bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bronchopulmonary dysplasia prediction models: a systematic review and meta-analysis with validation
Authors: Kwok T’ng Chang , Batey Natalie , Luu Ka Ling , Prayle Andrew , Sharkey Don 
Published: January 2023

Abstract
Prediction models could identify infants at the greatest risk of bronchopulmonary dysplasia (BPD) and allow targeted preventative strategies. We performed a systematic review and meta-analysis with external validation of identified models. Studies using predictors available before day 14 of life to predict BPD in very preterm infants were included. Two reviewers assessed 7628 studies for eligibility. Meta-analysis of externally validated models was followed by validation using 62,864 very preterm infants in England and Wales. A total of 64 studies using 53 prediction models were included totalling 274,407 infants (range 32–156,587/study). In all, 35 (55%) studies predated 2010; 39 (61%) were single-centre studies. A total of 97% of studies had a high risk of bias, especially in the analysis domain. Following meta-analysis of 22 BPD and 11 BPD/death composite externally validated models, Laughon’s day one model was the most promising in predicting BPD and death (C-statistic 0.76 (95% CI 0.70–0.81) and good calibration). Six models were externally validated in our cohort with C-statistics between 0.70 and 0.90 but with poor calibration. Few BPD prediction models were developed with contemporary populations, underwent external validation, or had calibration and impact analyses. Contemporary, validated, and dynamic prediction models are needed for targeted preventative strategies.

Impact

This review aims to provide a comprehensive assessment of all BPD prediction models developed to address the uncertainty of which model is sufficiently valid and generalisable for use in clinical practice and research.

Published BPD prediction models are mostly outdated, single centre and lack external validation.

Laughon’s 2011 model is the most promising but more robust models, using contemporary data with external validation are needed to support better treatments.
A phase I trial of LXS196, a protein kinase C (PKC) inhibitor, for metastatic uveal melanoma
Authors: Piperno-Neumann S. , Carlino M. S. , Boni V. , Loirat D. , Speetjens F. M. , Park J. J. , Calvo E. , Carvajal R. D. , Nyakas M. , Gonzalez-Maffe J. , Zhu X. , Shirley M. D. , Ramkumar T. , Fessehatsion A. , Burks H. E. , Yerramilli-Rao P. , Kapiteijn E. 
Published: January 2023

Abstract
Background
Up to 50% of patients with uveal melanoma develop metastases (MUM) with a poor prognosis and median overall survival of approximately 1 year.

Methods
This phase I study evaluated the safety, tolerability, pharmacokinetics, pharmacodynamics and efficacy of the oral protein kinase C inhibitor LXS196 in 68 patients with MUM (NCT02601378). Patients received LXS196 doses ranging from 100–1000 mg once daily (QD; n = 38) and 200–400 mg twice daily (BID; n = 30).

Results
First cycle dose-limiting toxicities (DLTs) were observed in 7/38 (18.4%) QD and 2/17 (11.8%) BID patients. Hypotension was the most common DLT, occurring at doses ≥500 mg/day, and manageable with LXS196 interruption and dose reduction. Median duration of exposure to LXS196 was 3.71 months (range: 1.81–15.28) for QD and 4.6 months (range: 0.33–58.32) for BID dosing. Clinical activity was observed in 6/66 (9.1%) evaluable patients achieving response (CR/PR), with a median duration of response of 10.15 months (range: 2.99–41.95); 45/66 had stable disease (SD) per RECIST v1.1. At 300 mg BID, the recommended dose for expansion, 2/18 (11.1%) evaluable patients achieved PR and 12/18 (66.7%) had SD.

Conclusion
These results suggest manageable toxicity and encouraging clinical activity of single-agent LXS196 in patients with MUM.
CSF1R inhibitors induce a sex-specific resilient microglial phenotype and functional rescue in a tauopathy mouse model
Authors: Johnson Noah R. , Yuan Peng , Castillo Erika , Lopez T. Peter , Yue Weizhou , Bond Annalise , Rivera Brianna M. , Sullivan Miranda C. , Hirouchi Masakazu , Giles Kurt , Aoyagi Atsushi , Condello Carlo 
Published: January 2023

AbstractMicroglia are central to pathogenesis in many neurological conditions. Drugs targeting colony-stimulating factor-1 receptor (CSF1R) to block microglial proliferation in preclinical disease models have shown mixed outcomes, thus the therapeutic potential of this approach remains unclear. Here, we show that CSF1R inhibitors given by multiple dosing paradigms in the Tg2541 tauopathy mouse model cause a sex-independent reduction in pathogenic tau and reversion of non-microglial gene expression patterns toward a normal wild type signature. Despite greater drug exposure in male mice, only female mice have functional rescue and extended survival. A dose-dependent upregulation of immediate early genes and neurotransmitter dysregulation are observed in the brains of male mice only, indicating that excitotoxicity may preclude functional benefits. Drug-resilient microglia in male mice exhibit morphological and gene expression patterns consistent with increased neuroinflammatory signaling, suggesting a mechanistic basis for sex-specific excitotoxicity. Complete microglial ablation is neither required nor desirable for neuroprotection and therapeutics targeting microglia must consider sex-dependent effects.
Thermodynamic architecture and conformational plasticity of GPCRs
Authors: Anantakrishnan Sathvik , Naganathan Athi N. 
Published: January 2023

AbstractG-protein-coupled receptors (GPCRs) are ubiquitous integral membrane proteins involved in diverse cellular signaling processes. Here, we carry out a large-scale ensemble thermodynamic study of 45 ligand-free GPCRs employing a structure-based statistical mechanical framework. We find that multiple partially structured states co-exist in the GPCR native ensemble, with the TM helices 1, 6 and 7 displaying varied folding status, and shaping the conformational landscape. Strongly coupled residues are anisotropically distributed, accounting for only 13% of the residues, illustrating that a large number of residues are inherently dynamic. Active-state GPCRs are characterized by reduced conformational heterogeneity with altered coupling-patterns distributed throughout the structural scaffold. In silico alanine-scanning mutagenesis reveals that extra- and intra-cellular faces of GPCRs are coupled thermodynamically, highlighting an exquisite structural specialization and the fluid nature of the intramolecular interaction network. The ensemble-based perturbation methodology presented here lays the foundation for understanding allosteric mechanisms and the effects of disease-causing mutations in GCPRs.
Gray matter volume drives the brain age gap in schizophrenia: a SHAP study
Authors: Ballester Pedro L. , Suh Jee Su , Ho Natalie C. W. , Liang Liangbing , Hassel Stefanie , Strother Stephen C. , Arnott Stephen R. , Minuzzi Luciano , Sassi Roberto B. , Lam Raymond W. , Milev Roumen , Müller Daniel J. , Taylor Valerie H. , Kennedy Sidney H. , Reilly James P. , Palaniyappan Lena , Dunlop Katharine , Frey Benicio N. 
Published: January 2023

AbstractNeuroimaging-based brain age is a biomarker that is generated by machine learning (ML) predictions. The brain age gap (BAG) is typically defined as the difference between the predicted brain age and chronological age. Studies have consistently reported a positive BAG in individuals with schizophrenia (SCZ). However, there is little understanding of which specific factors drive the ML-based brain age predictions, leading to limited biological interpretations of the BAG. We gathered data from three publicly available databases - COBRE, MCIC, and UCLA - and an additional dataset (TOPSY) of early-stage schizophrenia (82.5% untreated first-episode sample) and calculated brain age with pre-trained gradient-boosted trees. Then, we applied SHapley Additive Explanations (SHAP) to identify which brain features influence brain age predictions. We investigated the interaction between the SHAP score for each feature and group as a function of the BAG. These analyses identified total gray matter volume (group × SHAP interaction term β = 1.71 [0.53; 3.23]; pcorr < 0.03) as the feature that influences the BAG observed in SCZ among the brain features that are most predictive of brain age. Other brain features also presented differences in SHAP values between SCZ and HC, but they were not significantly associated with the BAG. We compared the findings with a non-psychotic depression dataset (CAN-BIND), where the interaction was not significant. This study has important implications for the understanding of brain age prediction models and the BAG in SCZ and, potentially, in other psychiatric disorders.
LAP1 supports nuclear adaptability during constrained melanoma cell migration and invasion
Authors: Jung-Garcia Yaiza , Maiques Oscar , Monger Joanne , Rodriguez-Hernandez Irene , Fanshawe Bruce , Domart Marie-Charlotte , Renshaw Matthew J. , Marti Rosa M. , Matias-Guiu Xavier , Collinson Lucy M. , Sanz-Moreno Victoria , Carlton Jeremy G. 
Published: January 2023

AbstractMetastasis involves dissemination of cancer cells away from a primary tumour and colonization at distal sites. During this process, the mechanical properties of the nucleus must be tuned since they pose a challenge to the negotiation of physical constraints imposed by the microenvironment and tissue structure. We discovered increased expression of the inner nuclear membrane protein LAP1 in metastatic melanoma cells, at the invasive front of human primary melanoma tumours and in metastases. Human cells express two LAP1 isoforms (LAP1B and LAP1C), which differ in their amino terminus. Here, using in vitro and in vivo models that recapitulate human melanoma progression, we found that expression of the shorter isoform, LAP1C, supports nuclear envelope blebbing, constrained migration and invasion by allowing a weaker coupling between the nuclear envelope and the nuclear lamina. We propose that LAP1 renders the nucleus highly adaptable and contributes to melanoma aggressiveness.
Improved cytosine base editors generated from TadA variants
Authors: Lam Dieter K. , Feliciano Patricia R. , Arif Amena , Bohnuud Tanggis , Fernandez Thomas P. , Gehrke Jason M. , Grayson Phil , Lee Kin D. , Ortega Manuel A. , Sawyer Courtney , Schwaegerle Noah D. , Peraro Leila , Young Lauren , Lee Seung-Joo , Ciaramella Giuseppe , Gaudelli Nicole M. 
Published: January 2023

AbstractCytosine base editors (CBEs) enable programmable genomic C·G-to-T·A transition mutations and typically comprise a modified CRISPR–Cas enzyme, a naturally occurring cytidine deaminase, and an inhibitor of uracil repair. Previous studies have shown that CBEs utilizing naturally occurring cytidine deaminases may cause unguided, genome-wide cytosine deamination. While improved CBEs that decrease stochastic genome-wide off-targets have subsequently been reported, these editors can suffer from suboptimal on-target performance. Here, we report the generation and characterization of CBEs that use engineered variants of TadA (CBE-T) that enable high on-target C·G to T·A across a sequence-diverse set of genomic loci, demonstrate robust activity in primary cells and cause no detectable elevation in genome-wide mutation. Additionally, we report cytosine and adenine base editors (CABEs) catalyzing both A-to-I and C-to-U editing (CABE-Ts). Together with ABEs, CBE-Ts and CABE-Ts enable the programmable installation of all transition mutations using laboratory-evolved TadA variants with improved properties relative to previously reported CBEs.
Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
Authors: Tan Jimin , Shenker-Tauris Nina , Rodriguez-Hernaez Javier , Wang Eric , Sakellaropoulos Theodore , Boccalatte Francesco , Thandapani Palaniraja , Skok Jane , Aifantis Iannis , Fenyö David , Xia Bo , Tsirigos Aristotelis 
Published: January 2023

AbstractInvestigating how chromatin organization determines cell-type-specific gene expression remains challenging. Experimental methods for measuring three-dimensional chromatin organization, such as Hi-C, are costly and have technical limitations, restricting their broad application particularly in high-throughput genetic perturbations. We present C.Origami, a multimodal deep neural network that performs de novo prediction of cell-type-specific chromatin organization using DNA sequence and two cell-type-specific genomic features—CTCF binding and chromatin accessibility. C.Origami enables in silico experiments to examine the impact of genetic changes on chromatin interactions. We further developed an in silico genetic screening approach to assess how individual DNA elements may contribute to chromatin organization and to identify putative cell-type-specific trans-acting regulators that collectively determine chromatin architecture. Applying this approach to leukemia cells and normal T cells, we demonstrate that cell-type-specific in silico genetic screening, enabled by C.Origami, can be used to systematically discover novel chromatin regulation circuits in both normal and disease-related biological systems.
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs
Authors: Han Alvin X. , Toporowski Amy , Sacks Jilian A. , Perkins Mark D. , Briand Sylvie , van Kerkhove Maria , Hannay Emma , Carmona Sergio , Rodriguez Bill , Parker Edyth , Nichols Brooke E. , Russell Colin A. 
Published: January 2023

AbstractThe first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated COVID-19 epidemics in a prototypical low- and middle-income country to investigate how testing rates, sampling strategies and sequencing proportions jointly impact surveillance outcomes, and showed that low testing rates and spatiotemporal biases delay time to detection of new variants by weeks to months and can lead to unreliable estimates of variant prevalence, even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of approximately 100 tests per 100,000 people per day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.
Apolipoprotein C3 facilitates internalization of cationic lipid nanoparticles into bone marrow-derived mouse mast cells
Authors: Alam Syed Benazir , Wang Feng , Qian Hui , Kulka Marianna 
Published: January 2023

AbstractMast cells (MCs), are hematopoetically-derived secretory immune cells that release preformed as well as de novo synthesized inflammatory mediators in response to activation by several stimuli. Based on their role in inflammatory responses, particularly in the lung and skin, MCs provide an effective target for anti-inflammatory therapeutic strategies. Drug-delivery of lipophilic payloads to MCs can be challenging due to their functionally distinct intracellular structures. In the present study, pH-sensitive cationic lipid-based nanoparticles (LNPs) composed of DODMA, DODAP or DOTAP lipids that encapsulated a GFP or eGFP plasmid were constructed using non-turbulent microfluidic mixing. This approach achieved up to 75–92% encapsulation efficiency. Dynamic light scattering revealed a uniformly sized and homogeneous dispersion of LNPs. To promote cellular internalization, LNPs were complexed with apolipoproteins, amphipathic proteins capable of binding lipids and facilitating their transport into cells. Cryo-TEM analysis showed that LNP structure was differentially modified when associated with different types of apolipoproteins. LNP preparations made up of DODMA or DODMA, DODAP and DOTAP lipids were coated with seven apolipoproteins (Apo A1, B, C3, D, E2, E4 and H). Differentiated bone-marrow derived mouse mast cells (BMMCs) were exposed to apolipoprotein-LNP and internalization was measured using flow cytometry. Out of all the apolipoproteins tested, ApoC3 most efficiently facilitated cellular internalization of the LNP into BMMCs as determined by GFP fluorescence using flow cytometry. These effects were confirmed in a less differentiated but also interleukin-3-dependent model of mouse mast cells, MC/9. ApoC3-LNP enhanced internalization by BMMC in a concentration-dependent manner and this was significantly increased when BMMC were pre-treated with inhibitors of actin polymerization, suggesting a dependence on intracellular shuttling. Activation of peroxisome proliferator-activated receptor gamma (PPARγ) decreased ApoC3-LNP internalization and reduced the expression of apolipoprotein E receptor 2 (ApoER2), suggesting that ApoC3-LNP binding to ApoER2 may be responsible for its enhanced internalization. Furthermore, ApoC3 fails to facilitate internalization of LNPs in Lrp8−/− KO BMMC that do not express ApoER2 on their cell surface. Altogether, our studies reveal an important role of ApoC3 in facilitating internalization of cationic LNPs into MCs.
Prion protein amino acid sequence influences formation of authentic synthetic PrPSc
Authors: Block Alyssa J. , York Taylor C. , Benedict Romilly , Ma Jiyan , Bartz Jason C. 
Published: January 2023

AbstractSynthetic prions, generated de novo from minimal, non-infectious components, cause bona fide prion disease in animals. Transmission of synthetic prions to hosts expressing syngeneic PrPC results in extended, variable incubation periods and incomplete attack rates. In contrast, murine synthetic prions (MSP) generated via PMCA with minimal cofactors readily infected mice and hamsters and rapidly adapted to both species. To investigate if hamster synthetic prions (HSP) generated under the same conditions as the MSP are also highly infectious, we inoculated hamsters with HSP generated with either hamster wild type or mutant (ΔG54, ΔG54/M139I, M139I/I205M) recombinant PrP. None of the inoculated hamsters developed clinical signs of prion disease, however, brain homogenate from HSPWT- and HSPΔG54-infected hamsters contained PrPSc, indicating subclinical infection. Serial passage in hamsters resulted in clinical disease at second passage accompanied by changes in incubation period and PrPSc conformational stability between second and third passage. These data suggest the HSP, in contrast to the MSP, are not comprised of PrPSc, and instead generate authentic PrPSc via deformed templating. Differences in infectivity between the MSP and HSP suggest that, under similar generation conditions, the amino acid sequence of PrP influences generation of authentic PrPSc.
Rapid prediction of secondary neurologic decline after traumatic brain injury: a data analytic approach
Authors: Podell Jamie , Yang Shiming , Miller Serenity , Felix Ryan , Tripathi Hemantkumar , Parikh Gunjan , Miller Catriona , Chen Hegang , Kuo Yi-Mei , Lin Chien Yu , Hu Peter , Badjatia Neeraj 
Published: January 2023

AbstractSecondary neurologic decline (ND) after traumatic brain injury (TBI) is independently associated with outcome, but robust predictors of ND are lacking. In this retrospective analysis of consecutive isolated TBI admissions to the R. Adams Cowley Shock Trauma Center between November 2015 and June 2018, we aimed to develop a triage decision support tool to quantify risk for early ND. Three machine learning models based on clinical, physiologic, or combined characteristics from the first hour of hospital resuscitation were created. Among 905 TBI cases, 165 (18%) experienced one or more ND events (130 clinical, 51 neurosurgical, and 54 radiographic) within 48 h of presentation. In the prediction of ND, the clinical plus physiologic data model performed similarly to the physiologic only model, with concordance indices of 0.85 (0.824–0.877) and 0.84 (0.812–0.868), respectively. Both outperformed the clinical only model, which had a concordance index of 0.72 (0.688–0.759). This preliminary work suggests that a data-driven approach utilizing physiologic and basic clinical data from the first hour of resuscitation after TBI has the potential to serve as a decision support tool for clinicians seeking to identify patients at high or low risk for ND.
3D printing of hollow geometries using blocking liquid substitution stereolithography
Authors: Bhanvadia Aftab A. , Farley Richard T. , Noh Youngwook , Nishida Toshikazu 
Published: January 2023

AbstractMicrometer scale arbitrary hollow geometries within a solid are needed for a variety of applications including microfluidics, thermal management and metamaterials. A major challenge to 3D printing hollow geometries using stereolithography is the ability to retain empty spaces in between the solidified regions. In order to prevent unwanted polymerization of the trapped resin in the hollow spaces—known as print-through—significant constraints are generally imposed on the primary process parameters such as resin formulation, exposure conditions and layer thickness. Here, we report on a stereolithography process which substitutes the trapped resin with a UV blocking liquid to mitigate print-through. We investigate the mechanism of the developed process and determine guidelines for the formulation of the blocking liquid. The reported method decouples the relationship between the primary process parameters and their effect on print-through. Without having to optimize the primary process parameters to reduce print-through, hollow heights that exceed the limits of conventional stereolithography can be realized. We demonstrate fabrication of a variety of complex hollow geometries with cross-sectional features ranging from tens of micrometer to hundreds of micrometers in size. With the framework presented, this method may be employed for 3D printing functional hollow geometries for a variety of applications, and with improved freedom over the printing process (e.g. material choices, speed and resulting properties of the printed parts).
Exploration of body weight in 115 000 young adult dogs of 72 breeds
Authors: Andersson L. , Emanuelson U. , Ringmark S. , Bjørnvad C. R. , Hedhammar Å. , Höglund K. 
Published: January 2023

AbstractHigh body weight (BW), due to large size or excess body fat, has been associated with developmental and metabolic alterations, and degenerative diseases in dogs. Study objectives were to determine mean BW in young adult dogs of different breeds, including changes over a 10-year period. Body weight data from the official Swedish hip dysplasia screening program were used, including data from dogs screened at 1–2.5 years of age, in breeds with ≥ 15 individual observations/year during 2007–2016. Mean BW per breed and sex was established from 114 568 dogs representing 72 breeds. Estimates of breed BW showed significant change in 33 (45%) breeds over the 10-year period. Body weight increased in five breeds (2–14% change) and decreased in 26 breeds (1–8% change). In two breeds, BW increased in male and decreased in female dogs. This observational study provides extensive breed BW data on young adult dogs. The change in breed BW, noted in almost half of the breeds, could be due to changes either in size or in body fat mass. In certain breeds, the change in BW over time might have an impact on overall health. Studies with simultaneous evaluation of BW and body condition over time are warranted.