bluuebunny/crossref_metadata_2025_split huggingface dataset:
Penalized deep partially linear cox models with application to CT scans of lung cancer patients
Authors: Sun Yuming , Kang Jian , Haridas Chinmay , Mayne Nicholas , Potter Alexandra , Yang Chi-Fu , Christiani David C , Li Yi 
Published: February 2024

AbstractLung cancer is a leading cause of cancer mortality globally, highlighting the importance of understanding its mortality risks to design effective patient-centered therapies. The National Lung Screening Trial (NLST) employed computed tomography texture analysis, which provides objective measurements of texture patterns on CT scans, to quantify the mortality risks of lung cancer patients. Partially linear Cox models have gained popularity for survival analysis by dissecting the hazard function into parametric and nonparametric components, allowing for the effective incorporation of both well-established risk factors (such as age and clinical variables) and emerging risk factors (eg, image features) within a unified framework. However, when the dimension of parametric components exceeds the sample size, the task of model fitting becomes formidable, while nonparametric modeling grapples with the curse of dimensionality. We propose a novel Penalized Deep Partially Linear Cox Model (Penalized DPLC), which incorporates the smoothly clipped absolute deviation (SCAD) penalty to select important texture features and employs a deep neural network to estimate the nonparametric component of the model. We prove the convergence and asymptotic properties of the estimator and compare it to other methods through extensive simulation studies, evaluating its performance in risk prediction and feature selection. The proposed method is applied to the NLST study dataset to uncover the effects of key clinical and imaging risk factors on patients’ survival. Our findings provide valuable insights into the relationship between these factors and survival outcomes.
Theory of Mind impairment in childhood narcolepsy type 1: a case–control study
Authors: Veneruso Marco , Del Sette Paola , Cordani Ramona , Lecce Serena , Pizza Fabio , Chiarella Lorenzo , Venturino Cristina , Nobili Lino , Plazzi Giuseppe 
Published: February 2024

Abstract
Narcolepsy type 1 is a central disorder of hypersomnolence characterized by excessive daytime sleepiness, cataplexy and other rapid eye movement sleep-related manifestations. Neurophysiological studies suggest that narcolepsy type 1 patients may experience impairment in emotional processing due to structural and functional changes in limbic structures and associated areas. However, the only study exploring narcolepsy behavioural responses found no impairment in the ability to recognize emotions, possibly due to compensatory mechanisms. The present study was designed to fill this gap in the literature by investigating the behavioural impairment related to emotional processing focusing on an advanced socio-cognitive skill, namely Theory of Mind, in paediatric narcolepsy type 1 patients. Twenty-two narcolepsy type 1 children and adolescents (six female; age range: 8.0–13.5) and 22 healthy controls matched for age and sex (six female; age range: 8.9–13.0) underwent a neuropsychological evaluation to assess socio-economic status, verbal abilities, working memory, social anxiety and Theory of Mind via a verbal task (i.e. Strange Stories task) and a visual task (i.e. Silent Films). Narcolepsy type 1 patients were also evaluated for disease severity. Patients exhibited impairment in Theory of Mind skills, as assessed both through both verbal (controls median = 8; patients median = 5; P = 0.009) and visual tasks (controls median = 8; patients median = 6; P = 0.003), compared to healthy controls. Correlation analyses showed that verbal and visual Theory of Mind was negatively related to narcolepsy severity (ρ = −0.45, P = 0.035 and ρ = −0.52, P = 0.012), and daytime sleepiness (ρ = −0.48, P = 0.025 and ρ = −0.45, P = 0.038). Our study shows a selective impairment in the Theory of Mind domain in children and adolescents with narcolepsy type 1. In addition, our results highlight a link between symptom severity and Theory of Mind, suggesting that lower Theory of Mind levels are associated with higher symptom severity. Further, longitudinal studies are needed to disentangle the direction of this relation and to disambiguate if narcolepsy severity impaired children’s Theory of Mind or if Theory of Mind skills modulate the severity of narcolepsy symptoms by providing a greater ability to avoid cataplexy.
Synthesis and biodegradation of atactic polymer based on 3-hydroxybutanoic acid
Authors: Yokaryo Hiroto , Nakayama Atsuyoshi , Kawasaki Norioki , Yamano Naoko , Ida Sayuri , Tokiwa Yutaka 
Published: February 2024

Abstract
Atactic poly[(R,S)-3-hydroxybutanoic acid] with varying enantiomer ratios was synthesized using a combination of renewable (R)-3-hydroxybutanoic acid and its racemic mixture. The melting temperature of the synthesized atactic polymers was consistently lower than that of poly[(R)-3-hydroxybutanoic acid], exhibiting a decreasing trend with an increasing enantiomer ratio. The biodegradability of the synthesized polymers was assessed through enzymatic and seawater degradation studies.
Léon Walras and Alfred Marshall: microeconomic rational choice or human and social nature?
Authors: Arena Richard , Caldari Katia 
Published: February 2024

Abstract
Alfred Marshall’s and Léon Walras’s works have often been compared in the literature, on the one hand underlining their several differences and on the other hand focussing on their possible resemblances building what was called ‘neoclassical economics. This interpretation failed to pay due attention, however, to a number of important aspects that in fact stand in the way of a proper understanding of these two authors’ contributions. This paper focuses on the analogies to be found between Walras’s and Marshall’s analyses of economic behaviour, which are related not to a supposed affiliation to a common neo-classical tradition but to a common conception of the relation between human economic agents and society.
Comprehensive Analysis of PKD1 and PKD2 by Long-Read Sequencing in Autosomal Dominant Polycystic Kidney Disease
Authors: Xu Dechao , Mao Aiping , Chen Libao , Wu Le , Ma Yiyi , Mei Changlin 
Published: February 2024

Abstract

Background
Autosomal dominant polycystic kidney disease (ADPKD) is mainly caused by heterogeneous variants in the PKD1 and PKD2 genes. Genetic analysis of PKD1 has been challenging due to homology with 6 PKD1 pseudogenes and high GC content.

Methods
A single-tube multiplex long-range-PCR and long-read sequencing-based assay termed “comprehensive analysis of ADPKD” (CAPKD) was developed and evaluated in 170 unrelated patients by comparing to control methods including next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification.

Results
CAPKD achieved highly specific analysis of PKD1 with a residual noise ratio of 0.05% for the 6 pseudogenes combined. CAPKD identified PKD1 and PKD2 variants (ranging from variants of uncertain significance to pathogenic) in 160 out of the 170 patients, including 151 single-nucleotide variants (SNVs) and insertion-deletion variants (indels), 6 large deletions, and one large duplication. Compared to NGS, CAPKD additionally identified 2 PKD1 variants (c.78_96dup and c.10729_10732dup). Overall, CAPKD increased the rate of variant detection from 92.9% (158/170) to 94.1% (160/170), and the rate of diagnosis with pathogenic or likely pathogenic variants from 82.4% (140/170) to 83.5% (142/170). CAPKD also directly determined the cis-/trans-configurations in 11 samples with 2 or 3 SNVs/indels, and the breakpoints of 6 large deletions and one large duplication, including 2 breakpoints in the intron 21 AG-repeat of PKD1, which could only be correctly characterized by aligning to T2T-CHM13.

Conclusions
CAPKD represents a comprehensive and specific assay toward full characterization of PKD1 and PKD2 variants, and improves the genetic diagnosis for ADPKD.
Mortality and comorbidities in a Nationwide cohort of HIV-infected adults: comparison to a matched non-HIV adults’ cohort, France, 2006–18
Authors: Vallée Alexandre , Majerholc Catherine , Zucman David , Livrozet Jean-Michel , Laurendeau Caroline , Bouée Stéphane , Prevoteau du Clary François 
Published: February 2024

Abstract

Background
Human immunodeficiency virus (HIV) remains a significant cause of morbidity and mortality worldwide. The aim of this study was to describe the mortality rate and associated comorbidities in a nationwide population-based cohort of persons living with HIV (PLWHIV) and to compare it with mortality in an age and gender-matched cohort of non-HIV individuals in France.

Methods
Using data from the French national health data system, we identified and included 173 712 PLWHIV (66.5% men) and 173 712 non-HIV participants (66.5% men) matched for age and gender. PLHIV were identified based on ICD-10 HIV diagnoses, HIV-specific laboratory tests, and/or prescriptions for antiretroviral therapy specific to HIV. Hazard ratios (HRs) of mortality were assessed using multiple Cox regression models.

Results
During the 13 years of follow-up (2006–18), we observed 20 018 deaths among PLWHIV compared with 6262 deaths among non-HIV participants (11.52% vs. 3.60%, P &lt; 0.001). The over-mortality of PLWHIV was expressed by univariable HR = 2.135 (2.072–2.199), which remained significant after adjustment for region, Complementary Universal Health Insurance and AME, with multivariable HR = 2.182 (2.118–2.248). The results remained significant after adjusting for comorbidities, including infectious diseases [HR = 1.587 (1.538–1.638)]. Notably, PLWHIV were more importantly associated with mortality in women [HR = 2.966 (2.767–3.180)], compared in men [HR = 1.961 (1.898–2.027)].

Conclusion
Although the life expectancy of PLWHIV has globally increased, the causes of death should be prioritized in prevention policies and care management. Gender-specific policies should be highlighted, as we observed a higher impact of HIV mortality in women.
“Yes, that’s me singing to myself”: Jackie Kay’s “These are not my clothes” as a Self-Affirming Narrative of Care in Old Age
Authors: Oró-Piqueras Maricel , Casado-Gual Núria , Vizcaíno Verónica 
Published: February 2024

Abstract
Fictional stories set in care homes have increased in the last decades and, with them, the perspectives from which care homes are constructed and represented have become diversified. Care home stories. Aging, disability, and long-term residential care. Transcript Verlag]. Through the alternative worlds that are offered by literary narratives, these stories allow the reader to glimpse into the increasingly varied possibilities of care that a residential settlement can offer. At the same time, they highlight the attributes attached to human beings once their bodies are not regarded as fully functional or able by their carers and society at large. Jackie Kay’s short story “These are not my clothes” (2011) presents a highly symbolic care-home narrative in which constant practices of depersonalized care and infantilization lead to the inevitable dehumanization of the residents and their eventual deterioration. Through the viewpoint of its female protagonist, Margaret, Kay creates a personal, poignant and, at times, also humorous narrative of care that undermines prevailing images of the so-called fourth age as a period of extreme cognitive deterioration. Drawing from theories of care and the interdisciplinary field of aging studies, especially in connection with theories of embodiment and old age and social approaches to aging, this article offers a close reading of Kay’s short story as both an assertive narrative on the fourth age, and as an insubordinate story of care, which can serve as a model to both gerontologists and care practitioners.
US payment policy for medications to treat opioid use disorder: landscape and opportunities
Authors: McGinty Emma E , White Sarah A , Eisenberg Matthew D , Palmer Nicole R , Brown C Hendricks , Saloner Brendan K 
Published: February 2024

Abstract
Offering patients medications for opioid use disorder (MOUD) is the standard of care for opioid use disorder (OUD), but an estimated 75%–90% of people with OUD who could benefit from MOUD do not receive medication. Payment policy, defined as public and private payers’ approaches to covering and reimbursing providers for MOUD, is 1 contributor to this treatment gap. We conducted a policy analysis and qualitative interviews (n = 21) and surveys (n = 31) with US MOUD payment policy experts to characterize MOUD insurance coverage across major categories of US insurers and identify opportunities for reform and innovation. Traditional Medicare, Medicare Advantage, and Medicaid all provide coverage for at least 1 formulation of buprenorphine, naltrexone, and methadone for OUD. Private insurance coverage varies by carrier and by plan, with methadone most likely to be excluded. The experts interviewed cautioned against rigid reimbursement models that force patients into one-size-fits-all care and endorsed future development and adoption of value-based MOUD payment models. More than 70% of experts surveyed reported that Medicare, Medicaid, and private insurers should increase payment for office- and opioid treatment program–based MOUD. Validation of MOUD performance metrics is needed to support future value-based initiatives.
Is more patient empowerment always better? Examining the moderating role of perceived physician’s argument quality
Authors: Zhai Jiajing , Nie Jinghong 
Published: February 2024

Abstract
Patient empowerment is an important concept in the study of physician–patient communication and is becoming increasingly popular in medical practices. However, previous studies have yielded inconsistent results regarding its effects. To reconcile these findings and establish a robust connection between empowerment and patient adherence, our study blends dyadic power theory with patient empowerment research. Using mixed methods, including both empirical modeling and controlled experiments, we found that patients who are equally empowered, as compared to those who are under- or over-empowered, exhibit a stronger dominance intention, which subsequently positively affects their adherence and satisfaction. Underlying this nonlinear influence of empowerment on adherence are two independent pathways: one channeling the effect through dominance intention and the other through perceived physician incompetence. Perceived physician’s argument quality represents a boundary condition. This research offers meaningful theoretical and practical implications to the literatures on patient empowerment and adherence by revealing the curvilinear relationship.
From Europe to Mexico: The Unexpected Journey of Thirty Jewish Families Escaping Nazism
Authors: Gleizer Daniela , Siman Yael 
Published: February 2024

Abstract
Despite Mexico’s highly restrictive policy toward Jewish refugees during the 1930s and the Second World War, nearly two thousand Jewish refugees fleeing from Nazism managed to enter the country. While previous historiography has primarily focused on government policies toward Jewish refugees, it has paid little attention to the experiences of those who actually arrived in Mexico. This article fills this gap by analyzing the forced migration and transit process of thirty Jewish refugee families who arrived in Mexico between 1937 and 1949. Mexico emerged as a crucial option for refugees throughout their flight when they utilized and established transnational links that would ultimately lay the groundwork for their rescue. By expanding the field of Holocaust studies to encompass the experiences of refugees in Latin America, this study provides important insights into the global dynamics of the Holocaust.
Staging a Boycott: Photographs of the Nazi Attack on Jewish-Owned Businesses in April 1933
Authors: Kreutzmüller Christoph 
Published: February 2024

Abstract
On April 1, 1933, the Nazi regime staged the brutal state-organized blockade of Jewish-owned businesses as a peaceful boycott. At the time, attempts to influence public opinion only worked to a limited extent. Both domestic and international papers were reluctant to print photos that represented the Nazi perspective too clearly. Yet astonishingly, the Nazi perspective prevails today. The photos made by the Nazis and their helpers to stage the “boycott” are dominant in exhibitions and publications. The “Nazi victory on the shopfront,” as The Guardian called it in 1933, has therefore turned into a belated victory on the “photo front.” This article analyzes the photos taken on April 1, 1933, deconstructs the propaganda messages embedded in them, and reconstructs the violence of the Nazi regime’s first systematic assault against the Jews in Germany.
Fish age reading using deep learning methods for object-detection and segmentation
Authors: Cayetano Arjay , Stransky Christoph , Birk Andreas , Brey Thomas 
Published: February 2024

Abstract
Determination of individual age is one essential step in the accurate assessment of fish stocks. In non-tropical environments, the manual count of ring-like growth patterns in fish otoliths (ear stones) is the standard method. It relies on visual means and individual judgment and thus is subject to bias and interpretation errors. The use of automated pattern recognition based on machine learning may help to overcome this problem. Here, we employ two deep learning methods based on Convolutional Neural Networks (CNNs). The first approach utilizes the Mask R-CNN algorithm to perform object detection on the major otolith reading axes. The second approach employs the U-Net architecture to perform semantic segmentation on the otolith image in order to segregate the regions of interest. For both methods, we applied a simple postprocessing to count the rings on the output masks returned, which corresponds to the age prediction. Multiple benchmark tests indicate the promising performance of our implemented approaches, comparable to recently published methods based on classical image processing and traditional CNN implementation. Furthermore, our algorithms showed higher robustness compared to the existing methods, while also having the capacity to extrapolate missing age groups and to adapt to a new domain or data source.
Outcomes and prognostic factors of repeat pulmonary metastasectomy
Authors: Kanzaki Ryu , Watari Hirokazu , Omura Akiisa , Kawagishi Sachi , Tanaka Ryo , Maniwa Tomohiro , Okami Jiro 
Published: February 2024

Abstract

OBJECTIVES
Information on prognostic factors after repeat pulmonary metastasectomy (PM) is limited, and outcomes after a third PM are not well documented.

METHODS
A single-institute retrospective study was conducted. Between 2000 and 2020, 68 patients underwent repeat PM for pulmonary metastases from various cancers. Outcomes and prognostic factors for the second PM and outcomes after the third PM were analysed.

RESULTS
This study included 39 men and 29 women. The mean age at second PM was 53.2 years old. The primary tumours were soft tissue sarcoma in 24 patients, colorectal cancer in 19 and osteosarcoma in 10. The interval between the first PM procedure and detection of pulmonary metastasis after the first PM (months) was ≤12 in 37 patients and &gt;12 in 31 patients. At the second PM, 20 patients underwent lobectomy or bilobectomy, and 48 underwent sublobar resection. Complete resection was achieved in 60 patients, and 52 patients experienced recurrence after the second PM. The 5-year relapse-free survival and overall survival rates after the second PM were 27% and 48%, respectively. Multivariable analysis revealed that the interval between the first PM and the subsequent detection of pulmonary metastasis (≤12 months) was a poor prognostic factor for both relapse-free survival and overall survival after the second PM. Seventeen patients underwent a third PM, 3 of whom achieved a 3-year disease-free survival.

CONCLUSIONS
Patients with a period of &gt;12 months between the first PM and the subsequent detection of pulmonary metastases showed favourable outcomes and are thus considered good candidates for second PM. A third PM may be beneficial for selected patients.
Earthquake Theorem for Cluster Algebras of Finite Type
Authors: Asaka Takeru , Ishibashi Tsukasa , Kano Shunsuke 
Published: February 2024

Abstract
We introduce a cluster algebraic generalization of Thurston’s earthquake map for the cluster algebras of finite type, which we call the cluster earthquake map. It is defined by gluing exponential maps, which is modeled after the earthquakes along ideal arcs. We prove an analogue of the earthquake theorem, which states that the cluster earthquake map gives a homeomorphism between the spaces of $\mathbb {R}^{\textrm {trop}}$- and $\mathbb {R}_{&gt;0}$-valued points of the cluster $\mathcal {X}$-variety. For those of type $A_{n}$ and $D_{n}$, the cluster earthquake map indeed recovers the earthquake maps for marked disks and once-punctured marked disks, respectively. Moreover, we investigate certain asymptotic behaviors of the cluster earthquake map, which give rise to “continuous deformations” of the Fock–Goncharov fan.
Epidemiological Characteristics and Outcome of Viral Respiratory Tract Infections in the First Year After Allogeneic Hematopoietic Cell Transplantation
Authors: Van Praet Jens T , Huysman Andreas , De Knijf Eline , De Buyser Stefanie , Snauwaert Sylvia , Van Droogenbroeck Jan , Lodewyck Tom , Schauwvlieghe Alexander , Selleslag Dominik , Reynders Marijke 
Published: February 2024

Abstract
Adverse outcomes of viral respiratory tract infections (RTIs) have been reported in recipients of allogeneic hematopoietic cell transplantation. Using a laboratory-developed multiparameter polymerase chain reaction in a consecutive series of 242 patients, we found the highest incidence of viral RTI in the preengraftment phase. The occurrence of multiple episodes of viral RTI or viral pneumonia was significantly associated with a higher hazard of nonrelapse mortality in the first year after transplantation. We observed a 90-day mortality of 19.7% after viral RTI, which was significantly different between patient groups stratified according to the immunodeficiency scoring index.
Unravelling the complex interplay between antibiotic consumption and adaptive changes in methicillin-resistant Staphylococcus aureus
Authors: van Hal Sebastiaan J , Jensen Slade O , Tong Stephen Y C , Bentley Stephen , Holden Matthew T 
Published: February 2024

Abstract

Objectives
This study aims to elucidate the genomic dynamics driving the emergence of antimicrobial resistance (AMR), with a specific focus on the interplay between AMR and antimicrobial usage.

Methods
We conducted a comprehensive analysis using a ST239 methicillin-resistant Staphylococcus aureus (MRSA) dataset over a continuous 12-year period from a single hospital. Genomic analyses were performed tracking the changes in MRSA populations, particularly the emergence of reduced vancomycin susceptibility, and assessing the impact of glycopeptide use on these emergence events.

Results
Our findings reveal a significant correlation between hospital glycopeptide usage and the selection of MRSA strains with reduced vancomycin susceptibility. Genomic analyses provided insights into the molecular mechanisms driving resistance emergence, including the slowing of the molecular clock rate in response to heightened antimicrobial consumption.

Conclusions
In conclusion, this study the highlights the complex dynamics between AMR and antimicrobial use at the hospital level. The observed correlation between antimicrobial consumption and the development of less susceptible MRSA strains underscores the importance of antimicrobial stewardship programmes and the establishment of optimal consumption thresholds for mitigating AMR effectively.