bluuebunny/crossref_metadata_2025_split huggingface dataset:
LATE RECURRENCE OF RETINAL DETACHMENT: INCIDENCE, CLINICAL FEATURES AND SURGICAL OUTCOMES
Authors: Anguita Rodrigo , Makuloluwa Achini , Sim Sing Yue , Flores-Sanchez Blanca , Roth Janice , Charteris David G 
Published: September 2023

ABSTRACT

Purpose:
To describe and evaluate demographics, clinical features, prognostic factors, rate of success of surgery, incidence and visual outcomes in patients with a late recurrence of rhegmatogenous retinal detachment(RRD) over a 10-year period at a large tertiary referral eye centre.

Methods:
A retrospective, observational case-series of patients with late recurrence of retinal detachment, defined as redetachment after at least 6 months of total reattachment in non-PVR RRD, after vitrectomy(PPV) surgery with gas tamponade.

Results:
39 patients with a late recurrence of RRD out of 16,396 RRD operations. The mean of time between the first RD surgery and redetachment was 122.7 weeks(SD 115). On presentation with late recurrence, 72% of eyes were pseudophakic and 64% were macula-off. In 28 eyes small breaks were found. 38% had established PVR,(PVR-C in 80 %). 95% underwent PPV. Gas was used in 61%.The initial secondary success rate was 41%. Initial BCVA was 1.32 logMAR(6/120) and final was 0.8 logMAR(6/38)(p-value 0.002).

Conclusion:
Late recurrence of retinal detachment is rare. It is characterized by small retinal breaks which may be difficult to visualise. Although cases can be treated with favourable anatomical results, visual outcomes are often less good, the success rate is lower.
Reproductive Factors and the Risk of Open Angle Glaucoma in Women
Authors: Kai Jia-Yan , Zhou Miao , Li Dan-Lin , Zhu Ke-Yao , Zhang Xiao-Feng , Pan Chen-Wei 
Published: September 2023

Précis:
There was a significant inverse linear relationship between age at menopause and open angle glaucoma (OAG). Late menarche (≥13 y) and a history of 5 or more deliveries were significantly associated with an increased risk of OAG.

Purpose:
To determine the association between reproductive factors including age at menarche, age at menopause, reproductive period, parity, and the risk of OAG in women.

Methods:
PubMed, Embase, Cochrane Library, and Web of Science were searched until February 9, 2022. Studies were included if they assessed the association between reproductive factors and OAG. The adjusted odds ratios (ORs) with relevant 95% CIs were extracted and pooled using fixed-effects models. Besides, we conducted dose-response analyses via the generalized least squares for trend method.

Results:
Seven articles including 18,618 women were identified in this review. The pooled results indicated that late age at menarche (≥13 y) was significantly associated with an increased risk of OAG (OR=1.76, 95% CI: 1.28, 2.43). Early menopause (<45 y) also significantly elevated the risk of OAG (OR=1.89, 95% CI: 1.23, 2.90) in categorical meta-analyses, consistent with the inverse linear relationship between menopausal age and the risk of OAG in dose-response analyses (P=0.002). In addition, women who had delivered at least 5 children were at significantly higher risk of OAG compared with those nulliparous (OR=2.35, 95% CI: 1.02, 5.39), and a J-shape relationship between parity and OAG was observed in dose-response analyses (P<0.001).

Conclusions:
Late menarche (≥13 y), early menopause (<45 y), and a history of 5 or more parturitions are possible risk factors for OAG. Longitudinal studies are warranted to further examine the relationships between reproductive factors and the risk of OAG.
Trabeculectomy in Eyes With High Myopia
Authors: Abe Ricardo Y. , Oltramari Laura , Vessani Roberto M. , Schimiti Rui B. , Magacho Leopoldo , Kanadani Fábio N. , Costa Vital P. 
Published: September 2023

Précis:
Primary trabeculectomy was safe and effective at lowering intraocular pressure (IOP) in patients with primary open angle glaucoma and high myopia.

Purpose:
To investigate the efficacy and safety of trabeculectomy in patients with glaucoma and high myopia.

Patient and Methods:
Retrospective case-control study. Glaucomatous patients with high myopia undergoing primary trabeculectomy surgery with at least 1 year of follow-up were compared with an age-matched control group without high myopia undergoing the same procedure. Surgical success was defined as: IOP ≤ 15 mm Hg with (qualified) or without (complete) antiglaucoma medications and at least 20% reduction from baseline IOP at the end of 48 months of follow-up.

Results:
We included a total of 90 eyes from 90 patients (45 eyes with high myopia and 45 controls). Within the 90 eyes, 70 eyes underwent trabeculectomy and 20 eyes underwent combined phacoemulsification and trabeculectomy. Although patients with high myopia had higher chances for failure (37% vs. 22%) compared with controls, the difference was not statistically significant (P=0.067). In the multivariable analysis, patients of African descent (P=0.043) and those with juvenile glaucoma (P=0.001) had more chances of failure, even after adjusting for myopia. There was no statistically significant difference between complication rates in both groups.

Conclusion:
Trabeculectomy was effective in reducing IOP in patients with high myopia and glaucoma, without the additional risk of complications compared with a control group.
KNEE OSTEONECROSIS AFTER SARS-COV 2 VIRUS INFECTION
Authors: Muñoz García Ana , Jiménez Martín Florencio , Hernández Herrero David 
Published: September 2023

ABSTRACT
Osteonecrosis after COVID-19 infection is a complex pathology with multifactorial origin. Factors such as infection itself with associated coagulopathy, as well as genetic mechanisms, and medications used for its treatment such as corticosteroids, may also be involved. The variability in the presentation makes diagnosis difficult, which, if done soon, can help delay progression and reduce morbidity and the need for surgery.
This report presents a case of knee osteonecrosis in a female patient who did not have previous knee pathology on imaging tests. She was diagnosed by magnetic resonance imaging months after hospital admission for SARS-COV 2 pneumonia, which required high-dose corticosteroid treatment.
Thermal threshold testing: call for a balance between the number of measurements and abnormalities in the diagnosis of sarcoidosis-associated small fiber neuropathy
Authors: Raasing Lisette R.M. , Veltkamp Marcel , Datema Mirjam , Grutters Jan C. , Vogels Oscar J.M. 
Published: September 2023

Abstract

Introduction:
Several recent studies of diagnosing small fiber neuropathy (SFN) have shown a lack of uniformity in thermal threshold testing (TTT) or quantitative sensory testing (QST) which makes it a challenge to compare the data. It is known that the chance of finding an abnormality increases with increasing number of measurements.

Objectives:
With this study, we first wanted to investigate whether TTT could benefit from a new approach focusing on the balance between the number of measurements, depending on the selection of parameters and measuring sites, and on number of abnormalities (NOAs). Second, we wanted to address the role of the method of levels (MLe) in possible desensitization during TTT measurements.

Methods:
One hundred seventeen participants were included (48 patients with sarcoidosis with probable SFN, 49 without SFN, and 20 healthy controls). Thermal threshold testing measurements and Small Fiber Neuropathy Screening List (SFNSL) questionnaire were used to assess SFN.

Results:
A combination of measuring all thermal threshold parameters at both feet except for MLe showed the best diagnostic performance. Increasing TTT NOAs correlates with the severity of SFN. Adding the SFNSL questionnaire further improves diagnostic performance.

Discussion:
Looking at TTT NOAs in all TTT parameters except for MLe at both feet should be considered as a new approach to improve the consistency and balance between the selection of TTT parameters, measuring sites, and definition of “abnormal QST.” Moreover, the SFNSL questionnaire is a valuable tool to quantify SFN symptoms and could improve SFN diagnosis.
Considering the Interaction between Surgical Approach and Timing on Complication Rates of Complex Orbital Fracture Repair
Authors: Flyer Benjamin E. , Feehs Kenneth R. , Maniscalco Brianna R. , Lacy Alexa L. , Slijepcevic Allison A. 
Published: September 2023

Objective:
The optimal approach and timing of complex orbital fracture repair is an unresolved issue that is complicated by unique clinical presentations and patient-specific considerations. Early surgical repair in less than 14 days is associated with fewer complications; however, there are no guidelines addressing the optimal timing for surgical repair. This study assesses the time of surgical repair and surgical outcomes of complex orbital fractures.

Methods:
Retrospective chart review from 2010 to 2022. Adult patients with orbital fractures are treated with surgical repair.

Results:
In all, 94 patients presented with orbital fractures and were treated with 108 surgeries. Postoperative complications: vision disturbance 33/108 (30.6%), gaze restriction 12/108 (11.1%), lid malposition 10/108 (9.3%), globe complication 13/108 (12.0%), and hardware issues 14/108 (13.0%). Postoperative complications were not significantly associated with the surgical approach used for fracture repair or the time of surgical repair.

Conclusion:
Postoperative complications following surgical repair of orbital fractures are not associated with surgical approach or time of repair following the initial injury.
The effects of aging on rod bipolar cell ribbon synapses
Authors: Shrestha Abhishek P , Rameshkumar Nirujan , Boff Johane Martins , Rajmanna Rhea , Chandrasegaran Thadshayini , Courtney Frederick E , Zenisek David , Vaithianathan Thirumalini 
Published: September 2023

AbstractThe global health concern posed by age-related visual impairment highlights the need for further research focused on the visual changes that occur during the process of aging. To date, multiple sensory alterations related to aging have been identified, including morphological and functional changes in inner hair cochlear cells, photoreceptors, and retinal ganglion cells. While some age-related morphological changes are known to occur in rod bipolar cells in the retina, their effect on these cells and on their connection to other cells via ribbon synapses remain elusive. To investigate the effects of aging on rod bipolar cells and their ribbon synapses, we compared synaptic calcium currents, calcium dynamics, and exocytosis in zebrafish (Danio rerio) that were middle-aged (MA,18 months) or old-aged (OA, 36 months). The bipolar cell terminal in OA zebrafish exhibited a decreased number of synaptic ribbons, an increased ribbon length, and a decrease in local Ca2+signals at the tested ribbon location with little change in the overall magnitude of the calcium current or exocytosis in response to brief pulses. Staining of the synaptic ribbons with antibodies specific for PKCα revealed shortening of the inner nuclear and plexiform layers (INL and IPL). These findings shed light on age-related changes in the retina that are related to synaptic ribbons and calcium signals.
Impact of Molecular Dynamics of Polyrotaxanes on Chondrocytes in Double Network Supramolecular Hydrogels under Physiological Thermomechanical Stimulation
Authors: Stampoultzis Theofanis , Rana Vijay Kumar , Guo Yanheng , Pioletti Dominique P. 
Published: September 2023

AbstractHyaline cartilage, a soft tissue enriched with a dynamic extracellular matrix, manifests as a supramolecular system within load-bearing joints. At the same time, the challenge of cartilage repair through tissue engineering lies in replicating intricate cellular-matrix interactions. This study attempts to investigate chondrocyte responses within double-network supramolecular hydrogels, tailored to mimic the dynamic molecular nature of hyaline cartilage. To this end, we infused non-covalent host-guest polyrotaxanes, by blending α-cyclodextrins as host molecules and polyethylene glycol as guests, into a gelatin-based covalent matrix, thereby enhancing its dynamic characteristics. Subsequently, chondrocytes were seeded into these hydrogels to systematically probe the effects of varied concentrations of introduced polyrotaxanes (instilling different levels of supramolecular dynamism in the hydrogel systems) on cellular responsiveness. Our findings unveiled an augmented level of cellular mechanosensitivity for supramolecular hydrogels compared to pure covalent-based systems. This is demonstrated by an increased mRNA expression of ion channels (TREK1, TRPV4, PIEZO1), signaling molecules (SOX9) and matrix remodeling enzymes (LOXL2). Such outcomes were further elevated upon external application of biomimetic thermomechanical loading that brought a stark increase in the accumulation of sulfated glycosaminoglycans and collagen. Overall, we found that matrix adaptability plays a pivotal role in modulating chondrocyte responses within double-network supramolecular hydrogels. These findings hold potential for advancing cartilage engineering within load-bearing joints.Graphical AbstractDouble network supramolecular hydrogels enhanced chondro-induction significantly compared to purely covalent-based hydrogels as indicated by enhanced accumulation of extracellular matrix molecules.
iLEC-DNA: Identifying Long Extra-chromosomal Circular DNA by Fusing Sequence-derived Features of Physicochemical Properties and Nucleotide Distribution Patterns
Authors: Abbasi Ahtisham Fazeel , Asim Muhammad Nabeel , Dengel Andreas , Ahmed Sheraz 
Published: September 2023

ABSTRACTLong extrachromosomal circular DNA (leccDNA) regulates several biological processes such as genomic instability, gene amplification, and oncogenesis. The identification of leccDNA holds significant importance to investigate its potential associations with cancer, autoimmune, cardiovascular, and neurological diseases. In addition, understanding these associations can provide valuable insights about disease mechanisms and potential therapeutic approaches. Conventionally, wet lab-based methods are utilized to identify leccDNA, which are hindered by the need for prior knowledge, and resource-intensive processes, potentially limiting their broader applicability. To empower the process of leccDNA identification across multiple species, the paper in hand presents the very first computational predictor. The proposed iLEC-DNA predictor makes use of SVM classifier along with sequence-derived nucleotide distribution patterns and physicochemical properties-based features. In addition, the study introduces a set of 12 benchmark leccDNA datasets related to three species, namely HM, AT, and YS. It performs large-scale experimentation across 12 benchmark datasets under different experimental settings using the proposed predictor and more than 140 baseline predictors. The proposed predictor outperforms baseline predictors across diverse leccDNA datasets by producing average performance values of 80.699%, 61.45% and 80.7% in terms of ACC, MCC and AUC-ROC across all the datasets. The source code of the proposed and baseline predictors is available athttps://github.com/FAhtisham/Extrachrosmosomal-DNA-Prediction.
Onsager’s variational principle in proliferating biological tissues, in presence of activity and anisotropy
Authors: Ackermann Joseph , Ben Amar Martine 
Published: September 2023

AbstractA hallmark of biological cells is their ability to proliferate and of tissues their ability to grow. This is common in morphogenesis and embryogenesis but also in pathological conditions such as tumour growth. To consider these tissues from a physical point of view, it is necessary to derive fundamental relationships, in particular for velocities and density components, taking into account growth terms, chemical factors and the symmetry of cells and tissues. The aim is then to develop a consistent coarse-grained approach to these complex systems, which exhibit proliferation, disorder, anisotropy and activity at small scales. To this end, Onsager’s variational principle allows the systematic derivation of flux-force relations in systems out of equilibrium and the principle of the extremum of dissipation, first formulated by Rayleigh and revisited by Onsager, finally leads to a consistent formulation for a continuous approach in terms of a coupled set of partial differential equations. Considering the growth and death rates as fluxes, as well as the chemical reactions driving the cellular activities, we derive the momentum equations based on a leading order physical expansion. Furthermore, we illustrate the different interactions for systems with nematic or polar order at small scales, and numerically solve the resulting system of partial differential equations in relevant biophysical growth examples. To conclude, we show that Onsager’s variational principle is useful for systematically exploring the different scenarios in proliferating systems, and how morphogenesis depends on these interactions.
Functional and phylogenetic β diversities and their link with clustering/overdispersion and uniqueness/redundancy
Authors: Pavoine Sandrine , Ricotta Carlo 
Published: September 2023

AbstractIn the recent decades, research on biodiversity in community ecology has been marked by the consideration of species’ evolutionary histories and biological traits, including those said functional as they relate to the functions a species has in ecosystems. Among the different spatial levels at which FP diversity can be quantified, less attention has been given to the definition of the general concept of between-communities (β) FP diversity than to those of local, within-communities (α) and regional, merged-communities (γ) FP diversities. Here we develop a new way for partitioning FP β diversity into elementary components to underline how and why FP β diversity differs from species β diversity, the latter reflecting only differences in species’ abundances between communities. As a reference example, we consider two distinct measures of FP β diversity: Rao’s dissimilarity coefficient (Qβ) that expresses an average dissimilarity between communities, and its transformation into an equivalent number of communities (Dβ).Thanks to analytical partitioning and simulations, we show thatQβandDβare connected differently with typical patterns of community structure. The search for the ecological and evolutionary processes that drive community assembly and the assessment of community resilience and stability have indeed revealed typical community structures: the local clustering of species with similar traits or shared evolutionary histories; and the local (α) or regional (γ) presence of functionally or phylogenetically redundant versus unique species. WhileQβandDβare both increasing functions of species β diversity and γ FP uniqueness,Qβincreases with FP clustering whileDβincreases with α FP redundancy. The selection of an index of β diversity for a given study depends on its objective, such as communication to conservation policy makers or theoretical study of the ecological and evolutionary processes of community assembly. To facilitate and secure this selection, we call, through our study, for the development of formal and precise definition(s) for FP β diversity in light of the concepts of clustering versus overdispersion, and redundancy versus uniqueness. In particular, we call for further research on when and why FP β diversity should increase with FP clustering.
Exercise training adaptations in liver glycogen and glycerolipids require hepatic AMP-activated protein kinase in mice
Authors: Hughey Curtis C. , Bracy Deanna P. , Rome Ferrol I. , Goelzer Mickael , Donahue E. Patrick , Viollet Benoit , Foretz Marc , Wasserman David H. 
Published: September 2023

ABSTRACTRegular exercise elicits adaptations in glucose and lipid metabolism that allow the body to meet energy demands of subsequent exercise bouts more effectively and mitigate metabolic diseases including fatty liver. Energy discharged during the acute exercise bouts that comprise exercise training may be a catalyst for liver adaptations. During acute exercise, liver glycogenolysis and gluconeogenesis are accelerated to supply glucose to working muscle. Lower liver energy state imposed by gluconeogenesis and related pathways activates AMP-activated protein kinase (AMPK), which conserves ATP partly by promoting lipid oxidation. This study tested the hypothesis that AMPK is necessary for liver glucose and lipid adaptations to training. Liver-specific AMPKα1α2 knockout (LAKO) and wild type (WT) mice completed sedentary and exercise training protocols. Liver nutrient fluxes were quantified at rest or during acute exercise following training. Liver metabolites and molecular regulators of metabolism were assessed. Training increased liver glycogen in WT mice, but not in LAKO mice. The inability to increase glycogen led to lower glycogenolysis, glucose production, and circulating glucose during acute exercise in trained LAKO mice. Deletion of AMPKα1α2 attenuated training-induced declines in liver diacylglycerides. In particular, training lowered the concentration of unsaturated and elongated fatty acids comprising diacylglycerides in WT mice, but not in LAKO mice. Training increased liver triacylglycerides and the desaturation and elongation of fatty acids in triacylglycerides of LAKO mice. These lipid responses were independent of differences in tricarboxylic acid cycle fluxes. In conclusion, AMPK is required for liver training adaptations that are critical to glucose and lipid metabolism.NEW & NOTEWORTHYThis study shows that the energy sensor and transducer, AMP-activated protein kinase, is necessary for an exercise training-induced: i) increase in liver glycogen that is necessary for accelerated glycogenolysis during exercise, ii) decrease in liver glycerolipids independent of TCA cycle flux, and iii) decline in the desaturation and elongation of fatty acids comprising liver diacylglycerides. The mechanisms defined in these studies have implications for use of regular exercise or AMPK-activators in patients with fatty liver.
ACE Configurator for ELISpot (ACE): Optimizing Combinatorial Design of Pooled ELISpot Assays with an Epitope Similarity Model
Authors: Lee Jin Seok , Karthikeyan Dhuvarakesh , Fini Misha , Vincent Benjamin G. , Rubinsteyn Alex 
Published: September 2023

ABSTRACTThe ELISpot assay is a powerfulin vitroimmunoassay that enables cost-effective quantification of antigen-specific T-cell reactivity. It is widely used in the context of cancer and infectious diseases to validate the immunogenicity of epitopes. While technological advances in hardware and software have kept pace with the need for increased throughput, assay design and deconvolution methodology have largely remained stagnant. Current methods for designing multiplexed ELISpot assays are restricted to preset configurations, lack support for high-throughput scenarios, and ignore peptide identity during pool assignment. We introduce the ACE Configurator for ELISpot (ACE) to address these gaps. ACE generates optimized peptide-pool assignments from highly customizable user inputs and handles positive peptide deconvolution using assay readouts. We present a novel sequence-aware pooling strategy, powered by a fine-tuned ESM-2 deep sequence model to identify immunologically similar peptides, reducing the number of false positives and subsequent confirmatory assays. To validate the performance of ACE using real-world datasets, we conducted a comprehensive benchmark study against various design heuristics, deconvolution methods, and experimental conditions, contextualizing design parameter choices with their impact on precision and number of total pools. Our results demonstrate ACE’s capacity to further increase precision of identified immunogenic peptides, maximizing experimental efficiency at the bench-side. ACE is freely available as an executable with a graphical user interface and command-line interfaces athttps://github.com/pirl-unc/ace.