bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Causality Problem in Focused Particle Transport
Authors: Strauss R D , van den Berg J P , Engelbrecht N E , Wijsen N 
Published: July 2023

Abstract
When perpendicular diffusion is included into the focused transport equation, certain assumptions of the perpendicular diffusion coefficient (including the well-known fieldline random walk limit) clearly lead to faster-than-light motion for relativistic particles, and transport that does not preserve causality in general. In this work we show that this discrepancy can be solved by including the effect of turbulence on particle drifts, especially the streaming term present in the focused transport equation, leading to a so-called drift reduction factor. We discuss this drift reduction factor, how it solves the above-mentioned causality problem, and its general implications for particle transport. Under certain simplifying assumptions we show the interplay between particle streaming (as a drift process) and perpendicular diffusion, and how these processes can be consistently coupled through the turbulent magnetic field.
Transmission of magnetic island modes across interplanetary shocks: comparison of theory and observations
Authors: Pitna A , Zank G P , Nakanotani M , Zhao L-L , Adhikari L , Safrankova J , Nemecek Z 
Published: July 2023

Abstract
Interplanetary shock waves are observed frequently in turbulent solar wind. They naturally enhance the temperature/entropy of the plasma through which they propagate. Moreover, many studies have shown that they also act as an amplifier of the fluctuations incident on the shock front. Solar wind turbulent fluctuations can be well described as the superposition of quasi-2D and slab components, the former being energetically dominant. In this paper, we address the interaction of fast forward shocks observed by the Wind spacecraft at 1 AU and quasi-2D turbulent fluctuations in the framework of the Zank et al. (2021) transmission model and we compare model predictions with observations. Our statistical study includes 378 shocks with varying upstream conditions and Mach numbers. We estimate the average ratio of the downstream observed and theoretically predicted power spectra within the inertial range of turbulence. We find that the distributions of this ratio for the whole set and for the subset of shocks that met the assumptions of the model, are remarkably close. We argue that a large statistical spread of the distributions of this ratio is governed by the inherent variation of the upstream conditions. Our findings suggest that the model predicts the downstream fluctuations with a good accuracy and that it may be adopted for a wider class of shocks than it was originally meant for.
UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data
Authors: Abe Ko , Shimamura Teppei 
Published: July 2023

Abstract
Factor analysis, ranging from principal component analysis to nonnegative matrix factorization, represents a foremost approach in analyzing multi-dimensional data to extract valuable patterns, and is increasingly being applied in the context of multi-dimensional omics datasets represented in tensor form. However, traditional analytical methods are heavily dependent on the format and structure of the data itself, and if these change even slightly, the analyst must change their data analysis strategy and techniques and spend a considerable amount of time on data preprocessing. Additionally, many traditional methods cannot be applied as-is in the presence of missing values in the data. We present a new statistical framework, unified nonnegative matrix factorization (UNMF), for finding informative patterns in messy biological data sets. UNMF is designed for tidy data format and structure, making data analysis easier and simplifying the development of data analysis tools. UNMF can handle a wide range of data structures and formats, and works seamlessly with tensor data including missing observations and repeated measurements. The usefulness of UNMF is demonstrated through its application to several multi-dimensional omics data, offering user-friendly and unified features for analysis and integration. Its application holds great potential for the life science community. UNMF is implemented with R and is available from GitHub (https://github.com/abikoushi/moltenNMF).
The power to act: dissecting distinctive elements of power and ownership in community organizing in England and Wales
Authors: Wood Jason 
Published: July 2023

Abstract
This paper considers the continuing evolution in England and Wales of the Alinsky tradition of broad-based community organizing, a process that seeks to build permanent and powerful alliances of local civil society institutions. The paper introduces some of the tenets of the Alinsky model of broad-based organizing and how this has been adapted to the UK context. Drawing on a leading charity that has pioneered this work, Citizens UK, the paper identifies five distinctive enablers of power and ownership found in community organizing: leadership, relationships, money, democratic behaviours, and actions. Taken together, broad-based community organizing offers an interesting alternative proposition for building community power and is a model that requires further academic, policy, and practitioner attention in the field of community development.
Circulating Cell-Free SEPT9 DNA Methylation in Blood Is a Biomarker for Minimal Residual Disease Detection in Head and Neck Squamous Cell Carcinoma Patients
Authors: Dietrich Dimo , Weider Simone , de Vos Luka , Vogt Timo Jakob , Färber Moritz , Zarbl Romina , Hunecke Alina , Glosch Ann-Kathrin , Gabrielpillai Jennis , Bootz Friedrich , Bauernfeind Franz-Georg , Kramer Franz-Josef , Kristiansen Glen , Brossart Peter , Strieth Sebastian , Franzen Alina 
Published: July 2023

Abstract

Background
Tumorous SEPT9 (septin 9, SEPTIN9) circulating cell-free DNA (ccfDNA) methylation in blood plasma is a powerful biomarker for diagnosis, molecular staging, prognosis, and recurrence monitoring in head and neck squamous cell carcinoma (HNSCC) patients. The present study aimed to evaluate the clinical performance of SEPT9 ccfDNA methylation to detect post-surgical minimal residual disease (MRD) in patients with localized or locally advanced HNSCC treated with curative intent.

Methods
We applied quasi-digital methylation-specific real-time PCR to quantify SEPT9 ccfDNA methylation levels 2 to 30 days post-surgically in plasma from n = 219 prospectively enrolled HNSCC patients. We tested the associations of SEPT9 ccfDNA methylation with clinicopathological parameters and used Kaplan–Meier and Cox proportional hazards analyses for univariate, pairwise bivariate, and multivariate analyses of disease-free survival.

Results
Of 219 patients, 26.5% (58/219) were post-surgically SEPT9 ccfDNA methylation positive. SEPT9 ccfDNA methylation positivity was significantly associated with tumor site, American Joint Committee on Cancer/Union for International Cancer Control (AJCC/UICC; 8th edition) tumor stage, nodal category and extracapsular extension, lymphatic and vascular invasion, and surgical margin. Bivariate Cox proportional hazards analysis proved post-surgical SEPT9 ccfDNA methylation positivity to be an independent prognostic factor tested together with AJCC/UICC tumor stage (SEPT9: hazard ratio [HR] = 2.43, 95% CI, 1.37–4.30, P = 0.002; AJCC/UICC stage: HR = 1.48, 95% CI, 1.11–1.98, P = 0.008).

Conclusions
Post-surgical SEPT9 ccfDNA methylation may aid to identify high-risk HNSCC patients who could benefit from an intensified adjuvant treatment and surveillance.
Niclosamide Enema for Active Distal Ulcerative Colitis: A Phase 1, Open-Label Study
Authors: Marafini Irene , De Cristofaro Elena , Salvatori Silvia , Calabrese Emma , Lolli Elisabetta , Monteleone Ivan , Franchi Luigi , Ciccocioppo Rachele , Glick Gary , Opipari Anthony , Monteleone Giovanni 
Published: July 2023

Abstract

Background
Oral and rectal formulations of 5-aminosalicylic acid are the first-line therapy for mild-to-moderate, distal ulcerative colitis (UC), but such a treatment is not effective in one-third of patients. Niclosamide is a small molecule, developed and approved as an orally administered drug to treat helminthic infections, with an excellent safety profile. Preclinical work showed that niclosamide is an anti-inflammatory agent, thereby providing the rationale to explore its safety and efficacy in patients with UC. This phase 1, open-label trial was aimed at assessing the safety of niclosamide formulated as an enema in patients with mild-to-moderate, distal UC, who relapsed on maintenance therapy with oral and/or rectal 5-aminosalicylic acid.

Methods
Seventeen patients with active UC received niclosamide enema (150 mg/60 mL) twice a day for 6 weeks. The primary endpoint was the safety of niclosamide treatment. Secondary endpoints included clinical remission and improvements in endoscopic Mayo/histologic scores. Endoscopic remission percentages exclude participants meeting criteria at baseline for endoscopic remission.

Results
Niclosamide was well tolerated by all 17 patients that were enrolled and treated. No serious adverse event was registered. Fifteen mild adverse events were registered in 6 patients and considered to be unrelated to the treatment. Clinical remission was achieved in 10 (59%) of 17 patients. Improvements of endoscopic Mayo score and histologic Geboes score were seen in 7 (58%) of 12 and 7 (41.2%) of 17 patients, respectively.

Conclusions
Niclosamide enema treatment is safe and well tolerated. Niclosamide improves clinical symptoms and endoscopic/histologic signs of UC; however, appropriately designed placebo-controlled clinical trials are required to confirm efficacy.
The identification of diurnal variations on circulating immune cells by finger prick blood sampling in small sample sizes: a pilot study
Authors: Bushell Dayna , Tan Jonathan Kah Huat , Smith Jessica , Moro Christian 
Published: July 2023

Abstract

Objective
There are well-described impacts of biological rhythms on human physiology. With the increasing push for routine blood tests for preventative medical care and clinical and physiological research, optimizing effectiveness is paramount. This study aimed to determine whether it is feasible to assess diurnal variations of peripheral lymphocyte prevalence using finger prick blood in a small sample size.

Methods
Using polychromatic flow cytometry, the prevalence of lymphocytes was assessed using 25 µL fingertip blood samples at 8 AM and 5 PM from 8 participants.

Results
TH cells and B cells showed significantly higher percentages in the 5 PM samples, whereas NK cells demonstrated a significantly higher morning percentage. T cells, leukocytes, and cytotoxic T cells showed no significant changes.

Conclusion
The detection of diurnal variations demonstrates that small blood volumes can be used to detect lymphocyte variations. The lower blood volume required provides a new testing method for clinical and research settings.
The luminous, hard state can’t be MAD
Authors: Fragile P Chris , Chatterjee Koushik , Ingram Adam , Middleton Matthew 
Published: July 2023

ABSTRACT
We present a straightforward argument for why the luminous, hard state of black hole X-ray binaries (BHXRBs) cannot always be associated with a magnetically arrested accretion disc (MAD). It relies on three core premises: (1) that the type-C quasi-periodic oscillation (QPO) is best explained by Lense–Thirring (LT) precession of a tilted, inner, hot flow; (2) that observed optical and infrared (IR) QPOs with the same or lower frequency as the type-C QPO suggest the jet, too, must precess in these systems; and (3) that numerical simulations of MADs show that their strong magnetic fields promote alignment of the disc with the black hole and, thereby, suppress LT precession. If all three premises hold true, then, at least whenever the optical and IR QPOs are observed alongside the type-C QPO, these systems cannot be in the MAD state. Extending the argument further, if the type-C QPO is always associated with LT precession, then it would rule out MADs anytime this timing feature is seen, which covers nearly all BHXRBs when they are in the luminous, hard and hard-intermediate states.
Maculopathies Referred to Neuro-Ophthalmology Clinic as Optic Neuropathies: A Case Series
Authors: Vosoughi Amir R. , Donaldson Laura , Micieli Jonathan A. , Margolin Edward A. 
Published: July 2023

Background:
The clinical features of maculopathies and optic neuropathies often overlap: Both present with decreased visual acuity and variable loss of color vision; thus, maculopathy can be misdiagnosed as optic neuropathy, leading to patient harm. We aimed to determine what findings and/or tests were most helpful in differentiating between optic neuropathy and maculopathy.

Methods:
A retrospective chart review of consecutive patients over 4.5 years who were referred to neuro-ophthalmology clinics with the diagnosis of optic neuropathy but whose final diagnosis was maculopathy. Patient demographics, mode of presentation, clinical profile, complete ophthalmological examination, results of all ancillary testing, and final diagnosis were recorded.

Results:
A total of 47 patients (27 women) were included. The median age was 55 years (range, 18–85). Most referrals were by ophthalmologists (72.3%) and optometrists (12.8%). The diagnosis of maculopathy was made in 51.1% of patients at the time of first neuro-ophthalmic consultation. Only 6.4% patients (3) had relative afferent pupillary defect. Benign disc anomalies (tilted, myopic, small, or anomalous discs) were present in 34.0%, and 21.3% had pathologic disc changes unrelated or secondary to maculopathy. Macular ocular coherence tomography (OCT) was abnormal in 84.4% (with outer retinal pathology in 42.2% and inner retina pathology in 17.8%). Retinal nerve fiber layer (RNFL) thickness was normal in 82.6% of patients.

Conclusions:
Macular OCT is a high-yield test in differentiating between optic neuropathy and maculopathy and should be obtained in patients with suspected optic neuropathies who have normal RNFL thickness. Macular dystrophies, particularly cone dystrophies, unspecified retinal disorders, and macular degeneration were the most common mimics of optic neuropathy. The diagnosis was often present on OCT of the macula. The presence of coexistent benign and pathological disc anomalies may lead to maculopathy being misdiagnosed as optic neuropathy.
Induction of antiviral gene expression by cyclosporine A, but not inhibition of cyclophilin A or B, contributes to its restriction of human coronavirus 229E infection in a lung epithelial cell line
Authors: Mamatis John E. , Gallardo-Flores Carla E. , Walsh Taylor , Sangwan Ujjwal , Colpitts Che C. 
Published: July 2023

AbstractThe development of antivirals with an extended spectrum of activity is an attractive possibility to protect against future emerging coronaviruses (CoVs). Cyclosporine A (CsA), a clinically approved immunosuppressive drug, has established antiviral activity against diverse unrelated viruses, including several CoVs. However, its antiviral mechanisms of action against CoV infection have remained elusive, precluding the rational design of non-immunosuppressive derivatives with improved antiviral activities. In this study, we evaluated the mechanisms of CsA against HCoV-229E infection in a human lung epithelial cell line. We demonstrate that the antiviral activity of CsA against HCoV-229E is independent of classical CsA target proteins, cyclophilin A or B, which are not required host factors for HCoV-229E in A549 cells. Instead, CsA treatment induces expression of antiviral genes in a manner dependent on interferon regulatory factor 1, but independent of classical interferon responses, which contributes to its inhibitory effect against HCoV-229E infection. Our results also point to a role for the HCoV-229E nucleoprotein in antagonizing activation of type I interferon, but we show that CsA treatment does not affect evasion of innate immune signaling pathways by HCoV-229E. Overall, our findings further the understanding of the antiviral mechanisms of CsA against CoV infection and highlight a novel immunomodulatory strategy to inhibit CoV infection that may inform future drug development efforts.
N-Acylethanolamine is a Source of Ethanolamine for Phosphatidylethanolamine Synthesis inTrypanosoma brucei
Authors: Jenni Aurelio , Bütikofer Peter 
Published: July 2023

AbstractThe Kennedy pathway is essential for survival ofTrypanosoma bruceiprocyclic and bloodstream form parasites in culture and provides the bulk of phosphatidylethanolamine and phosphatidylcholine for membrane biogenesis. The CDP-ethanolamine branch of the Kennedy pathway depends on a steady supply of ethanolamine to be functional. We now show that degradation of N-acylethanolamines, mediated at least in part byT. bruceifatty acid amide hydrolase (TbFAAH), represents an additional reaction to provide ethanolamine for phosphatidylethanolamine synthesis. Although TbFAAH is not essential for growth ofT. bruceiprocyclic forms in normal culture medium, it may be essential for ethanolamine production under conditions of limited availability of free ethanolamine in the environment, or in the insect vector or mammalian host.
How risk and ambiguity affect accounting conservatism
Authors: Fuad Fuad , Rohman Abdul , Yuyetta Etna Nur Afri , Zulaikha Zulaikha 
Published: July 2023

PurposeThis study aims to examine the diametrically opposite effects of probabilistic (risk) and nonprobabilistic uncertainty (ambiguity) on accounting conservatism.Design/methodology/approachThis study uses panel regression models with year and industry-fixed effects. It uses financial and market data from the communication and energy sectors of 24 countries, encompassing 1,946 firms and 5,838 firm-year observations.FindingsThe study reveals that conservatism is a rational response to risk. However, in the presence of higher ambiguity where uncertainty exceeds firm control and outcomes become unpredictable, management reduces conservative accounting practices. Robustness tests support the validity of these findings across different institutional frameworks, agency risks, sample selection and heterogeneity.Research limitations/implicationsThis study contributes to the existing literature by exploring the contrasting effects of risk and ambiguity on accounting conservatism. It enhances the understanding of how various institutional factors influence the asymmetric recognition of bad news compared to good news under conditions of uncertainty.Practical implicationsBy understanding the role of accounting conservatism in responding to uncertainties, regulators can develop more informed and effective policies that align with the dynamic nature of business environments.Originality/valueThis research provides novel and original ideas suggesting that the change in accounting conservatism is contingent upon the firms’ ambiguity or risk.
Does technological progress make OECD countries greener? New evidence from panel CS-ARDL
Authors: Nghiem Xuan-Hoa , Bakry Walid , Al-Malkawi Husam-Aldin N. , Farouk Sherine 
Published: July 2023

PurposeThis paper aims to examine the impact of information and telecommunication technologies (ICT-proxied by mobile phone subscription and Internet usage) on carbon dioxide (CO2) emissions in the Organization for Economic Cooperation and Development (OECD) countries from 1990 to 2018.Design/methodology/approachThe Cross-section Autoregressive Distributed Lag (CS-ARDL) model is employed to address the potential cross-section dependence problem. Common Correlated Effects Mean Group (CCEMG) and Augmented Mean Group (AMG) estimators are used to test for robustness of results.FindingsResults reveal contrasting effects of mobile phone subscription and Internet usage on CO2 emissions. While mobile phone penetration helps mitigate CO2 emissions, Internet usage tends to increase the emissions. Findings show that renewable energy is beneficial to the environment while economic growth is harmful to the environment. The effects of financial development and trade openness seem negligible.Practical implicationsThis study offers practical implications for policymakers. As different proxies of ICT could have contradictory impact on CO2, governments should be cautious against utilizing ICT to mitigate CO2. Findings point to the benefits of renewable energy in alleviating CO2 emissions. Therefore, governments are strongly advised to implement policies facilitating renewable energy consumption.Originality/valuePrevious studies ignored the problem of cross-section dependence which could lead to biased results and cause misleading inferences. This study aims to fill this void in the literature.
Translational or translationable? A call for ethno‐immersion in (empirical) bioethics research
Authors: Parsons Jordan A. , Johal Harleen Kaur , Parker Joshua , Romanis Elizabeth Chloe 
Published: July 2023

AbstractThe shift towards "empirical bioethics" was largely triggered by a recognition that stakeholders' views and experiences are vital in ethical analysis where one hopes to produce practicable recommendations. Such perspectives can provide a rich resource in bioethics scholarship, perhaps challenging the researcher's perspective. However, overreliance on a picture painted by a group of research participants—or on pre‐existing literature in that field—can lead to a biased view of a given context, as the subjectivity of data generated in these ways cannot (and should not wholly) be escaped. In response, we propose the implementation of a complementary approach of ethno‐immersion in bioethics research. By positioning oneself in the context being researched, the researcher can better understand the realities of that context. The researcher's understanding will, naturally, be subjective too. However, it will act as a better developed and more informed outsider view, when considering the picture painted by participants and previous studies, thus enabling the researcher to introduce more nuance when analysing data. We introduce this approach after examining what we call the context detachment problem, whereby some bioethics scholarship—empirical or otherwise—fails to reflect the reality of the healthcare setting it concerns. Our proposed ethno‐immersion (which differs from formal ethnography) is then explored as a response, highlighting its benefits, and answering the question of timing within a research project. Finally, we reflect on the applicability of our proposal to non‐empirical bioethics scholarship, concluding that it remains important but may require some adjustments.
What has Kant got to say about conscientious objection to reproductive health in South Africa?
Authors: Lekunze Fritz E. 
Published: July 2023

AbstractA woman's right to a safe legal abortion in South Africa conflicts with a health care professional's freedom of conscience. Conscientious objection or treatment refusal on the basis of conscience may be protected by the constitution but its morality has not been explored. This study uses Kantian Deontology to elucidate the ethical duties of health care professionals based on the Physician's Pledge. It concludes that conscience is morally empty and that health care professionals have a duty to treat all patients equally irrespective of the condition they present. Drawing on Kantian promise keeping, the study also concludes that health care professionals should place patients health and wellbeing above all other considerations. Using the categorical imperative, the study shows that health care professionals have a perfect duty not to refuse treatment. The study recommends that conscientious objection be rejected in all circumstances except where the psychological wellbeing of the health care professional will be affected. This can be achieved through legislative and professional body regulation of conscientious objection.