bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phage Therapy in Lung Transplantation: Current Status and Future Possibilities
Authors: Aslam Saima 
Published: November 2023

Abstract
Patients with chronic lung disease and lung transplantation have high rates of colonization and infection from multidrug-resistant (MDR) organisms. This article summarizes the current state of knowledge regarding phage therapy in the setting of lung transplantation. Phage therapy has been used in several lung transplant candidates and recipients on a compassionate use basis targeting mostly MDR gram-negative infections and atypical mycobacterial infections with demonstrated clinical safety. Phage biodistribution given intravenously or via nebulization has not been extensively studied, though preliminary data are presented. Phage interacts with both the innate and adaptive immune system; current literature demonstrates the development of serum neutralization in some cases of phage therapy, although the clinical impact seems variable. A summary of current clinical trials involving patients with chronic lung disease is presented, though none are specifically targeting lung transplant candidates or recipients. In addition to treatment of active infections, a variety of clinical scenarios may benefit from phage therapy, and well-designed clinical trials involving this vulnerable patient population are needed: pre- or peritransplantation use of phage in the setting of MDR organism colonization may lead to waitlisting of candidates currently declined by many centers, along with potential reduction of waitlist mortality rates and posttransplant infections; phage may be used for biofilm-related bronchial stent infections; and, finally, there is a possibility that phage use can affect allograft function and chronic rejection.
Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy
Authors: Grigson Susanna R , Giles Sarah K , Edwards Robert A , Papudeshi Bhavya 
Published: November 2023

Abstract
Bacteriophages, or phages, are viruses that infect bacteria shaping microbial communities and ecosystems. They have gained attention as potential agents against antibiotic resistance. In phage therapy, lytic phages are preferred for their bacteria killing ability, while temperate phages, which can transfer antibiotic resistance or toxin genes, are avoided. Selection relies on plaque morphology and genome sequencing. This review outlines annotating genomes, identifying critical genomic features, and assigning functional labels to protein-coding sequences. These annotations prevent the transfer of unwanted genes, such as antimicrobial resistance or toxin genes, during phage therapy. Additionally, it covers International Committee on Taxonomy of Viruses (ICTV)-an established phage nomenclature system for simplified classification and communication. Accurate phage genome annotation and nomenclature provide insights into phage–host interactions, replication strategies, and evolution, accelerating our understanding of the diversity and evolution of phages and facilitating the development of phage-based therapies.
Eager Term Rewriting For The Fracterm Calculus Of Common Meadows
Authors: Bergstra Jan A , Tucker John V 
Published: November 2023

Abstract
Eager equality is a novel semantics for equality in the presence of partial operations. We consider term rewriting for eager equality for arithmetic in which division is a partial operator. We use common meadows which are essentially fields that contain an absorptive element $\bot $. The idea is that term rewriting is supposed to be semantics preserving for non-$\bot $ terms only. We show soundness and adequacy results for eager term rewriting w.r.t. the class of all common meadows. However, we show that an eager term rewrite system which is complete for common meadows of rational numbers is not easy to obtain, if it exists at all.
Will supplemental cone beam computed tomography change the treatment plan of impacted maxillary canines based on 2D radiography? A prospective clinical study
Authors: Stoustrup Peter , Videbæk Anja , Wenzel Ann , Matzen Louise Hauge 
Published: November 2023

Abstract

Aim
To evaluate the impact of cone beam computed tomography (CBCT) on treatment planning for impacted maxillary canines; secondly, to identify CBCT factors influencing a change in the treatment plan; and thirdly, to assess 2D radiographic factors that can aid in selecting appropriate candidates for CBCT.

Material and methods
Patients with impacted maxillary canines and an overlap of a neighboring tooth in 2D radiographs and the suspicion of root resorption were referred for CBCT examination. An initial treatment plan was based on 2D radiographs, and the final treatment plan was established after the CBCT examination. Logistic regression analyses and t-tests were performed to evaluate differences in radiographic findings between the groups with and without a change in treatment plan.

Results
The study prospectively included 125 impacted canines, and 43 (34.4%) of them had a change in treatment plan after the CBCT examination. The most common change was a modification in the direction of cantilever traction (n = 28; 22.4%), while the least common was the change in decision to remove/keep the canine (n = 4; 3.2%). The size of the alpha and lateral angles had a significant impact on the decision to change the treatment plan. Other radiographic findings did not influence a change in treatment plan.

Conclusions
One-third of the canines had a change in treatment plan after supplemental CBCT examination. Canines with large alpha and lateral angles measured in the panoramic image were found to be significantly more likely to undergo changes in the initial direction of cantilever traction or changes to the canine extraction strategy following CBCT examination.
Routine stress testing in diabetic patients after percutaneous coronary intervention: the POST-PCI trial
Authors: Kim Hoyun , Kang Do-Yoon , Lee Jinho , Choi Yeonwoo , Ahn Jung-Min , Kim Seonok , Yoon Yong-Hoon , Hur Seung-Ho , Lee Cheol Hyun , Kim Won-Jang , Kang Se Hun , Park Chul Soo , Lee Bong-Ki , Suh Jung-Won , Choi Jae Woong , Kim Kee-Sik , Lee Su Nam , Park Seung-Jung , Park Duk-Woo 
Published: November 2023

Abstract

Background and Aims
The optimal follow-up surveillance strategy for high-risk diabetic patients with had undergone percutaneous coronary intervention (PCI) remains unknown.

Methods
The POST-PCI (Pragmatic Trial Comparing Symptom-Oriented versus Routine Stress Testing in High-Risk Patients Undergoing Percutaneous Coronary Intervention) study was a randomized trial comparing a follow-up strategy of routine functional testing at 1 year vs. standard care alone after high-risk PCI. Randomization was stratified according to diabetes status. The primary outcome was a composite of death from any cause, myocardial infarction, or hospitalization for unstable angina at 2 years.

Results
Among 1706 randomized patients, participants with diabetes (n = 660, 38.7%) had more frequent comorbidities and a higher prevalence of complex anatomical or procedural characteristics than those without diabetes (n = 1046, 61.3%). Patients with diabetes had a 52% greater risk of primary composite events [hazard ratio (HR) 1.52; 95% confidence interval (CI) 1.02–2.27; P = .039]. The 2-year incidences of the primary composite outcome were similar between strategies of routine functional testing or standard care alone in diabetic patients (7.1% vs. 7.5%; HR 0.94; 95% CI 0.53–1.66; P = .82) and non-diabetic patients (4.6% vs. 5.1%; HR 0.89; 95% CI 0.51–1.55; P = .68) (interaction term for diabetes: P = .91). The incidences of invasive coronary angiography and repeat revascularization after 1 year were higher in the routine functional-testing group than the standard-care group irrespective of diabetes status.

Conclusions
Despite being at higher risk for adverse clinical events, patients with diabetes who had undergone high-risk PCI did not derive incremental benefit from routine surveillance stress testing compared with standard care alone during follow-up.
Calling on the Third-party Privacy Control into Algorithmic Governance Framework: Linking Users’ Presumed Influence with Control Agency Theory
Authors: Huang Yangkun , Cao Xucheng 
Published: November 2023

AbstractIn the algorithmic society, personal privacy is exposed to ever-growing risks since the platform requires huge volumes of data for algorithm training. Globally, ordinary users, faced with the formidable platform and black-boxed algorithm, usually feel powerless against elusive privacy invasion and then have set about turning to third-party proxy institutions like the government and legislature to counterbalance the algorithmic privacy security framework. Starting from it, the present study examines what triggers users’ support for third-party proxy control, and a moderated serial mediation model has been estimated based on a Chinese cross-sectional sample (N = 661). Our research suggests that users’ algorithm awareness and their presumed algorithmic privacy risk to self and others (elders and minors) significantly predict their support, and serial mediating effects of the presumed algorithmic privacy risk can be more pronounced at the higher level of perceived effectiveness of platform policy. These findings help to identify the crucial role of algorithm awareness, which equips users to navigate risk and behave as responsible digital citizens, and also extend the influence of presumed influence model and the control agency theory in algorithmic contexts, making contributions in both theory and practice.
Effectiveness of Immunization Products Against Medically Attended Respiratory Syncytial Virus Infection: Generic Protocol for a Test-Negative Case-Control Study
Authors: van Roekel Caren , Poukka Eero , Turunen Topi , Nohynek Hanna , Presser Lance , Meijer Adam , Heikkinen Terho , Kramer Rolf , Begier Elizabeth , Teirlinck Anne C , Knol Mirjam J ,   PROMISE Investigators, Nair Harish , Campbell Harry , Bont Louis , Meijer Adam , Teirlinck Anne C , Knol Mirjam , Gideonse David , Backx Anoek , de Melker Hester , van Roekel Caren , Presser Lance , Turunen Topi , Nohynek Hanna , Poukka Eero , Saukkoriipi Annika , Paget John , van Summeren Jojanneke , Dückers Michel , Heikkinen Terho , Audenis Berta Gumí , Llavero Maica , Kragten Leyla , Kriek Lies , Faksová Kristýna , Giardini Michele , Emborg Hanne-Dorthe , Rocchi Francesca , Quiles Cintia Muñoz , Diez-Domingo Javier , Vernhes Charlotte , Demont Clarisse , Robin Aurelie , Neveu David , Marcelon Lydie , Bangert Mathieu , Kramer Rolf , Martyn Oliver , Bardone Corinne , Remy Vanessa , Chaves Sandra , Molnar Daniel , dos Santos Gael , Pirçon Jean-Yves , Rizkalla Bishoy , Turriani Elisa , Li Se , Melegh Noemie Napsugar , Joosten Philip , Moreno Victor Preckler , Shambulova Aigul , Cheret Arnaud , Quelard Delphine , Aerssens Jeroen , Weber Karin , Willame Corinne , Puggina Anna , Theis-Nyland Katherine , Nikolayeva Natalia , Kumar Veena , Beyhaghi Hadi , Shinde Vivek , Schmoele-Thoma Beate , Begier Elizabeth , Swanson Kena , Htar Tin Tin , Atwell Jessica , Aliabadi Negar , Deese Jen , Fell Deshayne , Lino Maria Maddalena , Turiga Monica-Flavia , Ahani Bahar 
Published: November 2023

AbstractMonitoring the real-life effectiveness of respiratory syncytial virus (RSV) products is of major public health importance. This generic protocol for a test-negative design study aims to address currently envisioned approaches for RSV prevention (monoclonal antibodies and vaccines) to study effectiveness of these products among target groups: children, older adults, and pregnant women. The generic protocol approach was chosen to allow for flexibility in adapting the protocol to a specific setting. This protocol includes severe acute respiratory infection (SARI) and acute respiratory infection (ARI), both due to RSV, as end points. These end points can be applied to studies in hospitals, primarily targeting patients with more severe disease, but also to studies in general practitioner clinics targeting ARI.
Renal outcomes in adults with HBV, HIV and HBV/HIV coinfection after 3 years of antiviral therapy in urban Tanzania
Authors: Wu En-Ling , Christian Beatrice , Rivera Adovich S , Fabian Emanuel , Macha Irene , Aris Eric , Mpangala Shida , Ulenga Nzovu , Mugusi Ferdinand , Murphy Robert L , Hawkins Claudia A 
Published: November 2023

Abstract

Background
An enhanced understanding of renal outcomes in persons with chronic HBV, HIV, and HBV/HIV coinfection is needed to mitigate chronic kidney disease in regions where HBV and HIV are endemic.

Objectives
To investigate changes in estimated glomerular filtration rate (eGFR) in adults with HBV, HIV or HBV/HIV enrolled in a 3 year prospective cohort study of liver outcomes in Dar es Salaam, Tanzania and initiated on antiviral therapy.

Methods
We compared eGFR between and within groups over time using mixed-effects models.

Results
Four hundred and ninety-nine participants were included in the analysis (HBV: 164; HIV: 271; HBV/HIV: 64). Mean baseline eGFRs were 106.88, 106.03 and 107.18 mL/min/1.73 m2, respectively. From baseline to Year 3, mean eGFR declined by 4.3 mL/min/1.73 m2 (95% CI −9.3 to 0.7) and 3.7 (−7.8 to 0.5) in participants with HBV and HIV, respectively, and increased by 5.1 (−4.7 to 14.9) in those with HBV/HIV. In multivariable models, participants with HBV had lower eGFRs compared with those with HIV or HBV/HIV and, after adjusting for HBV DNA level and hepatitis B e antigen (HBeAg) status, significantly lower eGFRs than those with HBV/HIV at all follow-up visits.

Conclusions
In this Tanzanian cohort, coinfection with HBV/HIV did not appear to exacerbate renal dysfunction compared with those with either infection alone. Although overall changes in eGFR were small, persons with HBV experienced lower eGFRs throughout follow-up despite their younger age and similar baseline values. Longer-term studies are needed to evaluate continuing changes in eGFR and contributions from infection duration and other comorbidities.
Value of pneumococcal PCR in respiratory samples for exclusion of pneumococcal pneumonia
Authors: Van Goethem Sam , Van Lint Philippe , Willems Philippe , Van Herendael Bruno , Hoet Katrien 
Published: November 2023

Abstract

Background
Streptococcus pneumoniae is the main aetiological agent in bacterial pneumonia. Therefore pneumococcal PCR is often included in respiratory multiplex PCR panels, both commercial and in-house. But respiratory PCR results for S. pneumoniae are difficult to interpret due to frequent non-pathogenic colonization on the mucosal surface of the upper airways with pneumococci or to cross-reaction of the PCR target in non-pneumococcal streptococci. In this study we investigated the value of lytA gene pneumococcal PCR in patients presenting with pneumonia.

Objectives
To assess the utility of lytA gene detection for S. pneumoniae in a respiratory multiplex quantitative PCR (qPCR) panel for patients presenting with pneumonia.

Methods
A retrospective study was conducted for lytA gene results as target for S. pneumoniae in hospitalized patients who were diagnosed with pneumonia and for which a respiratory multiplex PCR panel was performed. Patients were classified as ‘probable’, ‘possible’ or ‘unlikely’ of having a pneumococcal pneumonia.

Results
A sensitivity of 71.4% and specificity of 89.6% were found, corresponding to a negative predictive value and positive predictive value of 97.6% and 34.2%, respectively, when considering ‘probable’ versus ‘possible/unlikely’. In the PCR-positive cases we found a statistically significant difference in semi-quantitative Ct values between the ‘probable’ and the ‘possible/unlikely’ groups.

Conclusions
We conclude that a negative qPCR for the lytA gene in a respiratory sample is highly predictive of a negative S. pneumoniae culture and is possibly sufficient to exclude S. pneumoniae as a causative agent. Respiratory pneumococcal PCR has a high negative predictive value for pneumococcal disease but the positive predictive value is low.
Alcohol degradation, learning, and memory-enhancing effect of Acetobacter pasteurianus BP2201 in Caenorhabditis elegans model
Authors: Wen Xin , Yang Huazhong , Li Zhongqi , Chu Weihua 
Published: November 2023

Abstract

Aims
This study aimed to investigate the probiotic effects of Acetobacter pasteurianus BP2201, isolated from brewing mass, for the treatment of alcohol-induced learning and memory ability impairments in a Caenorhabditis elegans model.

Methods and results
Acetobacter pasteurianus BP2201 was examined for probiotic properties, including acid and bile salt resistance, ethanol degradation, antioxidant efficacy, hemolytic activity, and susceptibility to antibiotics. The strain displayed robust acid and bile salt tolerance, efficient ethanol degradation, potent antioxidant activity, and susceptibility to specific antibiotics. Additionally, in the C. elegans model, administering A. pasteurianus BP2201 significantly improved alcohol-induced learning and memory impairments.

Conclusions
Acetobacter pasteurianus BP2201 proves to be a promising candidate strain for the treatment of learning and memory impairments induced by alcohol intake.
Creation of a data commons for substance misuse related health research through privacy-preserving patient record linkage between hospitals and state agencies
Authors: Afshar Majid , Oguss Madeline , Callaci Thomas A , Gruenloh Timothy , Gupta Preeti , Sun Claire , Safipour Afshar Askar , Cavanaugh Joseph , Churpek Matthew M , Nyakoe-Nyasani Edwin , Nguyen-Hilfiger Huong , Westergaard Ryan , Salisbury-Afshar Elizabeth , Gussick Megan , Patterson Brian , Manneh Claire , Mathew Jomol , Mayampurath Anoop 
Published: November 2023

Abstract

Objectives
Substance misuse is a complex and heterogeneous set of conditions associated with high mortality and regional/demographic variations. Existing data systems are siloed and have been ineffective in curtailing the substance misuse epidemic. Therefore, we aimed to build a novel informatics platform, the Substance Misuse Data Commons (SMDC), by integrating multiple data modalities to provide a unified record of information crucial to improving outcomes in substance misuse patients.

Materials and Methods
The SMDC was created by linking electronic health record (EHR) data from adult cases of substance (alcohol, opioid, nonopioid drug) misuse at the University of Wisconsin hospitals to socioeconomic and state agency data. To ensure private and secure data exchange, Privacy-Preserving Record Linkage (PPRL) and Honest Broker services were utilized. The overlap in mortality reporting among the EHR, state Vital Statistics, and a commercial national data source was assessed.

Results
The SMDC included data from 36 522 patients experiencing 62 594 healthcare encounters. Over half of patients were linked to the statewide ambulance database and prescription drug monitoring program. Chronic diseases accounted for most underlying causes of death, while drug-related overdoses constituted 8%. Our analysis of mortality revealed a 49.1% overlap across the 3 data sources. Nonoverlapping deaths were associated with poor socioeconomic indicators.

Discussion
Through PPRL, the SMDC enabled the longitudinal integration of multimodal data. Combining death data from local, state, and national sources enhanced mortality tracking and exposed disparities.

Conclusion
The SMDC provides a comprehensive resource for clinical providers and policymakers to inform interventions targeting substance misuse-related hospitalizations, overdoses, and death.
‘Is It Too Late Now to Say Sorry?’
Authors: Kapoor Radhika 
Published: November 2023

Abstract
This article explores the use of remorse as a source of leniency at international criminal tribunals. It outlines the difficulties that beset international tribunals’ attempts to develop a clear, consistent conceptualization of the idea of remorse. Using a range of perspectives, it offers ways forward in terms of both comprehending remorse, as experienced by perpetrators of international crimes, and incorporating remorse into the present international criminal legal framework. In particular, it analyses how sincere expressions of remorse within the international criminal courtroom can signal and produce transformative effects for different players operating in the terrain of international criminal justice.
Critical assessment of the recent report on the gigaparsec-scale correlation of the orientations of large quasar groups
Authors: Fujii Hirokazu 
Published: November 2023

ABSTRACT
Recently, it was reported that large quasar groups (LQGs) identified from the Sloan Digital Sky Survey (SDSS) data release seven catalogue are not randomly oriented but preferentially aligned or orthogonal over scales 1–2 Gpc. To confirm this claim, I reproduced the same LQG sample and performed Sobolev tests of uniformity on the LQG orientation axes in the redshift space. Contrary to the original report based on the bimodal distribution of the LQG position angles in the sky, I found no departure from uniformity in the distribution of the LQG orientation axes. I also examined whether the LQGs are physical structures using a statistically more reliable data set constructed from the SDSS data release 16 (DR16) large-scale structure (LSS) quasar catalogue. Considering the Gaussian primordial density fluctuations and shot noise, I estimated the mass density contrasts of the LQGs from the number counts of the DR16 LSS quasars and found that most of the LQGs do not trace statistically significant high-density regions. I conclude that the LQG sample is a collection of unphysical chance associations and should not be used for any cosmological studies.
Robust cosmological inference from non-linear scales with k-th nearest neighbour statistics
Authors: Yuan Sihan , Abel Tom , Wechsler Risa H 
Published: November 2023

ABSTRACT
We present the methodology for deriving accurate and reliable cosmological constraints from non-linear scales ($\lt 50\, h^{-1}$ Mpc) with k-th nearest neighbour (kNN) statistics. We detail our methods for choosing robust minimum scale cuts and validating galaxy–halo connection models. Using cross-validation, we identify the galaxy–halo model that ensures both good fits and unbiased predictions across diverse summary statistics. We demonstrate that we can model kNNs effectively down to transverse scales of $r_{\rm p}\sim 3\, h^{-1}$ Mpc and achieve precise and unbiased constraints on the matter density and clustering amplitude, leading to a 2 per cent constraint on σ8. Our simulation-based model pipeline is resilient to varied model systematics, spanning simulation codes, halo finding, and cosmology priors. We demonstrate the effectiveness of this approach through an application to the Beyond-2p mock challenge. We propose further explorations to test more complex galaxy–halo connection models and tackle potential observational systematics.