bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building a Collaborative Environmental Governance for Sustainable Management of Volcanic Lake at The Dieng Plateau-Central Java Indonesia
Authors: Wahyono Ari , Yoga Gunawan Pratama , Subehi Luki , Rustini Hadiid Agita , Fakhrudin Muh , Apip Apip , Ridwansyah Iwan , Samir Octavianto 
Published: February 2025

Abstract
The Dieng Plateau in Central Java, Indonesia, is home to unique volcanic lakes with significant ecological and economic value. Effective environmental governance is critical for the sustainable management of volcanic lakes, particularly in regions prone to natural hazards like the Dieng Plateau. Several hazards have been reported, including phreatic explosions. This paper explores a multidisciplinary approach to environmental governance, integrating ecological sciences and social sciences, to ensure the sustainable management of these lakes. We investigated the necessity and challenges of establishing collaborative environmental governance mechanisms to address the complex issues surrounding Lake Menjer as volcanic lake management in the region. Based on an investigation of water quality and biodiversity, all nutrient inputs from anthropogenic activities promoted this lake’s degradation. The environmental degradation of the lake showed the absence of management institutions. Drawing upon multidisciplinary research and stakeholder engagement, this study aims to: 1) to analyze the trend of environmental degradation in Lake Menjer in terms of eutrophication; and 2) to evaluate the current governance structures and propose strategies for enhancing collaboration among the various stakeholders. We analyzed existing policies, institutional frameworks, and community participation models to identify gaps and opportunities for improving environmental governance practices. We also advocate for a holistic and sustainable approach to volcanic lake management that balances ecological conservation and socio-economic development in Lake Menjer by fostering collaboration and co-management approaches. Key recommendations include fostering inclusive decision-making processes and promoting knowledge exchange and capacity-building initiatives with collaborative environmental governance approaches.
Taylor’s Critique of Secularism from a Naturalist Perspective
Authors: Nicholson Hugh 
Published: February 2025

ABSTRACT
This article argues that Charles Taylor’s apologetic for religious belief in A Secular Age—in particular, his argument for the equivalence of the closed and open interpretations of the “immanent frame” of nature—is persuasive to the extent that the reader shares Taylor’s conviction that human-level structures of meaning are not subject to the standards of truth and verification operative in the natural sciences. Absent this assumption, an acceptance of a self-sufficient immanent order, although it does not lead inexorably to atheism, nevertheless contains an inherent bias away from the metaphysical claims of traditional religions. The article concludes by identifying a current in contemporary scientific thought that expands the conception of science beyond the classical nomothetic and reductionistic model presupposed in Taylor’s analysis at the same time that it challenges, as effectively as Taylor’s appeal to a premodern religious worldview, the modern “ethic of rational control” that is the dubious legacy of Descartes.
Structural insights into human PNPase in health and disease
Authors: Li Yi-Ching , Wang Chun-Hsiung , Patra Malay , Chen Yi-Ping , Yang Wei-Zen , Yuan Hanna S 
Published: February 2025

Abstract
Human polynucleotide phosphorylase (hPNPase) is a 3′-to-5′ exoribonuclease located in mitochondria, where it plays crucial roles in RNA degradation and RNA import. Mutations in hPNPase can impair these functions, leading to various mitochondrial dysfunctions and diseases. However, the mechanisms by which hPNPase switches between its roles as an RNA-degrading enzyme and an RNA carrier, as well as how disease-associated mutations may affect these distinct functions, remain unclear. In this study, we present cryo-electron microscopy structures of hPNPase, highlighting the flexibility of its S1 domains, which cap the ring-like RNA-degradation chamber and shift between two distinctive open and closed conformations. We further demonstrate by small-angle X-ray scattering and biochemical analyses that the disease-associated mutations P467S and G499R impair hPNPase’s stem-loop RNA-binding and degradation activities by limiting the S1 domain’s ability to transition from an open to closed state. Conversely, the D713Y mutation, located within the S1 domain, does not affect the RNA-binding affinity of hPNPase, but diminishes its interaction with Suv3 helicase for cooperative degradation of structured RNA. Collectively, these findings underscore the critical role of S1 domain mobility in capturing structured RNA for degradation and import, as well as its involvement in mitochondrial degradosome assembly. Our study thereby reveals the molecular mechanism of hPNPase in RNA binding and degradation, and the multiple molecular defects that could be induced by disease-linked mutations in hPNPase.
A C2H2 Zinc Finger Protein, OsZOS2-19, Modulates ABA Sensitivity and Cold Response in Rice
Authors: Zhang Di , Ding Xiaoping , Wang Zhijun , Li Wenyu , Li Lingling , Liu Ling , Zhou Huang , Yu Jianghui , Zheng Cheng , Wu HouXiong , Yuan Dingyang , Duan Meijuan , Liu Citao 
Published: February 2025

Abstract
Cold stress is a major factor limiting rice (Oryza sativa L.) productivity, making it crucial to understand the molecular mechanisms underlying stress responses to develop resilient crops. In this study, we characterized OsZOS2-19, a cold- and abscisic acid (ABA) -responsive C2H2 zinc finger protein, which functions as a transcriptional repressor. Overexpression of OsZOS2-19 in rice lines increases sensitivity both cold and ABA, reducing cold tolerance, disrupting osmotic balance, and impairing reactive oxygen species (ROS) scavenging. RNA sequencing revealed that OsZOS2-19 overexpression interfered with key stress-response pathways, including those associated with sugar metabolism and glutathione biosynthesis. These findings suggest that OsZOS2-19 negatively regulates cold tolerance and ABA sensitivity by modulating ROS accumulation and osmotic balance, offering new insights into cold adaptation in rice.
An alternative pathway to starch granule initiation unraveled in Chlamydomonas reinhardtii.
Authors: Courseaux Adeline , Deschamps Philippe , Dauvillée David 
Published: February 2025

Abstract
The initiation of starch granule synthesis remains a relatively poorly understood phenomenon. Recent advances enabled the establishment of a model explaining the synthesis of new starch granules in Arabidopsis thaliana. These characterizations revealed the involvement of both a specific starch synthase isoform (SS4) and of several non-enzymatic proteins in this process. In this work, we investigated whether the initiation of starch synthesis in the green microalgae Chlamydomonas reinhardtii involves the same machinery as those uncovered in the plant model. Our extensive phylogenetic analysis revealed that most of the key players that were identified in higher plants are not found in microalgae suggesting that a different pathway is taking place. We showed that restoration of ADP-glucose synthesis in a mutant strain devoid of any endogenous primers allowed normal starch synthesis, revealing the existence of an initiation mechanism in Chlamydomonas. Our biochemical characterizations revealed that starch synthase isoform 3 possesses the intrinsic capacity to initiate polysaccharide synthesis in vitro and could be one of the functions involved in starch initiation. Our work suggests that the initiation of starch synthesis in Chlamydomonas involves a different pathway to that described in Arabidopsis and that further efforts will be required to identify the proteins involved in this process.
Occupational history questionnaire for job coding and exposure assessment in systemic autoimmune rheumatic diseases
Authors: Dens Anne-Catherine , Celen Hannelore , Michiels Stijn , Doumen Michaël , Pazmino Sofia , Godderis Lode , Verschueren Patrick , Kromhout Hans , Ronsmans Steven , De Langhe Ellen 
Published: February 2025

Abstract

Objectives
Systemic autoimmune rheumatic diseases (SARDs) develop in genetically susceptible individuals when exposed to environmental factors, such as respirable crystalline silica (RCS) particles. Assessing occupational exposure in population-based studies is critical but resource-intensive, often requiring expert interviews. This study aimed to develop and validate a self-administered occupational history questionnaire that allows for International Standard Classification of Occupations (ISCO-68) coding and exposure assessment, as a cost-effective alternative to traditional interviews.

Methods
Seventy rheumatoid arthritis patients participated by completing a standardized telephone interview and the newly developed self-administered questionnaire. Participants were also asked to recruit two gender- and age-matched family members for comparison. Independent observers assigned ISCO-68 codes to the reported jobs, and a job exposure matrix was used to link each job to RCS exposure. Agreement between the interview and questionnaire was assessed by comparing reported working years, ISCO-68 job codes, and RCS exposure. Cohen’s κ and intraclass correlation were calculated to evaluate agreement and interobserver variability.

Results
Patient response rate was 77%, but family member controls had a low response rate (6.45%), likely impacted by the COVID-19 pandemic. Agreement for reported working years was 91%, with Cohen’s κ of 0.87 for ever/never RCS exposure. Manual ISCO coding introduced variability, but interobserver reliability remained high (ICC = 0.91).

Conclusion
In conclusion, the self-administered occupational history questionnaire provides a valid, cost-effective, and time-efficient alternative to telephone interviews for assessing occupational history and estimating RCS exposure in epidemiological research. Future studies should explore automated coding systems and improved strategies for control recruitment.
Cancer risk of Janus kinase inhibitors and biological disease-modifying antirheumatic drugs among older Americans with rheumatoid arthritis
Authors: Ahmed Shyfuddin , Pfeiffer Ruth M , Jackson Sarah S , Song Minkyo , Mariette Xavier , Seror Raphaèle , Engels Eric A 
Published: February 2025

Abstract

Objective
To examine cancer risk associated with Janus kinase inhibitors (JAKis) and biological DMARDs (bDMARDs) in patients with RA.

Methods
Case–control study of patients with RA age 65 years or older in the US Surveillance, Epidemiology, and End Results (SEER)-Medicare database during 2014–2019. Cases were individuals with a first cancer diagnosed in SEER registries (N = 12 463). Cancer-free controls (N = 38 345) were Medicare beneficiaries residing in SEER areas. Exposure to JAKis, tumour necrosis factor inhibitors (TNFis) and other bDMARDs was ascertained using prescription claims. Logistic regression was used to estimate adjusted odds ratios (ORs).

Results
1.9% of cases and 2.0% of controls were prescribed a JAKi. Among patients prescribed a JAKi, the median duration of documented exposure was 1.8 years. Overall cancer risk was not associated with exposure to JAKis (adjusted OR 1.04, 95% CI 0.87–1.26), TNFis (0.98, 0.92–1.05) or other bDMARDs (0.98, 0.90–1.07). However, JAKi exposure was associated with significantly increased risk of lung cancer (OR 1.40, 95% CI 1.06–1.87), especially in males (2.12, 1.14–3.94) and with &gt;2 years of JAKi exposure (1.52, 1.01–2.28). Among females, JAKi exposure was associated with lower risk of breast cancer (OR 0.62, 95% CI 0.39–0.97).

Conclusions
Among older adults with RA, JAKi exposure over a median of 1.8 years was not associated with an overall increase in cancer risk. However, lung cancer risk was elevated, supporting clinical caution in prescribing this medication class to smokers. Further research is needed to understand the role of the JAK/STAT pathway in cancer.
Rigid Corneal Lenses for Visual Rehabilitation in Infants With Unilateral Aphakia After Cataract Surgery: A Longitudinal Case Series
Authors: Yan Honggai , Li Li , Liang Tianwei 
Published: February 2025

Objectives:
This study investigated the safety of rigid corneal lenses in children with unilateral aphakia after cataract surgery and observed the visual rehabilitation longitudinally.

Methods:
This retrospective cohort study performed a 3-year follow-up of 21 infants (age 5.9±3.3 months) with unilateral congenital cataracts who started wearing rigid corneal contact lenses after cataract surgery. The basic presurgical patient information included chief complaint, intraocular pressure (IOP), axial length, corneal width, anterior segment, and fundus examination. The postsurgical visual acuity, IOP, and anterior segment were examined during regular postoperative follow-up visits. Keratometry was performed when contact lenses had to be changed.

Results:
Of the 21 patients, 15 were male and 6 were female. Before surgery, the affected and nonaffected eyes had similar IOP (9.5±3.5 vs. 9.2±2.8 mm Hg; P=0.502) and axial length (19.2±1.5 vs. 19.4±0.96; P=0.333). The corneal diameter in the affected eyes was smaller than in the nonaffected eyes (10.2±0.7 vs. 10.6±0.6 mm; P=0.002). After surgery, the logarithm of the minimum angle of resolution vision of the affected eyes improved gradually, showing values of 1.12±0.28, 0.78±0.37, and 0.62±0.38 at 1, 2, and 3 years after surgery, respectively. The respective values in the unaffected eyes were 0.58±0.14, 0.40±0.13, and 0.33±0.16. The mean keratometric astigmatism and keratometry 1 and 3 years after surgery were statistically similar (2.09±1.21 vs. 1.73±1.16 D, P=0.272; 44.82±3.15 vs. 44.39±2.75 D, P=0.324, respectively). No serious complications occurred during the follow-up.

Conclusion:
The rigid corneal lens is well tolerated and safe in aphakic eyes and can effectively improve children's visual acuity after unilateral cataract surgery. For patients able to receive rigid corneal lenses, intraocular lens implantation can be delayed until after the age of three.
Vasopressor Requirements in Antipsychotic Overdose
Authors: Tobarran Natasha , Kershner Emily K. , Cumpston Kirk L. , Chambers Andrew , Michienzi Avery , Rose S. Rutherfoord , Charlton Nathan , Wills Brandon K. 
Published: February 2025

Abstract

Purpose/Background
The antipsychotic class of medications has a varying degree of peripheral alpha antagonism resulting vasodilation and potentially hypotension. These hemodynamic changes may require treatment with crystalloids and vasopressors. The primary aim of this study was to evaluate the occurrence of hypotension after antipsychotic overdose and characterize vasopressor use.

Methods/Procedures
A retrospective cohort study was conducted by chart review of electronic records from 2 regional poison centers from January 1, 2004, to December 31, 2020. Inclusion criteria were single acute antipsychotic exposures evaluated in a health care facility and age >15. Exclusion criteria included missing data, minor or no effect outcomes, and polypharmacy overdose. The primary outcome was hypotension, which was defined as systolic blood pressure <90 mm Hg and/or MAP <65.

Findings/Results
There were 4488 single acute antipsychotic overdoses that presented to a healthcare facility after the initial search was conducted. After exclusions, there were 2070 cases with moderate or severe outcomes. The mean age was 42 (SD = 16), and 70% were female. There were 169 cases with hypotension. Of the hypotensive cases, 92% involved atypical antipsychotics, with quetiapine being the most common (n = 128, 76%). Vasopressor therapy was administered in 16/169 cases (9.9%). In the cases where vasopressor use was recorded, norepinephrine was used 12 times, dopamine 3 times, and phenylephrine once. No deaths were reported.

Implications/Conclusions
In antipsychotic overdoses that presented to a healthcare facility, hypotension was present in n = 169 (3.8%).

Conclusions
Among patient reports to 2 regional poison centers, we found that hypotension following acute antipsychotic overdose was infrequent and vasopressors are rarely administered.
Electronic Clinical Quality Measures for Prosthetic Joint Infection Diagnosis: Pitfalls and Potential
Authors: Miller Andy O. , Chin Amy S. , Carli Alberto V. , Sayegh George , Chee Diana , Buchalter Daniel B. , Simon Sam , Maclean Catherine H. 
Published: February 2025

ABSTRACT

Introduction:
Prosthetic joint infection (PJI) after total hip and knee arthroplasty (TJA) is a major cause of morbidity in orthopedics. Fully specified quality measures for PJI diagnosis are lacking. We aimed to specify and evaluate electronic clinical quality measures (eCQM) across different healthcare institutions.

Methods:
Measures were specified using an iterative process through which elements in the measures were identified and evaluated, and their capture optimized in the electronic health record (EHR). Measures were then retrospectively tested at three institutions. Performance on the measures at each institution, and across surgeons at one, was also assessed. Qualitative interviews with each institution identified technical, structural, and clinical reasons for poor performance on the measures.

Results:
Four of the five eCQMs could be implemented within the EHRs. Wide variations were found in measure performance. Qualitative interviews revealed differences in EHR coding, data not being shared within institutions, and focus on specific tests within the testing set as reasons for poor performance.

Conclusions:
Significant variability in posthetic joint infection eCQMs exists, driven both by variations in data availability and clinical practice. Electronic clinical quality measures hold significant potential to enhance diagnostic quality measurement, but successful implementation is highly dependent on process standardization, data accuracy, and adaptation of measures across healthcare settings.
Massive transfusion protocol prediction decision aids in an Australian trauma setting
Authors: Wangoo Kush , Nguyen Vinh Dat David , Byth Karen , Malik Rajesh , Coggins Andrew 
Published: February 2025

Background
Trauma patients may require activation of an emergent massive transfusion protocol (MTP). Several decision aids are designed to predict massive transfusion requirements but have not been widely studied in the Australasian setting.

Methods
Commonly used MTP decision aids were assessed for accuracy in injured patients at an urban Level 1 trauma centre. Consecutive cases were prospectively enrolled to a complete registry of thromboelastogram assays in trauma patients. Analysis was undertaken using receiver operating characteristic (ROC) curves, sensitivity and specificity.

Results
A total of 114 patients met inclusion criteria (56 received MTP). More detailed and military derived scores including McLaughlin and Larson demonstrated >90% specificity. Area under ROC curve results were similar to prior reports, but the ABC score performed less accurately than expected.

Conclusion
In the setting of traumatic haemorrhage, the available MTP prediction decision aids should be applied cautiously and used only in combination with on-going clinical judgement.
Rare coagulation factor deficiencies: a five-year experience from a single tertiary care center in South India
Authors: Suresh Nivedita , Kurian Bitty , Jeladharan Reshma , Sao Amrita , Sidharthan Neeraj , Abraham Reema Miria 
Published: February 2025

Objective
Rare coagulation factor deficiencies (RCFD) comprise a heterogeneous class of coagulation disorders due to deficiencies/abnormalities in coagulation factors other than factors VIII, IX and von Willebrand factor (VWF). Due to its rarity and varying geographic prevalence, bleeding characteristics and behaviour pattern are not known. Our aim was to study the frequency and clinical profile of RCFD, assess the severity of deficiency, evaluate blood component requirements and surgical outcomes.

Methods
This is a retrospective cohort study done at Advanced Coagulation Laboratory, Amrita Hospital, Kerala from September 2018 to October 2023. Clinical characteristics including bleeding phenotype were noted. The patients were diagnosed based on their complete coagulation workup.

Results
Total of 1019 patients were evaluated, 93 (9.1%) patients had RCFD. Males and females were 60 (64.5%) and 33 (35.5%), respectively (M : F ratio 2 : 1). Median age at diagnosis was 26 years (range: 2 months–74 years). Half the patients (47) had bleeding episodes, 23 (25%) patients were detected incidentally and 23 (25%) patients as a part of preoperative evaluation. Mucocutaneous bleeding was the commonest symptom. The most common RCFD was factor VII deficiency (40%). Transfusion/hemostatic support was required for 29 (31.2%) patients during their life time. No adverse outcome was noted in 27 (29%) patients who underwent surgeries.

Conclusion
Factor VII deficiency was the commonest RCFD. Only half of the patients with RCFD were symptomatic. RCFDs generally have a favorable surgical/ pregnancy outcome. Data from resource limited settings are lacking; more studies are required to formulate management guidelines.
The role of neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio as venous thromboembolism predictors in breast cancer patients pre- and post-therapy
Authors: Qian Alyssa , Zandi Armita , Bucciol Regan , Othman Maha 
Published: February 2025

Objectives
Breast cancer (BC) accounts for 12.3% of all cancer-associated venous thromboembolism (VTE). Platelet-to-lymphocyte ratio (PLR) and neutrophil-to-lymphocyte ratio (NLR) are recognized inflammatory biomarkers but have not been incorporated into thrombosis risk stratification models. We evaluated NLR and PLR as predictive biomarkers for VTE in BC patients to determine their optimal predictive cutoffs and net predictive value before and after treatment.

Methods
We conducted a prospective pilot study that involved 56 women with BC, recruited prior to treatment (chemotherapy and immunotherapy) initiation with at least 6-month monitoring for VTE. NLR and PLR were assessed pre and posttreatment.

Results
Five patients (8.9%) developed VTE. NLR and PLR increased significantly posttreatment (P = 0.001). Post, not pretreatment, NLR (P = 0.029) and PLR (P = 0.033) were significantly associated with VTE occurrence. Receiver Operating curve analysis indicated enhanced predictive capacity for VTE postimmunotherapy. Optimal posttreatment cutoffs were 3.6 for NLR and 280 for PLR, aligning with existing literature, with slightly elevated NLR.

Conclusions
Posttreatment NLR and PLR have higher predictability for VTE in patients receiving immunotherapy compared to chemotherapy. NLR outperforms PLR, particularly postimmunotherapy. This data holds promise for thrombosis risk stratification in the context of immunotherapy but requires evaluation in larger studies.