bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Impact of Pleural Fluid Streptococcus pneumoniae Polymerase Chain Reaction Testing in Children With Complicated Pneumonia
Authors: Ho Erin C , Olson Kaitlin E , Butler Molly , Birkholz Meghan , Miller Kristen , MacBrayne Christine E , Jung Sarah , Messacar Kevin , Asturias Edwin J , Dominguez Samuel R 
Published: August 2024

Abstract

Background
While Streptococcus pneumoniae (Spn) is the leading cause of pediatric complicated community-acquired pneumonia (cCAP), it is infrequently recovered by culture-based methods. We studied the real-world clinical impact of an Spn polymerase chain reaction (PCR) assay for pleural fluid.

Methods
This pre–post quasi-experimental cohort study compared pathogen detection, antibiotic usage, and outcomes in children hospitalized with cCAP requiring pleural effusion or empyema drainage at Children's Hospital Colorado between 2016 and 2023. Patients were compared across 2 diagnostic periods: pre-Spn PCR and post-Spn PCR. Cox proportional hazard models compared time from admission to pathogen detection, optimal therapy (narrowest pathogen-directed or guideline-recommended empiric therapy), and methicillin-resistant Staphylococcus aureus (MRSA) therapy discontinuation between periods.

Results
Compared to the pre-Spn PCR cohort (n = 149), the post-Spn PCR cohort (n = 79) was more likely to have a pathogen detected (73.4% post-PCR vs 38.9% pre-PCR, P &lt; .001), driven by more Spn detections (45.6% vs 14.1%, P &lt; .001). Time to pathogen detection during hospitalization was shorter in the post-Spn PCR period (P &lt; .001). The post-PCR cohort was more likely to receive optimal therapy (84.8% vs 53.0%, P &lt; .001), with shorter median times to optimal antibiotics (4.9 vs 10.0 days, P &lt; .001) and MRSA therapy discontinuation (1.5 vs 2.5 days, P = .03). There were no differences in hospital length of stay or readmissions.

Conclusions
Spn molecular testing of pleural fluid in children with cCAP resulted in significantly more microbiologic diagnoses and was associated with the optimization of antibiotics and decreased exposure to MRSA therapy, suggesting its clinical impact for pediatric complicated pneumonia.
Risk of Non–AIDS–Defining Events Is Lower in Antiretroviral Therapy (ART)–Naive Human Immunodeficiency Virus Controllers Than in Normal Progressors on Suppressive ART
Authors: Groenendijk Albert L , Miranda Afonso Pedro , Wit Ferdinand W N M , Blaauw Martinus J T , van Eekeren Louise E , Otten Twan , Vos Wilhelm A J W , Vadaq Nadira , dos Santos Jéssica C , van Lunzen Jan , van der Ven Andre , Rokx Casper , Verbon Annelies 
Published: August 2024

Abstract

Background
We aimed to compare the non-AIDS event (nADE) risk between normal progressors using antiretroviral therapy (NP-ART) and people with human immunodeficiency virus (HIV, PWH) who naturally control HIV infection (HIV controllers), as well as the risk of nADE following ART in HIV controllers.

Methods
The primary end point was the composite of cardiovascular disease, non-AIDS malignancy, or all-cause mortality, whichever came first. The role of ART in HIV controllers was assessed as a time-varying covariate.

Results
We included 1007 ART-naive HIV controllers (60 of them were elite controllers), 1510 early-ART (&lt;6 months after negative HIV test), and 15437 NP-ART (reference group), contributing 3813, 11 060, and 160 050 years of follow-up, respectively. HIV controllers had lower risk of the primary end point (hazard ratio [HR], 0.55; 95% confidence interval [CI]: .38–.81; P = .0023), all-cause mortality (adjusted HR [aHR], 0.45; 95% CI: .25–.79; P = .0054), and cardiovascular disease (aHR, 0.47; 95% CI: .22–.99; P = .046), but not non-AIDS malignancy (aHR, 0.74; 95% CI: .41–1.35; P = .33), compared with NP-ART. Among HIV controllers, each log10 lower baseline viral load further decreased the risk of a nADE (aHR, 0.54; 95% CI: .29–.99; P = .045). ART in HIV controllers did not reduce the risk of any nADE (aHR, 1.22; 95% CI: .66–2.29; P = .53).

Conclusions
HIV controllers had a lower n ADE risk than NP-ART, especially in those with low plasma viral loads. ART did not alter the nADE risk in HIV controllers. Our findings help clinicians to decide on prescribing ART in HIV controllers.
The Groupe d’Etude sur les Affections Inflammatoires Digestives (GETAID): 40 Years of a Family Story in Inflammatory Bowel Disease
Authors: Laharie David , Vuitton Lucine , Bourreille Arnaud , Bouhnik Yoram , Colombel Jean-Frédéric , Louis Edouard , Fumery Mathurin , Mailhat Charlotte , Mary Jean-Yves , Peyrin-Biroulet Laurent 
Published: August 2024

Abstract
The Groupe d’Etude sur les Affections Inflammatoires Digestives (GETAID) was founded in Paris in 1983 by Professor Robert Modigliani and colleagues. From the beginning, the aim of this international (France, Belgium, and Switzerland), multicenter, French-speaking group was to address clinical questions raised by patients or physicians in their daily practice or the inflammatory bowel disease community, by focusing on clinical research on treatments through randomized controlled trials, prospective cohorts, and cross-sectional studies, quantifying the severity of various facets of the disease when necessary for these studies. This very innovative approach has contributed to the advancement of knowledge in inflammatory bowel diseases by publishing more than 120 original articles in peer-reviewed journals throughout the GETAID’s 40-year history, most of them in top publications in gastroenterology and hepatology journals. In this paper, we will see what GETAID’s contribution has been over the last 4 decades and review the reasons for its success and forthcoming challenges.
Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure
Authors: Ishigohoka Jun , Bascón-Cardozo Karen , Bours Andrea , Fuß Janina , Rhie Arang , Mountcastle Jacquelyn , Haase Bettina , Chow William , Collins Joanna , Howe Kerstin , Uliano-Silva Marcela , Fedrigo Olivier , Jarvis Erich D , Pérez-Tris Javier , Illera Juan Carlos , Liedvogel Miriam 
Published: August 2024

Abstract
Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.
How Does an Integrated Pharmacist Add Value in the Management of Inflammatory Bowel Disease in the Era of Values-Based Healthcare?
Authors: Hilley Patrick , Wong Darren , De Cruz Peter 
Published: August 2024

Abstract
The World Health Organization has recommended that the management of chronic diseases such as inflammatory bowel disease (IBD) should be undertaken using an integrated approach delivered by a multidisciplinary team. Although the composition of an IBD multidisciplinary team has been well described, the inclusion of an IBD pharmacist as a core member has been more recent, with variable uptake within IBD services internationally. While pharmacists continue to play the traditional role of safe prescribing and monitoring of immunosuppressive therapies, their role within the IBD team is rapidly expanding; however, the value, in terms of both clinical outcomes as well as financial savings (where available), which they add to IBD services has been less well described. In this narrative review, we perform a comprehensive evaluation of the literature detailing the expanding roles that IBD pharmacists play and describe opportunities that exist for integrated pharmacists to add value to IBD service delivery. Medication and adherence counseling, immunosuppressive monitoring, uptake of biosimilars, therapeutic drug monitoring, health promotion and prevention appear to be key areas where integrated pharmacists can add the most value to IBD patients and services. In particular, integrated IBD pharmacists can improve patient outcomes via rigorous monitoring pre and post initiation of drug therapies; focused medication counseling; advice on improving adherence; implementation of novel approaches to medication usage, and; strategies to help sustain IBD service delivery. These data can be used to further build a case for those seeking to add pharmacists to their team/services. Future studies should focus on evaluating the impact of an integrated IBD pharmacist on quality-of-care delivery together with the clinical and financial value added to IBD services compared to services that lack an integrated IBD pharmacist role.
Sustained Spread of HIV-1 CRF55_01B in its Place of Origin: Dynamics and Hotspots
Authors: An Minghui , Zheng Chenli , Chen Lin , Li Hao , Zhang Yan , Gan Yongxia , Zhao Bin , Zhang Hui , Han Xiaoxu , Zhao Jin , Shang Hong 
Published: August 2024

Abstract

Background
Shenzhen, a city with a substantial mobile population, was identified as the first discovered region of human immunodeficiency virus-1 (HIV-1) CRF55_01B and epicenter of its severe epidemic. During the implementation of venue-based behavioral interventions and the “treat-all” policy, identifying the patterns of spread and transmission hotspots of CRF55_01B is imperative.

Methods
In this study, 1450 partial pol sequences, with demographic information, were collected from all newly diagnosed CRF55_01B infections in Shenzhen from 2008 to 2020. Molecular networks were constructed using the maximum likelihood and time-resolve phylogenies. Transmission rates, effective reproduction numbers (Re) of clusters, and viral dispersal were evaluated using Bayesian inference.

Results
In total, 526 sequences formed 114 clusters, including 7 large clusters. The status and size of clusters were strongly correlated with age, ethnicity, occupation, and CD4+ T-cell counts. The transmission rates of clusters were significantly higher than the national epidemic estimate. Four large clusters had Re exceeding 1 at the end of the sampling period. Immigrants from Guangdong and Hunan, along with local residents, were identified as the transmission hubs, with heterosexual men being the main source and MSM being the main destination. The virus exhibited a high movement frequency from individuals aged 30–49 years toward diverse age groups.

Conclusions
This study demonstrated that the hidden CRF55_01B transmissions continued despite current combined interventions in Shenzhen, and at-risk individuals susceptible to infection or transmission were identified, potentially serving as targets for more effective prevention and control of the local epidemic, thereby mitigating cross-regional spread nationwide due to population migration.
Development and validation of supervised machine learning multivariable prediction models for the diagnosis of Pneumocystis jirovecii pneumonia using nasopharyngeal swab PCR in adults in a low-HIV prevalence setting
Authors: Chew Rusheng , Woods Marion L , Paterson David L 
Published: August 2024

Abstract

Background
The global burden of the opportunistic fungal disease Pneumocystis jirovecii pneumonia (PJP) remains substantial. Polymerase chain reaction (PCR) on nasopharyngeal swabs (NPS) has high specificity and may be a viable alternative to the gold standard diagnostic of PCR on invasively collected lower respiratory tract specimens, but has low sensitivity. Sensitivity may be improved by incorporating NPS PCR results into machine learning models.

Methods
Three supervised multivariable diagnostic models (random forest, logistic regression and extreme gradient boosting) were constructed and validated using a 111-person Australian dataset. The predictors were age, gender, immunosuppression type and NPS PCR result. Model performance metrics such as accuracy, sensitivity, specificity and predictive values were compared to select the best-performing model.

Results
The logistic regression model performed best, with 80% accuracy, improving sensitivity to 86% and maintaining acceptable specificity of 70%. Using this model, positive and negative NPS PCR results indicated post-test probabilities of 84% (likely PJP) and 26% (unlikely PJP), respectively.

Conclusions
The logistic regression model should be externally validated in a wider range of settings. As the predictors are simple, routinely collected patient variables, this model may represent a diagnostic advance suitable for settings where collection of lower respiratory tract specimens is difficult but PCR is available.
Evolutionary history and origins of Dsr-mediated sulfur oxidation
Authors: Klier Katherine M , Martin Cody , Langwig Marguerite V , Anantharaman Karthik 
Published: August 2024

Abstract
Microorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (Dsr) functioning in either the reductive or reverse, oxidative direction. Dsr-mediated sulfite reduction is an ancient metabolism proposed to have fueled energy metabolism in some of Earth’s earliest microorganisms, whereas sulfur oxidation is believed to have evolved later in association with the widespread availability of oxygen on Earth. Organisms are generally believed to carry out either the reductive or oxidative pathway, yet organisms from diverse phyla have been discovered with gene combinations that implicate them in both pathways. A comprehensive investigation into the metabolisms of these phyla regarding Dsr is currently lacking. Here, we selected one of these phyla, the metabolically versatile candidate phylum SAR324, to study the ecology and evolution of Dsr-mediated metabolism. We confirmed that diverse SAR324 encode genes associated with reductive Dsr, oxidative Dsr, or both. Comparative analyses with other Dsr-encoding bacterial and archaeal phyla revealed that organisms encoding both reductive and oxidative Dsr proteins are constrained to a few phyla. Further, DsrAB sequences from genomes belonging to these phyla are phylogenetically positioned at the interface between well-defined oxidative and reductive bacterial clades. The phylogenetic context and dsr gene content in these organisms points to an evolutionary transition event that ultimately gave way to oxidative Dsr-mediated metabolism. Together, this research suggests that SAR324 and other phyla with mixed dsr gene content are associated with the evolution and origins of Dsr-mediated sulfur oxidation.
Glioblastoma multiforme in a patient with neurofibromatosis type 1: a case report and review of literature
Authors: Ayasa Laith A , Rahhal Sara , Najjar Alaa Khaled , Suboh Bashar N , Aliwaiai Mohammed , Daqour Ahmad M , Bakri Izzeddin 
Published: August 2024

Abstract
Glioblastoma multiforme (GBM) is a highly aggressive brain tumor. Individuals with neurofibromatosis type 1 (NF1) have an increased risk of developing GBM. We present a case report of a 44-year-old male with NF1 who developed GBM. NF1-associated GBM presents distinct molecular features and younger age at diagnosis compared to sporadic cases. Treatment typically follows standard protocols for GBM. Despite advancements in neuro-oncology, gaps in knowledge persist regarding NF1-associated GBM, including its prevalence, molecular mechanisms, and optimal treatment strategies. Larger studies and collaborative efforts are needed to address these gaps and enhance patient care.
Three-dimensional endoscopy in lumbar spine surgery as a novel approach for degenerative pathologies: a case report
Authors: Ma Alison , Xie Nathan , Reidy Joseph , Mobbs Ralph Jasper 
Published: August 2024

Abstract
Endoscopic spine surgery has evolved exponentially. However, the two-dimensional (2D) view results in lack of stereoscopic vision and depth perception, contributing to the steep learning curve. This case report recounts a world first trial of a three-dimensional (3D) endoscopic system that converts 2D to 3D images and explores its potential role in the surgical management of degenerative lumbar spine diseases. The 3D endoscopic system was used for two patient cases and both 2D and 3D images were displayed side by side and compared. Advantages of the 3D endoscopic system include increased perception of depth, rapid identification of bleeding points, and greater visualization of anatomical details. Field of view and exposure were identical in 2D and 3D views. Limitations include costs and need for additional equipment. Overall, 3D endoscopy improved depth perception, instrument manoeuvrability, and recognition of anatomical details. This case report can guide further research and training in endoscopic spine surgery.
Iatrogenic tracheal rupture in the elderly: a case report and review of tracheobronchial repair techniques
Authors: Chang Shantel , Cistulli David , Harden Michael 
Published: August 2024

Abstract
Tracheobronchial rupture is an extremely rare and potentially fatal complication. We present the case of a delayed presentation of an iatrogenic tracheobronchial rupture following orotracheal intubation, requiring veno-venous extracorporeal membrane oxygenator on standby. We review the clinical presentation, investigations, and management of tracheobronchial rupture, including conservative treatment and invasive surgical repair techniques.
Cardiac tamponade caused by a ruptured coronary aneurysm treated with open-chest hemostasis after esophageal cancer surgery: a case report
Authors: Hasegawa Makoto , Kikuchi Tomohiro , Yago Hiroki , Mitsui Dai , Matsuishi Akira , Tsumuraya Hideaki , Kaneta Akinao , Matsuida Hajime , Nirei Azuma , Hanayama Hiroyuki , Saze Zenichiro , Takase Shinya , Kono Koji 
Published: August 2024

Abstract
Cardiac tamponade is a rare postoperative complication of esophagectomy, with no previous reports of association with coronary artery aneurysm rupture. We present a case of cardiac tamponade caused by coronary aneurysm rupture following esophageal cancer surgery. A 68-year-old man with no history of heart disease underwent robotic subtotal esophagectomy for esophageal squamous cell carcinoma. He experienced intermittent chest pain on postoperative day (POD) 17. Echocardiography revealed increasing pericardial fluid, and pericardiocentesis on POD 34 revealed bloody pericardial fluid. Contrast-enhanced computed tomography and coronary angiography revealed a ruptured coronary aneurysm causing cardiac tamponade. Emergency surgery with a median sternotomy achieved hemostasis, and the patient recovered successfully. Cardiac tamponade after esophageal surgery, particularly from coronary aneurysm rupture, is rare. Prompt diagnosis and treatment are crucial for patient survival. Despite its risks, median sternotomy was effective in achieving rapid hemostasis and patient recovery in this case.
Transverse colonic volvulus presenting in a 19-year-old female with subsequent sigmoid volvulus
Authors: Stiene Jennifer , Barber Meghan , Silva Francisco Rodriguez , Halloran Sean J , Sferra Joseph J 
Published: August 2024

Abstract
Transverse colonic volvulus is exceptionally rare and is the rarest compared to sigmoid or cecal volvulus. This case report summarizes the care of a young 19-year-old woman who presented with transverse colonic volvulus. This woman came to the emergency room with abdominal pain, nausea, and vomiting, and she had no risk factors for a volvulus. This case report has the goal of raising awareness among those taking care of anyone coming in for abdominal pain. Volvulus is a serious issue and can be life threatening if not treated appropriately.
UNESCO and the Right to Science
Authors: Romano Cesare PR , Boggio Andrea 
Published: August 2024

Abstract
This chapter maps the right to science within the UN Educational, Scientific and Cultural Organization (UNESCO). The first part describes the origins of UNESCO and explains how science came to be part of its mission. Then, it discusses the high hopes the establishment of UNESCO created, particularly in the scientific field, the grand ambitions its leadership and the organization had, and the harsh political realities that tempered many of them. It describes the governance structure of UNESCO, paying particular attention to its standard-making process. UNESCO’s role in articulating international human rights standards is seldom recognized, but it is significant and, in the case of the right to science, paramount. The chapter reviews four recommendations: Recommendation on Science and Scientific Researchers (2017); Declaration of Ethical Principles in Relation to Climate Change (2017); Recommendation on Open Science (2021); and Recommendation on the Ethics of Artificial Intelligence (2021); three declarations regarding genetics and bioethics: Universal Declaration on Human Genome and Human Rights (1997); International Declaration on Human Genetic Data (2003); and Universal Declaration on Bioethics and Human Rights (2005); and two statements of expert meetings sponsored by UNESCO: Declaration on Science and the Use of Scientific Knowledge of the World Conference of Science (1999) and Venice Statement on the Right to Enjoy the Benefits of Scientific Progress and its Applications (2009). All these instruments give greater depth to the right to science.
An Ethics Lens for Nursing Leadership
Authors: Brown-Saltzman Katherine 
Published: August 2024

Abstract
With the innumerable skills required for the nursing leadership role, the demands of the work, and conflicting obligations, it is no wonder that an ethical lens can be so easily lost. Yet ethics is so central to every decision that is made, it should be the filter that is incorporated consistently. When ethics becomes the vista—whether considering the myriad of ethical conflicts, hiring practices, budgeting, limited resources, ethics supports, policy, motivational practices, or supporting the nurses’ voice—one has an opportunity to create an ethical environment. A leadership practice that utilizes a habituated ethics perspective may be more complex and may require a greater upfront effort. However, it will also be extraordinarily rich and will provide for outcomes that establish a foundation of thoughtful and ethically based governance. One’s own voice must walk the fine line of role modeling ethical mindfulness, owning moral authority, and acting with responsible courage. In firmly representing nursing’s core values, one has the opportunity and the responsibility to create the milieu that empowers moral agency. In this way, one honors nursing’s commitment to the profession that cherishes the moral obligations of caring for the sick and promoting health and well-being.