bluuebunny/crossref_metadata_2025_split huggingface dataset:
PICAFlow: a complete R workflow dedicated to flow/mass cytometry data, from pre-processing to deep and comprehensive analysis
Authors: Régnier Paul , Marques Cindy , Saadoun David 
Published: December 2023

Abstract

Summary
PICAFlow is a R-written integrative workflow dedicated to flow/mass cytometry data handling, from pre-processing to deep and comprehensive analysis. It is designed as a powerful all-in-one tool which contains all the necessary functions and packages presented in a user-friendly and ease-to-use fashion. PICAFlow also includes important features that are very frequently lacking in other close software, such as interactive R Shiny applications for real-time data transformation and compensation as well as normalization methods aiming to remove batch effects and unwanted inter- and intra-group heterogeneity. It also allows to perform dimensionality reduction, cell clustering (using different available approaches), as well as complementary statistical analyses and export different support for data interpretation and visualization.

Availability
PICAFlow is available as a R-written package hosted at the following GitHub repository: https://github.com/PaulRegnier/PICAFlow and is complemented by a fully detailed tutorial available at the following URL: https://paul-regnier.fr/tutoriel-picaflow/.
Modular brain network in volitional eyes closing: enhanced integration with a marked impact on hubs
Authors: Zhang Yi , Han Xiao , Ge Xuelian , Xu Tianyong , Wang Yanjie , Mu Jiali , Liu Fan 
Published: December 2023

Abstract
Volitional eyes closing would shift brain’s information processing modes from the “exteroceptive” to “interoceptive” state. This transition induced by the eyes closing is underpinned by a large-scale reconfiguration of brain network, which is still not fully comprehended. Here, we investigated the eyes-closing-relevant network reconfiguration by examining the functional integration among intrinsic modules. Our investigation utilized a publicly available dataset with 48 subjects being scanned in both eyes closed and eyes open conditions. It was found that the modular integration was significantly enhanced during the eyes closing, including lower modularity index, higher participation coefficient, less provincial hubs, and more connector hubs. Moreover, the eyes-closing-enhanced integration was particularly noticeable in the hubs of network, mainly located in the default-mode network. Finally, the hub-dominant modular enhancement was positively correlated to the eyes-closing-reduced entropy of BOLD signal, suggesting a close connection to the diminished consciousness of individuals. Collectively, our findings strongly suggested that the enhanced modular integration with substantially reorganized hubs characterized the large-scale cortical underpinning of the volitional eyes closing.
Expanding options of supportive care in IgA nephropathy
Authors: Maixnerova Dita , Hartinger Jan , Tesar Vladimir 
Published: December 2023

ABSTRACT
Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis worldwide, with a potentially serious prognosis. At present, management of IgAN is primarily based on therapeutic lifestyle changes, and excellent blood pressure control and maximized supportive treatment with the combination of inhibition of the renin–angiotensin–aldosterone system with either inhibitors of angiotensin-converting enzyme or angiotensin II receptor blockers and inhibitors of sodium-glucose cotransporter-2, and possibly in the future also with endothelin antagonists. Supportive care currently represents the cornerstone of treatment of IgAN. Targeted-release formulation of budesonide should replace systemic corticosteroids in patients with higher proteinuria and active histological lesions.
New treatment options are aimed at immunopathogenesis of IgAN including depletion or modulation of Galactose-deficient-Immunoglobulin A1–producing B cells, plasma cells, and the alternate and/or lectin pathway of complement. The exact place of monoclonal antibodies and complement inhibitors will need to be determined.
This article reviews potential supportive therapies currently available for patients with IgAN.
Understanding patient needs and predicting outcomes in IgA nephropathy using data analytics and artificial intelligence: a narrative review
Authors: Schena Francesco Paolo , Manno Carlo , Strippoli Giovanni 
Published: December 2023

ABSTRACT
This narrative review explores two case scenarios related to immunoglobulin A nephropathy (IgAN) and the application of predictive monitoring, big data analysis and artificial intelligence (AI) in improving treatment outcomes. The first scenario discusses how online service providers accurately understand consumer preferences and needs through the use of AI-powered big data analysis. The author, a clinical nephrologist, contemplates the potential application of similar methodologies, including AI, in his medical practice to better understand and meet patient needs. The second scenario presents a case study of a 20-year-old man with IgAN. The patient exhibited recurring symptoms, including gross haematuria and tonsillitis, over a 2-year period. Through histological examination and treatment with renin–angiotensin system blockade and corticosteroids, the patient experienced significant improvement in kidney function and reduced proteinuria over 15 years of follow-up. The case highlights the importance of individualized treatment strategies and the use of predictive tools, such as AI-based predictive models, in assessing treatment response and predicting long-term outcomes in IgAN patients. The article further discusses the collection and analysis of real-world big data, including electronic health records, for studying disease natural history, predicting treatment responses and identifying prognostic biomarkers. Challenges in integrating data from various sources and issues such as missing data and data processing limitations are also addressed. Mathematical models, including logistic regression and Cox regression analysis, are discussed for predicting clinical outcomes and analysing changes in variables over time. Additionally, the application of machine learning algorithms, including AI techniques, in analysing big data and predicting outcomes in IgAN is explored. In conclusion, the article highlights the potential benefits of leveraging AI-powered big data analysis, predictive monitoring and machine learning algorithms to enhance patient care and improve treatment outcomes in IgAN.
Systemic and targeted steroids for the treatment of IgA nephropathy
Authors: Locatelli Francesco , Del Vecchio Lucia , Ponticelli Claudio 
Published: December 2023

ABSTRACT
Immunoglobulin A nephropathy (IgAN) is a common glomerulonephritis partially correlated with mucosal immune system dysfunction. Progressive renal failure occurs in many patients, with about 30–50% of the patients with IgAN developing end-stage kidney disease (ESKD). Many treatments have been used for decades, despite uncertainty about their effectiveness and the ideal dose. Randomised controlled trials reported that systemic glucocorticoids can be an effective treatment for patients with persistent and significant proteinuria despite renin-angiotensin system inhibitors use possibly causing systemic side effects. The primary focus of IgAN management should be based on optimised supportive care, including renin-angiotensin system (RAS) blockade and now SGLT2 inhibitors. The novel targeted-release formulation (TRF) of budesonide has been tested to reduce the adverse events of systemic steroids by delivering the drug to the distal ileum. The local efficacy of TRF-budesonide may represent a novel and promising approach to treating IgAN. Two clinical trials showed that TRF-budesonide could significantly reduce proteinuria and haematuria and possibly preserve renal function while significantly reducing the side effects. However, the limited number of treated patients and the relatively short follow-up suggest caution before considering budesonide superior to the current six-months steroid pulses scheme. Long-term data on the efficacy and safety of TRF budesonide are awaited, together with the design of trials with a head-to-head comparison with systemic steroids before considering TRF-budesonide as the standard of care treatment for IgAN nephropathy.
Exploratory behavior is associated with the cognitive speed in male chestnut thrushes
Authors: Lou Yingqiang , Zou Yuqi , Fang Yun , Sun Yuehua 
Published: December 2023

Abstract
Intra-individual variation in cognitive abilities has been widely reported in animals. Recent studies have found that individual cognitive performance varies with personality traits in a wide range of animal taxa, with a speed-accuracy trade-off between cognition and personality traits. Few studies investigated whether these relationships change depending on different contexts. Here we investigate whether the personality trait (as measured by exploratory behavior in a novel environment) is associated with cognition (novel skill learning and spatial memory) in wild male chestnut thrushes Turdus rubrocanus. Using an experimental novel skill-learning task set-up, we found that fast-exploring individuals explored the experimental device (a cardboard with 8 opaque cups) sooner than slow-exploring individuals. Exploratory behavior was not associated with individual spatial memory performances or an individual’s capacity to learn the novel skill. Learning speed was positively associated with the difficulty of learning phases, and fast-exploring individuals used less trials to meet the learning criterion. In addition, fast-exploring individuals took less time to complete the 24-h spatial memory test, but the accuracy of the test was not significantly different between individuals who were more or less exploratory. We suggest that variation in personality traits associates with individual learning speed in cognitive tasks and that this relationship is context-dependent.
Serial troponin-I and long-term outcomes in subjects with suspected acute coronary syndrome
Authors: Pareek Manan , Kristensen Anna Meta Dyrvig , Vaduganathan Muthiah , Byrne Christina , Biering-Sørensen Tor , Højbjerg Lassen Mats Christian , Johansen Niklas Dyrby , Skaarup Kristoffer Grundtvig , Rosberg Victoria , Pallisgaard Jannik L , Mortensen Martin Bødtker , Maeng Michael , Polcwiartek Christoffer B , Frangeskos Julia , McCarthy Cian P , Bonde Anders Nissen , Lee Christina Ji-Young , Fosbøl Emil L , Køber Lars , Olsen Niels Thue , Gislason Gunnar H , Torp-Pedersen Christian , Bhatt Deepak L , Kragholm Kristian H 
Published: December 2023

Abstract

Aims
It is unclear how serial high-sensitivity troponin-I (hsTnI) concentrations affect long-term prognosis in individuals with suspected acute coronary syndrome (ACS).

Methods and results
Subjects who underwent two hsTnI measurements (Siemens TnI Flex® Reagent) separated by 1–7 h, during a first-time hospitalization for myocardial infarction, unstable angina, observation for suspected myocardial infarction, or chest pain from 2012 through 2019, were identified through Danish national registries. Individuals were stratified per their hsTnI concentration pattern (normal, rising, persistently elevated, or falling) and the magnitude of hsTnI concentration change (&lt;20%, &gt;20–50%, or &gt;50% in either direction). We calculated absolute and relative mortality risks standardized to the distributions of risk factors for the entire study population. A total of 20 609 individuals were included of whom 2.3% had died at 30 days, and an additional 4.7% had died at 365 days. The standardized risk of death was highest among persons with a persistently elevated hsTnI concentration (0–30 days: 8.0%, 31–365 days: 11.1%) and lowest among those with two normal hsTnI concentrations (0–30 days: 0.5%, 31–365 days: 2.6%). In neither case did relative hsTnI concentration changes between measurements clearly affect mortality risk. Among persons with a rising hsTnI concentration pattern, 30-day mortality was higher in subjects with a &gt;50% rise compared with those with a less pronounced rise (2.2% vs. &lt;0.1%).

Conclusion
Among individuals with suspected ACS, those with a persistently elevated hsTnI concentration consistently had the highest risk of death. In subjects with two normal hsTnI concentrations, mortality was very low and not affected by the magnitude of change between measurements.
Biosimilars engage in low levels of direct-to-physician marketing relative to reference biologics
Authors: Hyland Megan F , Carey Colleen M 
Published: December 2023

Abstract
Biosimilars have the potential to greatly reduce US spending on biologic drugs, but uptake of these competitor products varies. We used Open Payments data from 2014 to 2022 to proxy for direct-to-physician marketing and compared levels of activity between biologic and biosimilar drug manufacturers. Our analysis focused on 6 reference biologics that recently faced competition in the years immediately before and after the launch of the first biosimilar. We used Medicare Part B dosage units to measure market penetration of biosimilars and its relationship with biosimilar marketing activity. Last, we conducted a sensitivity test, comparing payments for primarily office- or hospital-based physicians, using affiliations constructed from Medicare Carrier claims. Reference biologic manufacturers greatly reduced the amount of direct-to-physician marketing in the post-launch period. Biosimilar manufacturers generally engaged in low levels of activity relative to the historic performance of reference biologics. These trends were consistent across office- and hospital-based physicians. The intensity of biosimilars' direct-to-physician marketing also had no apparent relationship with achieved market penetration. Our findings demonstrate that persistently high market shares of reference biologics cannot be explained by ongoing direct-to-physician marketing activities. At the same time, while such activities could educate physicians or induce switching, biosimilar entrants engaged in little direct-to-physician marketing.
Making care primary: Medicare's latest attempt at value-based primary care
Authors: Kumar Wasan , Adashi Eli Y , Kocher Bob 
Published: December 2023

Abstract
On June 8th, 2023, the Centers for Medicare and Medicaid Innovation (CMMI) announced the Making Care Primary (MCP) model, its latest attempt to transform primary care delivery for a value-based care payment system. The MCP is a decade-long multi-payer partnership with a voluntary risk-adjusted payment model for primary care organizations. It provides financial support for organizations to develop and implement a value-based care infrastructure and prospective payments per beneficiary for the delivery of primary care. The MCP consists of 3 tracks, ranging from lump-sum infrastructure payments to a fully prospective payment model with 1-sided risk. In turn, physicians need to meet a set criteria, such as quality outcomes, health-related social needs screening and referral, and high-touch chronic care management (CMMI; https://innovation.cms.gov/innovation-models/making-care-primary). While MCP is a well-planned effort, it is likely to suffer from some of the same pitfalls as prior CMS attempts to revolutionize primary care and may therefore exert unintended effects on market consolidation.
Comparing image quality and trachoma detection across three camera types from a survey in Kongwa, Tanzania
Authors: Aguwa Ugochi T , Mkocha Harran , Munoz Beatriz , Wolle Meraf A , Brady Christopher J , West Sheila K 
Published: December 2023

Abstract

Background
There is an increasing demand for photography for trachoma prevalence surveys. In previous studies, digital single lens reflex (DSLR) images were superior to smartphone images, but newer-model smartphones and/or lens attachments may be able to bridge this gap. This study compares the image quality and ability to detect trachomatous inflammation – follicular (TF) of three camera types: a DSLR Nikon camera, an iPhone SE and an iPhone 13 Pro with a cell scope.

Methods
We surveyed 62 children ages 1–7 y from two Tanzanian communities. Upper tarsal conjunctiva images of both eyes were graded for TF by two standardized graders. The McNemar's test and a logistic regression model were used for analyses.

Results
The DSLR camera malfunctioned during the study, thus the iPhone SE and iPhone 13 Pro with cell scope were both more likely to take high-quality, gradable photographs (88% and 86%, respectively) compared with the DSLR camera (69%) (p&lt;0.001 and p=0.02, respectively). TF was detected in gradable images from the iPhone SE (8.8%) and iPhone 13 Pro with cell scope (9.0%) at the same rate (p=1.0) as images from the DSLR camera (9.7%).

Conclusion
Smartphones with high-quality image capture, like the iPhone SE/13 Pro, have the potential for use in trachoma surveys if the proportion of gradable images can be improved.
Gender differences in the surgical management of trachomatous trichiasis: an exploratory analysis of global trachoma survey data, 2015–2019
Authors: Sullivan Kristin M , Harding-Esch Emma M , Batcho Wilfrid E , Issifou Amadou A Bio , Lopes Maria de Fátima Costa , Szwarcwald Celia Landmann , Vaz Ferreira Gomez Daniela , Bougouma Clarisse , Christophe Nassa , Kabore Martin , Bucumi Victor , Bella Assumpta L , Epee Emilienne , Yaya Georges , Trujillo-Trujillo Julian , Dejene Michael , Gebretsadik Fikre Seife , Gebru Genet , Kebede Fikreab , Mathewos Tsedeke , Cassama Eunice Texiera de Silva , Sanha Salimato , Barasa Ernest , Sultani Hadley Matendechero , Watitu Titus , Tekeraoi Rabebe , Kalua Khumbo M , Masika Michael P , Traoré Lamine , Minnih Abdallahi O , Abdala Mariamo , Massangaie Marília E , Win Ye , Apadinuwe Sue-Chen , Mishra Sailesh Kumar , Sharma Shekhar , Amza Abdou , Kadri Boubacar , Nassirou Beido , Mpyet Caleb D , Olobio Nicholas , Hussain Arif , Khan Asad Aslam , Jambi Garap , Ko Robert , Kello Amir B , Badiane Mouctar D , Sarr Boubacar , Dalmar Abdi , Elshafie Balgesa E , Kabona George E , Kaitaba Oscar , Mwingira Upendo , Simon Alistidia , Kanyi Sarjo , Awoussi Marcel S , Togbey Kwamy , Baayenda Gilbert , Francis Mugume , Tukahebwa Edridah M , Bakhtiari Ana , Keil Alexander P , Maselko Joanna , Westreich Daniel , Garae Mackline , Taleo Fasiah , Al-Khateeb Tawfik Q , Mwale Consity , Solomon Anthony W , Gower Emily W 
Published: December 2023

Abstract

Background
Trachomatous trichiasis (TT) is a painful, potentially blinding eye condition that can be managed through epilation or surgery. Women are affected by TT approximately twice as often as men and are believed to face gendered barriers to receiving surgical care to prevent vision loss.

Methods
We used data from 817 cross-sectional surveys conducted during 2015–2019 in 20 African countries to estimate the prevalence difference (PD) between female and male eyes for four outcomes potentially indicating gender-related differences in TT management: (1) received surgery and developed postoperative TT (PTT), (2) never offered surgery, (3) offered surgery but declined it, and (4) offered epilation but never offered surgery.

Results
The prevalence was modestly elevated among female eyes compared with male eyes for having PTT (PD:1.8 [95% confidence limits (CL): 0.6, 3.0]) and having declined surgery for the eye (PD: 6.2 [95% CL: 1.8, 10.7]). The proportion offered epilation was similar by gender (PD:0.5 [95% CL: −0.4, 1.3]), while never having been offered surgery was somewhat more prevalent among male eyes (PD: −2.1 [95% CL: −3.5, −0.7]).

Conclusions
Our results suggest potential gender differences in TT management. More research is needed to determine the causes and implications of the observed differences.
Treatment coverage of mass administration of azithromycin among children aged 1–11 months in 21 districts of Kebbi state, Nigeria
Authors: Wamyil-Mshelia Teyil , Madaki Suzie , Isiyaku Sunday , Shu'aibu Joy , Olobio Nicholas P , Aliero Attahiru A , Abdulsalam Muhammad , Taiwo Joshua , McDickoh Victor J 
Published: December 2023

Abstract

Background
The WHO recommends mass drug administration (MDA) as a strategy to deliver safe and cost-effective medicines to prevent and treat diseases. The antibiotic, azithromycin, has been used during MDA for the treatment and prevention of trachoma in Nigeria. Azithromycin has recently been shown to reduce infant mortality in communities receiving it for trachoma-elimination purposes in sub-Saharan Africa. This article reports on the implementation strategies for the safety and antimicrobial resistance of mass administration of azithromycin to children aged 1–11 mo using the trachoma programme platform in Kebbi state.

Methods
The mass administration of azithromycin among 1–11-mo-olds in Kebbi was implemented in three phases: (i) the preimplementation phase, during which specific activities were conducted to achieve government and community buy-in, ownership and capacity building; (ii) the implementation phase, which included the mass administration of azithromycin carried out by community volunteers (also known as community-directed distributors [CDDs]), monitoring (by health workers and independent monitors) and reporting of the distribution by all personnel; and (iii) the postimplementation phase, which included the validation of community data, where each item of community summary data is verified and checked for completeness and accuracy before uploading to the District Health Information System platform, where data are visualised, analysed and stored.

Results
In total, 97% of the target population received treatment; the remaining 3% were not treated due to signs of ill health, history of allergy to antibiotics, parental refusal or absence at the time of MDA. Children aged 1–11 mo accounted for 17% of the under-5 population, with females constituting 56% of the target population. In communities that were monitored, reports showed that only 5% lacked distribution materials (scales, slings or registers), &gt;80% correctly entered data into community registers and 5% of children were not treated due to inadequate azithromycin provided to the CDDs for distribution.

Conclusion
The implementation of azithromycin MDA for children aged 1–11 mo in Kebbi, utilising the trachoma platform, exhibited commendable coverage due to existing programme platform, healthcare and community structures, intensive advocacy and social mobilisation, real-time monitoring and progress-tracking strategies. It also demonstrated that the trachoma platform is suitable for implementing public health interventions, even after the elimination of trachoma in previously endemic districts.