bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of vegetation cover and its driving factors in the Qinling-Daba Mountains on regional scale for 1986-2019
Authors: Yonghui Yao , Baoguo Wang
Published: March 2023

The Qinling-Daba Mountains is the transitional zone of the north and south of China. The vegetation in this area, characterized by complexity, heterogeneity and transition, is particularly sensitive to global climate change and human activities. Based on the normalized vegetation index (NDVI) data of the growing season from 1986 to 2019, which was synthesized by Landsat series satellite data on Google Earth Engine, this paper uses the methods of spatial analysis and Geo-detectors to clarify dynamics of vegetation cover and its main driving factors in the Qinling-Daba Mountains. The results show that: (1) vegetation coverage in study area shows a U-shaped NDVI distribution pattern in latitude, anti-U-shaped patterns in longitude and with altitude ascending. (2) the dynamics of vegetation coverage can be divided into two periods according to the result of MK mutation test (the breakthrough increasing period around 2005) and the trend of NDVI change: the slow increasing period with an increasing rate of 0.25%/a from 1986 to 2004 (R20.74), and the rapid increasing period with an increasing rate of 0.30%/a from 2005 to 2019 (R20.92). (3) Soil type, landform, vegetation type, land use type and annual average temperature are the main driving factors of vegetation dynamics in the Qinling-Daba Mountains, while annual precipitation, population density and GDP are the secondary driving factors of vegetation dynamics. The land use type and land management policies in the Qinling-Daba Mountains have a strong impact on vegetation cover change, and the climate warming in recent decades plays more important role than precipitation on the vegetation dynamics. These results are of great significance to comprehensively understand the impact of global climate warming and human activities on the natural environment of the Qinling-Daba Mountains.
Horizontal transfer of probable chicken-pathogenicity chromosomal islands betweenStaphylococcus aureusandStaphylococcus agnetis
Authors: Rhoads Douglas D. , Pummil Jeff , Ekesi Nnamdi S. , Alrubaye Adnan A. K.
Published: March 2023

Staphylococcus agnetisis an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates ofS. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized twoS. agnetisosteomyelitis strains. TheS. agnetisgenome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes ofS. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates ofS. aureus.BLAST searches of the NCBI databases detect no similar MGEs outside ofS. aureusandS. agnetis.These MGEs encode no proteins related to those produced byStaphylococcus aureusPathogenicity Islands, which have been associated with the transition ofS. aureusfrom human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongstS. agnetisandS. aureus.Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.
Effect of egg production dynamics on the functional response of parasitoids
Authors: Aguirre María , Logarzo Guillermo , Triapitsyn Serguei , Diaz-Soltero Hilda , Hight Stephen , Bruzzone Octavio
Published: March 2023

Functional response describes the number of hosts attacked by a parasitoid in relation to host densities and plays an important role by connecting behavioral-level processes with community-level processes. Most functional response studies were carried out using simple experimental designs where the insects were confined to a plain and small arena with different host densities during a fixed period of time. With these designs, other factors that might affect the functional response of parasitoids were not analyzed, such as fecundity, age, and experience. We proposed a series of latent-variables Markovian models that comprised an integrated approach of functional response and egg production models to estimate the realized lifetime reproductive success of adult parasitoids. As a case study, we used the parasitoidsAnagyrus cachamaiandA. lapachosus(Hymenoptera: Encyrtidae), two candidate agents for neoclassical biocontrol of the Puerto Rican cactus pest mealybug,Hypogeococcussp. (Hemiptera: Pseudococcidae).Anagyrus cachamaiandA. lapachosuspresented a type III functional response. However, the two parasitoids behaved differently: forA. cachamai, the number of parasitized hosts decreased with female age and depended on the number of mature eggs that were available for oviposition, whereasA. lapachosushost parasitism increased with female age and was modulated by its daily egg load and previous experience. The tested species were assessed according to their physiology and prior experience. We estimated the number of mature eggs after emergence, egg production on the first day, egg production rate, proportion of eggs resorbed, egg resorption threshold, and egg storage capacity. The methodology presented may have large applicability in pest control, invasive species management, and conservation biology, as it has the potential to increase our understanding of the reproductive biology of a wide variety of species, ultimately leading to improved management strategies.
Beyond performance, competence, and recognition: Forging a science researcher identity in the context of research training
Authors: Pfeifer Mariel A. , Zajic C.J. , Isaacs Jared M. , Erickson Olivia A. , Dolan Erin L.
Published: March 2023

Background

Studying science identity development has been useful for understanding students’ continuation in science-related education and career paths. Yet, how science contexts shape students’ science identity development, especially as students engage in research at the undergraduate and graduate level, is still largely unexplored. Here we integrate science identity and professional identity theories to investigate how research training shapes science identity. We focus on a specialized form of science identity we call science researcher identity. We characterize how the features of an individual’s research experience, and their personal characteristics interact to influence whether and how they see themselves as a science researcher. We accomplished this in two phases of qualitative research. First, we surveyed 548 undergraduate researchers about how their research experience influenced their identity as a scientist. Then we interviewed 30 early career researchers, including undergraduate, postbaccalaureate, and doctoral students, about their views of themselves as researchers and how elements of their research training shaped their views.

Results

Early career researchers (ECRs) viewed themselves as either science students or science researchers. How ECRs recognized themselves depended on how they viewed the purpose of their daily work and the extent to which they perceived autonomy and intellectual responsibility in their research. Individual-level factors, including research and researcher conceptions, research skill perceptions, and career intentions, influenced whether ECRs identified as science students or science researchers. ECRs also recognized themselves more or less as researchers based on contextual factors like the nature of their work, social interactions, and their perceptions of the norms within their research group and institution. ECRs considered how individual and contextual factors affected their science researcher identity through a lens we call ‘sense-making.’ We further detail the processes ECRs use to make sense of their science identity and the factors that influence it.

Conclusions

We synthesized our findings to form a conceptual model of science researcher identity development, which hypothesizes relationships among constructs related to science identity and professional identity development. Our results advance theory related to science identity, offer avenues for future investigation, and inform efforts to promote science researcher identity development.
A dynamic foot model for predictive simulations of gait reveals causal relations between foot structure and whole body mechanics
Authors: D’Hondt Lars , De Groote Friedl , Afschrift Maarten
Published: March 2023

The unique structure of the human foot is seen as a crucial adaptation for bipedalism. Its arched shape makes it possible to stiffen the foot to withstand high loads when pushing off, without compromising the range of motion. Experimental studies demonstrated that manipulating foot stiffness had considerable effects on gait. In clinical practise, altered foot structure is associated with pathological gait. Yet our understanding of how foot structure influences gait mechanics is still poor. Here we used predictive simulations to explore causal relations between foot properties and whole-body gait. Our dynamic three-segment foot model with longitudinal arch improved gait predictions compared to one- and two-segment foot models and can explain measured ankle-foot kinematics and energetics. We identified three properties of the ankle-foot complex that are crucial for healthy walking: (1) compliant Achilles tendon, (2) stiff heel pad, (3) the ability to stiffen the foot. The latter requires sufficient arch height and contributions of plantar fascia, intrinsic and extrinsic foot muscles. Insufficient foot stiffness results in walking patterns with reduced push-off power. During terminal stance plantar fascia and intrinsic foot muscles transfer energy from the metatarsophalangeal to midtarsal joint, which further increases push-off power.
Memory Th1 cells modulate heterologous diseases through innate function
Authors: Rakebrandt Nikolas , Yassini Nima , Kolz Anna , Schorer Michelle , Lambert Katharina , Rauld Celine , Balazs Zsolt , Krauthammer Michael , Carballido José M. , Peters Anneli , Joller Nicole
Published: March 2023

Through immune memory, infections have a lasting effect on the host. While memory cells enable accelerated and enhanced responses upon re-challenge with the same pathogen, their impact on susceptibility to unrelated diseases is unclear. We identify a subset of memory T helper 1 (Th1) cells termed innate acting memory T (TIA) cells that originate from a viral infection and produce IFN-γ with innate kinetics upon heterologous challengein vivo. Activation of memory TIAcells is induced in response to IL-12 in combination with IL-18 or IL-33 but is TCR-independent. Rapid IFN-γ production by memory TIAcells is protective in subsequent heterologous challenge with the bacterial pathogenLegionella pneumophila. In contrast, antigen-independent re-activation of CD4+memory TIAcells accelerates disease onset in an autoimmune model of multiple sclerosis. Our findings demonstrate that memory Th1 cells can acquire additional TCR-independent functionality to mount rapid, innate-like responses that modulate susceptibility to heterologous challenges.
Early language dissociation in bilingual minds: Non-invasive magnetoencephalography evidence through a machine learning approach
Authors: Molinaro Nicola , Nara Sanjeev , Carreiras Manuel
Published: March 2023

Is language selection in balanced bilinguals decodable from neural activity? Previous research employing various neuroimaging methods has not yielded a conclusive answer to this issue. However, direct brain stimulation studies in bilinguals have detected different brain regions related to language production in separate languages. In the present MEG study, we addressed this question in a group of proficient Spanish-Basque bilinguals (N=45), who performed two tasks (picture naming and word reading). They were asked to name the line drawing or read the word out loud, either in Basque or Spanish, if the ink turned from black to green after one second (randomly, in 10% of trials). Sensor-level evoked activity was similar and could not be differentiated for the two languages in either task. Crucially however, decoding analyses classified the language used in both tasks, starting ∼100 ms after stimulus onset. Searchlight analyses revealed that activity detected in the right occipital-temporal sensors contributed the most to language decoding in the picture naming task, while the left occipital-temporal sensors contributed the most to decoding in word reading. The cross-task decoding analysis highlighted robust generalization effects from the picture naming to the word reading task in a later time interval. The present findings bridge the gap between non-invasive and invasive experimental evidence on bilingual lexical processing and provide novel evidence about the role of the two hemispheres in activating each language for picture naming and word reading.
A haplotype resolved chromosome-scale assembly of North American wild appleMalus fuscaand comparative genomics of the fire blightMfu10locus. Genome of the Pacific CrabappleMalus fusca
Authors: Mansfeld Ben N. , Yocca Alan , Ou Shujun , Harkess Alex , Burchard Erik , Gutierrez Benjamin , Nocker Steve van , Gottschalk Christopher
Published: March 2023

The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus×domestica). With a range extending from Alaska to Northern California,M. fuscais extremely hardy and disease resistant. The species represents an untapped genetic resource for development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization ofM. fuscahas been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation forM. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome ofM. fusca,identifying thousands of large variants. We further showed high sequence co-linearity with other domesticated and wildMalusspecies. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference-quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA-informed introgression breeding.
The intricate triangular interaction between protective microbe, pathogen, and host genetics determines fitness of the metaorganism
Authors: Griem-Krey Hanne , Petersen Carola , Hamerich Inga K. , Schulenburg Hinrich
Published: March 2023

The microbiota shapes host biology in numerous ways. One example is protection against pathogens, which is likely critical for host fitness in consideration of the ubiquity of pathogens. The host itself can affect abundance of microbiota or pathogens, which has usually been characterised in separate studies. To date, however, it is unclear how the host influences the interaction with both simultaneously and how this triangular interaction determines fitness of the host-microbe assemblage, the so-called metaorganism. To address this current knowledge gap, we focused on a triangular model interaction, consisting of the nematodeCaenorhabditis elegans, its immune-protective symbiontPseudomonas luridaMYb11, and its pathogenBacillus thuringiensisBt679. We combined the two microbes withC. elegansmutants with altered immunity and/or microbial colonisation, and found that (i) under pathogen stress, immunocompetence has a larger influence on metaorganism fitness than colonisation with the protective microbe, (ii) in almost all cases, MYb11 still improves fitness, and (iii) disruption of p38 MAPK signalling, which contributes centrally to immunity against Bt679, completely reverses the protective effect of MYb11, which further reduces nematode survival and fitness upon infection with Bt679. Our study highlights the complex interplay between host genetics, protective microbe, and pathogen in shaping metaorganism biology.
Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results
Authors: Baron Cantin , Cherkaoui Sarah , Therrien-Laperriere Sandra , Ilboudo Yann , Poujol Raphaël , Mehanna Pamela , Garrett Melanie E. , Telen Marilyn J. , Ashley-Koch Allison E. , Bartolucci Pablo , Rioux John D. , Lettre Guillaume , Des Rosiers Christine , Ruiz Matthieu , Hussin Julie G.
Published: March 2023

Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights into our understanding of the genetic control of metabolite levels. However, the biological interpretation of these associations remains challenging due to a lack of existing tools to annotate mGWAS gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we computed the shortest reactional distance (SRD) based on the curated knowledge of the KEGG database to explore its utility in enhancing the biological interpretation of results from three independent mGWAS, including a case study on sickle cell disease patients. Results show that, in reported mGWAS pairs, there is an excess of small SRD values and that SRD values and p-values significantly correlate, even beyond the standard conservative thresholds. The added-value of SRD annotation is shown for identification of potential false negative hits, exemplified by the finding of gene-metabolite associations with SRD ≤1 that did not reach standard genome-wide significance cut-off. The wider use of this statistic as an mGWAS annotation would prevent the exclusion of biologically relevant associations and can also identify errors or gaps in current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs that can be used to integrate statistical evidence to biological networks.
Are increasing honey bee colony losses attributed toVarroa destructorin New Zealand driven by miticide resistance?
Authors: McGruddy Rose A. , Bulgarella Mariana , Felden Antoine , Baty James W. , Haywood John , Stahlmann-Brown Philip , Lester Philip J.
Published: March 2023

The most devastating pest to honey bees (Apis mellifera) worldwide is the parasitic miteVarroa destructor. The development of miticide-resistant mite populations has been a major driver of colony loss in many countries. We investigated the threat Varroa poses to honey bee populations in New Zealand and tested the effectiveness of the two most popular chemical treatments used by beekeepers. Colony losses reported by New Zealand beekeepers have risen over five consecutive years from 2017 to 2021, as have the proportion of losses attributed to Varroa, with this parasite found to be the main driver of colony loss in 2021. Varroa resistance to miticide treatments flumethrin and amitraz was tested. The concentration of flumethrin required to kill 50% of the mites (LC50) was 156 μg/g, 13 times greater than the adjusted LC50value of 12 μg/g observed in a trial also conducted in New Zealand in 2003, thus indicating evidence of developing mite resistance to flumethrin in New Zealand. Molecular analyses searching for mutations in the Varroa genome known to be associated with flumethrin resistance found no evidence of such mutations, suggesting that any extant resistance to flumethrin has evolved independently in New Zealand. No evidence of resistance to amitraz was found, as the LC50value of 12 μg/g was lower than what was observed in the 2003 trial (110 μg/g). Further development of integrated pest management, such as gene-silencing RNA interference (RNAi) and selective breeding of Varroa-resistant bees, is needed to effectively manage a parasite that threatens global agriculture.
An experimental framework to assess biomolecular condensates in bacteria
Authors: Hoang Y , Azaldegui Christopher A. , Ghalmi Maria , Biteen Julie S. , Vecchiarelli Anthony G.
Published: March 2023

High-resolution imaging of biomolecular condensates in living cells is essential for correlating their properties to those observed throughin vitroassays. However, such experiments are limited in bacteria due to resolution limitations. Here we present an experimental framework that probes the formation, reversibility, and dynamics of condensate-forming proteins inEscherichia colias a means to determine the nature of biomolecular condensates in bacteria. We demonstrate that condensates form after passing a threshold concentration, maintain a soluble fraction, dissolve upon shifts in temperature and concentration, and exhibit dynamics consistent with internal rearrangement and exchange between condensed and soluble fractions. We also discovered that an established marker for insoluble protein aggregates, IbpA, has different colocalization patterns with bacterial condensates and aggregates, demonstrating its applicability as a reporter to differentiate the twoin vivo. Overall, this framework provides a generalizable, accessible, and rigorous set of experiments to probe the nature of biomolecular condensates on the sub-micron scale in bacterial cells.
Building and validating 5-feature models to predict preeclampsia onset time from electronic health record data
Authors: Ballard Hailey K , Yang Xiaotong , Mahadevan Aditya , Lemas Dominick J , Garmire Lana X
Published: March 2023

Background

Preeclampsia is a potentially fatal complication during pregnancy, characterized by high blood pressure and presence of proteins in the urine. Due to its complexity, prediction of preeclampsia onset is often difficult and inaccurate.

Methods

This study aims to create quantitative models to predict the onset gestational age of preeclampsia using electronic health records. We retrospectively collected 1178 preeclamptic pregnancy records from the University of Michigan Health System(UM) as the discovery cohort, and 881 records from the University of Florida Health System(UF) as the validation cohort. We constructed two Cox-proportional hazards models with Lasso regularization: one baseline model utilizing maternal and pregnancy characteristics, and the other full model with additional lab results, vital signs, and medications in the first 20 weeks of pregnancy. We built the models using 80% of the UM data and subsequently tested them on the remaining 20% UM data and validated with UF data. We further stratified the patients into high and low risk groups for preeclampsia onset risk assessment.

Findings

The baseline model reached C-indices of 0·64 and 0·61 in the 20% UM testing data and the UF validation data, respectively, while the full model increased these C-indices to 0·69 and 0·61 respectively. Both the baseline and full models contain five selective features, among which number of fetuses in the pregnancy, hypertension and parity are shared between the two models with similar hazard ratios. In the baseline model, history of complicated type II diabetes and a mood/anxiety disorder during the first 20 weeks of pregnancy were important. In the full model, maximum diastolic blood pressure in early pregnancy was the predominant feature.

Interpretation

Electronic health record data provide useful information to predict gestational age of preeclampsia onset. Stratification of the cohorts using five-predictor Cox-PH models provide clinicians with convenient tools to assess the patients’ onset time of preeclampsia.

Funding

This study was supported by grants through the NIEHS, NICHD, NIDDK, and NCATS.
An explainable deep learning classifier of bovine mastitis based on whole genome sequence data - circumventing the p>>>n problem
Authors: Kotlarz K. , Mielczarek M. , Biecek P. , Wojdak-Maksymiec K. , Suchocki T. , Topolski P. , Jagusiak W. , Szyda J.
Published: March 2023

The most serious drawback underlying the biological annotation of Whole Genome Sequence data is the p>>n problem, meaning that the number of polymorphic variants (p) is much larger than the number of available phenotypic records (n). Therefore, the major aim of the study was to propose a way to circumvent the problem by combining a LASSO logistic regression model with Deep Learning (DL). That was illustrated by a practical biological problem of classification of cows into mastitis-susceptible or mastitis-resistant, based on genotypes of Single Nucleotide Polymorphisms (SNPs) identified in their WGS. Among several DL architectures proposed via optimisation of DL hyperparameters using the Optuna software, imposed on different SNP sub-sets defined by LASSO logistic regressions with different penalty values, the architecture with 204,642 SNPs was selected as the best one. This architecture was composed of 2 layers with respectively 7 and 46 units per layer as well as respective drop-out rates of 0.210 and 0.358. The classification of the test data set resulted in the AUC=0.750, accuracy=0.650, sensitivity=0.600, and specificity=0.700 was selected as the best model and thus proceeded to genomic and functional annotations. Significant SNPs were selected based on the SHapley Additive exPlanation values transformed to Z-scores to assess the underlying type I-error. These SNPs were annotated to genes. As a final result, a single GO term related to the biological process and thirteen GO terms related to the molecular function were significantly enriched in the gene set that corresponded to the significant SNPs.

Author Summary

Our objective is to distinguish between cows that are susceptible and resistant to bovine mastitis by analysing their genomic data. However, we face a significant challenge due to the large number of single nucleotide polymorphisms (SNPs) and limited sample size. To address this challenge, we utilize two methods: feature selection algorithms and deep learning. We experiment with various ways of implementing these techniques and evaluate their performance on a validation set. Our findings reveal that the optimal approach can accurately predict a cow’s susceptibility or resistance status around 65% of the time. Additionally, we employ a technique to identify the most crucial SNPs and their biological functions. Our results indicate that some of these SNPs are related to immune response or protein synthesis pathways, implying that they may affect the cow’s health and productivity.
Mind of a dauer: Comparative connectomics reveals developmental plasticity
Authors: Yim Hyunsoo , Choe Daniel T. , Bae J. Alexander , Kang Hae-Mook , Nguyen Ken C.Q. , Choi Myung-kyu , Ahn Soungyub , Bahn Sang-kyu , Yang Heeseung , Hall David H. , Kim Jinseop S. , Lee Junho
Published: March 2023

A fundamental question in neurodevelopmental biology is how flexibly the nervous system changes during development. To address this, we reconstructed the complete connectome of dauer, an alternative developmental stage of nematodes with distinct behavioral characteristics, by volumetric reconstruction and automated synapse detection using deep learning. With the basic architecture of the nervous system preserved, structural changes in neurons, large or small, were closely associated with connectivity changes, which in turn evoked dauer-specific behaviors such as nictation. Graph theoretical analyses revealed significant dauer-specific rewiring of sensory neuron connectivity and increased clustering within motor neurons in the dauer connectome. We suggest that the nervous system in the nematode, probably animals in general, has evolved to respond to harsh environments by reversibly developing a quantitatively and qualitatively differentiated connectome.
Hepatic conversion of acetyl-CoA to acetate plays crucial roles in energy stresses
Authors: Wang Jinyang , Wen Yaxin , Zhao Wentao , Zhang Yan , Lin Furong , Ouyang Cong , Wang HuiHui , Yao Lizheng , Ma Huanhuan , Zhuo Yue , Huang Huiying , Shi Xiulin , Feng Liubin , Lin Donghai , Jiang Bin , Li Qinxi
Published: March 2023

Accumulating evidences indicate that acetate is increased in energy stresses such as diabetes mellitus and prolonged starvation. However, it is largely unknown how and where acetate is produced and what is its biological significance. We observed overproduction of acetate in an amount comparable to ketone bodies in patients and mice with diabetes or starvation. Mechanistically, ACOT 12&8 are dramatically upregulated in liver to convert FFA-derived acetyl-CoA to acetate and CoA. This conversion not only provides large amount of acetate which fuels brain preferentially rather than muscle, but also recycles CoA which is required for sustained fatty acid oxidation and ketogenesis. Taken together, we suggest that acetate is an emerging novel “ketone body” and may be used as a parameter to evaluate the progression of energy stress in the future.
De novoserine biosynthesis is protective in mitochondrial disease
Authors: Jackson Christopher B , Marmyleva Anastasiia , Awadhpersad Ryan , Monteuuis Geoffray , Mito Takayuki , Zamboni Nicola , Tatsuta Takashi , Vincent Amy E. , Wang Liya , Langer Thomas , Carroll Christopher J , Suomalainen Anu
Published: March 2023

Importance of serine as a metabolic regulator is well known in tumors and raising attention also in degenerative diseases. Recent data indicate thatde novoserine biosynthesis is an integral component of metabolic response to mitochondrial disease, but the roles of the response have remained unknown. Here, we report that glucose-drivende novoserine biosynthesis maintains metabolic homeostasis in energetic stress. Pharmacological inhibition of the rate-limiting enzyme, phosphoglycerate dehydrogenase (PHGDH), aggravated mitochondrial muscle disease, suppressed oxidative phosphorylation and mitochondrial translation, altered whole-cell lipid profiles and enhanced mitochondrial integrated stress response (ISRmt),in vivo,in skeletal muscle and in cultured cells. Our evidence indicates thatde novoserine biosynthesis is essential to maintain mitochondrial respiration, redox balance, and cellular lipid homeostasis in skeletal muscle with mitochondrial dysfunction. Our evidence implies that interventions activatingde novoserine synthesis may protect against mitochondrial failure in the skeletal muscle.

Bullet points

Serine becomes an essential amino acid in mitochondrial translation defects

Blockingde novoserine biosynthesis promotes progression of mitochondrial disease

De novoserine biosynthesis maintains phospholipid homeostasis upon mitochondrial insult

Serine biosynthesis sustains redox-balance and mitochondrial translation in disease
Fluorescent Sensors for Imaging Interstitial Calcium
Authors: Valiente-Gabioud Ariel A. , Suñer Inés Garteizgogeascoa , Idziak Agata , Fabritius Arne , Angibaud Julie , Basquin Jérome , Nägerl U. Valentin , Singh Sumeet Pal , Griesbeck Oliver
Published: March 2023

Calcium in interstitial fluids is central to systemic physiology and a crucial ion pool for entry into cells through numerous plasma membrane channels. Its study has been limited by the lack of methods that allow monitoring in tight inter-cell spaces at high spatio-temporal resolution. We engineered high performance ultra-low affinity genetically encoded calcium biosensors named GreenT-ECs. GreenT-ECs combine large fluorescence changes upon calcium binding and binding affinities (KD) ranging from 0.8 mM to 2.9 mM, making them uniquely tuned to calcium concentrations in extracellular organismal fluids. We validated GreenT-ECs in rodent hippocampal neurons and transgenic zebrafishin vivo, where the sensors enabled monitoring homeostatic regulation of tissue interstitial calcium. GreenT-ECs may become useful for recording very large calcium transients and for imaging calcium homeostasis in inter-cell structures in live tissues and organisms.
An intracellular phosphorus-starvation signal activates the PhoB/PhoR two-component system inSalmonella enterica
Authors: Bruna Roberto E. , Kendra Christopher G. , Pontes Mauricio H.
Published: March 2023

Bacteria acquire P primarily as inorganic orthophosphate (Pi, PO43-). Once internalized, Pi is rapidly assimilated into biomass during the synthesis of ATP. Because Pi is essential, but excessive ATP is toxic, the acquisition of environmental Pi is tightly regulated. In the bacteriumSalmonella enterica(Salmonella), growth in Pi-limiting environments activates the membrane sensor histidine kinase PhoR, leading to the phosphorylation of its cognate transcriptional regulator PhoB and subsequent transcription of genes involved in adaptations to low Pi. Pi limitation is thought to promote PhoR kinase activity by altering the conformation of a membrane signaling complex comprised by PhoR, the multicomponent Pi transporter system PstSACB and the regulatory protein PhoU. However, the identity of the low Pi signal and how it controls PhoR activity remain unknown. Here we characterize the PhoB-dependent and independent transcriptional changes elicited bySalmonellain response to P starvation, and identify PhoB-independent genes that are required for the utilization of several organic-P sources. We use this knowledge to identify the cellular compartment where the PhoR signaling complex senses the Pi-limiting signal. We demonstrate that the PhoB and PhoR signal transduction proteins can be maintained in an inactive state even whenSalmonellais grown in media lacking Pi. Our results establish that PhoR activity is controlled by an intracellular signal resulting from P insufficiency.
Pubertal growth spurt is not universal: Polymorphism in growth at adolescence and its possible origin
Authors: Henneberg Maciej , Rosset Iwona , Żądzińska Elżbieta
Published: March 2023

Objectives

Numerous studies of child growth conducted in industrialised countries showed presence of the phenomenon of the adolescent growth spurt to the extent that its presence became a dogma applied to humans as a species. However, earliest observations of growth at adolescence and also observations of adolescent growth conducted in small traditional societies do not show pubertal spurts consistently. Longitudinal observations of growth of individuals in present-day societies show strong polymorphism of the age at which puberty starts and ends and the magnitude of growth acceleration during puberty. Some normally developing individuals may not experience the pubertal growth spurt.

Design, Seeting, Participants

Longitudinal height growth data of 110 girls aged 6-18 years from homogenous socio-economic situation – one medical high school (=nursing college) in one large Polish city of Lodz.

Results

18 (16%) girls did not show statistically significant acceleration of body height growth while they reached the same adult height as their spurting peers. Girls who experienced growth spurt had the age at peak height velocity of 11.2 years and peak height velocity of 69.3 mm, comparable to those found in many other studies. There was a negative correlation of adult height with variation of individual accelerations (r-0.24, p=0.01) – girls whose accelerations differed less from year to year achieved greater adult heights.

Conclusions

Findings of no pubertal spurts in some individuals have been made in other samples studied by other authors, though rarely reported. It can be argued that slow growth at adolescence was more favourable in conditions of limited access to nutrition and medical care while polymorphisms determining fast, uneven growth became more prevalent after industrialisation that, together with progress in health sciences, relaxed natural selection on patterns of growth. Individuals who do not experience pubertal growth spurts, but are otherwise healthy, should not be subject to clinical interventions.

Summary Box

What is already known on this topic

Pubertal growth spurt in body height is considered a typical feature of postnatal development. There is a large polymorphism of the age at which the spurt occurs and of its intensity.

Individuals who do not experience the spurt, but are otherwise healthy, may be subject to uncesessary clinical interventions.

What this study adds

Among 110 female students of an urban secondary nursing college studied longitudinally from 6 to 16 years, 16% did not experience acceleration of growth at puberty.

Similar findings were reported in the literature from some non-Westernised communities and from European 19thcentury populations.
Ferroptosis propagates to neighboring cells via cell-cell contacts
Authors: Roeck Bernhard F. , Vorndran Michael R. H. , Garcia-Saez Ana J.
Published: March 2023

Ferroptosis is an iron-dependent form of regulated cell death characterized by accumulation of peroxidized lipids and plasma membrane disruption, whose molecular mechanism of execution remains poorly understood. Here, we developed a new optogenetic system, Opto-GPX4Deg, for light-induced degradation of the lipid reducing protein GPX4, which allows controlled ferroptosis induction with high precision in time and space. By using Opto-GPX4Deg to study cell death dynamics within the cellular population, we found that lipid peroxidation, followed by ferroptotic death, spread to neighboring cells in a distance-dependent manner. Remarkably, ferroptosis propagation showed a strong dependency on cell confluence and preferentially affected adjacent cells. Our findings establish cell death propagation as a feature of ferroptosis and provide new understanding of the mechanism involved.
Flight data-driven intelligent prediction for fuselage vibration of helicopter
Authors: Deng Jinghui , Cheng Qiyou , Lu Xing
Published: March 2023

Purpose

Helicopter fuselage vibration prediction is important to keep a safety and comfortable flight process. The helicopter vibration mechanism model is difficult to meet of demand for accurate vibration prediction. Thus, the purpose of this paper is to develop an intelligent algorithm for accurate helicopter fuselage vibration analysis.

Design/methodology/approach

In this research, a novel weighted variational mode decomposition (VMD)- extreme gradient boosting (xgboost) helicopter fuselage vibration prediction model is proposed. The vibration data is decomposed and reconstructed by the signal clustering results. The vibration response is predicted by xgboost algorithm based on the reconstructed data. The information transfer order between the controllable flight data and flight attitude are analyzed.

Findings

The mean absolute percentage error (MAPE), root mean square error (RMSE) and mean absolute error (MAE) of the proposed weighted VMD-xgboost model are decreased by 6.8%, 31.5% and 32.8% compared with xgboost model. The established weighted VMD-xgboost model has the highest prediction accuracy with the lowest mean MAPE, RMSE and MAE of 4.54%, 0.0162, and 0.0131, respectively. The attitude of horizontal tail and cycle pitch are the key factors to vibration.

Originality/value

A novel weighted VMD-xgboost intelligent prediction methods is proposed. The prediction effect of xgboost model is highly improved by using the signal-weighted reconstruction technique. In addition, the data set used is collected from actual helicopter flight process.
Participative leadership effects on followers' radical creativity: role of creative process engagement and supervisor support for creativity
Authors: Nabi Md. Nurun , Akter Mst. Marium
Published: March 2023

Purpose

Drawn on self-determination (SDT) and social cognitive theory (SCT), this study examines how participative leadership (PL) influences the creative process engagement of followers (CPE) on fostering followers' radical creativity (FRC) through the supervisor support for creativity (SSC). It also demonstrates the CPE as a cognitive mediator between PL and FRC and SSC as a behavioral moderator between PL and CPE in Asia's manufacturing settings.

Design/methodology/approach

The research is quantitative, and data are gathered using a questionnaire and a survey of Bangladesh's 252 textile and apparel industry respondents. SPSS 26 and SMART PLS 3.8 evaluated the measurement and structural models and other descriptive analyses for hypothesis testing and result confirmation.

Findings

The findings revealed that PL positively impacted followers' creative process engagement. Again, the CPE of followers was used to mediate PL and FRC to promote and determine radical creativity. Moreover, the research also found a substantial correlation between PL and the creative process involved in supervisor support for creativity, which increases followers' radical creativity.

Research limitations/implications

This study contributes to the current literature by extending the scope of PL, CPE, FRC, SDT and SCT theory incorporating supervisor support.

Practical implications

The findings showed that textile and apparel industry managers, leaders and practitioners could use participatory leadership to engage in collaborative leader-follower creativity goal setting, creativity-relevant thinking and talent flourishing to encourage and motivate creativity through supervisor support to followers to foster radical creativity.

Originality/value

The results demonstrate the colloquial expression in behavioral mechanism (creative process engagement) nurtured with the cognitive tool, shedding insight into the link between PL and radical creativity in followers (SSC for promoting radical creativity).
An exploration of the causal structure underlying crowdfunding: theoretical findings and practical implications
Authors: Linzalone Roberto , Ammirato Salvatore , Felicetti Alberto Michele
Published: March 2023

Purpose

Crowdfunding (CF) is a digital-financial innovation that, bypassing credit crisis, bank system rigidities and constraints of the capital market, is allowing new ventures and established companies to get the needed funds to support innovations. After one decade of research, mainly focused on relations between variables and outcomes of the CF campaign, the literature shows methodological lacks about the study of its overall behavior. These reflect into a weak theoretical understanding and inconsistent managerial guidance, leading to a 27% success ratio of campaigns. To bridge this gap, this paper embraces a “complex system” perspective of the CF campaign, able to explore the system's behavior of a campaign over time, in light of its causal loop structure.

Design/methodology/approach

By adopting and following the document model building (DMB) methodology, a set of 26 variables and mutual causal relations modeled the system “Crowdfunding campaign” and a data set based on them and crafted to model the “Crowdfunding campaign” with a causal loop diagram. Finally, system archetypes have been used to link the causal loop structure with qualitative trends of CF's behavior (i.e. the raised capital over time).

Findings

The research brought to 26 variables making the system a “Crowdfunding campaign.” The variables influence each other, thus showing a set of feedback loops, whose structure determines the behavior of the CF campaign. The causal loop structure is traced back to three system archetypes, presiding the behavior in three stages of the campaign.

Originality/value

The value of this paper is both methodological and theoretical. First, the DMB methodology has been expanded and reinforced concerning previous applications; second, we carried out a causation analysis, unlike the common correlation analysis; further, we created a theoretical model of a “Crowdfunding Campaign” unlike the common empirical models built on CF platform's data.
Influence of wind and rain environment on operational safety of intercity train running on the viaduct
Authors: Zeng Guang-Zhi , Li Zhi-Wei , Huang Sha , Chen Zheng-Wei
Published: March 2023

Purpose

Based on the aerodynamic loads and dynamic performances of trains, this study aims to investigate the effect of crosswinds and raindrops on intercity trains operating on viaducts to ensure the safe operation of intercity railways in metropolitan areas.

Design/methodology/approach

An approach coupled with the Euler multiphase model as well as the standard k-ɛ turbulence model is used to investigate the coupled flow feature surrounding trains and viaducts, including airflow and raindrops, and the numerical results are validated with those of the wind tunnel test. Additionally, the train’s dynamic response and the operating safety region in different crosswind speeds and rainfall is investigated based on train’s aerodynamic loads and the train wheel–rail dynamics simulation.

Findings

The aerodynamic loads of trains at varying running speeds exhibit an increasing trend as the increase of wind speed and rainfall intensity. The motion of raindrop particles demonstrates a significant similarity with the airflow in wind and rain environments, as a result of the dominance of airflow and the supplementary impacts of droplets. As the train’s operating speed ranged between 120 and 200 km/h and within a rainfall range of 20–100 mm/h, the safe operating region of trains decreased by 0.56%–7.03%, compared with the no-rain condition (0 mm/h).

Originality/value

The impact of crosswind speeds and rainfall on the train’s aerodynamic safety is studied, including the flow feature of crosswind and different particle-sized raindrops around the train and viaduct, aerodynamic loads coefficients suffered by the intercity train as well as the operating safety region of intercity trains on the viaduct.