bluuebunny/crossref_metadata_2025 huggingface dataset:
Variations in phase angle and handgrip strength in patients undergoing cardiac surgery: Prospective cohort study
Authors: Silva Taís K. , Perry Ingrid D. S. , Brauner Janete S. , Mancuso Aline C. B. , Souza Gabriela C. , Vieira Sílvia R. R.
Published: June 2023

Background

Bioimpedance phase angle (PA) is a measure of cell membrane integrity, whereas handgrip strength (HGS) is an evaluation of functional capacity. Although both are related to the prognosis of patients undergoing cardiac surgery, their changes over time are less known. This study followed variations in PA and HGS for 1 year in these patients, determining associations with clinical outcomes.

Methods

This prospective cohort study included 272 cardiac surgery patients. PA and HGS were measured at six predetermined times. The evaluated outcomes were surgery type; bleeding; time of surgery, cardiopulmonary bypass, aortic cross‐clamp, and mechanical ventilation; postoperative (PO) length of stay (LOS) in the intensive care unit (ICU) and hospital; and infections, hospital readmission, reoperation, and mortality.

Results

There were reductions in PA and HGS values after surgery, with total recovery beginning at 6 months for PA and 3 months for HGS. In the PA area under the curve (AUC), age, combined surgery, and sex (β = −9.66, P < 0.001; β = −252.85, P = 0.005; β = −216.56, P < 0.001, respectively) were predictors for PA‐AUC reduction. Stratified by sex, age (β = −93.54, P < 0.001) and PO LOS (β = −46.91, P = 0.003) were predictors for HGS‐AUC reduction in women, but only age was a predictor in men (β = −77.02, P = 0.010). PA and HGS had an effect in hospital LOS and ICU LOS.

Conclusion

Age, combined surgery, and female sex were predictors of reduced PA‐AUC, whereas reduced HGS‐AUC was predicted by age in both sexes and PO hospital LOS in women, which suggests that these factors could interfere in prognosis.
Understanding indigenous people's traditional Chinese medicinal plants harvesting preferences to guide sustainable management
Authors: Zhao Jingjing , Fan Linyu , Hu Sifan , Poha  , Jiayangji  , Wan Anita Kar Yan , Zeng Yan , Yang Yongchuan , Duan Beilu , Lee Tien Ming
Published: June 2023

Surging demand for medicinal plant products may lead to unsustainable harvesting practices, which could put pressure on wild populations. Yet little is known about indigenous harvesters' preferences on key traditional Chinese medicinal plant resources, and how these might affect sustainable use and management.

We conducted a discrete choice experiment with over 900 native Tibetan harvesters in the eastern Qinghai–Tibetan plateau in China, under a range of complex alternative livelihood, climate and environmental change, and land tenure and customs scenarios.

We used random parameter logit model with broad heterogeneity to estimate local Tibetan harvesters' preferences and their willingness to harvest, and latent class logit model to explore distinct within‐population groupings based on shared preferences, for designing possible interventions.

We uncovered three key findings with important management implications for medicinal plants. When given a choice, the local harvesters preferred not to harvest any herbs. However, if they opted to harvest, they preferred to harvest flowers and seeds, as compared to roots, and tended to use wooden tool (over the use of bare hands and iron tool).

Notably, the degree of compliance with village rules and customs, and ecological worldview interact with targeted plant parts and potential income from harvest to influence their harvesting preferences. Their choices were sensitive to scenario‐based changes to livelihood options.

Finally, our study revealed three distinct harvester groups with substantial heterogeneity. Specifically, two groups consisted of over 60% of the interviewed harvesters who appeared to have a strong preference for sustainable practices, while the remaining group lacks this tendency.

Overall, our results shed light on the importance of understanding the drivers of harvesting preferences and the heterogeneity of harvesting practices among indigenous people and their cultural and sustainability leanings, providing crucial insights for future sustainable use and management of wild and economically important medicinal plants in the grasslands of Qinghai–Tibetan Plateau and other regions.

Read the free Plain Language Summary for this article on the Journal blog.
Improved gross primary production estimation in rice fields through integrated multi‐scale methodologies
Authors: Lee Bora , Kwon Hyojung , Zhao Peng , Tenhunen John
Published: June 2023

Understanding productivity in agricultural ecosystems is important, as it plays a significant role in modifying regional carbon balances and capturing carbon in the form of agricultural yield. This study in particular combines information from flux determinations using the eddy covariance (EC) methodology, process‐based modeling of carbon gain, remotely (satellite) sensed vegetation indices (VIs), and field surveys to assess the gross primary production (GPP) of rice, which is a primary food crop worldwide. This study relates two major variables determining GPP. The first is leaf area index (LAI) and carboxylation capacity of the rice canopy (Vcuptake), and the second being MODIS remotely sensed vegetation indices (VIs). Success in applying such derived relationships has allowed GPP to be remotely determined over the seasonal course of rice development. The relationship to VIs of both LAI and Vcuptake was analyzed first by using the regression approaches commonly applied in remote sensing studies. However, the resultant GPP estimations derived from these generic models were not consistently accurate and led to a large proportion of underestimations. The new, alternative approach developed to estimate LAI and Vcuptake uses consistent development curves for rice (i.e., relies on consistent biological regulations of plant development). The modeled GPP based on this consistent development curve for both LAI and Vcuptake agreed with R2 from 0.76 to 0.92 (within the 95% confidence interval). The results of this study demonstrate that improved linkages between ground‐based survey data, eddy flux measurements, process‐based models, and remote sensing data can be constructed to estimate GPP in rice paddies. This study suggests further that the conceptual application of the consistent development curve, such as the combining of different scale measurements, has the potential to predict GPP better than the common practice of utilizing simple linear models, when seeking to estimate the critical parameters that influence carbon gain and agricultural yields.
Conventional specimen radiography in breast-conserving therapy: a useful tool for intraoperative margin assessment after neoadjuvant therapy?
Authors: Schäfgen Benedikt , Haller Annabelle , Sinn Hans-Peter , Feisst Manuel , Gomez Christina , Stieber Anne , Nees Juliane , Togawa Riku , Pfob André , Hennigs André , Hederer Johanna , Riedel Fabian , Fastner Sarah , Heil Jörg , Golatta Michael
Published: June 2023

Purpose

A previous study in our breast unit showed that the diagnostic accuracy of intraoperative specimen radiography and its potential to reduce second surgeries in a cohort of patients treated with neoadjuvant chemotherapy were low, which questions the routine use of Conventional specimen radiography (CSR) in this patient group. This is a follow-up study in a larger cohort to further evaluate these findings.

Methods

This retrospective study included 376 cases receiving breast-conserving surgery (BCS) after neoadjuvant chemotherapy (NACT) of primary breast cancer. CSR was performed to assess potential margin infiltration and recommend an intraoperative re-excision of any radiologically positive margin. The histological workup of the specimen served as gold standard for the evaluation of the accuracy of CSR and the potential reduction of second surgeries by CSR-guided re-excisions.

Results

362 patients with 2172 margins were assessed. The prevalence of positive margins was 102/2172 (4.7%). CSR had a sensitivity of 37.3%, a specificity of 85.6%, a positive predictive value (PPV) of 11.3%, and a negative predictive value (NPV) of 96.5%. The rate of secondary procedures was reduced from 75 to 37 with a number needed to treat (NNT) of CSR-guided intraoperative re-excisions of 10.

In the subgroup of patients with clinical complete response (cCR), the prevalence of positive margins was 38/1002 (3.8%), PPV was 6.5% and the NNT was 34.

Conclusion

This study confirms our previous finding that the rate of secondary surgeries cannot be significantly reduced by CSR-guided intraoperative re-excisions in cases with cCR after NACT. The routine use CSR after NACT is questionable, and alternative tools of intraoperative margin assessment should be evaluated.
Tailoring the performance of nanocellulose-based multilayer-barrier paperboard using biodegradable-thermoplastics, pigments, and plasticizers
Authors: Koppolu Rajesh , Lahti Johanna , Abitbol Tiffany , Aulin Christian , Kuusipalo Jurkka , Toivakka Martti
Published: June 2023

In this work a multilayer barrier paperboard was produced in a roll-to-roll process by slot-die coating of nanocellulose (microfibrillated cellulose or carboxymethylated cellulose nanofibrils) followed by extrusion coating of biodegradable thermoplastics (polylactic acid, polybutylene adipate terephthalate and polybutylene succinate). Hyperplaty kaolin pigments were blended in different ratios into nanocellulose to tailor the barrier properties of the multilayer structure and to study their influence on adhesion to the thermoplastic top layer. Influence of a plasticizer (glycerol) on flexibility and barrier performance of the multilayer structure was also examined. Water vapor permeance for the multilayer paperboard was below that of control single-layer thermoplastic materials, and oxygen permeance of the coated structure was similar or lower than that of pure nanocellulose films. Glycerol as a plasticizer further lowered the oxygen permeance and kaolin addition improved the adhesion at the nanocellulose/thermoplastic interface. The results provide insight into the role played by nanocelluloses, thermoplastics, pigments, and plasticizers on the barrier properties when these elements are processed together into multilayer structures, and paves the way for industrial production of sustainable packaging.
Predicting flow resistance in open-channel flows with submerged vegetation
Authors: Cui Hanwen , Felder Stefan , Kramer Matthias
Published: June 2023

In vegetated flows, hydrodynamic parameters, such as drag coefficient, frontal area and deflected canopy height, influence velocity distributions, mean velocity and flow resistance. Previous studies have focused on flow–structure interaction in sparse vegetation, dense vegetation or transitional canopies, respectively. To date, a unifying approach to estimate hydrodynamic properties of submerged vegetated flows across the full vegetation density spectrum is missing. Herein, published data sets across a wide range of vegetation conditions were re-analysed using a previously proposed four-layer velocity superposition model. For the investigated vegetation conditions, the velocity model was able to match measured velocity distributions and depth-averaged mean velocity. The contribution of each velocity layer to the mean velocity was analyzed, showing that the mixing layer is dominant in transitional canopies with shallow submergence, and that the log-law layer is dominant in denser canopies with deeper submergence. Based upon velocity distributions, an explicit equation for the Darcy–Weisbach friction factors was deduced that is able to predict flow resistance as function of relative submergence. While each velocity distribution could be well described with the four-layer model across the range of vegetation conditions, some data scatter in model parameters was observed. To improve predictive capabilities of the model, future research should focus on detailed velocity measurements with high spatial resolution.
On star-convex bodies with rotationally invariant sections
Authors: Zawalski Bartłomiej
Published: June 2023

We will prove that an origin-symmetric star-convex body K with sufficiently smooth boundary and such that every hyperplane section of K passing through the origin is a body of affine revolution, is itself a body of affine revolution. This will give a positive answer to the recent question asked by Bor, Hernández-Lamoneda, Jiménez de Santiago, and Montejano-Peimbert, though with slightly different prerequisites.
Concerning the photophysics of fluorophores towards tailored bioimaging compounds: a case study involving S100A9 inflammation markers
Authors: Steiner Simon T. , Maisuls Iván , Junker Anna , Fritz Günter , Faust Andreas , Strassert Cristian A.
Published: June 2023

A full understanding concerning the photophysical properties of a fluorescent label is crucial for a reliable and predictable performance in biolabelling applications. This holds true not only for the choice of a fluorophore in general, but also for the correct interpretation of data, considering the complexity of biological environments. In the frame of a case study involving inflammation imaging, we report the photophysical characterization of four fluorescent S100A9-targeting compounds in terms of UV–vis absorption and photoluminescence spectroscopy, fluorescence quantum yields (ΦF) and excited state lifetimes (τ) as well as the evaluation of the radiative and non-radiative rate constants (kr and knr, respectively). The probes were synthesized based on a 2-amino benzimidazole-based lead structure in combination with commercially available dyes, covering a broad color range from green (6-FAM) over orange (BODIPY-TMR) to red (BODIPY-TR) and near-infrared (Cy5.5) emission. The effect of conjugation with the targeting structure was addressed by comparison of the probes with their corresponding dye-azide precursors. Additionally, the 6-FAM and Cy5.5 probes were measured in the presence of murine S100A9 to determine whether protein binding influences their photophysical properties. An interesting rise in ΦF upon binding of 6-FAM-SST177 to murine S100A9 enabled the determination of its dissociation equilibrium constant, reaching up to KD = 324 nM. This result gives an outlook for potential applications of our compounds in S100A9 inflammation imaging and fluorescence assay developments. With respect to the other dyes, this study demonstrates how diverse microenvironmental factors can severely impair their performance while rendering them poor performers in biological media, showing that a preliminary photophysical screening is key to assess the suitability of a particular luminophore.
Deep learning-assisted radiomics facilitates multimodal prognostication for personalized treatment strategies in low-grade glioma
Authors: Rauch P. , Stefanits H. , Aichholzer M. , Serra C. , Vorhauer D. , Wagner H. , Böhm P. , Hartl S. , Manakov I. , Sonnberger M. , Buckwar E. , Ruiz-Navarro F. , Heil K. , Glöckel M. , Oberndorfer J. , Spiegl-Kreinecker S. , Aufschnaiter-Hiessböck K. , Weis S. , Leibetseder A. , Thomae W. , Hauser T. , Auer C. , Katletz S. , Gruber A. , Gmeiner M.
Published: June 2023

Determining the optimal course of treatment for low grade glioma (LGG) patients is challenging and frequently reliant on subjective judgment and limited scientific evidence. Our objective was to develop a comprehensive deep learning assisted radiomics model for assessing not only overall survival in LGG, but also the likelihood of future malignancy and glioma growth velocity. Thus, we retrospectively included 349 LGG patients to develop a prediction model using clinical, anatomical, and preoperative MRI data. Before performing radiomics analysis, a U2-model for glioma segmentation was utilized to prevent bias, yielding a mean whole tumor Dice score of 0.837. Overall survival and time to malignancy were estimated using Cox proportional hazard models. In a postoperative model, we derived a C-index of 0.82 (CI 0.79–0.86) for the training cohort over 10 years and 0.74 (Cl 0.64–0.84) for the test cohort. Preoperative models showed a C-index of 0.77 (Cl 0.73–0.82) for training and 0.67 (Cl 0.57–0.80) test sets. Our findings suggest that we can reliably predict the survival of a heterogeneous population of glioma patients in both preoperative and postoperative scenarios. Further, we demonstrate the utility of radiomics in predicting biological tumor activity, such as the time to malignancy and the LGG growth rate.
Comprehensive reliability evaluation of three types of connection of DC–DC converters: single‐phase, two‐phase, and parallel input‐series output
Authors: Mahmoudi Mohsen , Ajami Ali , Babaei Ebrahim
Published: June 2023

With the increasing use of power electronic converters, the reliability studies of these converters are essential. The most important factor in increasing the reliability of power converters is their structures. In this paper the reliability evaluation of a DC–DC converter with various connections including single‐phase, interleaved, and parallel‐input and series‐output (PISO) topologies is presented. In the first view, it seems that the interleave topology has high reliability, but considering the more presented detailed indexes, it is identified that the PISO structure has a higher reliability than the interleave structure. In this paper for better evaluation, the various topologies are considered which operate at full rated power and half power. To calculate the reliability of the converters the important parameters such as the thermal and electrical stresses of elements are considered. The Markov model is used to evaluate the reliability. In order to verify the presented studies and analysis, the DC–DC converters with single‐phase, interleaved, and PISO have been implemented. The experimental results show that the PISO topology has higher reliability.
Low‐ripple high‐efficiency AC‐DC rectifier with auxiliary compensator for hydrogen production
Authors: Zhang Li , Han Minxiao , Bao Weiqi , Dong Yijiang , Fan Yiwen , Liu Haijun
Published: June 2023

In hydrogen production, AC‐DC rectifiers must provide a high current and low voltage to the production load. This paper focuses on the efficient performance and elimination of the output ripple in these AC‐DC rectifiers. Unfortunately, efforts to reduce the current ripple often lead to lower efficiency, causing a contradiction. To address this issue, a low‐ripple high‐efficiency AC‐DC rectifier with an auxiliary compensator is proposed in this paper. The proposed rectifier can maximise efficiency while eliminating the current ripple, including the switching ripple and low‐frequency ripple. By incorporating a rectifier‐chopper and a buck circuit with a series‐connected capacitor, the auxiliary compensator, the solution provides an additional flow path for the current ripple at the rectifier output, successfully preventing the ripple from being output to the load. This paper offers a thorough exposition regarding the causative factors and sources of the switching and low‐frequency ripple. Furthermore, a detailed explication of the operating principle of the proposed rectifier system is provided. The losses and costs associated with auxiliary compensators are then analysed for persuasive purposes. Finally, simulation and experimental results verify the feasibility and superiority of the proposed rectifier.
Sensitivity Analysis on Odds Ratios
Authors: Leppälä Kalle
Published: June 2023

The classical Cornfield inequalities state that if a third confounding variable is fully responsible for an observed association between the exposure and the outcome variables, then the association between both the exposure and the confounder, and the confounder and the outcome, must be at least as strong as the association between the exposure and the outcome, as measured by the risk ratio. The work of Ding and VanderWeele on assumption-free sensitivity analysis sharpens this bound to a bivariate function of the 2 risk ratios involving the confounder. Analogous results are nonexistent for the odds ratio, even though the conversion from odds ratios to risk ratios can sometimes be problematic. We present a version of the classical Cornfield inequalities for the odds ratio. The proof is based on the mediant inequality, dating back to ancient Alexandria. We also develop several sharp bivariate bounds of the observed association, where the 2 variables are either risk ratios or odds ratios involving the confounder.
GDockScore: a graph-based protein–protein docking scoring function
Authors: McFee Matthew , Kim Philip M
Published: June 2023

Protein complexes play vital roles in a variety of biological processes, such as mediating biochemical reactions, the immune response and cell signalling, with 3D structure specifying function. Computational docking methods provide a means to determine the interface between two complexed polypeptide chains without using time-consuming experimental techniques. The docking process requires the optimal solution to be selected with a scoring function. Here, we propose a novel graph-based deep learning model that utilizes mathematical graph representations of proteins to learn a scoring function (GDockScore). GDockScore was pre-trained on docking outputs generated with the Protein Data Bank biounits and the RosettaDock protocol, and then fine-tuned on HADDOCK decoys generated on the ZDOCK Protein Docking Benchmark. GDockScore performs similarly to the Rosetta scoring function on docking decoys generated using the RosettaDock protocol. Furthermore, state-of-the-art is achieved on the CAPRI score set, a challenging dataset for developing docking scoring functions.

Availability and implementation

The model implementation is available at https://gitlab.com/mcfeemat/gdockscore.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis
Authors: Meyer Rhonda C , Weigelt-Fischer Kathleen , Tschiersch Henning , Topali Georgia , Altschmied Lothar , Heuermann Marc C , Knoch Dominic , Kuhlmann Markus , Zhao Yusheng , Altmann Thomas
Published: June 2023

Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
Influence of planets on debris discs in star clusters – I. The 50 au Jupiter
Authors: Wu Kai , Kouwenhoven M B N , Spurzem Rainer , Pang Xiaoying
Published: June 2023

Although debris discs may be common in exoplanet systems, only a few systems are known in which debris discs and planets coexist. Planets and the surrounding stellar population can have a significant impact on debris disc evolution. Here, we study the dynamical evolution of debris structures around stars embedded in star clusters, aiming to determine how the presence of a planet affects the evolution of such structures. We combine NBODY6++GPU and REBOUND to carry out N-body simulations of planetary systems in star clusters ($N=8\, 000$; Rh = 0.78 pc) for a period of 100 Myr, in which 100 solar-type stars are assigned 200 test particles. Simulations are carried out with and without a Jupiter-mass planet at 50 au. We find that the planet destabilizes test particles and speeds up their evolution. The planet expels most particles in nearby and resonant orbits. Remaining test particles tend to retain small inclinations when the planet is present, and fewer test particles obtain retrograde orbits. Most escaping test particles with speeds smaller than the star cluster’s escape speed originate from cold regions of the planetary system or from regions near the planet. We identify three regions within planetary systems in star clusters: (i) the private region of the planet, where few debris particles remain (40–60 au), (ii) the reach of the planet, in which particles are affected by the planet (0–400 au), and (iii) the territory of the planetary system, most particles outside which will eventually escape (0–700 au).
High Coverage Highly Accurate Long-Read Sequencing of a Mouse Neuronal Cell Line Using the PacBio Revio Sequencer
Authors: Manuel Juana G. , Heins Hillary B. , Crocker Sandra , Neidich Julie A. , Sadzewicz Lisa , Tallon Luke , Turner Tychele N.
Published: June 2023

Recently, Pacific Biosciences released a new highly accurate long-read sequencer called the Revio System that is projected to generate 30× HiFi whole-genome sequencing for the human genome within one sequencing SMRT Cell. Mouse and human genomes are similar in size. In this study, we sought to test this new sequencer by characterizing the genome and epigenome of the mouse neuronal cell line Neuro-2a. We generated long-read HiFi whole-genome sequencing on three Revio SMRT Cells, achieving a total coverage of 98×, with 30×, 32×, and 36× coverage respectively for each of the three Revio SMRT Cells. We performed several tests on these data including single-nucleotide variant and small insertion detection using GPU-accelerated DeepVariant, structural variant detection with pbsv, methylation detection with pb-CpG-tools, and generatingde novoassemblies with the HiCanu and hifiasm assemblers. Overall, we find consistency across SMRT Cells in coverage, detection of variation, methylation, andde novoassemblies for each of the three SMRT Cells.
Identification of tumor-specific MHC ligands through improved biochemical isolation and incorporation of machine learning
Authors: Mecklenbräuker Shima , Skoczylas Piotr , Biernat Paweł , Zaghla Badeel , Król-Józaga Bartłomiej , Jasiński Maciej , Pienkowski Victor Murcia , Sanecka-Duin Anna , Popp Oliver , Szatanek Rafał , Mertins Philipp , Kaczmarczyk Jan , Blum Agnieszka , Klatt Martin
Published: June 2023

Isolation of MHC ligands and subsequent analysis by mass spectrometry is considered the gold standard for defining targets for TCR-T immunotherapies. However, as many targets of high tumor-specificity are only presented at low abundance on the cell surface of tumor cells, the efficient isolation of these peptides is crucial for their successful detection. Here, we demonstrate how different isolation strategies, which consider hydrophobicity and post-translational modifications, can improve the detection of MHC ligands, including cysteinylated MHC ligands from cancer germline antigens or point-mutated neoepitopes. Furthermore, we developed a novel MHC class I ligand prediction algorithm (ARDisplay-I) that outperforms the current state-of-the-art and facilitates the assignment of peptides to the correct MHC allele. The model has other applications, such as the identification of additional MHC ligands not detected from mass spectrometry or determining whether the MHC ligands can be presented on the cell surface via MHC alleles not included in the study. The implementation of these strategies can augment the development of T cell receptor-based therapies (i.a. TIL1-derived T cells, genetically engineered T cells expressing tumor recognizing receptors or TCR-mimic antibodies) by facilitating the identification of novel immunotherapy targets and by enriching the resources available in the field of computational immunology.

Significance:

This study demonstrates how the isolation of different tumor-specific MHC ligands can be optimized when considering their hydrophobicity and post-translational modification status. Additionally, we developed a novel machine-learning model for the probability prediction of the MHC ligands’ presentation on the cell surface. The algorithm can assign these MHC ligands to their respective MHC alleles which is essential for the design of TCR-T immunotherapies.
Structural basis of CMKLR1 signaling induced by chemerin9
Authors: Zhang Xuan , Weiß Tina , Cheng Mary Hongying , Chen Siqi , Ambrosius Carla Katharina , Czerniak Anne Sophie , Li Kunpeng , Feng Mingye , Bahar Ivet , Beck-Sickinger Annette G. , Zhang Cheng
Published: June 2023

Chemokine-like receptor 1 (CMKLR1), also known as chemerin receptor 23 (ChemR23) or chemerin receptor 1, is a chemoattractant G protein-coupled receptor (GPCR) that responds to the adipokine chemerin and is highly expressed in innate immune cells, including macrophages and neutrophils. The signaling pathways of CMKLR1 can lead to both pro- and anti-inflammatory effects depending on the ligands and physiological contexts. To understand the molecular mechanisms of CMKLR1 signaling, we determined a high-resolution cryo-electron microscopy (cryo-EM) structure of the CMKLR1-Gisignaling complex with chemerin9, a nanopeptide agonist derived from chemerin, which induced complex phenotypic changes of macrophages in our assays. The cryo-EM structure, together with molecular dynamics simulations and mutagenesis studies, revealed the molecular basis of CMKLR1 signaling by elucidating the interactions at the ligand-binding pocket and the agonist-induced conformational changes. Our results are expected to facilitate the development of small molecule CMKLR1 agonists that mimic the action of chemerin9 to promote the resolution of inflammation.
Kinesin-14 HSET and KlpA are non-processive microtubule motors with load-dependent power strokes
Authors: Liu Xinglei , Rao Lu , Qiu Weihing , Gennerich Arne
Published: June 2023

Accurate chromosome segregation during cell division relies on coordinated actions of microtubule (MT)-based motor proteins in the mitotic spindle. Kinesin-14 motors play vital roles in spindle assembly and maintenance by crosslinking antiparallel MTs at the spindle midzone and anchoring spindle MTs’ minus ends at the poles. We investigate the force generation and motility of the Kinesin-14 motors HSET and KlpA, revealing that both motors function as non-processive motors under load, producing single power strokes per MT encounter. Each homodimeric motor generates forces of ∼0.5 pN, but when assembled in teams, they cooperate to generate forces of 1 pN or more. Importantly, cooperative activity among multiple motors leads to increased MT-sliding velocities. Our findings deepen our understanding of the structure-function relationship of Kinesin-14 motors and underscore the significance of cooperative behavior in their cellular functions.
Two-million-year-old microbial communities from the Kap København Formation in North Greenland
Authors: Fernandez-Guerra Antonio , Wörmer Lars , Borrel Guillaume , Delmont Tom O , Elberling Bo , Elvert Marcus , Eren A. Murat , Gribaldo Simonetta , Henriksen Rasmus Amund , Hinrichs Kai-Uwe , Jochheim Annika , Korneliussen Thorfinn S. , Krupovic Mart , Larsen Nicolaj K. , Perez-Laso Rafael , Pedersen Mikkel Winther , Pedersen Vivi K. , Ruter Anthony H. , Sand Karina K. , Sikora Martin , Steinegger Martin , Veseli Iva , Wang Yucheng , Zhao Lei , Žure Marina , Kjær Kurt H. , Willerslev Eske
Published: June 2023

Environmental DNA (eDNA) from the 2-million-year-old Kap København Formation of northern Greenland has revealed an ecosystem of plants and animals with no contemporary analogue1. Here, we reconstruct the microbial (bacterial, archaeal, and viral) communities that thrived at the site during this time. By leveraging a novel analytical framework that integrates taxonomic profiling, DNA damage estimates, and functional reconstructions, we identify and distinguish pioneer microbial communities from later permafrost microbial assemblages. We show that at the time of sediment deposition, the terrestrial input at the Kap København site originated from a palustrine wetland, suggesting warmer, non-permafrost conditions. During this period, the detection of methanogenic archaea and signals of their carbon metabolism is consistent with Kap København and similar northern ecosystems contributing moderate methane emissions. Intriguingly, we discover a remarkable nucleotide sequence similarity—exceeding 98%—between pioneer methanogens and present-day analogues in thawing permafrost. This aligns with the concept of “time-traveling” microbes2surviving across geological time and waiting for conditions to turn favourable rather than evolving to adapt to changing conditions. Importantly, in contrast to the plant and animal communities of the Kap København, a striking similarity in microbial composition to that of a contemporary thawing Arctic suggests that microbial communities may serve as the first indication of broader climate-driven ecosystem disruptions.
Structure of the N-RNA/P interface reveals mode of L/P attachment to the nucleocapsid of human metapneumovirus
Authors: Whitehead Jack D. , Decool Hortense , Leyrat Cédric , Carrique Loic , Fix Jenna , Eléouët Jean-François , Galloux Marie , Renner Max
Published: June 2023

Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The polymerase complex of HMPV consists of two obligate components, the L polymerase and its cofactor, the phosphoprotein P. During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within multimerized N nucleoproteins. An essential interaction between N and a C-terminal region of P is required for tethering of the L/P polymerase to the RNA template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how L/P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to polymerase activity assays and imaging of inclusion bodies in transfected cells. We report a 2.9 Å resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.
Biological embedding of childhood adversity - a multi-omics perspective on stress regulation
Authors: Zang Johannes C.S. , May Caroline , Marcus Katrin , Kumsta Robert
Published: June 2023

The experience of adversity in childhood can have life-long consequences on health outcomes. In search of mediators of this relationship, alterations of bio-behavioral and cellular regulatory systems came into focus, including those dealing with basic gene regulatory processes. Systems biology oriented approaches have been proposed to gain a more comprehensive understanding of the complex multiple interrelations between and within layers of analysis. We used co-expression based, supervised and unsupervised single and multi-omics system approaches to investigate the influence of childhood adversity on gene expression, protein expression and DNA methylation in CD14+monocytes of healthy adults before and after exposure to an experimental psychosocial stress protocol. Childhood adversity explained some variance at the single analyte level and within gene and protein co-expression structures. A single-omic, post stress gene expression model differentiated best between participants with a history of childhood adversity and controls in supervised analyses. In unsupervised analyses, a multi-omics based model showed best performance but separated participants based on sex only. Multi-omics analyses are a promising concept but might yield different results based on the specific approach taken and the omic-datasets supplied. Here, stress associated gene-expression pattern were most strongly associated with childhood adversity, and integrating multiple cellular layers did not results in better discriminatory performance. Currently, the capacity and yield of different omics-profiling methods might limit the full potential of integrative approaches.
Degree apprenticeships in the UK higher education institutions – are they viable?: Integrative literature review
Authors: Quew-Jones Rebecca Jane
Published: June 2023

Purpose

Apprenticeships for higher education institutes (HEIs) at degree and postgraduate levels in the UK have been challenging to provide, requiring increasingly complex collaboration and investment. This questions longer-term viability, creating a new perspective investigating evidence of value and impact for UK HEIs. This integrative literature review examines existing apprenticeship literature and showcases new knowledge for HEIs to update and inform future decision-making. Knowledge created offers a new framework, an “apprenticeship knowledge-based checklist model” and a perspective to explore further.

Design/methodology/approach

This integrative literature review examines apprenticeship provision viability for UK HEIs across several disciplines since commencement.

Findings

Analysis of selected studies across three research themes critiques potential apprenticeship practice for HEIs: stakeholder collaboration, widening participation and work-integrated learning. Results provided a new integrated perspective via governance levels: strategic, academic department, and teaching team.

Research limitations/implications

The research draws from multiple disciplines representing current literature in the HEI Apprenticeships field. However, the context in which programmes are delivered by HEIs and employers differs significantly, so factors continue to emerge.

Practical implications

Practical implications drawn from these findings aim to cultivate dialogue before embarking/withdrawing from HEI Apprenticeship programmes. It offers employers guidance expectations when partnering with university providers. For global apprenticeship provisions, it offers a checklist for re-valuating practice.

Originality/value

The research identified new knowledge implications from existing literature in a field experiencing rapid growth. It offers valuable contributions: a knowledge-based checklist model constructed for HEIs to evaluate existing and future viability provisions at each governance level. It is a catalyst for new practice approaches and an agenda for further research.
The HipScreen app for hip migration measurement and the advent of digital health technologies
Authors: Schreiber Jonathan
Published: June 2023

This commentary is on the original article by Kulkarni et al. on pages 1486–1492
of this issue.
A novel approach to automatic seizure detection using computer vision and independent component analysis
Authors: Garção Vicente M. , Abreu Mariana , Peralta Ana R. , Bentes Carla , Fred Ana , P. da Silva Hugo
Published: June 2023

Objective

Epilepsy is a neurological disease that affects ~50 million people worldwide, 30% of which have refractory epilepsy and recurring seizures, which may contribute to higher anxiety levels and poorer quality of life. Seizure detection may contribute to addressing some of the challenges associated with this condition, by providing information to health professionals regarding seizure frequency, type, and/or location in the brain, thereby improving diagnostic accuracy and medication adjustment, and alerting caregivers or emergency services of dangerous seizure episodes. The main focus of this work was the development of an accurate video‐based seizure‐detection method that ensured unobtrusiveness and privacy preservation, and provided novel approaches to reduce confounds and increase reliability.

Methods

The proposed approach is a video‐based seizure‐detection method based on optical flow, principal component analysis, independent component analysis, and machine learning classification. This method was tested on a set of 21 tonic–clonic seizure videos (5–30 min each, total of 4 h and 36 min of recordings) from 12 patients using leave‐one‐subject‐out cross‐validation.

Results

High accuracy levels were observed, namely a sensitivity and specificity of 99.06% ± 1.65% at the equal error rate and an average latency of 37.45 ± 1.31 s. When compared to annotations by health care professionals, the beginning and ending of seizures was detected with an average offset of 9.69 ± 0.97 s.

Significance

The video‐based seizure‐detection method described herein is highly accurate. Moreover, it is intrinsically privacy preserving, due to the use of optical flow motion quantification. In addition, given our novel independence‐based approach, this method is robust to different lighting conditions, partial occlusions of the patient, and other movements in the video frame, thereby setting the base for accurate and unobtrusive seizure detection.
Factors predicting proactive work behaviors among nurses: A descriptive predictive study
Authors: Htet Hsu Yee , Abhicharttibutra Kulwadee , Wichaikum Orn‐Anong
Published: June 2023

Aim

This study examined the level of proactive work behavior and predictability of education level, work engagement, transformational leadership of nurse managers, and organizational support on proactive work behaviors among nurses.

Background

Nurses face many challenges to provide quality nursing care as numbers of patients increase in particular as a result of COVID‐19 and human resource shortages worldwide, this includes Myanmar. Proactive work behavior is a critical factor in providing quality nursing care.

Methods

We collected data from 183 registered nurses in four university‐affiliated general hospitals in Myanmar by using stratified random sampling. Instruments included the Utrecht Work Engagement Scale, the Global Transformational Leadership Scale, the Survey of Perceived Organizational Support, and the Proactive Work Behavior Scale. Descriptive statistics and multiple regression were used to analyze data. Findings are reported according to the STROBE checklist.

Results

The overall level of proactive work behavior was perceived as moderate. Transformational leadership and work engagement were significant predictors of proactive work behaviors of nurses, explaining 33.0% of the total variance.

Conclusion

Findings provide that both transformational leadership and work engagement are significant predictors of proactive work behaviors which are important for improving the quality of patient care and organizational outcomes.

Implications for nursing and health policy

Nurse administrators and hospital directors should encourage nurses to voice ideas for improving the standard of work, provide opportunities for generating ideas, support resources for taking charge and preventing problems whilst also supporting the promotion of nurse managers' transformational leadership and nurses' work engagement.
Screw‐retained ceramic‐veneered/monolithic zirconia partial implant‐supported fixed dental prostheses: A 5 to 10‐year retrospective study on survival and complications
Authors: Zhang Yifan , Luo Jia , Di Ping , Chen Bo , Li Jianhui , Yu Ziyang , Lin Ye
Published: June 2023

Purpose

To assess the clinical performance of screw‐retained, ceramic‐veneered, monolithic zirconia partial implant‐supported fixed dental prostheses (ISFDP) over 5–10 years and to evaluate implant‐ and prosthesis‐related factors influencing treatment failure and complications.

Materials and methods

Partially edentulous patients treated with screw‐retained all‐ceramic ISFDPs with 2–4 prosthetic units with a documented follow‐up of ≥5 years after implant loading were included in this retrospective study. The outcomes analyzed included implant/prosthesis failure and biological/technical complications. Possible risk factors were identified using the mixed effects Cox regression analysis.

Results

A screened sample of 171 participants with 208 prostheses (95% of the restorations were splinted crowns without a pontic) supported by 451 dental implants were enrolled in this study. The mean follow‐up duration after prosthesis delivery was 82.4 ±17.2 months. By the end of the follow‐up period, 431 (95.57%) of the 451 implants remained functional at the implant level. At the prosthesis level, 185 (88.94%) of the 208 partial ISFDPs remained functional. Biological complications were observed in 67 implants (14.86%), and technical complications were observed in 62 ISFDPs (29.81%). Analysis revealed only emergence profiles (over‐contoured) as a significant risk factor for implant failure (P<0.001) and biological complications (P<0.001). Full‐coverage ceramic‐veneered zirconia prostheses had a significantly greater chance of chipping (P<0.001) compared with buccal‐ceramic‐veneered or monolithic zirconia prostheses.

Conclusions

Screw‐retained ceramic‐veneered, monolithic partial ISFDPs have a favorable long‐term survival rate. Over‐contoured emergence profile is a significant risk factor associated with implant failure and biological complications. Buccal‐ceramic‐veneered and monolithic zirconia partial ISFDPs lower the initial prevalence of chipping compared with a full‐coverage veneered design.
Hypoxia response protein HRM1 modulates the activity of mitochondrial electron transport chain in Arabidopsis under hypoxic stress
Authors: Tsai Kuen‐Jin , Suen Der‐Fen , Shih Ming‐Che
Published: June 2023

We studied Arabidopsis HYPOXIA‐RESPONSIVE MODULATOR 1 (HRM1), which belongs to a group of core hypoxia‐responsive genes that are conserved among plant species across great evolutionary distance.

The hrm1 mutants had lower survival rates and showed more damage than the wild‐type (WT) plants under hypoxic stress. Promoter analyses showed that HRM1 is regulated by EIN3 and RAP2.2 during hypoxia. Fluorescence tracing and immunogold labeling assays showed that HRM1 protein was enriched in mitochondria.

Co‐immunoprecipitation coupled with mass spectrometry and bimolecular fluorescence complementation assays showed that HRM1 associates with the complex‐I in mitochondria. Compared with the WT plants, metabolic activities related to the mitochondrial electron transport chain (mETC) were higher in hrm1 mutants during hypoxia. Loss of HRM1 caused de‐repression of mETC complex I, II, and IV activities and higher basal and maximum respiration rates under hypoxia.

Our results showed that through association with complex‐I, HRM1 attenuates mETC activity and modulates the respiratory chain under low oxygen. Compared with the regulatory system in mammalian, adjustment of mitochondrial respiration to low oxygen helps plants decrease reactive oxygen species production and is also critical for the submergence survival.