bluuebunny/crossref_metadata_2025_split huggingface dataset:
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis
Authors: Aihara Gohta , Clifton Kalen , Chen Mayling , Li Zhuoyan , Atta Lyla , Miller Brendan F , Satija Rahul , Hickey John W , Fan Jean 
Published: June 2024

Abstract

Motivation
Spatial omics data demand computational analysis but many analysis tools have computational resource requirements that increase with the number of cells analyzed. This presents scalability challenges as researchers use spatial omics technologies to profile millions of cells.

Results
To enhance the scalability of spatial omics data analysis, we developed a rasterization preprocessing framework called SEraster that aggregates cellular information into spatial pixels. We apply SEraster to both real and simulated spatial omics data prior to spatial variable gene expression analysis to demonstrate that such preprocessing can reduce computational resource requirements while maintaining high performance, including as compared to other down-sampling approaches. We further integrate SEraster with existing analysis tools to characterize cell-type spatial co-enrichment across length scales. Finally, we apply SEraster to enable analysis of a mouse pup spatial omics dataset with over a million cells to identify tissue-level and cell-type-specific spatially variable genes as well as spatially co-enriched cell types that recapitulate expected organ structures.

Availability and implementation
SEraster is implemented as an R package on GitHub (https://github.com/JEFworks-Lab/SEraster) with additional tutorials at https://JEF.works/SEraster.
Buen Vivir and Community Water Organisations in Colombia: Lessons for Social Work
Authors: Ramírez Ana Patricia Quintana 
Published: June 2024

Abstract
Buen Vivir is a path that Latin American peoples are following in the hope of decolonising the exclusionary economic and political relations imposed by external development. This paradigm, inherited from our ancestors, is claimed today in the search for a harmonious life with nature and in conditions of equality and solidarity among human beings. This Indigenous thinking coincides with the intention to articulate the theory and practice of community social work from an environmental perspective. As demonstrated by associations formed by rural and peri-urban inhabitants to manage water supply for human consumption in Colombia. From these groups, the discipline learns the importance of promoting unity among people, values of reciprocity in the distribution of water and, the conservation of nature through cultural practices inherited intergenerationally from indigenous, Afro and mestizo ancestors.
Unveiling serotonergic dysfunction of obsessive-compulsive disorder on prefrontal network dynamics: a computational perspective
Authors: Yin Lining , Yu Ying , Han Fang , Wang Qingyun 
Published: June 2024

Abstract
Serotonin (5-HT) regulates working memory within the prefrontal cortex network, which is crucial for understanding obsessive-compulsive disorder. However, the mechanisms how network dynamics and serotonin interact in obsessive-compulsive disorder remain elusive. Here, we incorporate 5-HT receptors (5-HT1A, 5-HT2A) and dopamine receptors into a multistable prefrontal cortex network model, replicating the experimentally observed inverted U-curve phenomenon. We show how the two 5-HT receptors antagonize neuronal activity and modulate network multistability. Reduced binding of 5-HT1A receptors increases global firing, while reduced binding of 5-HT2A receptors deepens attractors. The obtained results suggest reward-dependent synaptic plasticity mechanisms may attenuate 5-HT related network impairments. Integrating serotonin-mediated dopamine release into circuit, we observe that decreased serotonin concentration triggers the network into a deep attractor state, expanding the domain of attraction of stable nodes with high firing rate, potentially causing aberrant reverse learning. This suggests a hypothesis wherein elevated dopamine concentrations in obsessive-compulsive disorder might result from primary deficits in serotonin levels. Findings of this work underscore the pivotal role of serotonergic dysregulation in modulating synaptic plasticity through dopamine pathways, potentially contributing to learned obsessions. Interestingly, serotonin reuptake inhibitors and antidopaminergic potentiators can counteract the over-stable state of high-firing stable points, providing new insights into obsessive-compulsive disorder treatment.
Similar Efficacy of Mesalazine in Adult and Older Adult Ulcerative Colitis Patients: Post Hoc Analysis of a Randomized Noninferiority Trial of 1600 mg vs 400 mg Tablets
Authors: Safroneeva Ekaterina , Thorne Helen , Gerstner Ortrud , Laoun Raphaël 
Published: June 2024

Abstract

Background
The efficacy data on treatment in older adults are scarce, while the greatest increase in ulcerative colitis (UC) prevalence is observed in age groups of individuals 40 to 65 years of age and ≥65 years of age.

Aim
We assessed the difference in rates of clinical and endoscopic response and remission in UC adults (≤60 years) and older adults (&gt;60 years) treated with mesalazine.

Methods
We performed a post hoc analysis of data from a phase 3 noninferiority trial of 817 UC patients treated with mesalazine for 8 and additional 26 weeks in a double-blind and open-label study, respectively. We used Wilcoxon rank sum or chi-square test to analyze differences between groups and multivariable logistic regression to determine the associations between endoscopic remission as outcome (Mayo endoscopic subscore [MES] = 0 or ≤1) and independent variables including disease duration, baseline MES, age, sex, comedications, and comorbidities.

Results
Older adults had a longer disease duration, a higher number of comorbidities, concomitant medications, and higher baseline MES (2.38 ± 0.486 in older adults vs 2.26 ± 0.439 in adults; P = .008) compared with adults. We observed no difference in rates of combined clinical and endoscopic remission, clinical remission and response, and endoscopic remission and response at week 8 and 38 post-treatment. In addition to other well-known predictors of worse outcome, patients with ≥3 comedications were less likely to achieve an MES = 0 at week 8 and 38 and an MES ≤1 at week 38.

Conclusions
We observed similar efficacy of mesalazine in adult and older adult UC patients. The increased comedication number rather than age may decrease effectiveness of UC medications, highlighting the importance of healthy aging.
Cucktales: Race, Sex, and Enjoyment in the Reactionary Memescape
Authors: Baspehlivan Uygar 
Published: June 2024

Abstract
This article makes a critical contribution to the study of digital reactionary movements by tracing the resonant circulation of “the cuck” memes across various levels of racialized and gendered subjectivity. It argues that the cuck meme resonates through composing an affective narrative of deferred and stolen enjoyment at the intersection of personal, social, and international politics. It follows the meme’s digital movements across pornographic anxieties around the sexual prowess of the Black other (the personal), the Gamergate events of 2014 and its politics of geek masculine injury (the social), and the perceived threat of immigration to the enjoyment-space designated as the nation (the international). Throughout, the paper makes three contributions. First, it theorizes the structuring role played by enjoyment as a political factor in historically shaping political subjectivity. Second, it shows how this political factor animates the transnational politics of contemporary reactionary movements and how they affectively and discursively perceive their various political resentments through narratives of enjoyment. Third, it demonstrates how memes as specific technical-aesthetic products allow the common resonance and articulation of these various resentments to shape a site of rectification for an enjoyment that is felt to be lost.
Pediatric hypophosphatasia: avoid diagnosis missteps!
Authors: Whyte Michael P , McAlister William H , Mack Karen E , Mumm Steven , Madson Katherine L 
Published: June 2024

Vignette
Hypophosphatasia (HPP) is the dento-osseous disorder caused by deactivating mutation(s) of ALPL, the gene that encodes the “tissue-nonspecific” isoenzyme of alkaline phosphatase (TNSALP). In HPP, 3 natural substrates of cell-surface TNSALP accumulate extracellularly; phosphoethanolamine (PEA), inorganic pyrophosphate (PPi), and pyridoxal 5′-phosphate (PLP). Hypophosphatasemia together with elevated plasma levels of PEA, PPi, and PLP comprise its biochemical signature. PPi can inhibit mineralization and in extracellular excess can impair bone and tooth hardening and perhaps explain weak muscle. Autosomal dominant or autosomal recessive inheritance from among more than 400 mutations of ALPL largely accounts for HPP’s broad-ranging severity, greatest among all skeletal diseases. Pediatric HPP spans life-threatening perinatal and infantile forms, childhood forms, and odonto-HPP selectively featuring premature loss of deciduous teeth. ALPL gene testing and TNSALP supplementation therapy have bolstered familiarity with HPP, but there are new considerations for diagnosis. Herein, diagnosis of a boy’s mild childhood HPP was delayed by missteps involving his medical and dental history, physical examination, radiographic findings, and clinical laboratory studies. We review how pediatric HPP is now identified. Prompt diagnosis while appreciating the broad-ranging severity of HPP underlies the safe and effective management of this inborn-error-of-metabolism.
Subtle momentary effects of social media experiences: an experience sampling study of posting and social comparisons on connectedness and self-esteem
Authors: Desjarlais Malinda 
Published: June 2024

Abstract
Part of the current mental health crisis is attributed to the increasing reliance on social media for daily tasks. By understanding behavioral or cognitive patterns that influence facets of well-being in real-time within individuals, we can empower individuals to intentionally adjust their behavior, thereby enhancing these aspects. This study utilized an experience sampling method to investigate the real-time effects of social media-induced social comparisons and posting on self-esteem and connectedness. Six times per day for 5 days, 74 adults reported on their social media use in the previous hour and their experiences of connectedness and self-esteem. Multilevel modeling demonstrated statistically significant within-person associations. Social media-induced upward comparison was related to momentary decreases in self-esteem, and moments when individuals posted on social media were related to higher levels of connectedness. The findings emphasize that specific experiences on social media may produce immediate effects for connectedness and self-esteem.
Differential gene expression underlying epileptogenicity in patients with gliomas
Authors: Mortazavi Armin , Khan Anas U , Nieblas-Bedolla Edwin , Boddeti Ujwal , Bachani Muzna , Ksendzovsky Alexander , Johnson Kory , Zaghloul Kareem A 
Published: June 2024

Abstract

Background
Seizures are a common sequela for patients suffering from gliomas. Molecular properties are known to influence the initiation of seizures that may influence tumor growth. Different levels of gene expression with seizures related to gliomas remain unclear. We analyzed RNA sequencing of gliomas to further probe these differences.

Methods
Total RNA sequencing was obtained from The Cancer Genome Atlas—Lower-Grade Glioma project, comprised of 2021 World Health Organization classification low-grade gliomas, including IDH-mutant and IDH-wild type, to distinguish differential expression in patients who did and did not experience seizures. Utilizing QIAGEN Ingenuity Pathways Analysis, we identified canonical and functional pathways to characterize differential expression.

Results
Of 289 patients with gliomas, 83 (28.7%) had available information regarding seizure occurrence prior to intervention and other pertinent variables of interest. Of these, 50 (60.2%) were allocated to the seizure group. When comparing the level of RNA expression from these tumors between the seizure and non-seizure groups, 52 genes that were significantly differentially regulated were identified. We found canonical pathways that were altered, most significantly RhoGDI and semaphorin neuronal repulsive signaling. Functional gene analysis revealed tumors that promoted seizures had significantly increased functional gene sets involving neuronal differentiation and synaptogenesis.

Conclusions
In the setting of gliomas, differences in tumor gene expression exist between individuals with and without seizures, despite similarities in patient demographics and other tumor characteristics. There are significant differences in gene expression associated with neuron development and synaptogenesis, ultimately suggesting a mechanistic role of a tumor-neuron synapse in seizure initiation.
A phase 1 study of biweekly nab-paclitaxel/oxaliplatin/S-1/LV for advanced upper gastrointestinal cancers: TCOG T1216 study
Authors: Tsai Hui-Jen , Yang Shih-Hung , Hsiao Chin-Fu , Kao Hsiang-Fong , Su Yung-Yeh , Shan Yan-Shen , Yen Chia-Jui , Du Jeng-Shiun , Hsu Chiun , Wu I-Chen , Chen Li-Tzong 
Published: June 2024

Abstract

Background
Oxaliplatin- and fluoropyrimidine-based triplet regimens have demonstrated feasibility and efficacy in the treatment of upper gastrointestinal (UGI) cancers. Herein, we evaluate the feasibility and preliminary efficacy of biweekly nab-paclitaxel plus oxaliplatin and S-1/leucovorin (SOLAR) in chemonaïve UGI cancers.

Methods
A 3 + 3 phase 1 study was conducted to determine the maximal tolerated dose (MTD) of oxaliplatin in SOLAR (nab-paclitaxel [150 mg/m2 in D1], oxaliplatin [60, 75, or 85 mg/m2 in D1], and oral S-1/leucovorin [35 mg/m2 and 30 mg bid from D1 to D7]). The secondary endpoints were overall response rate (ORR), progression-free survival (PFS), overall survival (OS), and safety.

Results
Thirteen and 6 accruals were in the dose-escalation and MTD expansion cohorts, respectively. One of 6 patients at level III experienced dose-limiting toxicity (grade 3 diarrhea), which revealed that the MTD of oxaliplatin was 85 mg/m2. After a mean of 15.9 cycles of treatment, the most common treatment-related grade 3/4 toxicities were neutropenia (57.9%) and diarrhea (21.1%). The ORR was 63.2%. The median PFS and OS were 12.5 and 24.7 months, respectively.

Conclusion
The current study revealed the MTD of oxaliplatin and demonstrated the preliminary efficacy of SOLAR in UGI cancers, which deserves further investigation.

ClinicalTrials.gov Identifier
NCT03162510
Culture and Authoritarianism
Authors: Pearlman Wendy 
Published: June 2024

Abstract
Research on authoritarianism and culture highlights shared values, beliefs, behaviors, symbols, meanings, and affective orientations and considers how they shape and are shaped by the inception, resilience, functioning, and decline of autocratic rule. Reviewing scholarship on cases from around the world, the chapter traces how scholars increasingly shift away from older understandings of culture as a reified set of influences determining regime type and instead emphasize culture’s dynamic, intersubjective, and relational character. Some scholars treat culture as a contingent structure within which individual agency affects the likelihood of nondemocratic politics. Others track the cultural mechanisms through which autocrats establish rule and oppositionists challenge it. Still others consider how authoritarian power produces particular cultures which in turn reproduce authoritarian power, with legacies that sometimes outlast regimes themselves. This chapter considers what these wide-ranging works teach us about the complex linkages between authoritarianism and culture and suggests directions for new research.
Paradiplomacy in Hard Times: Cooperation and Confrontation in Subnational U.S.–China Relations
Authors: Jaros Kyle A , Newland Sara A 
Published: June 2024

Abstract
What becomes of subnational foreign engagement when international tensions rise? State-level U.S.–China relations offer insights into unresolved theoretical questions about the dynamics of what we call “paradiplomacy in hard times.” Whereas U.S. state governments expanded official engagements with China in the early 2010s, many states and cities have scaled back engagement and introduced anti-PRC measures in recent years amid worsening U.S.–China friction. We draw on an original dataset of state-level policy actions toward China (2012–2022) to assess patterns of variation across time and space in subnational U.S.–China relations, showing that subnational foreign relations in times of tension feature distinct dimensions of cooperation and confrontation. Meanwhile, we use a detailed case study of Indiana–China relations to develop insights into drivers of subnational cooperation and confrontation, highlighting the diverging interests and actions of the business community, state officials, federal officials, political parties, and Chinese government counterparts in shaping states’ foreign relations.
Deep learning with a small dataset predicts chromatin remodelling contribution to winter dormancy of apple axillary buds
Authors: Saito Takanori , Wang Shanshan , Ohkawa Katsuya , Ohara Hitoshi , Kondo Satoru 
Published: June 2024

Abstract
Epigenetic changes serve as a cellular memory for cumulative cold recognition in both herbaceous and tree species, including bud dormancy. However, most studies have discussed predicted chromatin structure with respect to histone marks. In the present study, we investigated the structural dynamics of bona fide chromatin to determine how plants recognize prolonged chilling during the initial stage of bud dormancy. The vegetative axillary buds of the ‘Fuji’ apple, which shows typical low temperature-dependent, but not photoperiod, dormancy induction, were used for the chromatin structure and transcriptional change analyses. The results were integrated using a deep-learning model and interpreted using statistical models, including Bayesian estimation. Although our model was constructed using a small dataset of two time points, chromatin remodelling due to random changes was excluded. The involvement of most nucleosome structural changes in transcriptional changes and the pivotal contribution of cold-driven circadian rhythm-dependent pathways regulated by the mobility of cis-regulatory elements were predicted. These findings may help to develop potential genetic targets for breeding species with less bud dormancy to overcome the effects of short winters during global warming. Our artificial intelligence concept can improve epigenetic analysis using a small dataset, especially in non-model plants with immature genome databases.
Induction chemotherapy followed by transoral laser microsurgery with or without adjuvant therapy for advanced hypopharyngeal cancer patients: A preliminary result
Authors: Chang Chia-Fan , Wang Ling-Wei , Yang Muh-Hwa , Chu Pen-Yuan 
Published: June 2024

Background:
Hypopharyngeal squamous cell carcinoma (HPSCC) has the poorest prognosis among head and neck cancers. Its treatment may significantly affect breathing, speaking, and swallowing. Induction chemotherapy (ICT) followed by transoral laser microsurgery (TLM) could reduce these adverse effects and achieve good outcomes.

Methods:
This was a retrospective study of 11 patients with advanced HPSCC. All patients underwent ICT and TLM alongside tailor-made adjuvant therapy based on the pathological features.

Results:
Adjuvant therapy was done in seven of 11 patients (64%). The 3-year disease-free survival and laryngeal preservation rates were 78% and 91%, respectively. At the last follow-up, 10 of 11 patients (91%) had no tracheostomy or feeding tube.

Conclusion:
ICT followed by TLM is an appropriate treatment for good tumor control in select patients with advanced HPSCC while preserving laryngeal function.
Factors Affecting Research Participation Among Specialist Dementia Nurses
Authors: Pepper Amy , Wolverson Emma , Harrison-Dening Karen 
Published: June 2024

Background
Research involvement and engagement is a vital aspect of nursing practice. However, research in dementia care remains limited compared to research focused on finding a cure, presenting a significant gap that specialist dementia nurses (Admiral Nurses) can help bridge by participating in research themselves and facilitating recruitment to research.

Objectives
This study aimed to assess the research involvement and support needs of Admiral Nurses and identify factors affecting their participation in research. This research is particularly timely as Dementia UK has launched its first research strategy, which necessitates strengthening research capacity within Admiral Nursing.

Methods
We used a mixed methods convergent parallel synthesis design, simultaneously collecting quantitative and qualitative data. An online survey was conducted in January 2023, targeting current Admiral Nurses across the United Kingdom. The survey included questions addressing demographics, research experience, goals, barriers, facilitators, and support needs. Data analysis involved descriptive statistics, frequencies, univariate analyses, and thematic analysis.

Results
A positive relationship was found between the highest level of academic achievement and current or previous research involvement, as well as interest in becoming involved in research in the future. Although most nurses recognized the importance of research, only half reported current or past research involvement, indicating a need for increased support. A lack of access and opportunities for peer discussion hindered engagement with research findings. Time constraints, lack of support, and low confidence were major barriers to research involvement. Support needs varied but included mentorship, coaching, and the potential for a community of practice for research.

Discussion
This survey of Admiral Nurses sheds light on their research involvement, support needs, and barriers to participation. Recognizing the significance of research while identifying challenges and support requirements is crucial for enhancing research capacity among these specialized nurses. This study contributes valuable insights into the world of specialist dementia nursing and lays the foundation for future strategies to increase research engagement in this field.