bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facial Palsy and the eyes: Epidemiology, Tear Film, and Meibomian gland dysfunction; a comparative analysis
Authors: Guerrero-de Ferran Caroline , Rivera-Alvarado Jocelyn I. , Bastán-Fabián Daniel , Del Castillo-Morales Alfredo , Velázquez-Valenzuela Fabiola , Valdez García Jorge E. 
Published: July 2023

AbstractPurposeTo describe the correlation between facial palsy of any etiology and Meibomian gland dysfunction and to report the tear film parameters found in patients with facial palsy diagnosis.DesignObservational, longitudinal, and comparative study.MethodsA sample of 20 patients with unilateral facial palsy was obtained its severity was staged using the House-Brackmann scale. A dry eye evaluation using an Oculus 5M keratograph was performed, which included infrared meibography, tear breakup time, and a dry eye questionnaire. Meibographies were analyzed using ImageJ software to determine the affected area.Results11 patients (55%) were female, mean age of diagnosis was 57.80 ± 18.28 (range of 22-80), 10 (50%) cases were due to Bell’s palsy. Tear breakup time was markedly reduced in the affected side but was statistically insignificant (p=0.2167) and tear meniscus height was much greater in the non-affected side (p=0.0199). Finally, Meibomian gland alterations were more evident in the affected side, with upper Meibomian glands having a loss of 29.55 ± 13.31 percent (p=0.0374) and lower glands presenting a loss 44.44 ± 16.9 percent (p=<0.001).ConclusionsA clear difference in Meibomian gland and tear film dynamics can be observed in paretic vs non paretic sides in the same patients. Multiple mechanisms contribute to this ailment, such as an incomplete blinking pattern and Meibomian gland dysfunction due to orbicularis oculi weakness. Software based analysis also showed a greater glandular area loss when compared to clinician’s analysis, which may help aide in therapeutic decisions for patients with meibomian gland dysfunction.
One-Year Follow-up of Young People with ME/CFS Following Infectious Mononucleosis by Epstein-Barr Virus
Authors: Pricoco Rafael , Meidel Paulina , Hofberger Tim , Zietemann Hannah , Mueller Yvonne , Wiehler Katharina , Michel Kaja , Paulick Johannes , Leone Ariane , Haegele Matthias , Mayer-Huber Sandra , Gerrer Katrin , Mittelstrass Kirstin , Scheibenbogen Carmen , Renz-Polster Herbert , Mihatsch Lorenz , Behrends Uta 
Published: July 2023

AbstractBackgroundInfectious mononucleosis, caused by the Epstein-Barr Virus (EBV-IM), has been linked to the development of myalgic encephalomyelitis/chronic fatigue-syndrome (ME/CFS) in children, adolescents, and young adults. Our study presents the first cohort of young individuals in Germany who were diagnosed with ME/CFS following EBV-IM.MethodsWe conducted a one-year follow-up of 25 young people diagnosed with ME/CFS at our specialized tertiary outpatient service by clinical criteria requiring post-exertional malaise and with documented EBV-IM as the triggering event. Demographic information, laboratory findings, frequency and severity of symptoms, physical functioning, and health-related quality of life (HRQoL) were assessed at first visit as well as 6 and 12 months later at follow-up visits.ResultsThe physical functioning and HRQoL of the cohort were significantly impaired, with young adults displaying more severe symptoms, as well as worsening of fatigue, physical and mental functioning, and HRQoL throughout the study, compared to adolescents. After one year, we found that 6/12 (54%) adolescents no longer met the diagnostic criteria for ME/CFS, indicating partial remission, while all young adults continued to fulfill the Canadian consensus criteria. Improvement in children was evident in physical functioning, symptom frequency and severity, and HRQoL, while young adults had little improvement. EBV serology and EBV DNA load did not correlate with distinct clinical features of ME/CFS, and clinical chemistry showed no evidence of inflammation. Remarkably, the median time from symptom onset to ME/CFS diagnosis was 13.8 (IQR: 9.1–34.9) months.ConclusionsME/CFS following EBV-IM in young people is a severely debilitating disease with diagnoses protracted longer than one year in many patients and only limited responses to conventional symptom-oriented medical care. Although younger children may have a better prognosis, their condition can fluctuate and significantly impact their HRQoL. Our data emphasize that biomarkers and effective therapeutic options are also urgently needed for this very young age group to better manage their medical condition and pave the way to recovery.
Gut microbiota and faecal cytokine profiles of rural Cambodian infants and links to early life nutrition and diarrhoeal episodes
Authors: Dalby Matthew J , Kiu Raymond , Serghiou Iliana R , Miyazaki Asuka , Acford-Palmer Holly , Tung Rathavy , Caim Shabhonam , Phillips Sarah , Kujawska Magdalena , Matsui Mitsuaki , Iwamoto Azusa , Taking Bunsreng , Cox Sharon E , Hall Lindsay J 
Published: July 2023

AbstractThe gut microbiota of infants in low-middle income countries like Cambodia remain underrepresented in microbiome research. This study aimed to explore the faecal gut microbiota composition and faecal cytokine profiles in a cohort of infants living in a rural province of Cambodia and explore the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants (96 samples in total) after 7 months of age were analysed using 16S rRNA amplicon sequencing to determine the composition of the microbiota. Bacterial strains were isolated and subjected to whole genome sequencing and genomic analysis and concentrations of faecal cytokines were also measured. Initially, we compared the effects of two sample collection methods due to the challenges of faecal sample collection and storage in a rural location. Storage of faecal samples in a DNA preservation solution retained a greater abundance ofBacteroides. Analyses of microbiota composition of samples stored in DNA preservation solution indicated thatBifidobacteriumwas the most abundant genus withBifidobacterium longumthe most abundant species, particularly in breastfed infants. Most infants had detectable pathogenic taxa indicating frequent pathogen exposure, withShigellaandKlebsiellamore abundant in infants with recent diarrheal illness. We did not detect antibiotic-associated perturbations in the gut microbiota, and no associations were found between the gut microbiota and infant growth. Genomic analysis of isolated strains indicated the presence of gene clusters encoding the ability to digest human milk oligosaccharides inB. longumandBifidobacterium breveisolates. The presence of antibiotic-resistant genes was also identified in potentially pathogenic species, as well as in beneficial genera includingBifidobacterium. Faecal cytokine analysis showed higher concentrations of Interlukin-1alpha and vascular endothelial growth factor in breastfed infants, which may influence the infant gut mucosal immune system. This study provides insights into an underrepresented population of rural Cambodian infants, emphasising the impact of pathogen exposure and breastfeeding on gut microbiota composition and faecal immune profiles.
A Versatile Tool for Precise Variant Calling in Mycobacterium tuberculosis Genetic Polymorphisms
Authors: Razzak Safina Abdul , Hasan Zahra , Azim M. Kamran , Kanji Akbar , Shakoor Sadia , Hasan Rumina 
Published: July 2023

AbstractBackgroundWhole genome sequencing (WGS) facilitates the diagnosis of multidrug-resistant MDR-TB through the interpretation of sequence variations (SV) inMycobacterium tuberculosis(MTB) genes. Information on phenotypic and genotypic resistance associations continues to evolve, it is important to identify SV within genes of interest. We developed an MTB-VCF variant calling pipeline that can compare against the reference genome for any gene of interest. We demonstrate its utility for calling SV in genes associated with Rifampicin (RIF), Isoniazid (INH), Ethambutol (EM), and Streptomycin (SM) resistance.MethodsMTB-VCF is a Python-based command line Variant Calling pipeline designed to streamline batch processing from raw reads (FastQ) files. SV called by MTB-VCF were compared with those identified by TBProfiler, KVARQ, CASTB, Mykrobe Predictor and Phy-ResSE pipelines. The sensitivity and Specificity of MTB-VCF SV calling were calculated against the drug susceptibility testing (DST) phenotype.ResultsMTB-VCF identified 868 SV present in 200 phenotypically resistant MDR-TB isolates. These were acrossrpsl, rrs, rpoB, inhA,katG,ahpC,gidB andembCAB genes. Of these, 684 SV were known to be associated with a resistance genotype, leading to a specificity of 97.75%. The SV called by the MTB-VCF was compared separately to resistance genotypes called by TB-Profiler, KvarQ, CASTB, Mykrobe Predictor, and PhyRes-SE pipelines, demonstrating a sensitivity of 99.5%.ConclusionThe MTB-VCF pipeline offers a rapid and accurate solution for identifying SV in target genes for interpretation later. It can be run in large batches, proving flexible computing that allows for the customization of core bioinformatic pipelines, enabling the analysis of WGS data from different technologies.
Phytoplankton tune local pH to actively modulate circadian swimming behavior
Authors: Ghoshal Arkajyoti , Dhar Jayabrata , Grossart Hans-Peter , Sengupta Anupam 
Published: July 2023

AbstractDiel vertical migration (DVM), the diurnal exodus of motile phytoplankton between the light- and nutrient-rich aquatic regions, is governed by endogenous biological clocks. Many species exhibit irregular DVM patterns wherein out-of-phase gravitactic swimming–relative to that expected due to the endogenous rhythm–is observed. How cells achieve and control this irregular swimming behavior, and its impact on biological fitness remain poorly understood. Combining local environmental monitoring with behavioral and physiological analyses of motile bloom-formingHeterosigma akashiwocells, we report that phytoplankton species modulate their DVM pattern by progressively tuning local pH, yielding physiologically equivalent yet behaviorally distinct gravitactic sub-populations which remain separated vertically within a visibly homogeneous cell distribution. Individual and population-scale tracking of the isolatedtopandbottomsub-populations revealed similar gravitactic (swimming speed and stability) and physiological traits (growth rate and maximum photosynthetic yield), suggesting that the sub-populations emerge due to mutual co-existence. Exposing the top (bottom) sub-population to the spent media of the bottom (top) counterpart recreates the emergent vertical distribution, while no such phenomenon was observed when the sub-populations were exposed to their own spent media. A model of swimming mechanics based on the quantitative analysis of cell morphologies confirms that the emergent sub-populations represent distinct swimming stabilities, resulting from morphological transformations after the cells are exposed to the spent media. Together with the corresponding night-time dataset, we present an integrated picture of the circadian swimming, wherein active chemo-regulation of the local environment underpins motility variations for potential ecological advantages via intraspecific division of labor over the day-night cycle. This chemo-regulated migratory trait offers mechanistic insights into the irregular diel migration, relevant particularly for modelling phytoplankton transport, fitness and adaptation as globally ocean waters see a persistent drop in the mean pH.One sentence summaryActive regulation of local pH diversifies the diel vertical migration of motile phytoplankton.
Phenotypic effect ofGBA1variants in individuals with and without Parkinson disease: the RAPSODI study
Authors: Toffoli M , Chohan H , Mullin S , Jesuthasan A , Yalkic S , Koletsi S , Menozzi E , Rahall S , Limbachiya N , Loefflad N , Higgins A , Bestwick J , Lucas-Del-Pozo S , Fierli F , Farbos A , Mezabrovschi R , Lee-Yin C , Schrag A , Moreno-Martinez D , Hughes D , Noyce A , Colclough K , Jeffries AR , Proukakis C , Schapira AHV 
Published: July 2023

ABSTRACTBackgroundVariants in theGBA1gene cause the lysosomal storage disorder Gaucher disease (GD). They are also risk factors for Parkinson disease (PD), and modify the expression of the PD phenotype.The penetrance ofGBA1variants in PD is incomplete, and the ability to determine who amongstGBA1variant carriers are at higher risk of developing PD, would represent an advantage for prognostic and trial design purposes.ObjectivesTo compare the motor and non-motor phenotype ofGBA1carriers and non-carriers.MethodsWe present the cross-sectional results of the baseline assessment from the RAPSODI study, an online assessment tool for PD patients andGBA1variant carriers. The assessment includes clinically validated questionnaires, a tap-test, the University of Pennsyllvania Smell Identification Test and cognitive tests. Additional, homogeneous data from the PREDICT-PD cohort were included.ResultsA total of 379 participants completed all parts of the RAPSODI assessment (89GBA1-negative controls, 169GBA1-negative PD, 47GBA1-positive PD, 47 non-affectedGBA1carriers, 27 GD). Eightysix participants were were recruited through PREDICT-PD (43 non-affectedGBA1carriers and 43GBA1-negative controls).GBA1-positive PD showed worse performance in visual cognitive tasks and olfaction compared toGBA1-negative PD patients. No differences were detected between non-affectedGBA1carriers carriers andGBA1-negative controls. No phenotypic differences were observed between any of the non-PD groups.ConclusionsOur results support previous evidence thatGBA1-positive PD has a specific phenotype with more severe non-motor symptoms. However, we did not reproduce previous findings of more frequent prodromal PD signs in non-affectedGBA1carriers.
Remote Digital Cognitive Assessment Reveals Cognitive Deficits Related to Hippocampal Atrophy in Autoimmune Limbic Encephalitis
Authors: Shibata Kengo , Attaallah Bahaaeddin , Tai Xin-You , Trender William , Hellyer Peter J. , Hampshire Adam , Irani Sarosh R , Manohar Sanjay G , Husain Masud 
Published: July 2023

AbstractAutoimmune Limbic Encephalitis (ALE) is a neurological disease characterised by inflammation of the limbic regions of the brain, mediated by pathogenic autoantibodies. Because cognitive deficits persist following acute treatment of ALE, the accurate assessment of long-term cognitive outcomes is important for clinical assessments and trials. However, evaluating cognition is costly and an unmet need for validated digital methods exists. We investigated whether remote digital methods could identify previously characterised cognitive impairments in ALE patients and would correlate with standard neuropsychological assessment and hippocampal volume. The cognitive performance of 21 chronic ALE patients along with 54 age-matched healthy controls was assessed with a battery of 12 cognitive tasks from the Cognitron online platform. ALE patients performed significantly worse in memory, visuospatial abilities, executive function, and language. No impairments in digit & spatial span, target detection (attention) and emotion discrimination were observed. The global score on the online cognitive tasks correlated significantly with the established Addenbrooke’s Cognitive Examination III (ACE) pen-and-paper test. Deficits in visuospatial processing and language were identified in ALE compared to controls using remote digital testing but not the ACE, highlighting higher sensitivity of computerised testing to residual cognitive impairment. Finally, the hippocampal volume of ALE patients and healthy controls correlated with online cognitive scores. Overall, these findings demonstrate that remote, online testing may facilitate the characterisation of cognitive profiles in complex neurological diseases.
US Exceptionalism? International Trends in Midlife Mortality
Authors: Dowd Jennifer Beam , Doniec Katarzyna , Zhang Luyin , Tilstra Andrea 
Published: July 2023

AbstractBackgroundRising midlife mortality in the United States (US) has raised concerns, particularly the increase in “deaths of despair” (due to drugs, alcohol, and suicide). While life expectancy is also stalling in other countries such as the UK, whether midlife mortality is rising outside the US is not known.MethodsWe document trends in midlife mortality in the US, UK and a group of 16 high-income countries in Western Europe, Australia, Canada, New Zealand, and Japan, as well as 7 Central and Eastern European (CEE) countries from 1990-2019. We use annual mortality data from the World Health Organization Mortality Database to analyze sex and age-specific (25-44, 45-54, and 55-64) age-standardized death rates across 13 major cause-of-death categories.FindingsUS midlife mortality rates worsened since 1990 for several causes of death including drug- related, alcohol-related, suicide, metabolic disease, nervous system disease, respiratory disease, and infectious/parasitic diseases. Deaths due to homicide, transport accidents, and cardiovascular disease declined overall since 1990 but saw recent increases or stalling of improvements. Midlife mortality has also recently increased in the UK for 45-54-year-olds, and in Canada, Poland, and Sweden among 25-44-year-olds.ConclusionThe US is increasingly falling behind not only high-income but also CEE countries heavily impacted by the post-Soviet mortality crisis of the 1990s. While levels of midlife mortality in the UK are substantially lower than in the US overall, there are signs that UK midlife mortality is worsening relative to the rest of Europe.
LigaNET: A multi-modal deep learning approach to predict the risk of subsequent anterior cruciate ligament injury after surgery
Authors: Han Mo , Singh Mallika , Karimi Davood , Kim Jin Young , Flannery Sean W. ,   BEAR Trial Team, Ecklund Kirsten , Murray Martha M. , Fleming Braden C. , Gholipour Ali , Kiapour Ata M. 
Published: July 2023

AbstractAnterior cruciate ligament (ACL) injuries are a common cause of soft tissue injuries in young active individuals, leading to a significant risk of premature joint degeneration. Postoperative management of such injuries, in particular returning patients to athletic activities, is a challenge with immediate and long-term implications including the risk of subsequent injury. In this study, we present LigaNET, a multi-modal deep learning pipeline that predicts the risk of subsequent ACL injury following surgical treatment. Postoperative MRIs (n=1,762) obtained longitudinally between 3 to 24 months after ACL surgery from a cohort of 159 patients along with 11 non-imaging outcomes were used to train and test: 1) a 3D CNN to predict subsequent ACL injury from segmented ACLs, 2) a 3D CNN to predict injury from the whole MRI, 3) a logistic regression classifier predict injury from non-imaging data, and 4) a multi-modal pipeline by fusing the predictions of each classifier. The CNN using the segmented ACL achieved an accuracy of 77.6% and AUROC of 0.84, which was significantly better than the CNN using the whole knee MRI (accuracy: 66.6%, AUROC: 0.70; P<.001) and the non-imaging classifier (accuracy: 70.1%, AUROC: 0.75; P=.039). The fusion of all three classifiers resulted in highest classification performance (accuracy: 80.6%, AUROC: 0.89), which was significantly better than each individual classifier (P<.001). The developed multi-modal approach had similar performance in predicting the risk of subsequent ACL injury from any of the imaging sequences (P>.10). Our results demonstrate that a deep learning approach can achieve high performance in identifying patients at high risk of subsequent ACL injury after surgery and may be used in clinical decision making to improve postoperative management (e.g., safe return to sports) of ACL injured patients.
Methodological approach to sleep state misperception in insomnia disorder: comparison between multiple nights of actigraphy recordings and a single night of polysomnography recording
Authors: Maltezos Antonia , Perrault Aurore A. , Walsh Nyissa A. , Phillips Emma-Maria , Gong Kirsten , Tarelli Lukia , Smith Dylan , Cross Nathan E. , Pomares Florence B. , Gouin Jean-Philippe , Dang-Vu Thien Thanh 
Published: July 2023

ABSTRACTRationaleSleep state misperception (SSM) represents the discrepancy between objectively recorded and subjectively perceived measures of sleep, including sleep onset latency (SOL), sleep duration (TST) and wake duration (WASO). The severity of SSM is higher in insomnia disorder (INS) compared to other populations. SSM is typically assessed in-lab during one night with polysomnographic (PSG) recording or at-home with actigraphy recordings over multiple days, both complemented by subjective sleep reports. Both methods of data collection have their specific strengths and weaknesses, and provide sleep measures that may differ, especially in individuals with sleep disorders. The extent to which the methods and environment of data collection impact measures of sleep misperception remains unclear. This study aimed at providing a comprehensive assessment of SSM in INS and good sleepers (GS) by comparing recordings performed for one night in-lab (PSG and night review) and during several nights at-home (actigraphy and sleep diaries).MethodsFifty-seven INS and 29 GS wore an actigraphy device and filled a sleep diary for two weeks at-home. They subsequently completed a PSG recording and filled a night review the next morning in-lab. Sleep perception index (subjective/objective × 100; in %) of SOL, WASO and TST were computed and compared between methods and groups.ResultsWe found that GS and INS exhibit opposite patterns of sleep misperception. GS displayed a tendency to overestimate TST and WASO but correctly perceived SOL. The degree of misperception was similar across methods within the GS group. In contrast, INS underestimated their TST and overestimated their SOL both in-lab and at-home, yet the severity of misperception (i.e., degree of mismatch) of SOL was larger at-home than in-lab. Finally, INS overestimated WASO only in-lab while correctly perceiving it at-home. While only the degree of TST misperception was stable across methods in INS, misperception of SOL and WASO were dependent on the method used.ConclusionsWe found that GS and INS exhibit opposite patterns and severity of sleep misperception. While the degree of misperception in GS was similar across methods, we found that only sleep duration misperception was reliably detected by both in-lab and at-home methods in INS. Our results highlight that, when assessing sleep misperception in individuals with insomnia disorder, the method of data collection should be carefully considered in relation to the main sleep outcomes of interest.
Evaluating steroid hormone receptor interactions using the live-cell NanoBRET proximity assay
Authors: Huggins Rosemary J , Hosfield David , Ishag-Osman Amira , Lee Keemin , Ton-That Elia , Greene Geoffrey L. 
Published: July 2023

AbstractSteroid hormone receptors play a crucial role in the development and characterization of the majority of breast cancers. These receptors canonically function through homodimerization, but physical interactions between different hormone receptors play a key role in cell functions as well. The estrogen receptor (ERα) and progesterone receptor (PR), for example, are involved in a complex set of interactions known as ERα/PR crosstalk. Here, we developed a valuable panel of nuclear receptor expression plasmids specifically for use in NanoBRET assays to assess nuclear receptor homo- and heterodimerization. We demonstrate the utility of this assay system by assessing ERα/PR physical interaction in the context of the endocrine therapy resistance- associated ERα Y537S mutation. We identify a role of the ERα Y537S mutation beyond that of constitutive activity of the receptor; it also increases ERα/PR crosstalk. In total, the NanoBRET assay provides a novel avenue for investigating hormone receptor crosstalk. Future research may use this system to assess the effects of other clinically significant hormone receptor mutations on hormone receptor crosstalk.