciniphilawhile exhibiting antimicrobial activity against someBacteroidesandClostridiumspecies. To further explore the direct effect ofA. muciniphilaon lipid and glucose metabolism, we monocolonized eitherA. muciniphilaorBacteroides thetaiotaomicronto GF mice.A. muciniphilamonocolonization decreased CD36 expression in the jejunum and improved glucose metabolism, with decreased levels of multiple classes of fatty acids determined using plasma metabolomic analysis.

Conclusion

Our study confirmed a direct role ofA. muciniphilain energy metabolism, which was induced by microbial actions of IX. These highlight new treatment strategies for preventing metabolic syndrome by boosting the gut microbiota with food components.
A multi-tiered mechanical mechanism shapes the early neural plate
Authors: Inman Angus , Lutton Judith E. , Spiritosanto Elisabeth , Tada Masazumi , Bretschneider Till , Haas Pierre A. , Smutny Michael
Published: June 2023

The formation of complex tissues during embryonic development requires an intricate spatiotemporal coordination of local mechanical processes regulating global tissue morphogenesis. Here, we uncover a novel mechanism that mechanically regulates the shape of the anterior neural plate (ANP), a vital forebrain precursor, during zebrafish gastrulation. Combiningin vivoandin silicoapproaches we reveal that the ANP is shaped by global tissue flows regulated by distinct force generating processes. We show that mesendoderm migration and E-cadherin-dependent differential tissue interactions control distinct flow regimes in the neuroectoderm. Initial opposing flows lead to progressive tissue folding and neuroectoderm internalisation which in turn provide forces driving ANP tissue reshaping. We find that convergent extension is dispensable for internalisation but required for ANP tissue extension. Our results highlight how spatiotemporal regulation and coupling of different mechanical processes between tissues in the embryo controls the first folding event in the developing brain.
Entrepreneurial decisions: viewing the affordable loss heuristic from an economic well-being perspective
Authors: Reddy Colin David
Published: June 2023

Purpose

This article conceptualises how the economic well-being of an entrepreneurial household affects its members' mental accounting process to establish its affordable loss for a plunge decision.

Design/methodology/approach

The article used research literature to analyze the resources available for entrepreneurial endeavours against a household's ability to maintain acceptable minimum material living standards, juxtaposing income and wealth against competing consumption and investment opportunities.

Findings

Mentally accounting for whether household resources can meet minimum material living standards is central to entrepreneurs' ability to raise affordable loss and decide to invest in a new venture. The article proposes that entrepreneurial households establish affordable loss by availing their money exceeding that required to maintain acceptable minimum material living standards. In low-income households, the author assumes that members are not employed and can thus avail their time (versus money) towards affordable loss.

Originality/value

Economic well-being introduces mental accounts of income and wealth and a hedonic reference outcome in the material living standards of households required to meet basic needs. The article introduces the tension entrepreneurial households face between using their income and wealth towards investing in a new business and maintaining their material living standards. It introduces the idea that a loss can be “affordable” according to an entrepreneurial household's ability to remain above its acceptable minimum material living standard. This view prompts scholars to consider a household unit of analysis and avoid assuming an entrepreneur makes the plunge decision in isolation.
Augmenter of liver regeneration promotes drug resistance of acute lymphoblastic leukemia through the alteration of mitochondrial functions and the inhibition of the mitochondrial apoptosis pathway
Authors: Zhou Jingwen , Zhou Ying , Yuan Shiyi , Li Yifei , Xiao Wenrui , Zhang Ping , Lou Shifeng , Shen Yan
Published: June 2023

Background

Acute T lymphoblastic leukemia (T‐ALL) occurs in 25% of adults diagnosed with Acute lymphocytic leukemia (ALL), and drug resistance is still a clinical obstacle. Augmenter of liver regeneration (ALR) is important to ALL drug resistance and is involved in the regulation of mitochondrial function; we speculated that the high expression of ALR in T‐ALL promotes drug resistance through the alteration of mitochondrial function and the inhibition of the mitochondrial apoptosis pathway.

Method

We silenced and overexpressed ALR in the T‐ALL cell lines that were untreated or treated with dexamethasone (DXM) or methotrexate (MTX). Apoptosis, proliferation, reactive oxygen species and ATP productions, mitochondrial membrane potential, and mitochondrial respiratory chain complex expression in cells were examined. The data were collated to comprehensively evaluate the effects of ALR expression change on mitochondrial function and drug resistance in T‐ALL cells.

Results

ALR knockdown led to the inhibition of proliferation, an increase in apoptosis, and the promotion of the cells' sensitivity to drugs. It also showed mitochondrial dysfunction. ALR knockdown actived the mitochondrial apoptosis pathway. The treatment of ALR knockdown T‐ALL cells with MTX or DXM further altered the mitochondrial function of T‐ALL cells and actived the mitochondrial apoptosis pathway. Overexpression of ALR promoted cell proliferation and drug resistance, reduced apoptosis, protected mitochondrial function, and inhibited the mitochondrial apoptosis pathway.

Conclusion

T‐ALL resistance caused by ALR through the alteration of mitochondrial function is associated with the inhibition of the mitochondrial apoptosis pathway.
Study of surface damage in silicon by irradiation with focused rubidium ions using a cold-atom ion source
Authors: Xu S. , Li Y. , Verheijen M. A. , Kieft E. R. , Vredenbregt E. J. D.
Published: June 2023

Cold-atom ion sources have been developed and commercialized as alternative sources for focused ion beams (FIBs). So far, applications and related research have not been widely reported. In this paper, a prototype rubidium FIB is used to study the irradiation damage of 8.5 keV beam energy Rb+ ions on silicon to examine the suitability of rubidium for nanomachining applications. Transmission electron microscopy combined with energy dispersive x-ray spectroscopy is applied to silicon samples irradiated by different doses of rubidium ions. The experimental results show a duplex damage layer consisting of an outer layer of oxidation without Rb and an inner layer containing Rb mostly at the interface to the underlying Si substrate. The steady-state damage layer is measured to be 23.2(±0.3) nm thick with a rubidium staining level of 7(±1) atomic percentage.
Reflections on Improving Women’s Experiences of Mentorship in Canadian Coaching
Authors: Kramers Sara , Bean Corliss , Hummell Caroline , Allan Veronica , Johnson Andrea , Turnnidge Jennifer
Published: June 2023

Despite recent advancements for women in leadership roles, women remain underrepresented in sport coaching contexts. Mentorship has been advocated as a potential avenue for advancing and sustaining the careers of women coaches. In line with this, national sporting bodies have implemented mentorship programs to pair new and aspiring women coaches with senior leaders. While recent evaluations show promising results, research is needed to understand how these programs are conceptualized, implemented, and experienced by program participants. The purpose of this study was to qualitatively explore stakeholders’ experiences in two Canadian women in coaching mentorship programs. Perspectives were gathered from 21 Canadian sport stakeholders that included program mentees, mentors, and staff. Data were analyzed using a reflexive thematic approach. Findings demonstrate the need for purposefully recruiting both mentor and mentee coaches to sustain meaningful partnerships. Additionally, participants highlighted the need for sport organizations to situate women in coaching as a priority and engage in sponsorship and long-term planning for sustaining women’s advancements in coaching. This study explores women in coaching mentorship programs from multiple perspectives, which may inform future formalized mentorship opportunities for women coaches by addressing identified challenges and barriers.
Cheap gulp foraging of a giga-predator enables efficient exploitation of sparse prey
Authors: Videsen Simone K. A. , Simon Malene , Christiansen Fredrik , Friedlaender Ari , Goldbogen Jeremy , Malte Hans , Segre Paolo , Wang Tobias , Johnson Mark , Madsen Peter T.
Published: June 2023

The giant rorqual whales are believed to have a massive food turnover driven by a high-intake lunge feeding style aptly described as the world’s largest biomechanical action. This high-drag feeding behavior is thought to limit dive times and constrain rorquals to target only the densest prey patches, making them vulnerable to disturbance and habitat change. Using biologging tags to estimate energy expenditure as a function of feeding rates on 23 humpback whales, we show that lunge feeding is energetically cheap. Such inexpensive foraging means that rorquals are flexible in the quality of prey patches they exploit and therefore more resilient to environmental fluctuations and disturbance. As a consequence, the food turnover and hence the ecological role of these marine giants have likely been overestimated.
Cooperative assembly of a designer peptide and silk fibroin into hybrid nanofiber gels for neural regeneration after spinal cord injury
Authors: Feng Feng , Song Xiyong , Tan Zan , Tu Yujie , Xiao Longyou , Xie Pengfei , Ma Yahao , Sun Xiumin , Ma Junwu , Rong Limin , He Liumin
Published: June 2023

Local reconstruction of a permissive environment with biomaterials is a promising strategy to treat spinal cord injury (SCI). We reported a hybrid hydrogel fabricated from a small functional self-assembling peptide (F-SAP) and large silk fibroin (SF). The diffusion of SF micelles into F-SAP solution was driven by the dynamic synergy between osmotic pressure and F-SAP/SF electrostatic interactions, resulting in the rearrangement of SF micelles and the formation of rod-like filaments with axes nearly perpendicular to F-SAP nanofibers. Spectroscopy analysis, including circular dichroism, Raman and fluorescence, indicated conformation changes of SF from random coil to β sheet, which contributed to enhanced mechanical properties of the resultant hybrid hydrogel. Furthermore, the F-SAP/SF hybrid hydrogel coupled with controlled release of NT-3 provided a permissive environment for neural regeneration by providing nanofibrous substrates for regenerating axons, inflammatory modulation and remyelination, consequently resulting in improved locomotion and electrophysiological properties. This hydrogel could be used as a long-term stent in vivo for the treatment of SCI.
Predictive Population Dynamics of Escherichia coli O157:H7 and Salmonella enterica on Plants: a Mechanistic Mathematical Model Based on Weather Parameters and Bacterial State
Authors: Brandl Maria T. , Ivanek Renata , Allende Ana , Munther Daniel S.
Published: June 2023

Fruits and vegetables are important sources of foodborne disease. Novel approaches to improve the microbial safety of produce are greatly lacking.
Comprehensive essentiality analysis of the
Mycobacterium kansasii
genome by saturation transposon mutagenesis and deep sequencing
Authors: Levendosky Keith , Janisch Niklas , Quadri Luis E. N.
Published: June 2023

Mycobacterium kansasii
(
Mk
) is an opportunistic pathogen that is frequently isolated from urban water systems, posing a health risk to susceptible individuals. Despite its ability to cause tuberculosis-like pulmonary disease, very few studies have probed the genetics of this opportunistic pathogen. Here, we report a comprehensive essentiality analysis of the
Mk
genome. Deep sequencing of a high-density library of
Mk Himar1
transposon mutants revealed that 86.8% of the chromosomal thymine–adenine (TA) dinucleotide target sites were permissive to insertion, leaving 13.2% TA sites unoccupied. Our analysis identified 394 of the 5,350 annotated open reading frames (ORFs) as essential. The majority of these essential ORFs (84.8%) share essential mutual orthologs with
Mycobacterium tuberculosis
(
Mtb
). A comparative genomics analysis identified 139
Mk
essential ORFs that share essential orthologs in four other species of mycobacteria. Thirteen
Mk
essential ORFs share orthologs in all four species that were identified as being not essential, while only two
Mk
essential ORFs are absent in all species compared. We used the essentiality data and a comparative genomics analysis reported here to highlight differences in essentiality between candidate
Mtb
drug targets and the corresponding
Mk
orthologs. Our findings suggest that the
Mk
genome encodes redundant or additional pathways that may confound validation of potential
Mtb
drugs and drug target candidates against the opportunistic pathogen. Additionally, we identified 57 intergenic regions containing four or more consecutive unoccupied TA sites. A disproportionally large number of these regions were located upstream of
pe
/
ppe
genes. Finally, we present an essentiality and orthology analysis of the
Mk
pRAW-like plasmid, pMK1248.

IMPORTANCE

Mk
is one of the most common nontuberculous mycobacterial pathogens associated with tuberculosis-like pulmonary disease. Drug resistance emergence is a threat to the control of
Mk
infections, which already requires long-term, multidrug courses. A comprehensive understanding of
Mk
biology is critical to facilitate the development of new and more efficacious therapeutics against
Mk
. We combined transposon-based mutagenesis with analysis of insertion site identification data to uncover genes and other genomic regions required for
Mk
growth. We also compared the gene essentiality data set of
Mk
to those available for several other mycobacteria. This analysis highlighted key similarities and differences in the biology of
Mk
compared to these other species. Altogether, the genome-wide essentiality information generated and the results of the cross-species comparative genomics analysis represent valuable resources to assist the process of identifying and prioritizing potential
Mk
drug target candidates and to guide future studies on
Mk
biology.
Potential Role of Lysine Acetylation and Autophagy in Brown Film Formation and Postripening of Lentinula edodes Mycelium
Authors: Chu Ting , Shang Junjun , Jian Huahua , Song Chunyan , Yang Ruiheng , Bao Dapeng , Tan Qi , Tang Lihua
Published: June 2023

Mycelial BF formation and postripening of
L. edodes
affects the quality and quantity of its edible fruiting bodies. In this study, we explored the role of protein KAC in this biological process, with the aim of optimizing the cultivation and yield of
L. edodes
.
Short-Term Pretreatment with Melatonin Increases the Resistance of Barley Plants to the Subsequent Action of Cadmium
Authors: Danilova E. D. , Zlobin I. E. , Efimova M. V.
Published: June 2023

The effect of short-term and long-term root treatment with melatonin on growth parameters, photochemical activity of PSII, content of basic photosynthetic pigments, lipid peroxidation, and accumulation of inorganic ions in barley plants under the action of cadmium chloride was studied. It was shown for the first time that the protective effect of phytomelatonin during short-term treatment is manifested in a decrease in the toxic effect of cadmium on the content of photosynthetic pigments and the accumulation of cadmium ions in the shoots and roots of barley plants. The protective effect of melatonin is based on its ability to reduce the intensity of oxidative stress by maintaining the level of carotenoids and increasing the activity of antioxidant enzymes. The effectiveness of short-term use of melatonin in a number of indicators exceeds its protective effect from long-term exposure. The data obtained indicate the possibility of using melatonin as a substance that induces the state of plant priming upon subsequent exposure to cadmium.
Gastric duplication cyst of a bifid pancreas: cause of recurrent vomiting
Authors: Pina-Prata Rita , Rosa Filipa , Fontes Inês , Morão Sofia
Published: June 2023

An infant girl first presented with recurrent episodes of non-bilious vomiting, having had five hospitalisations over the following months because of dehydration. Laboratory data showed no inflammatory response, normal pancreatic amylase, but increased lipase levels (between 67 and 425 U/L). Several abdominal ultrasound studies suggested an intestinal duplication cyst on left hypochondrium and, later, a dilated and irregular pancreatic duct. CT showed a bifid tailed pancreas and a change in the cyst’s characteristics. A communication with the pancreatic duct was hypothesised, which was confirmed on MR cholangiopancreatography. On laparoscopic surgery, the cyst was confirmed to be at the end of the caudal side of the pancreatic bifid tail, having no communication with the stomach. Cystectomy with partial pancreatectomy was performed with pathological findings confirming a gastric duplication cyst originating from the pancreatic bifid tail. At latest follow-up, 4 months after surgery, she remains asymptomatic.
Challenges in diagnosis and therapeutic options for metastatic prostate cancer to the right ventricle
Authors: Sanchez-Nadales Alejandro , Khanna-Neicheril Radhika , Asher Craig R , Lopez David
Published: June 2023

Our patient presented with right-sided heart failure symptoms and found to have a large mass protruding into the heart’s right ventricle. Cardiac MRI delineated the morphological and tissue characteristics of the tumour. Although 18-fluorodeoxyglucose positron emission tomography (PET) did not reveal an intracardiac mass, the lesion was well demonstrated by Fluciclovine F18 PET/CT.
Risk factors for irinotecan-induced liver injury: a retrospective multicentre cross-sectional study in China
Authors: Han Jun , Liu Jianhua , Yu Zaoqin , Huang Rui , Zhao Li , Xu Yi , Chen Min , He Guangzhao , Song Qiuyan , Li Wei , Zhang Chengliang
Published: June 2023

Objectives

The hepatotoxicity of irinotecan has been widely implicated in the treatment of multiple solid tumours. However, there are few studies on the influencing factors of irinotecan-induced hepatotoxicity. Herein, we investigated the risk factors for irinotecan-induced liver injury among 421 patients receiving irinotecan-based regimens (IBRs).

Design

Retrospective multi-centre cross-sectional study.

Setting

This study surveyed four hospitals in China.

Participants

After excluding participants with missing variables, we retrospectively collected the demographic, clinical and therapeutic data of 421 patients who received IBRs in four hospitals between January 2020 and December 2021 and divided the patients into two groups: those without liver injury and those with liver injury.

Results

The 421 enrolled patients were grouped (liver injury group: n=92; control group: n=329) according to their hepatic biochemical monitoring parameters. In our study, the multivariate logistic regression results showed that three to four cycles of chemotherapy (OR (95% CI): 2.179 (1.272 to 3.733); p=0.005) and liver metastasis (OR (95% CI): 1.748 (1.079 to 2.833); p=0.023) were independent risk factors for irinotecan-induced liver injury. The Cox proportional hazards model demonstrated that alcohol consumption history (OR (95% CI): 2.032 (1.183 to 3.491); p=0.010) and a cumulative dose of irinotecan ≥1000 mg (OR (95% CI): 0.362 (0.165 to 0.792); p=0.011) were significantly correlated with the onset time of irinotecan-induced liver injury.

Conclusions

These findings suggest that patients with liver metastasis or who received three to four cycles of chemotherapy should undergo rigorous liver function monitoring to prevent or reduce the incidence of irinotecan-induced liver injury. Moreover, patients with a history of alcohol consumption should also be closely monitored.