bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the small aperture intraocular lens: depth of focus and the role of refraction and preoperative corneal astigmatism in visual performance
Authors: Vukich John , Thompson Vance , Yeu Elizabeth , Wiley William F. , Bafna Shamik , Koch Douglas D. , Lin Ling , Michna Magda 
Published: July 2024

Purpose:
To evaluate depth of focus (DOF) and visual acuities (VAs) by manifest refractive spherical equivalent (MRSE) and degree of preoperative corneal astigmatism with the IC-8 small aperture intraocular lens (SA IOL) (Apthera).

Setting:
21 investigational sites in the United States.

Design:
Prospective, multicenter, open-label, parallel-group, nonrandomized, examiner-masked, 1-year clinical study.

Methods:
Included patients had cataract and ≤1.5 diopters (D) preoperative corneal astigmatism. Patients received either the SA IOL in 1 eye targeted to −0.75 D and a monofocal or monofocal toric IOL in the other targeted to plano (SA IOL group) or bilateral monofocal/monofocal toric IOLs targeted to plano (control group). Monocular and binocular assessments included defocus curves and uncorrected VAs (distance, intermediate, and near) by postoperative MRSE; monocular VAs were assessed by degree of preoperative corneal astigmatism.

Results:
The SA IOL group (n = 343) achieved 0.82 D additional binocular DOF vs the control group (n = 110), and SA IOL eyes achieved 0.91 D additional monocular DOF over fellow eyes. Across all MRSEs, the SA IOL group achieved monocular uncorrected VAs of 20/40 or better and binocular uncorrected VAs of 20/32 or better across all distances. In addition, SA IOL eyes with higher (1.0-1.5 D) vs lower (<1.0 D) preoperative corneal astigmatism achieved equivalent monocular uncorrected VAs.

Conclusions:
The SA IOL provides increased DOF vs monofocal/monofocal toric IOLs and consistent monocular and binocular vision across several postoperative MRSEs and up to 1.5 D of preoperative corneal astigmatism, giving patients with cataract and mild astigmatism the potential for an extended range of vision and reliable visual outcomes.
Vulvar Inspection During Cervical Cancer Screening Procedures: The Ugly Reality
Authors: Preti Mario , Anderson Karin , Venturino Ezio , Maggino Tiziano , Carozzi Francesca , Robba Eleonora , Vieira-Baptista Pedro , Borella Fulvio , Barchi Laura , Bevilacqua Federica , Gallio Niccolò , Barbierato Ilaria , Pollano Benedetta , Cavallero Camilla , Gardner-Medwin Samuel , Benedetto Chiara , Bucchi Lauro 
Published: July 2024

Abstract
Vulvar examination during procedures for cervical carcinoma screening (CCS) can be a valid chance for early diagnosis of vulvar diseases and precancerous lesions. With this aim an online questionnaire was sent to the members of the Italian Cervical Carcinoma Screening Group (GISCi) from either first level group (FLG, Pap/human papillomavirus test sampling) or second level group (SLG, colposcopy and treatments) to assess if and how vulvar examination was performed. 86% of FLG and 90.2% of SLG report performing vulvar examination prior to CCS procedures. 15% of SLG cannot manage basic vulvar diseases and they refer patients to specialized center. 54.3% underline lack of standardized protocol in case of vulvar disease detection. Despite most health care professionals report examining the vulva during CCS procedures, vulvar cancer early diagnosis is still challenging.
Dietary protein splanchnic uptake and digestibility via stable isotope tracers
Authors: Cox Jake , Wilkinson Daniel James , Atherton Philip James , Smith Kenneth 
Published: July 2024

Purpose of review
Dietary proteins are broken down into peptides across the gastrointestinal tract, with skeletal muscle being a primary deposition site for amino acids in the form of incorporation into, for example, metabolic and structural proteins. It follows that key research questions remain as to the role of amino acid bioavailability, of which protein digestibility and splanchnic sequestration (absorption and utilization) of amino acids are determining factors, impact upon muscle protein synthesis (MPS) in clinical states.

Recent findings
Elevated splanchnic amino acid uptake has been implicated in anabolic resistance (i.e. attenuated anabolic responses to protein intake) observed in ageing, though it is unclear whether this limits MPS. The novel ‘dual stable isotope tracer technique’ offers a promising, minimally invasive approach to quantify the digestion of any protein source(s). Current work is focused on the validation of this technique against established methods, with scope to apply this to clinical and elderly populations to help inform mechanistic and interventional insights.

Summary
Considerations should be made for all facets of protein quality; digestibility of the protein, absorption/utilization and subsequent peripheral bioavailability of amino acids, and resultant stimulation of MPS. Stable isotope tracer techniques offer a minimally invasive approach to achieve this, with wide-ranging clinical application.
Mesorhizobium retamae sp. nov., a novel non-nodulating and non-nitrogen-fixing species isolated from the root nodules of Retama raetam sampled in Tunisia
Authors: Ben Gaied Roukaya , Sbissi Imed , Tarhouni Mohamed , Huber Katharina , Wolf Jacqueline , Neumann-Schaal Meina , Nouioui Imen , Ghodhbane-Gtari Faten , Gtari Maher 
Published: July 2024

A comprehensive polyphasic taxonomic investigation integrating taxongenomic criteria was conducted on strain IRAMC:0171T isolated from the root nodules of Retama raetam in Tunisia. This Gram-stain-negative and aerobic bacterium thrived within a temperature range of 5–45 °C, optimal at 28 °C, and tolerated salt concentrations from 0–6 % NaCl, with an optimal range of 0–3 %. It displayed pH tolerance from pH 4 to 10, thriving best at pH 6.8–7.5. Chemotaxonomically, strain IRAMC:0171T was characterized by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and phosphatidylethanolamine as polar lipids. Its predominant fatty acid composition was C18 : 1
ω7c (61.2 %), and the primary ubiquinone was Q10 (97 %). Analysis of the 16S rRNA gene of strain IRAMC:0171T showed 99.08 % similarity to Mesorhizobium waimense ICMP 19557T, Mesorhizobium amorphae ACCC 19665T, and Mesorhizobium huakuii IAM 14158. However, digital DNA–DNA hybridization and average nucleotide identity analyses revealed values ranging from 21.1 to 25.2 % and 77.05 to 82.24 %, respectively, signifying significant deviation from established species demarcation thresholds. Phylogenetic studies, encompassing 16S rRNA, whole-genome-based tree reconstruction, and core protein analysis, positioned strain IRAMC:0171T closest to Mesorhizobium terrae KCTC 72278T and ‘Mesorhizobium hungaricum’ UASWS1009T, forming together a distinct branch within the genus Mesorhizobium. In consideration of this comprehensive data, we propose strain IRAMC:0171T (=DSM 112841T=CECT 30767T) as the type strain of a new species named Mesorhizobium retamae sp. nov.
Artificial Intelligence Algorithms in Nailfold Capillaroscopy Image Analysis: A Systematic Review
Authors: Emam Omar S. , Ebadi Jalal Mona , Garcia-Zapirain Begonya , Elmaghraby Adel S. 
Published: July 2024

ABSTRACTBackgroundNon-invasive imaging modalities offer a great deal of clinically significant information that aid in the diagnosis of various medical conditions. Coupled with the never-before-seen capabilities of Artificial Intelligence (AI), uncharted territories that offer novel innovative diagnostics are reached. This systematic review compiled all studies that utilized AI in Nailfold Capillaroscopy as a future diagnostic tool.Methods and FindingsFive databases for medical publications were searched using the keywords artificial intelligence, machine learning, deep learning and nailfold capillaroscopy to return 105 studies. After applying the eligibility criteria, 10 studies were selected for the final analysis. Data was extracted into tables that addressed population characteristics, AI model development and nature and results of their respective performance. We found supervised deep learning approaches to be the most commonly used (n= 8). Systemic Sclerosis was the most commonly studied disease (n= 6). Sample size ranged from 17,126 images obtained from 289 participants to 50 images from 50 participants. Ground truth was determined either by experts labelling (n= 6) or known clinical status (n= 4). Significant variation was noticed in model training, testing and feature extraction, and therefore the reporting of model performance. Recall, precision and Area Under the Curve were the most used metrics to report model performance. Execution times ranged from 0.064 to 120 seconds per image. Only two models offered future predictions besides the diagnostic output.ConclusionsAI has demonstrated a truly remarkable potential in the interpretation of Nailfold Capillaroscopy by providing physicians with an intelligent decision-supportive tool for improved diagnostics and prediction. With more validation studies, this potential can be translated to daily clinical practice.
Paternal genome elimination creates contrasting evolutionary trajectories in male and female citrus mealybugs
Authors: Mongue Andrew J. , Woodman Tamsin , Marshall Hollie , Garber Arkadiy , Franco José C. , McCutcheon John P. , Ross Laura 
Published: July 2024

AbstractMost studies of sex-biased genes explore their evolution in familiar chromosomal sex determination systems, leaving the evolution of sex differences under alternative reproductive systems unknown. Here we explore the system of paternal genome elimination employed by mealybugs (Hempitera: Pseudococcidae) which have no sex chromosomes. Instead, all chromosomes are autosomal and inherited in two copies, but sex is determined by the ploidy of expression. Females express both parental alleles, but males reliably silence their paternally inherited chromosomes, creating genome-wide haploid expression in males and diploid expression in females. Additionally, sons do not express alleles directly inherited from their fathers, potentially disrupting the evolution of male-benefitting traits. To understand how these dynamics impact molecular evolution, we generated sex-specific RNAseq, a new gene annotation, and whole-genome population sequencing of the citrus mealybug,Planococcus citri. We found that genes expressed primarily in females hold more variation and evolve more quickly than those expressed in males or both sexes. Conversely, more adaptation occurs in genes expressed mainly in males than those expressed in females. Put together, paternal genome elimination appears to slow change on the male side but, by increasing selective scrutiny, increase the amount of adaptation in these genes. These results expand our understanding of evolution in a non-mendelian genetic system and the data we generated should prove useful for future research on this pest insect.
Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference
Authors: Lareau Caleb A. , Chapman Michael S. , Penter Livius , Nawy Tal , Pe’er Dana , Ludwig Leif S. 
Published: July 2024

AbstractSequencing mitochondrial DNA (mtDNA) variants from single cells has resolved clonality and lineage in native human samples and clinical specimens. Prior work established that heteroplasmic mtDNA variants can be used to delineate clonality in hematopoiesis, but they have limited ability to reconstruct cellular phylogenies. However, a recent report by Wenget al. challenges the current paradigm by describing an unprecedented number of shared mtDNA variants between cells that reportedly resolve high-resolution phylogenetic trees. We re-examined the claims of Wenget al., and identified two major points of concern regarding this unprecedented connectedness. First, shared variants between cells are disproportionately detected in a single molecule per cell, and second, these variants are enriched 10–20-fold at the edges of mtDNA molecules, reminiscent of artifacts reported in other sequencing approaches. Further, our analyses show that pruning low support and likely artificial mtDNA variants removes nearly all of the reported phylogenetic structure. Thus, we strongly caution against using mtDNA variant calling workflows that rely on minimal evidence, including the computational pipeline introduced in Wenget al., as variants with high connectedness and low evidence are likely artifacts that lead to the construction of false phylogenies.
Biomarker Discovery in Alzheimer’s and Neurodegenerative Diseases using Nucleic Acid-Linked Immuno-Sandwich Assay
Authors: Ashton Nicholas J. , Benedet Andrea L. , Di Molfetta Guglielmo , Pola Ilaria , Anastasi Federica , Fernández-Lebrero Aida , Puig-Pijoan Albert , Keshavan Ashvini , Schott Jonathan , Tan Kubra , Montoliu-Gaya Laia , Isaacson Richard , Bongianni Matilde , Tolassi Chiara , Cantoni Valentina , Alberici Antonella , Padovani Alessandro , Zanusso Gianluigi , Pilotto Andrea , Borroni Barbara , Suárez-Calvet Marc , Blennow Kaj , Zetterberg Henrik 
Published: July 2024

ABSTRACTINTRODUCTIONRecent advancements in immunological methods accurately quantify biofluid biomarkers for identifying Alzheimer’s pathology and neurodegeneration. Despite this progress, more biomarkers, ideally in blood, are needed for effective patient management and disease monitoring for Alzheimer’s disease (AD) and other neurodegenerative proteinopathies.METHODSWe employed the Nucleic Acid-Linked Immuno-Sandwich Assay (NULISA™) central nervous system (CNS) panel for biomarker quantification in plasma, serum and cerebrospinal fluid (CSF) of patients with AD, mild cognitive impairment, Lewy body dementia, progranulin (GRN) mutation carriers and matched controls.RESULTSNULISA™ identified p-tau217 and NfL as the most significantly deregulated plasma biomarkers in the AD continuum andGRNmutation carriers, respectively. Importantly, numerous novel and significant proteomic changes were observed in each disease comparison, which included proteins involved in synaptic processing, inflammation, microglial reactivity, TDP-43 and α-synuclein pathology. Plasma and serum act as complimentary biofluids.CONCLUSIONWe highlight the potential of next-generation biomarker identification tools, such as NULISA™, to detect novel proteomic features that incorporate established biomarkers like p-tau217 and NfL. These findings highlight the importance of continued biomarker discovery to enhance patient management, improve treatment decisions, and better understand the complexities of neurodegenerative disorders.
Evaluation of Hepatitis B core related antigen (HBcrAg) as a biomarker in cohorts from the United Kingdom and South Africa
Authors: Downs Louise O , Delphin Marion , Schalwyk Marije van , Hugo Susan , Gabriel Shiraaz , Lumley Sheila F , Waddilove Elizabeth , Wang Tingyan , Lara Catherine de , Babbs Arran , Wareing Sue , Fengou Polyxeni , Andersson Monique I , Glashoff Richard , Martin Jacqueline , Ansari M. Azim , Agarwal Kosh , Dusheiko Geoffrey , Taljaard Jantjie , Preiser Wolfgang , Barnes Eleanor , Kelly Gavin , Carey Ivana , Shimakawa Yusuke , Maponga Tongai , Matthews Philippa C 
Published: July 2024

ABSTRACTIntroductionBetter understanding of hepatitis B virus (HBV) biomarkers is needed. We evaluated Hepatitis B core related antigen (HBcrAg), in the United Kingdom (UK) and South Africa (SA).MethodsWe undertook a cross-sectional retrospective observational study of adults with chronic HBV infection from the UK (n=142) and SA (n=211). We recorded clinical and laboratory parameters and quantified HBcrAg. We report HBcrAg distribution, relationship with other biomarkers, and performance in risk stratification based on point of care test (POCT) thresholds.ResultsSA and UK cohorts were similar in sex and age (p>0.05), but significantly different in ethnicity, HIV coinfection, HBeAg-positivity and proportion with HBV viral load (VL) >200,000 IU/ml (all p<0.001). More of the untreated SA population had HBcrAg >5.3 log10U/ml compared to the UK (33% vs 9% respectively, p<0.0001). HBcrAg ≥4.3 log10U/ml (corresponding to a positive POCT) was 100% sensitive and 92% specific for predicting VL >200,000 IU/ml in the UK, but not SA. HBcrAg positively correlated with alanine transferase (ALT) (p<0.001 in UK, p<0.01 in SA), and fibrosis/cirrhosis by APRI score (p = 0.03 in UK and p=0.008 in SA), but not by elastography or FIB-4 scores.DiscussionHBcrAg distribution and relationship with other biomarkers differs between settings. HBcrAg (including POCT) may be a useful proxy for VL, but less so as a marker of disease progression, Its use needs tailoring to represent diverse populations.
Lung function may recover after coal mine fire smoke exposure: a longitudinal cohort study
Authors: Holt Nicolette R , Smith Catherine L , Gao Caroline X , Borg Brigitte , Lane Tyler J , Brown David , Ikin Jillian F , Makar Annie , McCrabb Thomas , Thomas Mikayla , Nilsen Kris , Thompson Bruce R , Abramson Michael J 
Published: July 2024

ABSTRACTBackground and objectiveThe 2014 Hazelwood coalmine fire exposed residents in nearby Morwell to high concentrations of particulate matter <2·5 µm (PM2·5) for approximately 6 weeks. This analysis aimed to evaluate the long-term impact on respiratory health.MethodsAdults from Morwell and the unexposed town of Sale completed validated respiratory questionnaires and performed spirometry, gas transfer and oscillometry 3·5-4 years (Round 1) and 7·3-7·8 years (Round 2) after the fire. Individual PM2·5exposure levels were estimated using chemical transport models mapped onto participant-reported time-location data. Mixed-effects regression models were fitted to analyse associations between PM2·5exposure and outcomes, controlling for key confounders.ResultsFrom 519 (346 exposed) Round 1 participants, 329 (217 exposed) participated in Round 2. Spirometry and gas transfer in Round 2 were mostly lower compared with Round 1, excepting FVC (increased) and FEV1(minimal change). The effect of mine fire-related PM2·5exposure changed from a negative effect in Round 1 to no effect in Round 2 for both pre-(p=0·005) and post-bronchodilator FVC (p=0·032). PM2·5was not associated with gas transfer in either round. For post-bronchodilator reactance and area under the curve, a negative impact of PM2·5in Round 1 showed signs of recovery in Round 2 (both p<0·001).ConclusionIn this novel study evaluating long-term respiratory outcomes after medium-duration high concentration PM2·5exposure, the attenuated associations between exposure and respiratory function may indicate some recovery in lung function. With increased frequency and severity of landscape fires observed globally, these results inform public health policies and planning.KEY MESSAGESEvidence is currently lacking on the long-term sequelae of high concentration PM2·5exposure, from extreme wildfire events lasting weeks to months, on lung physiology and function. We found that previously observed deficits in adult lung function, measured using spirometry, gas transfer and oscillometry 3.5 years after a prolonged coal mine fire, may recover in the longer-term. With increased frequency of prolonged landscape fires observed globally, these results inform public health policies and planning.
Ototoxicity-related Changes in GABA Immunolabeling Within the Rat Inferior Colliculus
Authors: Holt Avril Genene , Griffith Ronald D. , Lee Soo D. , Asako Mikiya , Buras Eric , Yalcinoglu Selin , Altschuler Richard A. 
Published: July 2024

AbstractSeveral studies suggest that hearing loss results in changes in the balance between inhibition and excitation in the inferior colliculus (IC). The IC is an integral nucleus within the auditory brainstem. The majority of ascending pathways from the lateral lemniscus (LL), superior olivary complex (SOC), and cochlear nucleus (CN) synapse in the IC before projecting to the thalamus and cortex. Many of these ascending projections provide inhibitory innervation to neurons within the IC. However, the nature and the distribution of this inhibitory input have only been partially elucidated in the rat.The inhibitory neurotransmitter, gamma aminobutyric acid (GABA), from the ventral nucleus of the lateral lemniscus (VNLL), provides the primary inhibitory input to the IC of the rat with GABA from other lemniscal and SOC nuclei providing lesser, but prominent innervation. There is evidence that hearing related conditions can result in dysfunction of IC neurons. These changes may be mediated in part by changes in GABA inputs to IC neurons. We have previously used gene micro-arrays in a study of deafness-related changes in gene expression in the IC and found significant changes in GAD as well as the GABA transporters and GABA receptors (Holt 2005). This is consistent with reports of age and trauma related changes in GABA (Bledsoe et al, 1995; Mossop et al, 2000; Salvi et al, 2000). Ototoxic lesions of the cochlea produced a permanent threshold shift. The number, intensity, and density of GABA positive axon terminals in the IC were compared in normal hearing and deafened rats. While the number of GABA immunolabeled puncta was only minimally different between groups, the intensity of labeling was significantly reduced. The ultrastructural localization and distribution of labeling was also examined. In deafened animals, the number of immuno gold particles was reduced by 78% in axodendritic and 82% in axosomatic GABAergic puncta. The affected puncta were primarily associated with small IC neurons. These results suggest that reduced inhibition to IC neurons contribute to the increased neuronal excitability observed in the IC following noise or drug induced hearing loss. Whether these deafness-diminished inhibitory inputs originate from intrinsic or extrinsic CNIC sources awaits further study.
Mechano-mediated M2 macrophage polarization and immune suppression in stiffened tumor microenvironment
Authors: Sapudom Jiranuwat , Tipay Paul , Teo Jeremy CM 
Published: July 2024

AbstractThe tumor microenvironment (TME), which is composed of various cell types and the extracellular matrix (ECM), plays crucial roles in cancer progression and treatment outcomes. However, the impact of the mechanical properties of the ECM, specifically collagen fibril alignment and crosslinking, on macrophage behavior and polarization is less understood. To investigate this, we reconstituted 3D collagen matrices to mimic the physical characteristics of the TME. Our results demonstrated that stiffening the matrix through the alignment or crosslinking of collagen fibrils promotes macrophage polarization toward the anti-inflammatory M2 phenotype. This phenotype is characterized by increased expression of CD105 and CD206 and a distinct cytokine secretion profile. The increased stiffness and aligned fibrils activate mechanotransduction pathways, notably integrin β1 and PI3K signaling, leading to increased IL-4 secretion, which acts in an autocrine manner to further promote M2 polarization. Interestingly, these stiffened microenvironments also suppressed the proinflammatory response. In coculture experiments with breast cancer cell lines (MDA-MB-231 and MCF-7), macrophages within stiffened or aligned matrices significantly increased cancer cell proliferation and invasion. These findings suggest that the mechanical properties of the ECM, specifically its alignment and crosslinking, create a more favorable environment for tumor progression by modulating macrophage activity. Overall, our study underscores the critical role of ECM mechanics in shaping immune cell behavior within the TME, highlighting the potential for therapies that target ECM properties and macrophage polarization to inhibit cancer progression and enhance treatment efficacy.