bluuebunny/crossref_metadata_2025_split huggingface dataset:
EFFECT OF PHYSICIAN FACE MASK USE ON POSTINJECTION ENDOPHTHALMITIS
Authors: Fortes Blake H. , Astafurov Konstantin V. , Hodge David O. , Smith Wendy M. , Barkmeier Andrew J. , Olsen Timothy W. , Iezzi Raymond , Bakri Sophie J. 
Published: August 2022

Purpose:
To examine the impact of physician face mask use on the rates and outcomes of postinjection endophthalmitis.

Methods:
A multicenter retrospective, comparative cohort study comparing endophthalmitis rate and visual acuity of eyes that developed endophthalmitis after antivascular endothelial growth factor injections at Mayo Clinic Rochester (MCR) and at Mayo Clinic Health System sites depending on physician masking.

Results:
A total of 164,824 injections were performed at MCR and Mayo Clinic Health System sites. Of these, 66,098 injections were in the no mask group and 98,726 injections were in the mask group. Overall, there were no differences in the rates of infectious endophthalmitis in the no mask versus mask cohorts (overall: no mask: 20 cases [0.0303%] vs. mask: 41 cases (0.0415%); P = 0.24; infectious: no mask: 12 cases [0.018%] versus mask: 13 cases [0.0132%]; P = 0.42). At MCR alone, there was a significant reduction in infectious endophthalmitis between the no mask versus mask groups (no mask: 9 cases [0.0297%] versus mask: 2 cases [0.003%]; P < 0.001). Only 2 cases of infectious endophthalmitis occurred at MCR after the face mask policy was implemented (1 in 30,000 injections). At presentation and at 6 months, the average visual acuity was similar for patients who developed endophthalmitis between the no mask versus mask groups.

Conclusion:
Physician face mask use did not affect the rate or outcome of postinjection endophthalmitis. However, there was a significant reduction at MCR after masking along with other quality improvement measures, including performance of injections in a dedicated procedure room and preparation of patients by nurses, that led to a low rate of endophthalmitis.
RHEGMATOGENOUS RETINAL DETACHMENT AFTER INITIATION OF PILOCARPINE HYDROCHLORIDE OPHTHALMIC SOLUTION 1.25% FOR TREATMENT OF PRESBYOPIA
Authors: Eton Emily A. , Zhao Peter Y. , Johnson Mark W. , Rao Rajesh C. , Huvard Michael J. 
Published: August 2022

Background/Purpose:
Retinal detachment has previously been reported in association with topical miotic use for the treatment of glaucoma. Pilocarpine hydrochloride 1.25% was recently approved by the Food and Drug Administration for the treatment of presbyopia, with no reports of associated retinal detachments in the clinical trial data.

Methods:
Case report.

Results:
Two novel cases of unilateral retinal detachment occurring within 10 days of the initiation of pilocarpine 1.25% for the treatment of presbyopia were described. The patients were pseudophakic men in their 60s or 70s with preexisting retinal detachment risk factors, such as high myopia, lattice degeneration, and prior retinal detachment. Both affected eyes were treated with pars plana vitrectomy and gas endotamponade with an uncomplicated postoperative course.

Conclusion:
Retinal detachment may be associated with the use of pilocarpine 1.25%. Caution should be used when considering prescribing this medication in patients with preexisting retinal abnormality.
The Concept of Strength Through Synergy Applied to the Search of Powerful Prognostic Biomarkers in Gastroesophageal Cancer
Authors: Delgado Bolton Roberto C. , Calapaquí Terán Adriana K. , Fanti Stefano , Giammarile Francesco 
Published: August 2022

Abstract
Integrating clinical and pathological data together with imaging-derived information, such as radiomics and sarcopenia status, creating new combined biomarkers that increase the prognostic value compared with each of them used independently. The concept of strength through synergy, applicable in so many areas of life, is also demonstrated in this area of science and opens up innumerable pathways for improving patient care in cancer. This is as an example on how we can explore and make the most of all the information we already have (clinical, pathological, imaging), without the need for new invasive tests.
18F-FDG PET/CT in Urethral Metastases From Bladder Cancer
Authors: Beyhan Ediz , Baykal Koca Sevim , Yücetaş Uğur , Çermik Tevfik Fikret , Ergül Nurhan 
Published: August 2022

Abstract
Urethral metastasis of bladder cancer after surgery is rare. We present a 63-year-old man who had surgery for invasive bladder carcinoma and prostate adenocarcinoma 4 years ago and referred for urethral hemorrhage. 18F-FDG PET/CT was performed for restaging and showed intense linear 18F-FDG activity in the proximal urethra. The patient underwent urethrectomy, and histopathology determined urethral metastasis.
Osteomyelitis and Gentamicin-PMMA Chains
Authors: Février Agathe , Boursot Charles , Tannugi Kévin Cohen 
Published: August 2022

Abstract
In chronic osteomyelitis, effective local antibiotic therapy after surgical debridement can be achieved by implantation of gentamicin-PMMA chains. The gentamicin concentrations at the site of infection are higher than that after systemic application of the same antibiotic. The appearance of this treatment is a particular aspect from a radiological point of view. Even if this is rare, these images deserve to be known when looking for osteomyelitis. We report a case of a 21-year-old man from Russia who had a bone scan in the context of chronic osteomyelitis persisting since a shin splints operation in a context of bilateral trauma in his country with antibiotic beads application.
Motivation as a Predictor of Aphasia Treatment Outcomes
Authors: Weatherill Maryanne , Tibus Elizabeth O. , Rodriguez Amy D. 
Published: August 2022

Purpose:
Motivation is a complex phenomenon that can influence a person's ability to make progress in treatment. We sought to understand how motivation is currently measured and utilized in aphasia rehabilitation by identifying treatment studies that (1) include measurement of motivation and (2) use motivation to predict treatment response.

Method:
A scoping review was conducted by systematically searching PubMed, CINAHL, EBSCO, Ovid MEDLINE, and APA PsycInfo using the following search terms: (measurement OR treatment OR rehabilitation OR predict*) AND (motiv* OR engagement OR adherence OR compliance) AND (aphasia OR dysphasia).

Results:
Two studies met our inclusion criteria. Motivation was measured differently across studies. No studies used motivation to predict treatment outcomes.

Discussion/Conclusions:
Despite the importance of motivation in aphasia rehabilitation success, studies that include its measurement are sparse. Additional research is needed and should include development of measurement tools and evaluation of the predictive value of motivation on treatment outcomes.
Is There a Relationship Between Cortisol and Treatment Response in Chronic Aphasia?
Authors: Gravier Michelle L. , Hula William D. , Johnson Jeffrey P. , Autenreith Alyssa , Dickey Michael Walsh 
Published: August 2022

Purpose:
To evaluate whether levels of cortisol, a stress-related hormone, predicted response to intensive speech–language intervention for individuals with chronic aphasia (IWA). Secondary analyses explored baseline cortisol levels, change following intervention, association between cortisol levels and aphasia severity, self-reported communicative distress, and chronic stress.

Method:
Afternoon salivary cortisol levels were measured in 14 IWA during the first and last weeks of a 4-week intensive speech–language intervention epoch. Behavioral outcome measures were collected pre- and postintervention.

Results:
Cortisol levels did not significantly predict treatment response in this sample of IWA, although a positive trend was present. Baseline cortisol levels were not abnormally elevated, did not change from pre- to postintervention, and were not significantly correlated with any of the behavioral outcome measures.

Discussion:
Although afternoon salivary cortisol levels did not robustly predict treatment response in this participant sample, future studies may be warranted that include IWA with elevated levels of cortisol at pretreatment.
Neutral genetic diversity in mixed mating systems
Authors: Uyenoyama Marcy K. 
Published: August 2022

ABSTRACTSystems of reproduction differ with respect to the magnitude of neutral genetic diversity maintained in a population. In particular, the partitioning of reproductives into mating types and regular inbreeding have long been recognized as key factors that influence effective population number. Here, a range of reproductive systems (full gonochorism, full hermaphroditism, androdioecy, and gynodioecy) are compared with respect to the maintenance of neutral genetic diversity. The analysis assumes anisogamy, with reproduction limited by the availability of large gametes (ova or seeds) but not small gametes (sperm or pollen). Levels of neutral genetic diversity respond to the relative proportions of gonochores and hermaphrodites in different ways under androdioecy versus gynodioecy. The manner in which effective number, sex-specific viability differences, and the evolving quantitative trait of the population influence the level of neutral genetic diversity is described across the systems of reproduction studied.
Stricter protocols combined with a clinical serum biomarker can increase replicability and causality for dietary intervention studies. Plus empirical data on BPA regrettable substitutions
Authors: Perdue W. Lewis , Reus Victor I. , van Breemen Richard B. , Muchiri Ruth N. , Yeamans-Irwin Rebecca L. 
Published: August 2022

ABSTRACTEffective regulation of harmful environmental chemicals found in wide variety of consumer products and consumables has been thwarted by the lack of agreement between government scientists and university/academic laboratories regarding the quantification of significant human harms. This is particularly relevant regarding plastic-derived chemicals (PDCs), such as Bisphenol A, now that the federal CLARITY-BPA program has failed to achieve any credible, human-significant scientific consensus. Because of this disagreement, direct, clinical human experimental data is vital to resolving this situation. In an effort to develop direct human-relevant data, some academic investigators have employed dietary intervention studies in an attempt to shed light on the controversy. Unfortunately, dietary intervention efforts thus far have not demonstrated causality or replicability.Investigators of this study propose a novel human dietary intervention protocol that can be both replicable and causal. This first-of-a-kind dietary intervention study explores a potential causal relationship between human serum levels of BPA and High-Sensitivity C-Reactive Protein (hsCRP), a proven clinical indicator of inflammation. Investigators used the equivalent of a USDA-defined typical diet followed by a PDC-reduced diet to compare blood levels of hsCRP. This proof-of-concept investigation is the first to use an easily accessible, medically-accepted clinical laboratory test to directly measure human health effects of PDC reduction.Unexpected phenomena discovered during the investigation offer study protocol modifications to enhance widespread replicability, and economically practical expansion to a substantial proportion of the approximately 84,000 mostly unregulated chemicals found in the human environment. In addition, our LC/MS-MS results offer the first direct quantitative human clinical evidence (of which we are aware) confirming the existence of regrettable substitutions in which product manufacturers have reduced BPA usage while substituting Bisphenol analogues that appear to equal or exceed BPA human toxicity. Bolstered by the unexpected results in this proof-of-concept investigation, novel lessons and techniques described herein may further specific and improved methods and best practices that can enable future dietary interventions to produce replicable, causal human results.
Recombination shapes 2022 monkeypox outbreak
Authors: Yeh Ting-Yu , Hsieh Zih-Yu , Feehley Michael C. , Feehley Patrick J. , Contreras Gregory P. , Su Ying-Chieh , Hsieh Shang-Lin , Lewis Dylan A. 
Published: August 2022

SummaryBackgroundOn July 23, 2022, the WHO declared monkeypox outbreak a global health emergency. Here we analyze monkeypox virus (MPXV) sequences during 2022 pandemic to investigate whether the virus is adapting for better survival and transmission among the human population.MethodsBy studying tandem repeats (TRs) and linkage disequilibrium (LD), we analyzed 415 MPXV sequences from January 1 to July 20, 2022 worldwide.FindingThe 2022 MPXV population has diverged into 4 lineages and 11 subgroups based on various TRs and their copy numbers. LD analysis also shows that virus has evolved into 3 new lineages. We identify 8 new recombinants (six from Slovenia, one from Australia, one from Italy) using TR analysis and 3 recombinants (two from Germany, one from Spain) using LD analysis.ConclusionOur results indicate that the MPXV genome is evolving and expanding quickly during the 2022 pandemic. We conclude that in combination with genomic surveillance, TR analysis, as well as LD analysis, are useful tools with which to monitor and track phylogenetic dynamics and recombination of monkeypox transmission.
Human photoreceptor cell transplants integrate into human retina organoids
Authors: Wagner Felix , Carrera Roberto , Kurth Thomas , Michalakis Stylianos , Naumann Ronald , Zuzic Marta , Neumann Katrin , Gourau Olivier , Busskamp Volker , Karl Mike O. 
Published: August 2022

AbstractCell transplantation is a promising therapeutic approach to recover loss of neurons and vision in patient retinas. So far, human photoreceptor transplants restored some visual function in degenerating mouse retina. Whether retinal cell transplants also integrate into human retina, and how to optimize this for different pathologies are still unknown. Here, we sought to determine if human retina organoids generated from pluripotent stem cells might assist cell replacement therapy development in a human-to-human setting. Models for intra- and subretinal cell transplantation strategies were explored: Photoreceptor donor cells carrying a transgenic fluorescent reporter were enriched from acutely dissociated human retinal organoids. Donor cells were precisely transplanted by microinjection into the retina of host organoids, but high cell numbers might require multiple injections posing potential damage. Alternatively, donor cells were transplanted in large numbers by placing them in subretinal-like contact to the apical organoid surface. Using postmitotic retinal organoids (age >170-days) as a source for donor cells and as hosts, we show that six weeks after subretinal-like transplantation, large clusters of photoreceptors reproducibly incorporate into the host retina. Transplanted clusters frequently are located within or across the host photoreceptor layer, include cone and rod photoreceptors, and become infiltrated by cell processes of host Müller glia, indicative of structural integration. Histological and ultrastructural data of virally-labeled photoreceptor transplants show characteristic morphological and structural features of polarized photoreceptors: inner segments and ribbon synapses, and donor-host cell contacts develop contributing to the retinal outer limiting membrane. These results demonstrate that human retinal organoids provide a preclinical research system for cell replacement therapies.Graphical abstract
Mutations within the cGMP-binding domain of CNGA1 causing autosomal recessive retinitis pigmentosa in human and animal model
Authors: Kandaswamy Surabhi , Zobel Lena , John Bina , Santhiya Sathiyaveedu Thyagarajan , Bogedein Jacqueline , Przemeck Gerhard K.H. , Gailus-Durner Valérie , Fuchs Helmut , Biel Martin , de Angelis Martin Hrabĕ , Graw Jochen , Michalakis Stylianos , Amarie Oana Veronica 
Published: August 2022

ABSTRACTRetinitis pigmentosa is a group of progressive inherited retinal dystrophies that may present clinically as part of a syndromic entity or as an isolated (nonsyndromic) manifestation. In a family suffering from retinitis pigmentosa, we identified a missense variation in CNGA1 affecting the cyclic nucleotide binding domain (CNBD) and characterized a mouse model developed with mutated CNBD. A gene panel analysis comprising 105 known RP genes was used to analyze a family with autosomal-recessive retinitis pigmentosa (arRP) and revealed that CNGA1 was affected. From sperm samples of ENU mutagenesis derived F1 mice, we re-derived a mutant with a Cnga1 mutation. Homozygous mutant mice, developing retinal degeneration, were examined for morphological and functional consequences of the mutation. In the family, we identified a rare CNGA1 variant (NM_001379270.1) c.1525G>A; (p.Gly509Arg), which co-segregated among the affected family members. Homozygous Cnga1 mice harboring a (ENSMUST00000087213.12) c.1526A>G (p.Tyr509Cys) mutation showed progressive degeneration in the retinal photoreceptors from 8 weeks on. This study supports a role for CNGA1 as a disease gene for arRP and provides new insights on the pathobiology of cGMP-binding domain mutations in CNGA1-RP.
PeTriBERT : Augmenting BERT with tridimensional encoding for inverse protein folding and design
Authors: Dumortier Baldwin , Liutkus Antoine , Carré Clément , Krouk Gabriel 
Published: August 2022

AbstractProtein is biology workhorse. Since the recent break-through of novel folding methods, the amount of available structural data is increasing, closing the gap between data-driven sequence-based and structure-based methods. In this work, we focus on the inverse folding problem that consists in predicting an amino-acid primary sequence from protein 3D structure. For this purpose, we introduce a simple Transformer model from Natural Language Processing augmented 3D-structural data. We call the resulting model PeTriBERT: Proteins embedded in tridimensional representation in a BERT model. We train this small 40-million parameters model on more than 350 000 proteins sequences retrieved from the newly available AlphaFoldDB database. Using PetriBert, we are able to in silico generate totally new proteins with a GFP-like structure. These 9 of 10 of these GFP structural homologues have no ressemblance when blasted on the whole entry proteome database. This shows that PetriBert indeed capture protein folding rules and become a valuable tool for de novo protein design.
Pelagibacter phage Skadi - An abundant polar specialist that exemplifies ecotypic niche specificity among the most abundant viruses on Earth
Authors: Buchholz Holger H. , Bolaños Luis M. , Bell Ashley G. , Michelsen Michelle L. , Allen Michael J. , Temperton Ben 
Published: August 2022

AbstractBacteria in the SAR11 clade are the most abundant members of surface marine bacterioplankton and are a critical component of global biogeochemical cycles. Similarly, pelagiphages that predate SAR11 are both ubiquitous and highly abundant in the oceans. These viruses are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called Skadi isolated from the Western English Channel using a cold-water ecotype of SAR11 (HTCC1062) as bait. Skadi is closely related to the globally dominant pelagiphage HTVC010P. We show that, along with other HTVC010P-type viruses, Skadi belongs to a distinct viral family within the order Caudovirales for which we propose the name Ubiqueviridae. Metagenomic read recruitment identifies Skadi as one of the most abundant pelagiphages on Earth. Skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of Skadi host-range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Read mapping from the Global Ocean Viromes project (GOV2) showed that relative abundance of Skadi correlated negatively with temperature, and positively with nutrients, available oxygen and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed-bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
DeepIFC: virtual fluorescent labeling of blood cells in imaging flow cytometry data with deep learning
Authors: Timonen Veera A. , Kerkelä Erja , Impola Ulla , Penna Leena , Partanen Jukka , Kilpivaara Outi , Arvas Mikko , Pitkänen Esa 
Published: August 2022

ABSTRACTImaging flow cytometry (IFC) combines flow cytometry with microscopy, allowing rapid characterization of cellular and molecular properties via high-throughput single-cell fluorescent imaging. However, fluorescent labeling is costly and time-consuming. We present a computational method called DeepIFC based on the Inception U-Net neural network architecture, able to generate fluorescent marker images and learn morphological features from IFC brightfield and darkfield images. Furthermore, the DeepIFC workflow identifies cell types from the generated fluorescent images and visualizes the single-cell features generated in a 2D space. We demonstrate that rarer cell types are predicted well when a balanced data set is used to train the model, and the model is able to recognize red blood cells not seen during model training as a distinct entity. In summary, DeepIFC allows accurate cell reconstruction, typing and recognition of unseen cell types from brightfield and darkfield images via virtual fluorescent labeling.
Cellular and computational models reveal environmental and genetic interactions in MMUT-type methylmalonic aciduria
Authors: Ramon Charlotte , Traversi Florian , Bürer Céline , Froese D. Sean , Stelling Jörg 
Published: August 2022

AbstractMMUT-type methylmalonic aciduria is a rare inherited metabolic disease caused by the loss of function of the methylmalonyl-CoA mutase (MMUT) enzyme. Patients develop symptoms resembling those of primary mitochondrial disorders, but the underlying causes of mitochondrial dysfunction remain unclear. Here, we examined environmental and genetic interactions in MMUT deficiency using a combination of computational modeling and cellular models to decipher pathways interacting with MMUT. Immortalized fibroblast (hTERT BJ5ta) MMUT-KO (MUTKO) clones displayed a mild mitochondrial impairment in standard glucose-based medium, but they did not to show increased reliance on respiratory metabolism nor reduced growth or viability. Consistently, our modeling predicted MUTKO specific growth phenotypes only for lower extracellular glutamine concentrations. Indeed, two of three MMUT-deficient BJ5ta cell lines showed a reduced viability in glutamine-free medium. Further, growth on 183 different carbon and nitrogen substrates identified increased NADH (nicotinamide adenine dinucleotide) metabolism of BJ5ta and HEK293 MUTKO cells compared to controls on purine- and glutamine-based substrates. With this knowledge, our modeling predicted 13 reactions interacting with MMUT that potentiate an effect on growth, primarily those of secondary oxidation of propionyl-CoA, oxidative phosphorylation and oxygen diffusion. Of these, we validated 3-hydroxyisobutytyl-CoA hydrolase (HIBCH) in the secondary propionyl-CoA oxidation pathway. Altogether, these results suggest compensation for the loss of MMUT function by increasing anaplerosis through glutamine or by diverting flux away from MMUT through the secondary propionyl-CoA oxidation pathway, which may have therapeutic relevance.1sentence take-home messageBy perturbing metabolic pathways through genetic and environmental interventions in cellular and computational models of MMUT-type methylmalonic aciduria, we identified glutamine and secondary oxidative propionyl-CoA oxidation pathways as being important in the disease.