bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation and pilot testing of a multidisciplinary model of care to mainstream genomic testing for paediatric inborn errors of immunity
Authors: Yanes Tatiane , Sullivan Anna , Barbaro Pasquale , Brion Kristian , Hollway Georgina , Peake Jane , McNaughton Peter 
Published: March 2023

AbstractMolecular diagnosis of paediatric inborn errors of immunity (IEI) influences management decisions and alters clinical outcomes, through early use of targeted and curative therapies. The increasing demand for genetic services has resulted in growing waitlists and delayed access to vital genomic testing. To address this issue, the Queensland Paediatric Immunology and Allergy Service, Australia, developed and evaluated a mainstreaming model of care to support point-of-care genomic testing for paediatric IEI. Key features of the model of care included a genetic counsellor embedded in the department, state-wide multidisciplinary team meetings, and variant prioritisation meetings to review whole exome sequencing (WES) data. Of the 62 children presented at the MDT, 43 proceeded to WES, of which nine (21%) received a confirmed molecular diagnosis. Changes to treatment and management were reported for all children with a positive result, including curative hematopoietic stem cell transplantation (n = 4). Four children were also referred for further investigations of variants of uncertain significance or additional testing due to ongoing suspicion of genetic cause after negative result. Demonstrating engagement with the model of care, 45% of the patients were from regional areas and on average, 14 healthcare providers attended the state-wide multidisciplinary team meetings. Parents demonstrated understanding of the implications of testing, reported minimal decisional regret post-test, and identified benefits to genomic testing. Overall, our program demonstrated the feasibility of a mainstreaming model of care for paediatric IEI, improved access to genomic testing, facilitated treatment decision-making, and was acceptable to parents and clinicians alike.
An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation
Authors: Bhat Khalid H. , Priyadarshi Saurabh , Naiyer Sarah , Qu Xinyan , Farooq Hammad , Kleiman Eden , Xu Jeffery , Lei Xue , Cantillo Jose F. , Wuerffel Robert , Baumgarth Nicole , Liang Jie , Feeney Ann J. , Kenter Amy L. 
Published: March 2023

AbstractThe mouse Igh locus is organized into a developmentally regulated topologically associated domain (TAD) that is divided into subTADs. Here we identify a series of distal VH enhancers (EVHs) that collaborate to configure the locus. EVHs engage in a network of long-range interactions that interconnect the subTADs and the recombination center at the DHJH gene cluster. Deletion of EVH1 reduces V gene rearrangement in its vicinity and alters discrete chromatin loops and higher order locus conformation. Reduction in the rearrangement of the VH11 gene used in anti-PtC responses is a likely cause of the observed reduced splenic B1 B cell compartment. EVH1 appears to block long-range loop extrusion that in turn contributes to locus contraction and determines the proximity of distant VH genes to the recombination center. EVH1 is a critical architectural and regulatory element that coordinates chromatin conformational states that favor V(D)J rearrangement.
Variable microtubule architecture in the malaria parasite
Authors: Ferreira Josie L. , Pražák Vojtěch , Vasishtan Daven , Siggel Marc , Hentzschel Franziska , Binder Annika M. , Pietsch Emma , Kosinski Jan , Frischknecht Friedrich , Gilberger Tim W. , Grünewald Kay 
Published: March 2023

AbstractMicrotubules are a ubiquitous eukaryotic cytoskeletal element typically consisting of 13 protofilaments arranged in a hollow cylinder. This arrangement is considered the canonical form and is adopted by most organisms, with rare exceptions. Here, we use in situ electron cryo-tomography and subvolume averaging to analyse the changing microtubule cytoskeleton of Plasmodium falciparum, the causative agent of malaria, throughout its life cycle. Unexpectedly, different parasite forms have distinct microtubule structures coordinated by unique organising centres. In merozoites, the most widely studied form, we observe canonical microtubules. In migrating mosquito forms, the 13 protofilament structure is further reinforced by interrupted luminal helices. Surprisingly, gametocytes contain a wide distribution of microtubule structures ranging from 13 to 18 protofilaments, doublets and triplets. Such a diversity of microtubule structures has not been observed in any other organism to date and is likely evidence of a distinct role in each life cycle form. This data provides a unique view into an unusual microtubule cytoskeleton of a relevant human pathogen.
Growth anisotropy of the extracellular matrix shapes a developing organ
Authors: Harmansa Stefan , Erlich Alexander , Eloy Christophe , Zurlo Giuseppe , Lecuit Thomas 
Published: March 2023

AbstractFinal organ size and shape result from volume expansion by growth and shape changes by contractility. Complex morphologies can also arise from differences in growth rate between tissues. We address here how differential growth guides the morphogenesis of the growing Drosophila wing imaginal disc. We report that 3D morphology results from elastic deformation due to differential growth anisotropy between the epithelial cell layer and its enveloping extracellular matrix (ECM). While the tissue layer grows in plane, growth of the bottom ECM occurs in 3D and is reduced in magnitude, thereby causing geometric frustration and tissue bending. The elasticity, growth anisotropy and morphogenesis of the organ are fully captured by a mechanical bilayer model. Moreover, differential expression of the Matrix metalloproteinase MMP2 controls growth anisotropy of the ECM envelope. This study shows that the ECM is a controllable mechanical constraint whose intrinsic growth anisotropy directs tissue morphogenesis in a developing organ.
Crevasse refreezing and signatures of retreat observed at Kamb Ice Stream grounding zone
Authors: Lawrence J. D. , Washam P. M. , Stevens C. , Hulbe C. , Horgan H. J. , Dunbar G. , Calkin T. , Stewart C. , Robinson N. , Mullen A. D. , Meister M. R. , Hurwitz B. C. , Quartini E. , Dichek D. J. G. , Spears A. , Schmidt B. E. 
Published: March 2023

AbstractIce streams flowing into Ross Ice Shelf are presently responsible for around 10% of the mass flux from West Antarctica, with the noteworthy exception of Kamb Ice Stream, which stagnated in the late 1800s. The subsequent reduction in ice supply led to grounding-line retreat at the coastal margin where Kamb transitions into the floating Ross Ice Shelf. Grounding-line migration is linked to broader changes in ice-sheet mass balance and sea level, but our understanding of related ice, ocean and seafloor interactions is limited by the difficulty in accessing these remote regions. Here we report in situ observations from an underwater vehicle deployed at Kamb that show how fine-scale variability in ice and ocean structure combine to influence a diversity of ice–ocean interactions. We found a stratified water column within a tenth of a degree of freezing at the ice base and mapped basal crevasses with supercooled water and active marine ice formation. At the seafloor, we interpret parallel ridges as crevasse impressions left as the ice lifted off during grounding-line retreat. These observations from a recently ungrounded sub-shelf environment illuminate both the geomorphological signatures of past grounding-line retreat and the fine-scale sensitivity of ongoing ice–ocean interactions to ice topography.
Resonant plasmonic micro-racetrack modulators with high bandwidth and high temperature tolerance
Authors: Eppenberger Marco , Messner Andreas , Bitachon Bertold Ian , Heni Wolfgang , Blatter Tobias , Habegger Patrick , Destraz Marcel , De Leo Eva , Meier Norbert , Del Medico Nino , Hoessbacher Claudia , Baeuerle Benedikt , Leuthold Juerg 
Published: March 2023

AbstractResonant modulators encode electrical data onto wavelength-multiplexed optical carriers. Today, silicon microring modulators are perceived as promising to implement such links; however, they provide limited bandwidth and need thermal stabilization systems. Here we present plasmonic micro-racetrack modulators as a potential successor of silicon microrings: they are equally compact and compatible with complementary-metal–oxide–semiconductor-level driving voltages, but offer electro-optical bandwidths of 176 GHz, a 28 times improved stability against operating temperature changes and no self-heating effects. The temperature-resistant organic electro-optic material enables operation at 85 °C device temperature. We show intensity-modulated transmission of up to 408 Gbps at 12.3 femtojoules per bit with a single resonant modulator. Plasmonic micro-racetrack modulators offer a solution to encode high data rates (for example, the 1.6 Tbps envisioned by next-generation communications links) at a small footprint, with low power consumption and marginal, if no, temperature control.
In silico tissue generation and power analysis for spatial omics
Authors: Baker Ethan A. G. , Schapiro Denis , Dumitrascu Bianca , Vickovic Sanja , Regev Aviv 
Published: March 2023

AbstractAs spatially resolved multiplex profiling of RNA and proteins becomes more prominent, it is increasingly important to understand the statistical power available to test specific hypotheses when designing and interpreting such experiments. Ideally, it would be possible to create an oracle that predicts sampling requirements for generalized spatial experiments. However, the unknown number of relevant spatial features and the complexity of spatial data analysis make this challenging. Here, we enumerate multiple parameters of interest that should be considered in the design of a properly powered spatial omics study. We introduce a method for tunable in silico tissue (IST) generation and use it with spatial profiling data sets to construct an exploratory computational framework for spatial power analysis. Finally, we demonstrate that our framework can be applied across diverse spatial data modalities and tissues of interest. While we demonstrate ISTs in the context of spatial power analysis, these simulated tissues have other potential use cases, including spatial method benchmarking and optimization.
Relationship between postpartum depression and plasma vasopressin level at 6–8 weeks postpartum: a cross-sectional study
Authors: Kashkouli Masoumeh , Jahanian Sadatmahalleh Shahideh , Ziaei Saeideh , Kazemnejad Anoshirvan , Saber Ashraf , Darvishnia Hamid , Azarbayjani Khadijeh 
Published: March 2023

AbstractPostpartum depression (PPD) is the most important postpartum mood disorder due to its significant effect on both the infant and family health. Arginine vasopressin (AVP) has been suggested as a hormonal agent involved in the development of depression. The purpose of this study was to investigate the relationship between the plasma concentrations of AVP and the score of Edinburgh Postnatal Depression Scale (EPDS). This cross-sectional study was conducted in 2016–2017 in Darehshahr Township, Ilam Province, Iran. In the first phase, 303 pregnant women, who were at 38 weeks, met the inclusion criteria, and were not depressed (according to their EPDS scores) were included in the study. In the 6–8 week postpartum follow-up, using the EPDS, 31 depressed individuals were diagnosed and referred to a psychiatrist for confirmation. The maternal venous blood samples of 24 depressed individuals still meeting the inclusion criteria and 66 randomly selected non-depressed subjects were obtained to measure their AVP plasma concentrations with ELISA assay. There was a significant positive relationship between plasma AVP levels and the EPDS score (P = 0.000, r = 0.658). Also the mean plasma concentration of AVP was significantly higher in the depressed group (41.35 ± 13.75 ng/ml) than in the non-depressed group (26.01 ± 7.83 ng/ml) (P < 0.001). In a multiple logistic regression model for various parameters, increased vasopressin levels were associated with increased odds of PPD (OR = 1.15, 95% CI = 1.07–1.24, P = 0.000). Furthermore, multiparity (OR = 5.45, 95% CI = 1.21–24.43, P = 0.027) and non-exclusive breastfeeding (OR = 13.06, 95% CI = 1.36–125, P = 0.026) were associated with increased odds of PPD. Maternal gender preference (having a baby of desired and desired sex) decreased the odds of PPD (OR = 0.13, 95% CI = 0.02–0.79, P = 0.027 and OR = 0.08, 95% CI = 0.01–0.5, P = 0.007). AVP seems to be a contributor to clinical PPD by affecting the hypothalamic–pituitary–adrenal (HPA) axis activity. Furthermore, primiparous women had significantly lower EPDS scores.
Alcobiosis, an algal-fungal association on the threshold of lichenisation
Authors: Vondrák Jan , Svoboda Stanislav , Zíbarová Lucie , Štenclová Lenka , Mareš Jan , Pouska Václav , Košnar Jiří , Kubásek Jiří 
Published: March 2023

AbstractAlcobiosis, the symbiosis of algae and corticioid fungi, frequently occurs on bark and wood. Algae form a layer in or below fungal basidiomata reminiscent of the photobiont layer in lichens. Identities of algal and fungal partners were confirmed by DNA barcoding. Algal activity was examined using gas exchange and chlorophyll fluorescence techniques. Carbon transfer from algae to fungi was detected as 13C, assimilated by algae, transferred to the fungal polyol. Nine fungal partners scattered across Agaricomycetes are associated with three algae from Trebouxiophycae: Coccomyxa sp. with seven fungal species on damp wood, Desmococcus olivaceus and Tritostichococcus coniocybes, both with a single species on bark and rain-sheltered wood, respectively. The fungal partner does not cause any obvious harm to the algae. Algae enclosed in fungal tissue exhibited a substantial CO2 uptake, but carbon transfer to fungal tissues was only detected in the Lyomyces-Desmococcus alcobiosis where some algal cells are tightly enclosed by hyphae in goniocyst-like structures. Unlike lichen mycobionts, fungi in alcobioses are not nutritionally dependent on the algal partner as all of them can live without algae. We consider alcobioses to be symbioses in various stages of co-evolution, but still quite different from true lichens.
Synchrony to a beat predicts synchrony with other minds
Authors: Wohltjen Sophie , Toth Brigitta , Boncz Adam , Wheatley Thalia 
Published: March 2023

AbstractSynchrony has been used to describe simple beat entrainment as well as correlated mental processes between people, leading some to question whether the term conflates distinct phenomena. Here we ask whether simple synchrony (beat entrainment) predicts more complex attentional synchrony, consistent with a common mechanism. While eye-tracked, participants listened to regularly spaced tones and indicated changes in volume. Across multiple sessions, we found a reliable individual difference: some people entrained their attention more than others, as reflected in beat-matched pupil dilations that predicted performance. In a second study, eye-tracked participants completed the beat task and then listened to a storyteller, who had been previously recorded while eye-tracked. An individual’s tendency to entrain to a beat predicted how strongly their pupils synchronized with those of the storyteller, a corollary of shared attention. The tendency to synchronize is a stable individual difference that predicts attentional synchrony across contexts and complexity.
Drug–target interaction prediction based on protein features, using wrapper feature selection
Authors: Abbasi Mesrabadi Hengame , Faez Karim , Pirgazi Jamshid 
Published: March 2023

AbstractDrug–target interaction prediction is a vital stage in drug development, involving lots of methods. Experimental methods that identify these relationships on the basis of clinical remedies are time-taking, costly, laborious, and complex introducing a lot of challenges. One group of new methods is called computational methods. The development of new computational methods which are more accurate can be preferable to experimental methods, in terms of total cost and time. In this paper, a new computational model to predict drug–target interaction (DTI), consisting of three phases, including feature extraction, feature selection, and classification is proposed. In feature extraction phase, different features such as EAAC, PSSM and etc. would be extracted from sequence of proteins and fingerprint features from drugs. These extracted features would then be combined. In the next step, one of the wrapper feature selection methods named IWSSR, due to the large amount of extracted data, is applied. The selected features are then given to rotation forest classification, to have a more efficient prediction. Actually, the innovation of our work is that we extract different features; and then select features by the use of IWSSR. The accuracy of the rotation forest classifier based on tenfold on the golden standard datasets (enzyme, ion channels, G-protein-coupled receptors, nuclear receptors) is as follows: 98.12, 98.07, 96.82, and 95.64. The results of experiments indicate that the proposed model has an acceptable rate in DTI prediction and is compatible with the proposed methods in other papers.
Multidimensional variability in ecological assessments predicts two clusters of suicidal patients
Authors: Bonilla-Escribano Pablo , Ramírez David , Baca-García Enrique , Courtet Philippe , Artés-Rodríguez Antonio , López-Castromán Jorge 
Published: March 2023

AbstractThe variability of suicidal thoughts and other clinical factors during follow-up has emerged as a promising phenotype to identify vulnerable patients through Ecological Momentary Assessment (EMA). In this study, we aimed to (1) identify clusters of clinical variability, and (2) examine the features associated with high variability. We studied a set of 275 adult patients treated for a suicidal crisis in the outpatient and emergency psychiatric departments of five clinical centers across Spain and France. Data included a total of 48,489 answers to 32 EMA questions, as well as baseline and follow-up validated data from clinical assessments. A Gaussian Mixture Model (GMM) was used to cluster the patients according to EMA variability during follow-up along six clinical domains. We then used a random forest algorithm to identify the clinical features that can be used to predict the level of variability. The GMM confirmed that suicidal patients are best clustered in two groups with EMA data: low- and high-variability. The high-variability group showed more instability in all dimensions, particularly in social withdrawal, sleep measures, wish to live, and social support. Both clusters were separated by ten clinical features (AUC = 0.74), including depressive symptoms, cognitive instability, the intensity and frequency of passive suicidal ideation, and the occurrence of clinical events, such as suicide attempts or emergency visits during follow-up. Initiatives to follow up suicidal patients with ecological measures should take into account the existence of a high variability cluster, which could be identified before the follow-up begins.
An innovative wireless electrochemical card sensor for field-deployable diagnostics of Hepatitis B surface antigen
Authors: Teengam Prinjaporn , Tangkijvanich Pisit , Chuaypen Natthaya , Chailapakul Orawon 
Published: March 2023

AbstractA wireless-based detection utilizing an innovative electrochemical card (eCard) sensor controlled by a smartphone was developed for targeting Hepatitis B surface antigen (HBsAg). A simple label-free electrochemical platform allows a convenient operation for point-of-care diagnosis. A disposable screen-printed carbon electrode was modified straightforwardly layer-by-layer with chitosan followed by glutaraldehyde, allowing a simple but effective, reproducible, and stable method for covalently immobilizing antibodies. The modification and immobilization processes were verified by electrochemical impedance spectroscopy and cyclic voltammetry. The smartphone-based eCard sensor was used to quantify HBsAg by measuring the change in current response of the [Fe(CN)6]3-/4- redox couple before and after the presence of HBsAg. Under the optimal conditions, the linear calibration curve for HBsAg was found to be 10–100,000 IU/mL with a detection limit of 9.55 IU/mL. The HBsAg eCard sensor was successfully applied to detect 500 chronic HBV-infected serum samples with satisfactory results, demonstrating the excellent applicability of this system. The sensitivity and specificity of this sensing platform were found to be 97.75% and 93%, respectively. As illustrated, the proposed eCard immunosensor offered a rapid, sensitive, selective, and easy-to-use platform for healthcare providers to rapidly determine the infection status of HBV patients.
Effects of occipital-atlas stabilization on the upper cervical spine rotation combinations: an in vitro study
Authors: Hidalgo-García César , Lorente Ana I. , López-de-Celis Carlos , Lucha-López María Orosia , Rodríguez-Sanz Jacobo , Maza-Frechín Mario , Tricás-Moreno José Miguel , Krauss John , Pérez-Bellmunt Albert 
Published: March 2023

AbstractThe purpose of this study is to compare axial rotation range of motion for the upper cervical spine during three movements: axial rotation, rotation + flexion + ipsilateral lateral bending and rotation + extension + contralateral lateral bending before and after occiput-atlas (C0–C1) stabilization. Ten cryopreserved C0–C2 specimens (mean age 74 years, range 63–85 years) were manually mobilized in 1. axial rotation, 2. rotation + flexion + ipsilateral lateral bending and 3. rotation + extension + contralateral lateral bending without and with a screw stabilization of C0–C1. Upper cervical range of motion and the force used to generate the motion were measured using an optical motion system and a load cell respectively. The range of motion (ROM) without C0–C1 stabilization was 9.8° ± 3.9° in right rotation + flexion + ipsilateral lateral bending and 15.5° ± 5.9° in left rotation + flexion + ipsilateral lateral bending. With stabilization, the ROM was 6.7° ± 4.3° and 13.6° ± 5.3°, respectively. The ROM without C0–C1 stabilization was 35.1° ± 6.0° in right rotation + extension + contralateral lateral bending and 29.0° ± 6.5° in left rotation + extension + contralateral lateral bending. With stabilization, the ROM was 25.7° ± 6.4° (p = 0.007) and 25.3° ± 7.1°, respectively. Neither rotation + flexion + ipsilateral lateral bending (left or right) or left rotation + extension + contralateral lateral bending reached statistical significance. ROM without C0–C1 stabilization was 33.9° ± 6.7° in right rotation and 28.0° ± 6.9° in left rotation. With stabilization, the ROM was 28.5° ± 7.0° (p = 0.005) and 23.7° ± 8.5° (p = 0.013) respectively. The stabilization of C0–C1 reduced the upper cervical axial rotation in right rotation + extension + contralateral lateral bending and right and left axial rotations; however, this reduction was not present in left rotation + extension + contralateral lateral bending or both combinations of rotation + flexion + ipsilateral lateral bending.