bluuebunny/crossref_metadata_2025_split huggingface dataset:
Family supplemented patient monitoring after surgery (SMARTER): process evaluation of a complex intervention in Uganda
Authors: Hewitt-Smith Adam , Bulamba Fred , Nanimambi Juliana , Adong Lucy Ruth , Emacu Bernard , Kabaleta Mary , Khanyalano Justine , Hussein Maiga Ayub , Mugume Charles , Nakibuule Joanitah , Nandyose Loretta , Sejja Martin , Weere Winfred , Pearse Rupert M. , Stephens Timothy 
Published: May 2024

AbstractBackgroundImproving outcomes after surgery in Africa is a priority. The SMARTER Pilot Trial was a step-wedge cluster-randomised trial of family member supplemented vital signs monitoring after surgery. A concurrent process evaluation provides contextual understanding of intervention delivery.MethodsMixed methods approach with qualitative data sources including field notes from a research team diary and focus group discussions. Deductive analysis used the consolidated framework for implementation research. Quantitative data evaluating the efficacy of family members recognising abnormal vital signs and reporting them to nursing staff were collected following a prespecified intervention review held after two months.FindingsFocus group discussions were conducted with 16 nurses and research assistants. Field notes included 88 episodes documented throughout the trial in a research team diary. Quantitative data were collected in the final 397 patients following ethics amendments. Intervention facilitators included: relative advantage, inner context factors including tension for change and relative priority, and individual characteristics centred around knowledge and beliefs. Available resources, culture, and compatibility were identified as important barriers, with a smaller negative influence from self-efficacy and intervention complexity. Family members recognised 91.3% (42/46) of abnormal sets of vital signs and communicated 100% (42/42) of these to a member of the nursing or medical team. The team responded 90.5% (38/42) of the time.InterpretationFamily members were able to supplement nurse led monitoring of patients after surgery. This complex intervention was affected by context specific positive and negative influences. Scaling this intervention requires careful consideration of local context during planning.Trial registrationSMARTER Pilot Trial registered onclinicaltrials.gov-NCT04341558
Optimal algorithms for controlling infectious diseases in real time using noisy infection data
Authors: Beregi Sandor , Parag Kris V. 
Published: May 2024

AbstractDeciding when to enforce or relax non-pharmaceutical interventions (NPIs) based on real-time outbreak surveillance data is a central challenge in infectious disease epidemiology. Reporting delays and infection under-ascertainment, which characterise practical surveillance data, can misinform decision-making, prompting mistimed NPIs that fail to control spread or permitting deleterious epidemic peaks that overload healthcare capacities. To mitigate these risks, recent studies propose more data-insensitive strategies that trigger NPIs at predetermined times or infection thresholds. However, these strategies often increase NPI durations, amplifying their substantial costs to livelihood and life-quality. We develop a novel model-predictive control algorithm that optimises NPI decisions by jointly minimising their cumulative, future risks and costs over stochastic epidemic projections. Our algorithm is among the earliest to realistically incorporate uncertainties underlying both the generation and surveillance of infections. We find, except under extremely delayed reporting, that our projective approach outperforms data-insensitive strategies and show that earlier decisions strikingly improve real-time control with reduced NPI costs. Moreover, we expose how surveillance quality, disease growth and NPI frequency intrinsically limit our ability to flatten epidemic peaks or dampen endemic oscillations and why this potentially makes Ebola virus more controllable than SARS-CoV-2. Our algorithm provides a general framework for guiding optimal NPI decisions ahead-of-time and identifying the key factors limiting practical epidemic control.
KIPK and KIPK-LIKE1 suppress overbending during negative hypocotyl gravitropic growth
Authors: Xiao Yao , Zourelidou Melina , Bassukas Alkistis E. Lanassa , Weller Benjamin , Janacek Dorina P. , Schulz Lukas , Brajkovic Sarah , Šimura Jan , Ljung Karen , Kuster Bernhard , Hammes Ulrich Z. , Li Jia , Schwechheimer Claus 
Published: May 2024

ABSTRACTPlants use environmental cues, such as the direction of gravity or the direction, quantity and quality of light, to orientate organ and plant growth. During germination of angiosperm seeds in the soil, hypocotyl elongation is directed by negative gravitropism responses such that the seedling can reach the light for photosynthesis and autotrophic growth. Hypocotyl elongation in the soil, however, also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of hypocotyl bending, in that KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector after obstacle avoidance. At the same time, we find that the highly homologous KIPKL2 (KIPK-LIKE2) must be functionally distinct. We further find that KIPK, and likely also KIPKL1, phosphorylate BRXL2 (BREVIS RADIX LIKE2) and ARKs (ARMADILLO REPEAT KINESINs), that mutants of both KIPK phosphorylation substrates share the overbending phenotype withkipk kipkl1mutants, and thatKIPKandKIPKL1act synergistically with the ARK-regulatoryNEK6(NIMA-RELATED PROTEIN KINASE6). We propose that KIPK and KIPKL1 regulate ARK kinesins and thereby cortical microtubules for efficient gravitropic hypocotyl bending.
Clonal spheroids capture functional and genetic heterogeneity of head and neck cancer
Authors: Pandey Jyoti , Malik Md. Zubbair , Shyanti Ritis K , Parashar Palak , Kujur Praveen K , Mishra Deepali , Tailor Dhanir , Lee Jee Min , Kataria Tejinder , Gupta Deepak , Verma Hitesh , Malhotra Sanjay V , Kateriya Suneel , Tandon Vibha , Chaturvedi Rupesh , Singh Rana P 
Published: May 2024

AbstractHead and neck cancer squamous cell carcinoma (HNSCC) cells exhibit both structural and functional diversity, making them valuable models for understanding tumor heterogeneity at clinical levels. In this study, we generated single-cell-derived spheroids (SCDS) from HNSCC cell lines and patient tumor cells using scaffold- and non-scaffold-based methods to assess this variability. A distinct structural variability among these SCDS, categorized as hypo- and hyperproliferative spheroids based on size, was observed. Hyperproliferative spheroids demonstrated heightened proliferative and tumorigenic potential and increased sensitivity to cisplatin and radiation, while hypoproliferative spheroids exhibited enhanced migratory capabilities. Single-cell RNA sequencing (scRNA-seq) of hypo- and hyperproliferative spheroids provided insights into the transcriptional landscape of HNSCC cells, validating the observed structural and functional heterogeneities within primary tumors. These functionally and genetically characterized spheroids offer valuable tools for the development of next-generation therapeutics.Statement of SignificanceEstablishment and characterization of single-cell-derived spheroids from head and neck cancer cells, employing scaffold and non-scaffold materials, demonstrate functional and genetic heterogeneity. Single-cell analysis reveals correlations between genetic diversity and spheroid functionality. These characterized spheroids offer potential for advancing therapeutics development.
A microfluidic platform forin situstudies of bacteria electroporation
Authors: Volkov Ivan L. , Khaji Zahra , Johansson Magnus , Tenje Maria 
Published: May 2024

AbstractElectroporation of dye-labelled bio-molecules has proven to be a valuable alternative to fluorescent protein fusion for single-molecule tracking in living cells. However, control over cell viability, electroporation efficiency and environment conditions before, during and after electroporation is difficult to achieve in bulk experiments. Here, we present a microfluidic platform capable of single-cell electroporation within situmicroscopy and demonstrate delivery of DNA into bacteria. Via real time observation of the electroporation process, we find that the effect of electrophoresis plays an important role when performing electroporation in a miniaturized platform and show that its undesired action can be balanced by using bipolar electrical pulses. We suggest that a low temperature of the sample during electroporation is important for cell viability due to temperature-dependant viscoelastic properties of the cell membrane. We further found that the presence of low conductive liquid between cells and the electrodes leads to a voltage divider effect which strongly influences the success of on-chip electroporation. Finally, we conclude that electroporation is intrinsically a highly stochastic process that is difficult to fully control via external parameters and envision that the microfluidic system presented here, capable of single-cell read-out, can be used for further fundamental studies to increase our understanding of the electroporation process.
Developmental and conditional regulation of DAF-2/INSR ubiquitination inCaenorhabditis elegans
Authors: Falsztyn Ivan B. , Taylor Seth M. , Baugh L. Ryan 
Published: May 2024

ABSTRACTInsulin/IGF signaling (IIS) regulates developmental and metabolic plasticity. Conditional regulation of insulin-like peptide expression and secretion promotes different phenotypes in different environments. However, IIS can also be regulated by other, less-understood mechanisms. For example, stability of the only known insulin/IGF receptor inC. elegans, DAF-2/INSR, is regulated by CHIP-dependent ubiquitination. Disruption ofchn-1/CHIPreduces longevity inC. elegansby increasing DAF-2/INSR abundance and IIS activity in adults. Likewise, mutation of a ubiquitination site causesdaf-2(gk390525)to display gain-of-function phenotypes in adults. However, we show that this allele displays loss-of-function phenotypes in larvae, and that its effect on IIS activity transitions from negative to positive during development. In contrast, the allele acts like a gain-of-function in larvae cultured at high temperature, inhibiting temperature-dependent dauer formation. Disruption ofchn-1/CHIPcauses an increase in IIS activity in starved L1 larvae, unlikedaf-2(gk390525). CHN-1/CHIP ubiquitinates DAF-2/INSR at multiple sites. These results suggest that the sites that are functionally relevant to negative regulation of IIS vary in larvae and adults, at different temperatures, and in nutrient-dependent fashion, revealing additional layers of IIS regulation.ARTICLE SUMMARYInsulin-like signaling plays a critical role in helping animals adapt to different environmental conditions. Differences in abundance of insulin molecules drive differences in insulin signaling, affecting growth, metabolism, and resistance to stressful conditions. Previous work in the roundwormC. elegansshowed that targeted degradation of the insulin receptor also regulates insulin signaling. We show here that this process is affected by developmental stage, nutrient availability, and temperature, revealing additional ways that insulin-like signaling is regulated in this valuable animal model.
Structural basis of promiscuous inhibition ofListeriavirulence activator PrfA by oligopeptides
Authors: Hainzl Tobias , Scortti Mariela , Lindgren Cecilia , Grundström Christin , Krypotou Emilia , Vázquez-Boland José A. , Sauer-Eriksson A. Elisabeth 
Published: May 2024

AbstractThe facultative pathogenListeria monocytogenesuses a master regulator, PrfA, to tightly control the fitness-costly expression of its virulence factors. We found that PrfA activity is repressed via competitive occupancy of the binding site for the PrfA-activating cofactor glutathione by exogenous nutritional oligopeptides. The inhibitory peptides show different sequence and physicochemical properties, but how such wide variety of oligopeptides can bind PrfA was unclear. Using crystal structure analysis of PrfA complexed with inhibitory tri- and tetrapeptides, we show here that the binding promiscuity is due to the ability of PrfA β5 in the glutathione-binding tunnel to establish parallel or antiparallel β-sheet-like interactions with the peptide backbone. Spacious tunnel pockets provide additional flexibility for unspecific peptide accommodation while providing selectivity for hydrophobic residues. Hydrophobic contributions from two adjacent peptide residues appears to be critical for PrfA inhibitory binding. In contrast to glutathione, peptide binding prevents the conformational change required for PrfA activation and formation of the DNA-binding helix-turn-helix motifs, effectively inhibiting virulence expression.
Functional Heterogeneity of Voice-Encoding Cortex Revealed by Clinical Language Mapping
Authors: Harford Emily E. , Rupp Kyle M. , Welch William P. , Al-Ramadhani Ruba , Ghuman Avniel , Holt Lori L. , Abel Taylor J. 
Published: May 2024

AbstractRegions in the superior temporal sulcus and gyrus have been heavily implicated in voice-selective responses in human auditory cortex. Despite an apparent specialization for the encoding of human voice, research outside the auditory domain suggests that these areas likely participate in additional neural processes including speech processing and production. The aim of the current study was to combine results of electrophysiological recording and clinical stimulation mapping procedures in patients undergoing stereoelectroencephalography (sEEG) to explore potential functional heterogeneity in voice-encoding cortex. Both channels that demonstrated voice-encoding properties and channels critically implicated in language functioning were heavily concentrated in the left STG/S. Analysis of functional overlap revealed channels in the posterior STG/S that appear to be involved in both voice encoding and language. Strength of voice encoding in these functionally diverse sites was not significantly different from sites that were implicated in voice encoding alone. Our findings add to prior observations of functional heterogeneity in the STG/S and contribute to proposed models of speech perception. We discuss these results in the context of the utility of electrophysiological methods in mapping cortical networks and identifying regions essential for functioning.
Homomorphic Encryption: An Application to Polygenic Risk Scores
Authors: Knight Elizabeth , Yolou Israel , Li Jiaqi , Kockan Can , Jensen Matthew , Gerstein Mark 
Published: May 2024

AbstractBackgroundPolygenic risk scores (PRS) have emerged as a powerful tool in precision medicine, enabling personalized risk assessments for complex diseases. However, using sensitive genomic data in PRS calculations raises concerns about privacy and security. Fully Homomorphic Encryption (FHE) offers a promising solution by allowing computations on encrypted data, preserving the privacy of both genomic information and PRS models.ResultsIn this study, we present a novel application of FHE for secure and private PRS calculations using the CKKS protocol within the Lattigo library. Our approach involves a three-party system: clients (doctors with sensitive genetic data), modelers developing a PRS (academics or a company), and evaluators (a “local hospital” running the models while maintaining data confidentiality). We demonstrate the feasibility and accuracy of our protocol by applying it to synthetic datasets of various sizes and a robust 110k-SNP model for schizophrenia. The normal PRS calculation results are essentially identical to the encrypted calculation: between the two resultsR2is .999 & MSE is 2.27×10−6. Moreover, while the encrypted calculation is roughly 1000 times slower than conventional non-encrypted ones (when only considering the core PRS calculation), it is quite feasible on a single-CPU node - e.g. running on ° 1100 individuals with ° 110k SNPS took six minutes and°65G memory on a laptop computer. In addition, we investigate the impact of encryption parameters (modulus) on this computational time and accuracy in detail.ConclusionBy enabling secure PRS calculations on encrypted genomic data, our approach addresses the pressing need for privacy-preserving solutions in the era of precision medicine. The ability to perform accurate risk assessments while maintaining patient confidentiality paves the way for broader adoption of PRS and personalized medicine in healthcare, particularly with the advent of large-scale computing power.
Oxydifficidin, a potentNeisseria gonorrhoeaeantibiotic due to DedA assisted uptake and ribosomal protein RplL sensitivity
Authors: Kan Jingbo , Morales Adrian , Hernandez Yozen , Ternei Melinda A. , Lemetre Christophe , Maclntyre Logan W. , Biais Nicolas , Brady Sean F. 
Published: May 2024

AbstractGonorrhea, which is caused byNeisseria gonorrhoeae, is the second most reported sexually transmitted infection worldwide. The increasing appearance of isolates that are resistant to approved therapeutics raises the concern that gonorrhea may become untreatable. Here, we serendipitously identified oxydifficidin as a potentN. gonorrhoeaeantibiotic through the observation of aBacillus amyloliquefacienscontaminant in a lawn ofN. gonorrhoeae. Oxydifficidin is active against both wild- type and multidrug-resistantN. gonorrhoeae. It’s potent activity results from a combination of DedA- assisted uptake into the cytoplasm and the presence of an oxydifficidin-sensitive ribosomal protein L7/L12 (RplL). Our data indicates that oxydifficidin binds to the ribosome at a site that is distinct from other antibiotics and that L7/L12 is uniquely associated with its mode of action. This study opens a potential new avenue for addressing antibiotic resistant gonorrhea and underscores the possibility of identifying overlooked natural products from cultured bacteria, particularly those with activity against previously understudied pathogens.
The C-terminal tails of GroEL and its mitochondrial and chloroplastic homologs adopt polyproline II helices
Authors: Rodríguez Cristian Segura , López-Sánchez Rubén , Laurents Douglas Vinson 
Published: May 2024

ABSTRACTThe chaperonin GroEL and its mitochondrial and chloroplastic homologs mHsp60 and Cpn60 are large barrel-like oligomeric proteins. Chaperonins facilitate folding by isolating nascent chains in their hollow interior and undergoing conformational transitions driven by ATP hydrolysis. Due to their vital importance, the structure of GroEL and its homologs have been extensively studied by X-ray crystallography and CryoEM, revealing one or two rings each of which contains seven subunits. Each subunit has three folded domains and a twenty-four residue C-terminal extension. Whereas this C-terminal tail has been reported to bind and stimulate the folding of the client protein, it appears to be invisible or blurry, which suggests disorder. The objective of this study is to characterize conformational preferences in the C-terminal tails of GroEL, mHsp60 and representative Cpn60s using circular dichroism and nuclear magnetic resonance spectroscopies. The tails of GroEL and mHsp60 consist of two segments. The first is rich in residues typical of intrinsically disordered proteins and the second segment consists exclusively (GroEL) or almost entirely (mHsp60) of Gly and Met residues. The spectroscopic results evince that these C-terminal extensions are not wholly disordered but adopt polyproline II helices whose populations are higher in the second Gly/Met-rich segment. Whereas the C-terminal segments of chloroplastic chaperonins are Gly-poor, they are rich in proline and also adopt polyproline II helix conformations. These results provide insight into the function of chaperonin C-terminal tails.
Thermal variation influences the transcriptome of the major malaria vectorAnopheles stephensi
Authors: Pathak Ashutosh K , Quek Shannon , Sharma Ritu , Shiau Justine C , Thomas Matthew B. , Hughes Grant L. , Murdock Courtney C 
Published: May 2024

ABSTRACTThe abundance and distribution of ectotherms is being shaped at unprecedented scales by human-induced climate change. Unraveling molecular adaptations to thermal variation is prescient. Vector-borne diseases are of particular concern and although mosquitoes are responsible for most of the 621 million cases annually, their response to temperature is not well characterized. We describe the transcriptome of the major vector for human malaria,Anopheles stephensimaintained under a diurnal temperature regime (DTR) totaling 9°C and daily means of 20°C, 24°C and 28°C respectively. Gene expression profiles were examined in the midguts and carcasses of adult mosquitoes from one to 19 days post-blood meal. Differences in temporal expression profiles at each temperature revealed a total of 3,106 and 3,590 genes in the carcasses and midguts respectively and analyzed further to make three inferences. First, we identified genes with shared temporal expression profiles across all three temperatures, suggesting their indispensability to mosquito life history. Second, tolerance to 20 DTR 9°C and 28 DTR 9°C was associated with a larger and more diverse repertoire of gene products compared to 24 DTR 9°C; assuming physiological costs scale accordingly, this finding could explain the fitness trade-offs underlying the unimodal effect of temperature. Third, the long duration of our study revealed two general trends in gene expression, representative of a coordinated, tissue- and temperature-specific response to blood meal digestion, managing oxidative stress, and reproduction. Our results suggest how temperature could regulate the mosquito’s capacity to transmitPlasmodiumparasites and offer a reference point for understanding ectotherm adaptation.
Microtubule dynamic instability is sensitive to specific biological viscogensin vitro
Authors: Molines Arthur T. , Edrington Claire H. , Tetlalmatzi Sofía Cruz , Chang Fred , Brouhard Gary J. 
Published: May 2024

AbstractCytoplasm is a viscous, crowded, and heterogeneous environment, and its local viscosity and degree of macromolecular crowding have significant effects on cellular reaction rates. Increasing viscosity slows down diffusion and protein conformational changes, while increasing macromolecular crowding speeds up reactions. As a model system for cellular reactions, microtubule dynamics are slowed downin vivowhen cytoplasm concentration is increased by osmotic shifts, indicating a dominant role for viscosity in microtubule reaction pathways. In the cell, viscosity is determined by diverse species of “biological viscogens”, including glycerol, trehalose, intermediate metabolites, proteins, polymers, organelles, and condensates. Here we showin vitrothat microtubule dynamic instability is sensitive to specific viscogen species, particularly glycerol. We found that increasing viscosity with glycerol or trehalose slowed microtubule growth, slowed microtubule shrinkage, and increased microtubule lifetimes, similar to the “freezing” observed previouslyin vivo. Increasing viscosity with a globular protein, bovine serum albumin, increased microtubule growth rates, as its viscous effects may be balanced against its macromolecular crowding effects. At matched viscosities, glycerol had an outsized effect on microtubule lifetimes, rescues, and nucleation compared to other viscogens. Increasing viscosity did not, however, increase the intensity of EB3-GFP comets, indicating that GTP hydrolysis is unaffected by buffer conditions. We propose that glycerol exerts its distinct effect on microtubule dynamic instability by stabilizing the microtubule lattice after phosphate release. Effects of specific viscogens may modulate many cellular reaction rates within local environments of cytoplasm.