bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Subphenotypes of Staphylococcus aureus Bacteremia
Authors: Swets Maaike C , Bakk Zsuzsa , Westgeest Annette C , Berry Karla , Cooper George , Sim Wynne , Lee Rui Shian , Gan Tze Yi , Donlon William , Besu Antonia , Heppenstall Emily , Tysall Luke , Dewar Simon , de Boer Mark , Fowler Vance G , Dockrell David H , Thwaites Guy E , Pujol Miquel , Pallarès Natàlia , Tebé Cristian , Carratalà Jordi , Szubert Alexander , Groeneveld Geert H , Russell Clark D
Published: June 2024

Background

Staphylococcus aureus bacteremia (SAB) is a clinically heterogeneous disease. The ability to identify subgroups of patients with shared traits (subphenotypes) is an unmet need to allow patient stratification for clinical management and research. We aimed to test the hypothesis that clinically relevant subphenotypes can be reproducibly identified among patients with SAB.

Methods

We studied 3 cohorts of adults with monomicrobial SAB: a UK retrospective observational study (Edinburgh cohort, n = 458), the UK ARREST trial (n = 758), and the Spanish SAFO trial (n = 214). Latent class analysis was used to identify subphenotypes using routinely collected clinical data without considering outcomes. Mortality and microbiologic outcomes were then compared between subphenotypes.

Results

Included patients had predominantly methicillin-susceptible SAB (1366 of 1430, 95.5%). We identified 5 distinct, reproducible clinical subphenotypes: (A) SAB associated with older age and comorbidity, (B) nosocomial intravenous catheter-associated SAB in younger people without comorbidity, (C) community-acquired metastatic SAB, (D) SAB associated with chronic kidney disease, and (E) SAB associated with injection drug use. Survival and microbiologic outcomes differed between the subphenotypes. Mortality was highest in subphenotype A and lowest in subphenotypes B and E. Microbiologic outcomes were worse in subphenotype C. In a secondary analysis of the ARREST trial, adjunctive rifampicin was associated with increased mortality in subphenotype B and improved microbiologic outcomes in subphenotype C.

Conclusions

We have identified reproducible and clinically relevant subphenotypes within SAB and provide proof of principle of differential treatment effects. Through clinical trial enrichment and patient stratification, these subphenotypes could contribute to a personalized medicine approach to SAB.
Disturbance in the potential cardiovascular–bone–skeletal muscle axis and morbidity and mortality in patients undergoing haemodialysis: the Q-Cohort Study
Authors: Arase Hokuto , Yamada Shunsuke , Taniguchi Masatomo , Ooboshi Hiroaki , Tsuruya Kazuhiko , Kitazono Takanari , Nakano Toshiaki
Published: June 2024

Background

Disturbances in the cardiovascular system, bone and skeletal muscle are independent risk factors for death among patients receiving haemodialysis (HD). However, the combined impact of disorders of these three organs on morbidity and mortality is unclear in the HD population.

Methods

A total of 3031 Japanese patients on maintenance HD were prospectively followed. The outcomes were all-cause mortality, major adverse cardiovascular events (MACE) and bone fracture. Patients were divided into four groups (G1–G4) according to the baseline number of diseased organs represented as histories of cardiovascular disease and bone fractures and the presence of low skeletal muscle mass as follows: G1, no organ; G2, one organ; G3, two organs; G4, three organs. Multivariable-adjusted survival models were used to analyse associations between the number of diseased organs and outcomes.

Results

During a 4-year follow-up, 499 deaths, 540 MACE and 140 bone fractures occurred. In the Cox proportional hazards model, the risk for all-cause mortality was significantly higher in G2, G3 and G4 than in G1 as the reference {hazard ratio: G2, 2.16 [95% confidence interval (CI) 1.65–2.84], G3, 3.10 [95% CI 2.27–4.23] and G4, 3.11 [95% CI 1.89–5.14]}. Similarly, the risks for developing MACE and bone fractures were significantly elevated as the number of organ disorders increased.

Conclusions

Multiple disorders of the cardiovascular–bone–skeletal muscle axis are strong predictors of morbidity and mortality in patients undergoing HD.
Forward programming of human induced pluripotent stem cells via the ETS variant transcription factor 2: rapid, reproducible, and cost-effective generation of highly enriched, functional endothelial cells
Authors: Rieck Sarah , Sharma Kritika , Altringer Carlotta , Hesse Michael , Triantafyllou Christos , Zhang Yanhui , Busskamp Volker , Fleischmann Bernd K
Published: June 2024

Aims

Endothelial cell (EC) dysfunction plays a key role in the initiation and progression of cardiovascular disease. However, studying these disorders in ECs from patients is challenging; hence, the use of human induced pluripotent stem cells (hiPSCs) and their in vitro differentiation into ECs represents a very promising approach. Still, the generation of hiPSC-derived ECs (hECs) remains demanding as a cocktail of growth factors and an intermediate purification step are required for hEC enrichment. Therefore, we probed the utility of a forward programming approach using transgenic hiPSC lines.

Methods and results

We have used the transgenic hiPSC line PGP1 ETV2 isoform 2 to explore the in vitro differentiation of hECs via doxycycline-dependent induction of the ETS variant transcription factor 2 (ETV2) and compared these with a standard differentiation protocol for hECs using non-transgenic control hiPSCs. The transgenic hECs were highly enriched without an intermediate purification step and expressed—as non-transgenic hECs and human umbilical vein endothelial cells—characteristic EC markers. The viability and yield of transgenic hECs were strongly improved by applying EC growth medium during differentiation. This protocol was successfully applied in two more transgenic hiPSC lines yielding reproducible results with low line-to-line variability. Transgenic hECs displayed typical functional properties, such as tube formation and LDL uptake, and a more mature phenotype than non-transgenic hECs. Transgenic hiPSCs preferentially differentiated into the arterial lineage; this was further enhanced by adding a high concentration of vascular endothelial growth factor to the medium. We also demonstrate that complexing lentivirus with magnetic nanoparticles and application of a magnetic field enables efficient transduction of transgenic hECs.

Conclusion

We have established a highly efficient, cost-effective, and reproducible differentiation protocol for the generation of functional hECs via forward programming. The transgenic hECs can be genetically modified and are a powerful tool for disease modelling, tissue engineering, and translational purposes.
Cognitive functions and the brain-derived neurotrophic factor in patients with mild autonomous cortisol secretion
Authors: Barlas Tugba , Aksu Muhammed Hakan , Cerit Ethem Turgay , Yalcin Mehmet Muhittin , Akturk Mujde , Balos Toruner Fusun , Karakoc Mehmet Ayhan , Eroglu Altinova Alev
Published: June 2024

Context

The impact of abnormal cortisol secretion on cognitive functions in patients with mild autonomous cortisol secretion (MACS) remains uncertain.

Objective

To assess cognitive functions, determine serum brain-derived neurotrophic factor (BDNF) concentration in patients with MACS, and investigate the association between cognitive subdomains and BDNF.

Methods

We prospectively recruited 84 participants—28 patients with MACS, 28 patients with nonfunctional adrenal adenoma (NFAA), and 28 control subjects matched for age, gender, body mass index (BMI), visceral adiposity, and educational level. The serum BDNF concentration of participants was measured. The Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition–focused interviews and Montreal Cognitive Assessments (MoCA) were carried out by an experienced psychiatrist.

Results

Patients with MACS had a higher serum BDNF concentration than the NFAA (P = .001), while that of patients with NFAA was lower than the controls (P = .044). Linear regression analysis revealed BMI and morning cortisol after overnight 1 mg dexamethasone (DST) were mostly associated with BDNF (P < .05). No significant difference was found in MoCA scores between MACS and NFAA groups (P = .967), whereas those were lower than the control group (P = .004). When the cognitive subdomains were examined separately, MACS group performed higher memory score than NFAA (P = .045), but lower language scores than both the NFAA (P = .024) and control groups (P < .001). In the whole group, BDNF concentration was positively correlated with memory score (r = 0.337, P = .002), whereas DST was negatively correlated with language score (r = −0.355, P = .008).

Conclusion

Low-grade hypercortisolism is associated with elevated BDNF concentrations, which may be a protective factor for memory function in patients with MACS relative to those with NFAA.
Understanding the incidence of atrial fibrillation and stroke in hypertrophic cardiomyopathy patients: insights from Danish nationwide registries
Authors: Zörner Christopher R , Schjerning Anne-Marie , Jensen Morten Kvistholm , Christensen Alex Hørby , Tfelt-Hansen Jacob , Tønnesen Jacob , Riis-Vestergaard Lise Da , Middelfart Charlotte , Rasmussen Peter Vibe , Gislason Gunnar , Hansen Morten Lock
Published: June 2024

Aims

The treatment of atrial fibrillation (AF) in hypertrophic cardiomyopathy (HCM) can be challenging since AF aggravates symptoms and increases the risk of stroke. Which factors contribute to the development of AF and stroke in HCM remains unknown. The aim of this study was to determine the incidence of AF and stroke in HCM patients and identify the risk factors.

Methods and results

Using Danish national registries, all HCM patients from 2005 to 2018 were included. The association between HCM, incident AF, and stroke was investigated using multivariable Cox proportional hazards analysis. Cumulative incidences were calculated using the Aalen–Johansen estimator. Among the 3367 patients without prevalent AF, 24% reached the endpoint of incident AF with death as a competing risk. Median follow-up time was 4 years. Atrial fibrillation incidence was equal between sexes and increased for patients with ischaemic heart disease [IHD; hazard ratio (HR) 1.33, 95% confidence interval (CI) 1.08–1.63], hypertension (HT) (HR 1.36, 95% CI 1.14–1.67), and obstructive HCM (HR 1.27, 95% CI 1.05–1.52). Seven per cent developed stroke, with no difference detected stratifying for the presence of AF. Sub-analysis revealed that when AF was treated with oral anticoagulants (OACs), stroke was less likely (HR 0.4, 95% CI 0.18–0.86, P = 0.02). However, 34% of patients were not receiving adequate anticoagulation following AF diagnosis.

Conclusion

Obstructive HCM, HT, and IHD were associated with increased risk of AF. Prevalent AF alone was not predictive of stroke; however, AF patients treated with OAC were significantly less likely to develop stroke, suggesting that this development is driven by the protective effect of OAC. Despite this, 34% of patients did not receive OAC.
Effectiveness of physical activity interventions on undergraduate students’ mental health: systematic review and meta-analysis
Authors: Huang Kevin , Beckman Emma M , Ng Norman , Dingle Genevieve A , Han Rong , James Kari , Winkler Elisabeth , Stylianou Michalis , Gomersall Sjaan R
Published: June 2024

This systematic review and meta-analysis assessed the effectiveness of physical activity interventions on undergraduate students’ mental health. Seven databases were searched and a total of 59 studies were included. Studies with a comparable control group were meta-analysed, and remaining studies were narratively synthesized. The included studies scored very low GRADE and had a high risk of bias. Meta-analyses indicated physical activity interventions are effective in reducing symptoms of anxiety (n = 20, standardized mean difference (SMD) = −0.88, 95% CI [−1.23, −0.52]), depression (n = 14, SMD = −0.73, 95% CI [−1.00, −0.47]) and stress (n = 10, SMD = −0.61, 95% CI [−0.94, −0.28]); however, there was considerable heterogeneity (anxiety, I2 = 90.29%; depression I2 = 49.66%; stress I2 = 86.97%). The narrative synthesis had mixed findings. Only five studies reported being informed by a behavioural change theory and only 30 reported intervention fidelity. Our review provides evidence supporting the potential of physical activity interventions in enhancing the mental health of undergraduate students. More robust intervention design and implementation are required to better understand the effectiveness of PA interventions on mental health outcomes.
CsPHRs-CsJAZ3 incorporates phosphate signaling and jasmonate pathway to regulate catechin biosynthesis in Camellia sinensis
Authors: Li Linying , Zhang Xueying , Li Da , Su Hui , He Yuqing , Xu Zelong , Zhao Yao , Hong Yiyi , Li Qingsheng , Xu Ping , Hong Gaojie
Published: June 2024

Catechins constitute abundant metabolites in tea and have potential health benefits and high economic value. Intensive study has shown that the biosynthesis of tea catechins is regulated by environmental factors and hormonal signals. However, little is known about the coordination of phosphate (Pi) signaling and the jasmonic acid (JA) pathway on biosynthesis of tea catechins. We found that Pi deficiency caused changes in the content of catechins and modulated the expression levels of genes involved in catechin biosynthesis. Herein, we identified two transcription factors of phosphate signaling in tea, named CsPHR1 and CsPHR2, respectively. Both regulated catechin biosynthesis by activating the transcription of CsANR1 and CsMYB5c. We further demonstrated CsSPX1, a Pi pathway repressor, suppressing the activation by CsPHR1/2 of CsANR1 and CsMYB5c. JA, one of the endogenous plant hormones, has been reported to be involved in the regulation of secondary metabolism. Our work demonstrated that the JA signaling repressor CsJAZ3 negatively regulated catechin biosynthesis via physical interaction with CsPHR1 and CsPHR2. Thus, the CsPHRs–CsJAZ3 module bridges the nutrition and hormone signals, contributing to targeted cultivation of high-quality tea cultivars with high fertilizer efficiency.
Evaluation of phenotypic and genotypic methods for the identification and characterization of bacterial isolates recovered from catheter-associated urinary tract infections
Authors: Varney Adam M , Mannix-Fisher Eden , Thomas Jonathan C , McLean Samantha
Published: June 2024

Aims

Urinary tract infections are the most common hospital-acquired infection, 80% of which are associated with catheterization. Diagnostic methods may influence the reported identities of these pathogens, and phenotypic testing under laboratory conditions may not reflect infection phenotypes. This study aimed to evaluate the efficacy of diagnostic methods and whether medium composition alters phenotypes by characterizing catheter-associated urinary tract infection isolates from a UK hospital.

Methods and results

We compared five bacterial identification methods, including biochemical testing, matrix-assisted laser desorption/ionization biotyping, and genome sequencing, finding differences in genus- or species-level identifications. Antibiotic susceptibility comparisons between phenotypic assays and genomic predictions showed high agreement only in multidrug-resistant strains. To determine whether growth rate and biofilm formation were affected by medium composition, strains were grown in both planktonic and biofilm states. Low planktonic growth and significant biofilm formation were observed in artificial urine compared to rich laboratory media, underscoring the importance of assay design.

Conclusions

This study highlights the risks of relying on a single diagnostic method for species identification, advocating for whole-genome sequencing for accuracy. It emphasizes the continued importance of phenotypic methods in understanding antibiotic resistance in clinical settings and the need for characterization conditions that mirror those encountered by pathogens in the body.
Using patient portals for large-scale recruitment of individuals underrepresented in biomedical research: an evaluation of engagement patterns throughout the patient portal recruitment process at a single site within the All of Us Research Program
Authors: Beaton Maura , Jiang Xinzhuo , Minto Elise , Lau Chun Yee , Turner Lennon , Hripcsak George , Chaudhari Kanchan , Natarajan Karthik
Published: June 2024

Objective

To evaluate the use of patient portal messaging to recruit individuals historically underrepresented in biomedical research (UBR) to the All of Us Research Program (AoURP) at a single recruitment site.

Materials and Methods

Patient portal-based recruitment was implemented at Columbia University Irving Medical Center. Patient engagement was assessed using patient’s electronic health record (EHR) at four recruitment stages: Consenting to be contacted, opening messages, responding to messages, and showing interest in participating. Demographic and socioeconomic data were also collected from patient’s EHR and univariate logistic regression analyses were conducted to assess patient engagement.

Results

Between October 2022 and November 2023, a total of 59 592 patients received patient portal messages inviting them to join the AoURP. Among them, 24 445 (41.0%) opened the message, 8983 (15.1%) responded, and 3765 (6.3%) showed interest in joining the program. Though we were unable to link enrollment data with EHR data, we estimate about 2% of patients contacted ultimately enrolled in the AoURP. Patients from underrepresented race and ethnicity communities had lower odds of consenting to be contacted and opening messages, but higher odds of showing interest after responding.

Discussion

Patient portal messaging provided both patients and recruitment staff with a more efficient approach to outreach, but patterns of engagement varied across UBR groups.

Conclusion

Patient portal-based recruitment enables researchers to contact a substantial number of participants from diverse communities. However, more effort is needed to improve engagement from underrepresented racial and ethnic groups at the early stages of the recruitment process.
Disambiguation of acronyms in clinical narratives with large language models
Authors: Kugic Amila , Schulz Stefan , Kreuzthaler Markus
Published: June 2024

Objective

To assess the performance of large language models (LLMs) for zero-shot disambiguation of acronyms in clinical narratives.

Materials and Methods

Clinical narratives in English, German, and Portuguese were applied for testing the performance of four LLMs: GPT-3.5, GPT-4, Llama-2-7b-chat, and Llama-2-70b-chat. For English, the anonymized Clinical Abbreviation Sense Inventory (CASI, University of Minnesota) was used. For German and Portuguese, at least 500 text spans were processed. The output of LLM models, prompted with contextual information, was analyzed to compare their acronym disambiguation capability, grouped by document-level metadata, the source language, and the LLM.

Results

On CASI, GPT-3.5 achieved 0.91 in accuracy. GPT-4 outperformed GPT-3.5 across all datasets, reaching 0.98 in accuracy for CASI, 0.86 and 0.65 for two German datasets, and 0.88 for Portuguese. Llama models only reached 0.73 for CASI and failed severely for German and Portuguese. Across LLMs, performance decreased from English to German and Portuguese processing languages. There was no evidence that additional document-level metadata had a significant effect.

Conclusion

For English clinical narratives, acronym resolution by GPT-4 can be recommended to improve readability of clinical text by patients and professionals. For German and Portuguese, better models are needed. Llama models, which are particularly interesting for processing sensitive content on premise, cannot yet be recommended for acronym resolution.
All of whom? Limitations encountered using All of Us Researcher Workbench in a Primary Care residents secondary data analysis research training block
Authors: LaPolla Fred Willie Zametkin , Barber Grossi Marco , Chen Sharon , Guo Tai Wei , Havranek Kathryn , Jebb Olivia , Nguyen Minh Thu , Panganamamula Sneha , Smith Noah , Sundaresh Shree , Yu Jonathan , Mayer Gabrielle
Published: June 2024

Objectives

The goal of this case report is to detail experiences and challenges experienced in the training of Primary Care residents in secondary analysis using All of Us Researcher Workbench. At our large, urban safety net hospital, Primary Care/Internal Medicine residents in their third year undergo a research intensive block, the Research Practicum, where they work as a team to conduct secondary data analysis on a dataset with faculty facilitation. In 2023, this research block focused on use of the All of Us Researcher Workbench for secondary data analysis.

Materials and Methods

Two groups of 5 residents underwent training to access the All of Us Researcher Workbench, and each group explored available data with a faculty facilitator and generated original research questions. Two blocks of residents successfully completed their research blocks and created original presentations on “social isolation and A1C” levels and “medical discrimination and diabetes management.”

Results

Departmental faculty were satisfied with the depth of learning and data exploration. In focus groups, some residents noted that for those without interest in performing research, the activity felt extraneous to their career goals, while others were glad for the opportunity to publish. In both blocks, residents highlighted dissatisfaction with the degree to which the All of Us Researcher Workbench was representative of patients they encounter in a large safety net hospital.

Discussion

Using the All of Us Researcher Workbench provided residents with an opportunity to explore novel questions in a massive data source. Many residents however noted that because the population described in the All of Us Researcher Workbench appeared to be more highly educated and less racially diverse than patients they encounter in their practice, research may be hard to generalize in a community health context. Additionally, given that the data required knowledge of 1 of 2 code-based data analysis languages (R or Python) and work within an idiosyncratic coding environment, residents were heavily reliant on a faculty facilitator to assist with analysis.

Conclusion

Using the All of Us Researcher Workbench for research training allowed residents to explore novel questions and gain first-hand exposure to opportunities and challenges in secondary data analysis.
Application of functional genomics for domestication of novel non-model microbes
Authors: Bales Margaret K , Vergara Michael Melesse , Eckert Carrie A
Published: June 2024

With the expansion of domesticated microbes producing biomaterials and chemicals to support a growing circular bioeconomy, the variety of waste and sustainable substrates that can support microbial growth and production will also continue to expand. The diversity of these microbes also requires a range of compatible genetic tools to engineer improved robustness and economic viability. As we still do not fully understand the function of many genes in even highly studied model microbes, engineering improved microbial performance requires introducing genome-scale genetic modifications followed by screening or selecting mutants that enhance growth under prohibitive conditions encountered during production. These approaches include adaptive laboratory evolution, random or directed mutagenesis, transposon-mediated gene disruption, or CRISPR interference (CRISPRi). Although any of these approaches may be applicable for identifying engineering targets, here we focus on using CRISPRi to reduce the time required to engineer more robust microbes for industrial applications.

One-Sentence Summary

The development of genome scale CRISPR-based libraries in new microbes enables discovery of genetic factors linked to desired traits for engineering more robust microbial systems.
Vanin-2 is expressed in peripheral blood T cells and upregulated in patients with systemic lupus erythematosus
Authors: Liu Chen , Alimu Xiayidan , Zeng Xingyue , Bahabayi Ayibaota , Gao Yiming , Hu Yuzhe , Chen Yang , Zhao Junjie , Lian Xinran , Zheng Mohan , Liu Tianci , Wang Pingzhang
Published: June 2024

Members of the vanin gene family include VNN1, VNN2, and VNN3 in humans. Although the functions of vanins have been widely examined in myeloid cells, their expression and functions have not been clarified in T lymphocytes. This study aimed to elucidate the significance of Vanin-2 (VNN2) on human peripheral blood T lymphocytes and study its expression in systemic lupus erythematosus (SLE). The differential expression of Vanins was analyzed by bioinformatics. VNN2 expressions in peripheral blood T-cell subsets were analyzed by single-cell RNA sequencing data and flow cytometry. Changes of VNN2 expression before and after T-cell activation were further clarified by western blot. The function of VNN2+ cells was studied by granzyme B (GZMB) and perforin detection. Changes in VNN2+ proportions in T-cell subsets of patients with SLE were further analyzed. In the present study, only VNN2 among vanins showed distinguishable expression in T cells. VNN2+ percentages were higher in CD8+ T cells those in CD4+ T cells. VNN2+ T cells were with a higher memory T-cell composition. VNN2 expression was significantly increased after T-cell stimulation. VNN2+ T cells had higher levels of GZMB and perforin secretion than VNN2− T cells. Clinically, VNN2+ percentages in T cells of patients with SLE were upregulated. Together, these data suggested that VNN2 is expressed in peripheral blood T cells characterized more GZMB and perforin secretion, and increased VNN2+ T cells in patients with SLE could reflect altered T-cell functions in vivo.
Incident diabetes among older Asian, Native Hawaiian, and Pacific Islander women with breast cancer
Authors: Koric Alzina , Chang Chun-Pin Esther , Lee Yuan-Chin Amy , Wei Mei , Lee Catherine J , Tao Randa , Wang Jing , Tay Djin , Hashibe Mia
Published: June 2024

Background

The risk of diabetes among Asian, Native Hawaiian, and Pacific Islander (ANHPI) women after breast cancer is unclear. This study estimated the risk of incident type II diabetes in older ANHPI and older non-Hispanic White (NHW) women with breast cancer from the US National Cancer Institute’s Surveillance, Epidemiology, and End Results (SEER) Medicare linked claims.

Methods

A matched cohort of 7122 older ANHPI and 21 365 older NHW women with breast cancer were identified from SEER-Medicare between 2000 and 2017. To assess the risk of incident type II diabetes after breast cancer, hazard ratios (HRs) and 95% confidence intervals (95% CI) were estimated using the Cox proportional-hazards regression model.

Results

During the mean 8 years of follow-up, 9.3% of older women with breast cancer developed incident type II diabetes. In comparison with older NHW women, older ANHPI women without a known history of diabetes had an elevated risk of diabetes after breast cancer, with strong associations observed for Pacific Islander (HR = 3.09, 95% CI = 1.43 to 6.67), Vietnamese (HR = 2.12, 95% CI = 1.33 to 2.36), and Filipino (HR = 2.02, 95% CI = 1.57 to 2.59) women with breast cancer, adjusting for potential confounders. Among ANHPI women with breast cancer, more baseline comorbidities and obesity were risk factors for developing incident type II diabetes.

Conclusion

ANHPI women diagnosed with breast cancer had an elevated risk of type II diabetes compared with older NHW women with breast cancer. Routine monitoring and management of diabetes are warranted in older ANHPI women with breast cancer.
Fragments and semiophores: on the educational values of monuments as ephemeral heritage
Authors: Mendel Maria
Published: June 2024

Based on several cases, this article develops a thought inspired by the Journal of Philosophy of Education’s special issue on the Educational Value of Monuments (55.3). The article is a reflection about the locations which make statues able to be transformed materially and semiotically, and which provoke discussion about what is to be learnt by understanding the monument as a fragment and semiophore. I argue that the monument—located in a specific place which makes its contextual meaning—represents fragments, in Latin fractures or cracks, as an expression of the violence inflicted on an imaginary whole. Defining and accepting a monument as a fragment allows us to understand each change that may happen to it—including removal or relocation—as an incentive to learn about the meanings of new wholes and to consciously respond to them. On the one hand, this can effectively stop mimetic pressures to reproduce aggression towards monuments. On the other, it can create a ground for shaping an ethical attitude of co-responsibility for a common world that is not exclusively human. The strictly educational sense of the proposed redefinition of the monument would be to radicalize sensitivity to its inherent feature, which is its fragmentary nature, resulting in the fragility of the heritage it co-creates in the space of commonality. In the proposed understanding of the monument, apart from the emphasis on significant fragmentation, an important role is played by the decisive abandonment of the anthropocentric perspective. In the new perspective of the common world, the monument becomes an ephemeral heritage, and its most current educational value seems to lie there.
The devil, the detail, and the data
Authors: Garrett Andrew D
Published: June 2024

Digitalization has created a world awash with data from sources almost unimaginable 50 years ago. Using recent examples from climate change, the COVID-19 pandemic, official statistics, and artificial intelligence, the address will illustrate the importance of understanding the data generating process and the data about the data. It will be argued that statisticians and other data professionals have an increasingly important role to play as advocates for well-defined and well documented data generation—particularly as the distinction between inputs and outputs becomes blurred. For the Society, this does not represent a shift away from statistics, rather it re-establishes the link to our roots.
Measuring Expenditure with a Mobile App: Do Probability-Based and Nonprobability Panels Differ?
Authors: Jäckle Annette , Cornesse Carina , Wenz Alexander , Couper Mick P
Published: June 2024

In this case study, we examine a novel aspect of data collected in a typical probability and a typical nonprobability panel: mobile app data. The data were collected in Great Britain in 2018, using the Innovation Panel of the UK Household Longitudinal Study and the Lightspeed online access panel. Respondents in each panel were invited to participate in a month-long study, reporting all their daily expenditures in the app. In line with most of the research on nonprobability and probability-based panel data, our results indicate differences in the data gathered from these data sources. For example, more female, middle-aged, and highly educated people with higher digital skills and a greater interest in their finances participated in the nonprobability app study. Our findings also show that resulting differences in the app spending data are difficult to eliminate by weighting. The only data quality aspect for which we do not find evidence of differences between the nonprobability and probability-based panel is behavior in using the spending app. This finding is contrary to the argument that nonprobability online panel participants try to maximize their monetary incentive at the expense of data quality. However, this finding is in line with some of the scarce existing literature on response behavior in surveys, which is inconclusive regarding the question of whether nonprobability online panel participants answer questions less conscientiously than probability-based panel respondents. Since the two panels in our case study differ in more aspects than the sample selection procedure, more research in different contexts is necessary to establish generalizability and causality.
Integrated biomarker profiling for enhanced heart failure management: a comprehensive study on the application of chemiluminescence detection of GDF-15 and multi-index models
Authors: Zhang Ju , Zhang Jiajia , Huang Chengyi , Wu Ting , Jin Peipei
Published: June 2024

Background

Growth differentiation factor 15 (GDF-15) holds promise as a novel marker for heart failure. However, current detection methods fall short of meeting essential clinical requirements.

Objectives

The aim of this investigation was to assess the clinical significance of serum GDF-15 detection through the chemiluminescence method and to enhance its clinical application for predicting and evaluating heart failure in patients.

Methods

A total of 122 patients were included in the study. Serum GDF-15 levels were assessed using the chemiluminescence method and compared with results for NT-proBNP, N-terminal pro-brain natriuretic peptide (NT-proBNP), growth stimulation expressed gene 2 (ST2), high-sensitivity C-reactive protein (hs-CRP), and left ventricular ejection fraction (LVEF). Additionally, we conducted an analysis to evaluate the correlation between these indicators and heart failure events.

Results

LVEF, ST2, NT-proBNP, and GDF-15 exhibited significant associations with heart failure. In the multivariate proportional hazard analysis, subsequent to adjusting for the effects of other markers, however, only LVEF and GDF-15 retained their associations with heart failure events. Notably, GDF-15 emerged as the exclusive marker suitable for diagnosing heart failure with preserved ejection fraction.

Conclusion

The chemiluminescence method proved efficient in the rapid and sensitive detection of GDF-15 in patients with heart failure. Additionally, GDF-15 combined with other markers created a robust multi-index model. This model is valuable for heart failure diagnosis, treatment, and monitoring, with broad clinical applicability.
Efficacy of Polyunsaturated Fatty Acids as a Treatment for Post-traumatic Stress Disorder: A Systematic Review
Authors: Capple Kathryn A , Kostas-Polston Elizabeth A , Engler Mary B , Lai Choang , Froelicher Erika Sivarajan
Published: June 2024

Introduction

Post-traumatic stress disorder (PTSD) is a prevalent health condition among members of the military. Although the efficacy of pharmacological and psychiatric interventions for PTSD has been well studied, there are limited data on the effects of omega-3 (n-3) polyunsaturated fatty acid (PUFA) interventions on PTSD. The use of PUFAs shows promise because of their neuroprotective effects. Thus, this systematic review will synthesize the current state of the evidence regarding the effectiveness of PUFA treatment for PTSD.

Materials and Methods

Using the PubMed, PsychINFO, Embase, and CINAHL databases, a search of the literature was conducted using the search terms “posttraumatic-stress-disorder, combat disorders, trauma-related-stress-disorder, omega-3, fatty acid, and polyunsaturated fatty acids” to identify articles published from January 1, 2008, to January 1, 2024, that focused on PUFA interventions for PTSD. A total of 281 articles were identified. Following exclusions and quality assessments using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) criteria proposed by Cochrane, 6 randomized controlled trials (RCTs) and preclinical studies were chosen for inclusion, and data were then extracted into a data matrix for final synthesis and analysis.

Results

The RCTs (n = 3) showed no significant effect of PUFAs in the prevention of PTSD symptom onset. Among preclinical studies (n = 3), PUFAs resulted in a significant decrease in anxiety-like behavior and fear memory and an increase in spatial learning and memory. The quality of evidence among the 6 RCTs and preclinical studies using the Cochrane GRADE criteria ranged from low to high.

Conclusions

The results from this systematic review suggest that more evidence is needed before making any recommendations for the clinical use of dietary PUFAs in the management of PTSD symptoms.
Factors influencing mortality in COVID-19-associated mucormycosis: The international ID-IRI study
Authors: Sahin Meyha , Yilmaz Mesut , Mert Ali , Naghili Behrouz , Ravanbakhsh Fatemeh , Varshochi Mojtaba , Darazam Ilad Alavi , Ebrahimi Mohammad Javad , Moafi Maral , Tehrani Hamed Azhdari , Mahboob Amjad , Rashid Naveed , Khan Ejaz Ahmed , Hakamifard Atousa , Eser-Karlidag Gülden , Babamahmoodi Abdolreza , El-Kholy Amani , Mosawi Sayed Hussain , Albayrak Ayşe , Al Ramahi Jamal Wadi , Addepalli Syam Kumar , Özer Balin Şafak , Khan Asfandiyar , Pandya Nirav , Gurbuz Esra , Sincan Gülden , Azami Hadia , Dumlu Rıdvan , Khedr Reham , Ripon Rezaul Karim , Alkan Sevil , Kose Şükran , Ceylan Bahadır , Erdem Hakan
Published: June 2024

The emergence of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), triggered a global pandemic. Concurrently, reports of mucormycosis cases surged, particularly during the second wave in India. This study aims to investigate mortality factors in COVID-19-associated mucormycosis (CAM) cases, exploring clinical, demographic, and therapeutic variables across mostly Asian and partly African countries. A retrospective, cross-sectional analysis of CAM patients from 22 medical centers across eight countries was conducted, focusing on the first 3 months post-COVID-19 diagnosis. Data collected through the ID-IRI included demographics, comorbidities, treatments, and outcomes. A total of 162 CAM patients were included. The mean age was 54.29 ± 13.04 years, with 54% male. Diabetes mellitus (85%) was prevalent, and 91% had rhino-orbital-cerebral mucormycosis. Surgical debridement was performed in 84% of the cases. Mortality was 39%, with advanced age (hazard ratio [HR] = 1.06, [P < .001]), rituximab use (HR = 21.2, P = .05), and diabetic ketoacidosis (HR = 3.58, P = .009) identified as risk factors. The mortality risk increases by approximately 5.6% for each additional year of age. Surgical debridement based on organ involvement correlated with higher survival (HR = 8.81, P < .001). The utilization of rituximab and diabetic ketoacidosis, along with advancing age, has been associated with an increased risk of mortality in CAM patients. A combination of antifungal treatment and surgical intervention has demonstrated a substantial improvement in survival outcomes.
Tidal features and disc thicknesses of edge-on galaxies in the SDSS Stripe 82
Authors: Skryabina Maria N , Adams Kyle R , Mosenkov Aleksandr V
Published: June 2024

We examine deep optical images of edge-on galaxies selected from the Sloan Digital Sky Survey (SDSS) Stripe 82. The entire sample consists of over 800 genuine edge-on galaxies with spectroscopic redshifts out to $z\sim 0.2$. To discern the faintest details around the galaxies, we use three different data sources with a photometric depth of down to 30 mag arcsec$^{-2}$ in the r band: SDSS Stripe 82, Hyper Suprime-Cam Strategic Program, and DESI Legacy Imaging Surveys. Our analysis of the deep images reveals a variety of low surface brightness features. 49 galaxies exhibit prominent tidal structures, including tidal tails, stellar streams, bridges, and diffuse shells. Additionally, 56 galaxies demonstrate peculiar structural features such as lopsided discs, faint warps, and dim polar rings. Overall, we detect low surface brightness structures in 94 galaxies out of 838, accounting for 11  per cent of the sample. Notably, the fraction of tidal structures is only 5.8  per cent, which is significantly lower than that obtained in modern cosmological simulations and observations. Previous studies have shown that strongly interacting galaxies have stellar discs about 1.5–2 times thicker than those without apparent interactions. In an analysis where tidal features are carefully masked for precise disc axis ratio measurements, we show that discs of galaxies with tidal features are 1.33 times thicker, on average, than control galaxies that do not have visible tidal features. Furthermore, we find that edge-on galaxies with tidal structures tend to have a higher fraction of oval and boxy discs than galaxies without tidal features.
Inner walls or vortices? Crescent-shaped asymmetries in ALMA observations of protoplanetary discs
Authors: Ribas Á , Clarke Cathie J , Zagaria Francesco
Published: June 2024

Crescent-shaped asymmetries are common in millimetre observations of protoplanetary discs and are usually attributed to vortices or dust overdensities. However, they often appear on a single side of the major axis and roughly symmetric about the minor axis, suggesting a geometric origin. In this work, we interpret such asymmetries as emission from the exposed inner cavity walls of inclined discs and use them to characterize their vertical extent. Here we focus on the discs around CIDA 9 and RY Tau, first modelling their observations in visibility space with a simple geometric prescription for the walls, and then exploring more detailed radiative transfer models. Accounting for the wall emission yields significantly better residuals than purely axisymmetric models, and we estimate the dust scale height of these systems to be 0.4 au at 37 au for CIDA 9 and 0.2 au at 12 au for RY Tau. Finally, we identify crescent-shaped asymmetries in twelve discs, nine of which have constraints on their orientation – in all cases, the asymmetry appears on the far-side of the disc, lending support to the hypothesis that they are due to their inner rims. Modelling this effect in larger samples of discs will help to build a statistical view of their vertical structure.
The effect of interstellar medium on LVK’s black holes
Authors: Ghodla Sohan
Published: June 2024

Gravitational radiation alone is not efficient in hardening the orbit of a wide binary black hole (BBH). By employing a toy model for the interstellar medium (ISM) surrounding BBHs, here we discuss the effect of this baryonic medium on BBH dynamics. Depending on the BBH’s mass, we show that a binary surrounded by an isotropic cold neutral medium (i.e. an asymptotic temperature $T_{\infty } \approx 100$ K) with a time-averaged particle density of $\langle n_\mathrm{ H} \rangle = \mathcal {O}(1)$ cm$^{-3}$ can play a significant role in hardening the binary orbit over a $\mathcal {O}(10^9)$ yr time-scale. Additionally, this causes the black hole’s mass to grow at a rate ${\propto} m^2$. We thus discuss the impact of the ISM on the LIGO-Virgo-KAGRA (LVK) observables and quantify the properties of the ISM under which the latter could act as an additional important pathway for driving a subset of LVK’s BBH mergers.
Very metal-poor stars I: a catalogue derived from LAMOST DR9
Authors: Hou Xiaokun , Zhao Gang , Li Haining
Published: June 2024

In this paper, a semisupervised machining learning technique had been utilized to analyse low-resolution stellar spectra from Large sky Area Multi-Object fiber Spectroscopic Telescope (LAMOST) Data Release 9 (DR9). We identified approximately 111 000 potential very metal-poor stars. Estimation of their stellar parameters ($T_{\rm eff}$, ${\rm log}\, \rm {g}$, [Fe/H]) indicate that over 99 per cent are metal-poor ([Fe/H] < −1.0), comprising 32 631 very metal-poor ([Fe/H] < −2.0), 702 extremely metal-poor ([Fe/H] < −3.0) and 30 ultra metal-poor ([Fe/H] < −4.0) stars. Based on kinematic characteristics, stars were categorized into thick disc-like, thin disc-like, and halo-like groups. We analysed their metallicity distributions (MDs) with respect to vertical height ($|Z|$) and orbital eccentricity (e). Thick disc-like stars in current sample show a clear trend of decreasing metallicty with increasing $|Z|$ or e for the ranges −3.0 $\lt $ [Fe/H] $\lt $ −1.2 and $|Z|$$\lt $ 3 kpc. Conversely, thin disc-like stars in current sample exhibit a slight increase in the fraction of more metal-poor stars with $|Z|$ for the ranges −3.0 $\lt $ [Fe/H] $\lt $ −1.2 and $|Z|$$\lt$ 1 kpc, but no obvious correlation with e. Additionally, we confirmed the presence of two prominent substructures among halo-like stars. One exhibits a high eccentricity ($e\ \gt\ 0.8$) orbit and higher metallicity, while the other follows a retrograde orbit with moderate eccentricity ($e\sim 0.6$) and lower metallicity. We believe they are related to the merger events known as Gaia Sausage and Sequoia, respectively. Furthermore, our observations indicate that the Sequoia has lower eccentricity and metallicity compared to the Gaia Sausage.
Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning
Authors: Sharma Sudip , Kumar Sudhir
Published: June 2024

Phylogenomic analyses of long sequences, consisting of many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred relationships can be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.
Zika virus non-coding RNAs antagonize antiviral responses by PKR-mediated translational arrest
Authors: Pallarés Horacio M , González López Ledesma María Mora , Oviedo-Rouco Santiago , Castellano Luciana A , Costa Navarro Guadalupe S , Fernández-Alvarez Ana J , D’Andreiz María Josefina , Aldas-Bulos Victor Daniel , Alvarez Diego E , Bazzini Ariel A , Gamarnik Andrea V
Published: June 2024

Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that causes severe outbreaks in human populations. ZIKV infection leads to the accumulation of small non-coding viral RNAs (known as sfRNAs) that are crucial for evasion of antiviral responses and for viral pathogenesis. However, the mechanistic understanding of how sfRNAs function remains incomplete. Here, we use recombinant ZIKVs and ribosome profiling of infected human cells to show that sfRNAs block translation of antiviral genes. Mechanistically, we demonstrate that specific RNA structures present in sfRNAs trigger PKR activation, which instead of limiting viral replication, enhances viral particle production. Although ZIKV infection induces mRNA expression of antiviral genes, translation efficiency of type I interferon and interferon stimulated genes were significantly downregulated by PKR activation. Our results reveal a novel viral adaptation mechanism mediated by sfRNAs, where ZIKV increases its fitness by repurposing the antiviral role of PKR into a proviral factor.