bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cancer and Aging
Authors: Deimling Gary T. 
Published: January 2025

Abstract
Cancer has been called a disease of the elderly since most cancers occur in individuals older than 65 years of age. The American Cancer Society in 2023 indicated that cancer’s incidence increases greatly with age, and that 57% of those diagnosed in the past year are 65 or older. Furthermore, as the US population ages, it is estimated that this will increase to 70% by 2030. This chapter provides a conceptual approach to identifying the complex vulnerabilities that being a cancer survivor confers, including those of advancing age. These are discussed in the context of the multimorbidities that older adults experience as well as the health disparities linked to both gender and race. The chapter continues to review foundational and recent research on these issues along with findings from the authors’ National Cancer Institute-funded research at the Cancer Survivors Research Program (CSRP) and concludes with narratives provided by survivors who participated in their research.
Physical Functioning and Disability
Authors: Deimling Gary T. 
Published: January 2025

Abstract
Physical functioning is an important indicator of health across the life course. The effects of cancer on a survivor’s overall physical functioning may persist for up to 20 years after cancer treatment. Moreover, when added to the functional difficulties linked to late-life comorbidities, functional problems that often result from cancer or its treatment can ultimately result in survivors’ inability to participate in valued social and recreational activities, which in turn can translate into an erosion of overall quality of life. This chapter examines the foundational and recent research on cancer and physical functioning and disability, including research conducted at the Cancer Survivors Research Program (CSRP) and concludes with survivors’ narratives on these issues.
Psychosocial Distress
Authors: Deimling Gary T. 
Published: January 2025

Abstract
Research documenting the nature, severity, and persistence of psychosocial distress reported by cancer patients began more than 30 years ago and continues to be a central aspect of cancer research. Cancer manifests all the critical attributes of a serious and, for some, a traumatic life event, one that can be characterized by loss and crisis. Even with successful treatment, cancer often leaves a variety of physical health and functional problems that can have serious implications for psychosocial well-being. The focus of this chapter is on specific forms of psychosocial distress that occur among older adult survivors of cancer, focusing on depression, anxiety, and cancer-related worries, including fears of recurrence. As in preceding chapters, a conceptual framework is suggested that integrates the review of foundational as well as recent research, including findings from the Cancer Survivors Research Project (CSRP), culminating in a review of survivors’ narratives.
Adaptation, Appraisal, and Coping
Authors: Deimling Gary T. 
Published: January 2025

Abstract
An important theme in the psycho-oncology literature for nearly two decades has been the adaptation process. Treating adaptation as an ongoing process, one that can both mediate and moderate the impact of cancer-related stressors on adjustment outcomes, is an essential feature of the stress–coping paradigm. From this perspective, stressors related to cancer either may or may not culminate in distress outcomes depending on the adaptations that survivors make in response to having cancer. A key aspect of this process is the stress appraisal process and the application of specific coping strategies. Other important factors are the individual’s dispositional characteristics, such as optimism, and their personality. This chapter examines foundational and recent research on stress appraisal and coping resources used to adapt to cancer, including findings from the Cancer Survivors Research Program (CSRP) and survivors’ narratives.
Becoming Psychodynamic
Authors: Rinaldi Matthew 
Published: January 2025

Abstract
This guidebook covers the theory and technical aspects that trainees will learn in the course of their first psychodynamic psychotherapy case. From the common factors model, the book builds progressively the psychotherapeutic skills required to become more psychodynamic to enable deeper, longer-lasting change in patients. The book covers themes including why psychodynamic psychotherapy is effective, mistakes, training patient anxiety, the frame, the analytic stance, defences, working with difference, the working alliance, enactments, countertransference, projection and projective identification, reverie, containment, transference, interpretations, dreams, working through, ending, supervision, assessment, adapted models of psychodynamic psychotherapy, and personal therapy. Traditional psychoanalytic research is blended with current neuroscientific evidence and psychological experiments. The trainee is encouraged to reflect on their own practice, develop their individual style, and to follow appropriate recommended further reading.
Your feelings about your first case
Authors: Rinaldi Matthew 
Published: January 2025

Abstract
The first psychodynamic psychotherapy case will cause a range of feelings for the new trainee. By identifying them before starting, the trainee is more able to identify subsequent countertransference responses, offer a neutral space and, therefore, helpful psychodynamic psychotherapy. This chapter supports the trainee to identify their feelings about their first case, and explains why this is important using a case example from the author’s own experience of a ‘mistake’. Space is created for personal reflection and the trainee is encouraged to take this information to their supervision. Training requirements are also discussed, particularly the anxiety that can be induced by the need for a patient to stay for a particular length of time, and the super-ego response that trainees might experience on starting this new way of working, which detracts them from their natural analytic stance.
Building your psychotherapy skills
Authors: Rinaldi Matthew 
Published: January 2025

Abstract
The frame of psychodynamic psychotherapy allows the therapeutic work to exist and supports the therapist by building an internal guide. The first priority in therapy is to establish the frame, and the components of this frame are elaborated in this chapter. This includes timings, frequency of sessions, breaks, the environment, virtual work, contact between sessions, confidentiality, physical contact, process notes, money, clothing, and appearance. The fundamentals of the frame are related to attachment research. Attacks on the frame are described and a model for working with these is suggested.
Effect of numerical resolution on synthetic observables of simulated coronal loops
Authors: Breu C A , De Moortel I , Peter H , Solanki S K 
Published: January 2025

ABSTRACT
Increasingly realistic simulations of the corona are used to predict synthetic observables for instruments onboard both existing and upcoming heliophysics space missions. Synthetic observables play an important role in constraining coronal heating theories. Choosing the spatial resolution of numerical simulations involves a trade-off between accuracy and computational cost. Since the numerical resolution affects not only the scale of structures that can be resolved, but also thermodynamic quantities such as the average coronal density, it is important to quantify the effect on synthesized observables. Using 3D radiative magnetohydrodynamic simulations of coronal loops at three different grid spacings, from 60 km down to 12 km, we find that changes in numerical resolution lead to differences in thermodynamic quantities and stratification as well as dynamic behaviour. Higher grid resolution results in a more complex and dynamic atmosphere. The resolution affects the emission intensity as well as the velocity distribution, thereby affecting synthetic spectra derived from the simulation. The distribution of synthetic coronal loop strand sizes changes as more fine-scale structure is resolved. A number of parameters, however, seem to start to saturate from our chosen medium grid resolution on. Our study shows that while choosing a sufficiently high resolution matters when comparing forward-modelled observables with data from current and future space missions, for most purposes not much is gained by further increasing the resolution beyond a grid spacing of 24 km, which seems to be adequate for reproducing bulk loop properties and forward-modelled emission, representing a good trade-off between accuracy and computational resource.
Fungal-Derived tRNAs Are Expressed and Aminoacylated in Orchid Mitochondria
Authors: Warren Jessica M , Ceriotti Luis F , Sanchez-Puerta M Virginia , Sloan Daniel B 
Published: January 2025

Abstract
Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer, including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom horizontal gene transfer are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that some fungal-derived tRNA genes in the transferred region are transcribed, post-transcriptionally modified, and aminoacylated. In contrast, all the transferred protein-coding sequences appear to be pseudogenes. These findings show that fungal horizontal gene transfer has altered the composition of the orchid mitochondrial tRNA pool and suggest that these foreign tRNAs function in translation. The exceptional capacity of tRNAs for horizontal gene transfer and functional replacement is further illustrated by the diversity of tRNA genes in the C. maculata mitogenome, which also include genes of plastid and bacterial origin in addition to their native mitochondrial counterparts.
The ribosome as a platform to coordinate mRNA decay
Authors: Müller Martin B D , Becker Thomas , Denk Timo , Hashimoto Satoshi , Inada Toshifumi , Beckmann Roland 
Published: January 2025

Abstract
Messenger RNA (mRNA) homeostasis is a critical aspect of cellular function, involving the dynamic interplay between transcription and decay processes. Recent advances have revealed that the ribosome plays a central role in coordinating mRNA decay, challenging the traditional view that free mRNA is the primary substrate for degradation. This review examines the mechanisms whereby ribosomes facilitate both the licensing and execution of mRNA decay. This involves factors such as the Ccr4–Not complex, small MutS-related domain endonucleases, and various quality control pathways. We discuss how translational fidelity, as well as the presence of nonoptimal codons and ribosome collisions, can trigger decay pathways such as nonstop decay and no-go decay. Furthermore, we highlight the direct association of canonical exonucleases, such as Xrn1 and the Ski-exosome system, with the ribosome, underscoring the ribosome’s multifaceted role as a platform for regulatory processes governing mRNA stability. By integrating recent findings, this review offers a comprehensive overview of the structural basis of how ribosomes not only facilitate translation but also serve as critical hubs for mRNA decay coordination.
DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells
Authors: Frezza Valentina , Chellini Lidia , Riccioni Veronica , Bonvissuto Davide , Palombo Ramona , Paronetto Maria Paola 
Published: January 2025

Abstract
Ewing sarcomas (ESs) are biologically aggressive tumours of bone and soft tissues caused by chromosomal translocations yielding in-frame fusion proteins driving the neoplastic transformation. The DNA/RNA helicase DHX9 is an important regulator of cellular processes often deregulated in cancer. Using transcriptome profiling, our study reveals cancer-relevant genes whose splicing is modulated by DHX9. Immunodepletion experiments demonstrate that DHX9 impacts on the recruitment of U2 small nuclear RNP (snRNP) onto the pre-mRNA. Analysis of structure and sequence features of DHX9 target exons reveal that DHX9-sensitive exons display shorter flanking introns and contain HNRNPC and TIA1 consensus motifs. A prominent target of DHX9 is exon 11 in the Cortactin (CTTN) gene, which is alternatively spliced to generate isoforms with different activities in cell migration and tumour invasion. Alternative inclusion of the exon 11 in CTTN gene is one of the most recurrent isoform switches in multiple cancer types, thus highlighting the pivotal role of DHX9 in defining the tumour phenotype. Biochemical analyses reveal that DHX9 binding promotes the recruitment of U2snRNP, SF3B1, and SF3A2 to the splice sites flanking exon 11. These findings uncover a new role of DHX9 in the control of co-transcriptional splicing in ES, which may represent a new druggable target to counteract ES malignancy.
Strategic base modifications refine RNA function and reduce CRISPR–Cas9 off-targets
Authors: Zhang Kaisong , Shen Wei , Zhao Yunting , Xu Xinyan , Liu Xingyu , Qi Qianqian , Huang Siqi , Tian Tian , Zhou Xiang 
Published: January 2025

Abstract
In contrast to traditional RNA regulatory approaches that modify the 2′-OH group, this study explores strategic base modifications using 5-carboxylcytosine (ca5C). We developed a technique where ca5C is transformed into dihydrouracil via treatment with borane-pyridine complex or 2-picoline borane complex, leading to base mutations that directly impact RNA functionality. This innovative strategy effectively manages CRISPR–Cas9 system activities, significantly minimizing off-target effects. Our approach not only demonstrates a significant advancement in RNA manipulation but also offers a new method for the precise control of gene editing technologies, showcasing its potential for broad application in chemical biology.
Tumor cells upregulate neurotransmitter GABA in the choroid plexus through STAT6-Bestrophin1 signaling, promoting leptomeningeal dissemination
Authors: Das Diganta , Iyer Mukund , Nakamura Brooke , Sedighi Saman , Hsu Angela , Danilov Camelia , LaViolette Peter S , Connelly Jennifer , Chow Frances , Neman Josh 
Published: January 2025

Abstract

Background
Leptomeningeal dissemination (LMD) occurs when tumor cells interact with choroid plexus epithelium (CPE) to gain access to cerebrospinal fluid (CSF) in the brain’s meninges and ventricular system. This disease is particularly devastating for patients due to our limited understanding and few therapeutic options. The leptomeningeal CSF is a nutritionally deprived microenvironment for tumor cells. Despite this, LMD tumor cells survive by taking up and metabolizing the neurotransmitter GABA from the CSF. However, we currently lack evidence on how CSF-GABA levels are altered and how tumor cells communicate with the choroid plexus epithelium to increase GABA levels in the LMD microenvironment. Herein, we examined the interactions between CPEs and tumor cells that make CSF more hospitable to LMD growth.

Methods
We utilized primary choroid plexus, breast cancer cell and patient-derived breast and lung to brain metastatic cells along with in-vivo modeling along with STAT6 inhibitor and IL13 gene knockdown.

Results
We show breast and lung cancer cells derived-IL13 activates STAT6 signaling in choroid plexus. Subsequently, choroid plexus upregulates GABA-synthesizing enzyme GAD67 and GABA-permeable channel Bestrophin-1, all leading to elevated neurotransmitter GABA levels in the cerebrospinal fluid. Moreover, we show a significant reduction of Bestrophin1 in choroid plexus when tumor-derived IL13 is knocked down or when treated with brain permeable STAT6 specific inhibitor AS1517499, leading to increased survival.

Conclusions
Overall, these findings reveal a novel STAT6-Bestrophin1-GABA axis in choroid plexus and its therapeutic targeting can lead to favorable outcomes in leptomeningeal disease.
High Incidence and Duration of Antibiotic Use Among a Cohort of Men Who Have Sex With Men in Seattle, Washington
Authors: Zane Gregory K , Barbee Lindley A , Duerr Ann , Golden Matthew R , Manhart Lisa E , Dimitrov Dobromir , Khosropour Christine 
Published: January 2025

Abstract

Background
Doxycycline postexposure prophylaxis (doxy-PEP) effectively prevents bacterial sexually transmitted infections (STIs) but may increase antibiotic pressure. Little is known about longitudinal antibiotic use among men who have sex with men (MSM), a key population for doxy-PEP.

Methods
We analyzed data from a prospective cohort of MSM in Seattle, Washington, from 2016 to 2018, prior to the introduction of doxy-PEP. Antibiotic use and reason for prescription were self-reported in weekly surveys and extracted from medical records. We characterized antibiotic use across 49 weeks of follow-up, stratified by specific antibiotics of interest and reasons for prescription. Incidence rates (IRs) were calculated for the number of incident events of antibiotic initiation per 100 person-years (PY) at risk. We assessed factors associated with antibiotic initiation using negative binomial regression to estimate adjusted incidence rate ratios (IRRs).

Results
Among 140 participants, 68.6% (n = 96) received at least 1 antibiotic during follow-up, resulting in an overall IR of 264.5 events of antibiotic initiation per 100 PY and 1696 total days of antibiotic use. STI treatment was the most common reason for antibiotic initiation (IR, 153.5 events per 100 PY; 462 days); however, treatment for other conditions contributed most to overall days of antibiotic use (IR, 42.6 events per 100 PY; 947 days). An age of 25–39 years (IRR, 1.54 [95% confidence interval {CI}, 1.02–2.32]) and a history of bacterial STIs &lt;12 months prior to enrollment (IRR, 1.81 [95% CI, 1.12–2.93]) were significantly associated with higher incidence of antibiotic initiation.

Conclusions
Antibiotic consumption among this population was very high. Our analysis provides a necessary foundation for assessing the potential impacts of doxy-PEP.
A Longitudinal Description of the Health-Related Quality of Life Among Individuals at High Risk After SARS-CoV-2 Infection: A Dutch Multicenter Observational Cohort Study
Authors: Vergouwe Magda , Birnie Emma , van Veelen Sarah , Biemond Jason J , Appelman Brent , Peters-Sengers Hessel , de Bree Godelieve J , Popping Stephanie , Wiersinga W Joost ,   TURN-COVID Study Group, Welkers Matthijs R A , van Ittersum Frans J , van der Loeff Maarten F Schim , Bomers Marije K , Kersten Marie José , Hazenberg Mette D , Heijmans Jarom , van der Valk Marc , Kemper E Marleen , van den Berge Marcel , Ammerlaan Heidi S M , Berrevoets Marvin A H , van Alphen Robbert J , Douma Renée A , Leyten Eliane M S , van Nieuwkoop Cees , van Marum Rob J , Rosendaal Frits R , de Boer Mark G J , Oude Lashof Astrid M L , van Vonderen Marit G A , Wagenaar Jiri F P , Stalenhoef Janneke E , van de Veerdonk Frank , Hassing Robert-Jan , Soetekouw Robin , Moeniralam Hazra S , van Osch Frits 
Published: January 2025

Abstract

Background
Health-related quality of life (HRQoL) data post–COVID-19 in patients with medical conditions associated with severe disease are lacking. Here, we assess the longitudinal impact of COVID-19 on HRQoL and employment status in individuals at high risk.

Methods
This multicenter prospective cohort study included individuals at high risk for severe disease who were hospitalized or not-hospitalized with SARS-CoV-2 infection (September 2021–February 2024). Questionnaires about HRQoL and employment status were collected at 3, 6, and 12 months post–COVID-19 and retrospectively recalled and reported for pre–COVID-19. With a mixed effects model, we assessed the course of and risk factors for changes in HRQoL utility score.

Results
Among 332 individuals (median age, 59.8 years [IQR, 48.8–67.1]; 50.6% female), 184 (55.4%) were hospitalized for COVID-19 (intensive care unit admission, 12.0%). High-risk factors included solid organ transplantation (19.6%), hematologic malignancies (28.0%), and immunosuppressive medication use (56.6%). The median HRQoL utility score declined from 0.85 (IQR, 0.74–1.00) pre–COVID-19 to 0.81 (0.70–0.92) 12 months post–COVID-19 (P = .007). Solid organ transplant recipients and patients requiring oxygen therapy were at risk for an HRQoL decrease over 1 year. At 12 months, 45.3% of all employed responders had reported sick leave related to COVID-19 symptoms. Employed patients who reported sick leave had lower median HRQoL utility scores (0.81 [IQR, 0.72–0.91]) than those who did not (0.89 [0.86–1.00], P = .002).

Conclusions
Solid organ transplant recipients and individuals requiring oxygen therapy experience a substantial HRQoL decline over 12 months post–COVID-19. Moreover, almost half of employed participants reported COVID-19–related sick leave, correlating with lower HRQoL. This highlights the continuous burden of COVID-19 for this vulnerable population and supports the implementation of preventive approaches.
Effect of laparoscopic cholecystectomy on plasma levels of EETs, arachidonic acids derived lipid mediators
Authors: Sarı İsmail , Bolat Hacı , Özmen Esma , Köse Burcu , Ayan Durmuş 
Published: January 2025

Abstract

Background
Epoxyeicosatrienoic acids (EETs) are closely associated with lipoprotein metabolism, and changes in lipid profiles potentially affect their levels and functions. Given the alterations in lipid metabolism after cholecystectomy, this study aimed to investigate the levels of four EET regioisomers (free and esterified) and lipid profiles in patients with cholelithiasis after laparoscopic cholecystectomy (LC) and explore correlations between these parameters.

Methods
This prospective study involved 40 patients with symptomatic cholelithiasis who underwent LC. Plasma EETs and serum total cholesterol, triglyceride, high-density lipoprotein (HDL), very low-density lipoprotein, low-density lipoprotein, and body mass index (BMI) values were determined preoperatively and after 6 months of LC.

Results
After LC, triglyceride and very low-density lipoprotein levels increased while TC decreased. BMI values increased significantly after the operation. Despite plasma EET levels decreasing remarkably after surgery, this change did not reach statistical significance. A significant correlation was observed between preoperative levels of 8,9- and 11,12-EET and pre-and post-operative HDL. There was a significant negative correlation between the EET levels measured before and after surgery and the change in BMI values.

Conclusions
In this study, we observed significant changes in lipid profile 6 months after LC. While HDL, low-density lipoprotein, and EET levels showed a decreasing trend post-surgery, this change was not statistically significant. This trend and their significant correlations may indicate a complex relationship between HDL and EET metabolism. In addition, the negative correlation between EET levels and BMI changes highlights the need for further research to elucidate the metabolic impact and weight regulation of EETs after LC.
Becoming authentic: A social conception of the self
Authors: Mortimer Samuel A 
Published: January 2025

Abstract
Two approaches to authenticity have gained currency in the recent analytic philosophical literature. The first takes authenticity to be a property of how people act (authentic agency). The second takes it to be a property of who people are (authentic self). This paper motivates both views, then argues that there is a dependency between the two: the exercise of authentic agency depends on the possession of an authentic self, while the possession of an authentic self relies on the prior exercise of authentic agency. On a particular, individualist conception of the self, this leads to a paradox. This paradox is resolved if one instead adopts a social conception of the self, according to which the self is partially ontologically constituted by other agents (a ‘we’, rather than an ‘I’).