bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case 328
Authors: Agostinis Cristina , Lupi Elide 
Published: April 2024

History A 45-year-old female patient with diffuse osteoarticular pain, particularly low back pain, was referred by a rheumatologist for an updated radiologic evaluation. The patient had experienced these symptoms for many years and was diagnosed with human leukocyte antigen B27–negative spondyloarthritis approximately 11 years prior, based on findings of bilateral erosive sacroiliitis at pelvic radiography ( Fig 1A ) and bone scintigraphy with technetium 99m methylene diphosphonate ( Fig 1B ). After 3 years of treatment with a tumor necrosis factor–α inhibitor (adalimumab), which was effective for pain, the patient was lost to follow-up. At the current presentation, approximately 8 years after being lost to follow-up, the patient presented with worsening low back pain. The presence of nonobstructing kidney stones on US images confounded the underlying cause of worsening pain. The patient also experienced fatigue and depressed mood. Routine blood tests revealed a normal blood cell count, creatinine level of 0.64 mg/dL (56.58 μmol/L) (normal range, 0.30–1.1 mg/dL [26.52–97.24 mmol/L]), C-reactive protein level of 1.1 mg/dL (normal, <1 mg/dL), and vitamin D level of 21 ng/mL (52.42 nmol/L) (normal range, 30–100 ng/mL [74.88–249.60 nmol/L]). Noncontrast MRI of the thoracic and lumbar spine ( Fig 2 ), MRI of the sacroiliac joints ( Fig 3 ), and CT of the abdomen and pelvis ( Fig 4 ) were performed.
Clinical and Genomic Landscape of RAS Mutations in Gynecologic Cancers
Authors: Son Ji , Zhang Yingao , Lin Heather , Mirallas Oriol , Alvarez Ballesteros Pablo , Nardo Mirella , Clark Natalie , Hillman R. Tyler , Campbell Erick , Holla Vijaykumar , Johnson Amber M. , Biter Amadeo B. , Yuan Ying , Cobb Lauren P. , Gershenson David M. , Jazaeri Amir A. , Lu Karen H. , Soliman Pamela T. , Westin Shannon N. , Euscher Elizabeth D. , Lawson Barrett C. , Yang Richard K. , Meric-Bernstam Funda , Hong David S. 
Published: April 2024

Abstract

Purpose:
We aimed to describe RAS mutations in gynecologic cancers as they relate to clinicopathologic and genomic features, survival, and therapeutic implications.

Experimental Design:
Gynecologic cancers with available somatic molecular profiling data at our institution between February 2010 and August 2022 were included and grouped by RAS mutation status. Overall survival was estimated by the Kaplan–Meier method, and multivariable analysis was performed using the Cox proportional hazard model.

Results:
Of 3,328 gynecologic cancers, 523 (15.7%) showed any RAS mutation. Patients with RAS-mutated tumors were younger (57 vs. 60 years nonmutated), had a higher prevalence of endometriosis (27.3% vs. 16.9%), and lower grades (grade 1/2, 43.2% vs. 8.1%, all P &lt; 0.0001). The highest prevalence of KRAS mutation was in mesonephric-like endometrial (100%, n = 9/9), mesonephric-like ovarian (83.3%, n = 5/6), mucinous ovarian (60.4%), and low-grade serous ovarian (44.4%) cancers. After adjustment for age, cancer type, and grade, RAS mutation was associated with worse overall survival [hazard ratio (HR) = 1.3; P = 0.001]. Specific mutations were in KRAS (13.5%), NRAS (2.0%), and HRAS (0.51%), most commonly KRAS G12D (28.4%) and G12V (26.1%). Common co-mutations were PIK3CA (30.9%), PTEN (28.8%), ARID1A (28.0%), and TP53 (27.9%), of which 64.7% were actionable. RAS + MAPK pathway-targeted therapies were administered to 62 patients with RAS-mutated cancers. While overall survival was significantly higher with therapy [8.4 years [(95% confidence interval (CI), 5.5–12.0) vs. 5.5 years (95% CI, 4.6–6.6); HR = 0.67; P = 0.031], this effect did not persist in multivariable analysis.

Conclusions:
RAS mutations in gynecologic cancers have a distinct histopathologic distribution and may impact overall survival. PIK3CA, PTEN, and ARID1A are potentially actionable co-alterations. RAS pathway-targeted therapy should be considered.
Fracture Risk Among Stroke Survivors According to Poststroke Disability Status and Stroke Type
Authors: Lee Dagyeong , Cho In Young , Chang Won Hyuk , Yoo Jung Eun , Choi Hea Lim , Park Junhee , Shin Dong Wook , Han Kyungdo 
Published: April 2024

BACKGROUND:
Stroke survivors face physical and cognitive challenges, leading to an increased dependency and a higher fall risk. We aimed to investigate the impact of poststroke disability and stroke type on fracture risk at various sites compared with matched controls.

METHODS:
This retrospective cohort study used data from the Korean National Health Insurance System database (2010–2018), including patients with stroke and 1:1 matched controls. Stroke survivors were grouped based on the presence and severity of their poststroke disability and stroke type. The primary outcome was a newly diagnosed fracture, analyzed by Cox proportional hazard regression analyses adjusting for potential confounders.

RESULTS:
Among 223 358 stroke survivors (mean age, 64.8±10.9 years; 61.2% men), 16 344 fractures occurred during a mean follow-up of 3.7±2.5 years. In matched controls (n=322 161; mean age, 65.4±11.2 years; 61.3% men), 20 398 fractures were identified. Stroke survivors had increased overall fracture risk compared with matched controls (adjusted hazard ratio [aHR], 1.40 [95% CI, 1.37–1.43]). Specifically, hip fracture risk was even greater in stroke survivors (incidence rate per 1000 person-years, 4.7 [95% CI, 4.5–4.8]; aHR, 2.42 [95% CI, 2.30–2.55]) than controls (incidence rate, 2.2 [95% CI, 2.1–2.3]). The risk of vertebral fractures (aHR, 1.29 [95% CI, 1.25–1.34]) and other fractures (aHR, 1.19 [95% CI, 1.15–1.23]) was also higher than that of the control group. Hip fracture risk was the highest among stroke survivors with severe poststroke disability (aHR, 4.82 [95% CI, 4.28–5.42]), although vertebral or other fracture risk was the highest among those with mild poststroke disability. No significant difference in fracture risk was found between hemorrhagic and ischemic stroke survivors when stratified by disability status.

CONCLUSIONS:
Our findings showed increased subsequent fracture risk among stroke survivors, particularly those with poststroke disability and for hip fracture. Bone health assessment and treatment should be emphasized as an essential part of stroke management.
Groundwater decline has negatively affected the well-preserved amphibian community of Doñana National Park (SW Spain)
Authors: Díaz-Paniagua Carmen , Florencio Margarita , de Felipe Miguel , Ramírez-Soto Mamen , Román Isidro , Arribas Rosa 
Published: April 2024

Abstract
The success of amphibian conservation efforts is highly dependent on the preservation of amphibian breeding habitats. Doñana National Park contains an abundance of ponds with heterogeneous characteristics, which has historically favoured its amphibian community. However, most of the park’s ponds are groundwater dependent, and aquifer overexploitation outside the park is leading to shorter hydroperiods and even desiccation in the pond network. This problem has been exacerbated by the scarcity of rain over the last decade. In 2021-2022, we surveyed the occurrence of the park’s 11 amphibian species, with a view to comparing our findings with those from the last previous survey in 2003-2004. We mapped the species occurrence within the park for the two survey periods. While all 11 amphibian species could still be found in Doñana, their occurrence had decreased across the board. In 2003-2004, 6 species were present across more than 50% of the sampling area. In contrast, 18 years later, such was the case for only two species (Pelophylax perezi and Hyla meridionalis). Declines were greatest for Epidalea calamita, followed by Pelobates cultripes, Triturus pygmaeus, and Lissotriton boscai. The mean number of species per sampling unit (i.e., grid cell) dropped from 4.3 to 3.1. To preserve Doñana’s amphibian community, it is important to restore the park’s pond network, which implies reducing regional groundwater overexploitation.
Taxonomy of Naumann’s and dusky, red-throated and black-throated thrush complexes (Aves: Turdidae) using morphological and molecular characteristics
Authors: An Boyang , Yin Danyang , Huang Songlin , Mohamed Nassoro , Li Bo 
Published: April 2024

Abstract
Species are the basic units in evolution and biodiversity and thus a reasonable species classification is essential to assess and protect biodiversity. The classifications of the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes are not well defined in Turdidae (Aves, Passeriformes). Herein, we use qualitative and quantitative morphological characters and molecular data to review the taxonomy of these thrush complexes. These four thrushes can be distinguished with qualitative features of feather color and striping. These birds cannot be divided by quantitative features, which only work on two groups of thrush complexes. Phylogenetic analysis based on mitochondrial genes indicate that all haplotypes might be divided into two monophyletic clades corresponding to two groups of thrush complexes. According to coalescence-based species delimitation and the gen-morph species concept, these two groups of thrush complexes should be separated as two distinctive species (T. naumanni and T. ruficollis) and including two subspecies per species. This species classification is also supported by gene flow analysis. There is a significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis using a few microsatellite loci. This leads to a pattern of nuclear-mitochondrial discordance between the two birds that can be explained by several potential mechanisms. This study provides the first comprehensive classification of the two thrush complexes on a population level using morphological and molecular characteristics, which will be useful in expanding our understanding of species division among thrush complexes.
International Lawyers as Hope Mongers: How Did We Come to Believe That Democracy Was Here to Stay?
Authors: Aral Işıl 
Published: April 2024

Abstract
It is common these days to lament the recession of democracy around the world. The way scholars address the issue of democratic backsliding shows that there is a significant gap between the expectation about democracy’s anticipated course of development and the current state of affairs. This article argues that the expectation that democracy would consolidate over time was produced by the progress narrative of democratic governance discourses. Drawing on narratology, it conducts a discourse analysis to demonstrate that today’s dismay about the recession of democracy is due to an unwarranted expectation that was created by the progress narrative of democratic governance discourses. It focuses on the periodisation of history in the construction of these discourses and investigates how scholars used the Cold War – post-Cold War dichotomy to create a progress narrative.
The Interdecadal Changes in the Spatial Structure of the South Pacific Oscillation and Its Implication for ENSO Diversity
Authors: Min Qingye , Zhang Renhe 
Published: April 2024

Abstract
The South Pacific Oscillation (SPO), characterized by a north–south dipole-like pattern of sea level pressure anomalies, is one of the key factors in understanding tropical–extratropical interactions in the South Pacific. We show that in boreal summer (June–August), the center of the northern lobe sea level pressure anomalies in the SPO is shifted to the east gradually after the 1960–70s. This study focuses on the relationship between the boreal summer SPO and following winter El Niño–Southern Oscillation (ENSO) diversity before and after the eastward shift of the SPO’s subtropical lobe. The eastward shift of the SPO’s subtropical lobe altered both the seasonal footprint mechanism and the trade wind charging mechanism associated with the SPO and thus profoundly influenced the ENSO diversity. It is revealed that when the northern lobe of the SPO shifts to the west of its average location, it tends to strengthen the eastern Pacific (EP) El Niño mainly via the seasonal footprint mechanism. But after the SPO’s northern lobe shifts to the east of its average location, it tends to promote the development of central Pacific (CP) El Niño mainly via the trade wind charging mechanism. The changes in the spatial structure of convection over the tropical Pacific and Indian Oceans may be one of the possible causes for the eastward shift in the SPO’s northern lobe. The findings in the present study have implications for a better understanding of ENSO diversity.

Significance Statement
Previous studies have demonstrated that the South Pacific Oscillation (SPO), as an important El Niño–Southern Oscillation (ENSO) precursor in the South Pacific, has the potential to provide an enhancement of the prediction of specific ENSO flavor. However, the historical variation in the SPO’s spatial structure and related changes in the relationship with the diversity of ENSO are still unclear. In this paper, we show that the subtropical lobe of the boreal summer (June–August) SPO is shifted to the east gradually after the 1960–70s. The changes in the spatial structure have also altered both the seasonal footprint mechanism and the trade wind charging mechanism which play important roles in the developmental processes of different types of ENSO. Our work highlights the importance of the interdecadal changes in the spatial structure of the SPO in understanding the relationship between the SPO and ENSO diversity.
From principles to practice: Clarifying new obligations under Victoria’s Mental Health and Wellbeing Act 2022
Authors: Katterl Simon 
Published: April 2024

Objective To explain the new test for complying with the mental health principles under the Mental Health and Wellbeing Act 2022 (Vic). Conclusion The principles carry over limitations from the previous Mental Health Act 2014 (Vic) while also containing new features. The ‘all reasonable efforts to comply’ and ‘proper consideration’ tests resemble the existing test under section 38(1) of the Charter of Human Rights and Responsibilities Act 2006 (Vic) that also apply to public mental health services. Taking these duties together, public mental health services, including hospital and community mental health boards, clinical directors and clinical governance processes, will need to show concrete evidence of specific rights and/or principles being deliberated in their decisions.
Rheological properties of magnesium bentonite and sepiolite suspensions after dynamic ageing at high temperatures
Authors: Christidis Georgios E. , Athanasakis Nikolaos , Marinakis Dimitrios 
Published: April 2024

AbstractThe rheological properties of three Na-activated, trioctahedral Mg-bentonites (hectorite clay from the CMS Source Clay Project repository, saponite clay from Spain and stevensite clay from Rhassoul, Morocco) and a sepiolite clay from Greece were examined after dynamic ageing at temperatures up to 230°C. The 5% w/v suspensions were prepared by dispersing the clay mineral samples in distilled water. The suspensions underwent dynamic, thermal ageing for 16 h before determination of the viscosity, filtration loss, filter cake thickness and pH and the concentration of dissolved Na+ and Mg2+. Thermal ageing contributed to the dispersion of clay particles, with a direct effect on plastic and apparent viscosity, introducing pseudoplastic behaviour. With the exception of the stevensite clay at 230°C that displayed limited dissolution at 230°C and partial conversion to kerolite, the clays were stable at high temperatures. The Na-activation of all clays except for stevensite was not adversely affected by thermal ageing. Thermal ageing of stevensite at 230°C facilitated Na exchange and yielded suspension with high viscosity and low filtrate loss. Only the suspensions of hectorite and those of stevensite aged at 230°C met with American Petroleum Institute specifications. The thermal behaviour and rheological properties of the clays might be interpreted according to the intrinsic properties of the clay minerals, such as layer charge and charge distribution.
Study on the regulatory alienation effect of China's Environmental Protection Tax Law during the strict epidemic control period: based on a sample test of 1000 tax personnel
Authors: Ming-jun Chen , Jian-ya Zhou 
Published: April 2024

AbstractThe enactment of the Environmental Protection Tax Law was a major event in the process of China's economic and social development. This law has achieved certain results in the first two years since enactment, but there have also been many problems. During the three-year strict pandemic control period, the normal process of Environmental Protection Tax Law implementation was impacted, causing alienation and reducing the quality of implementation. This study empirically reveals the alienation mechanism in the implementation of the Environmental Protection Tax Law by taking 1000 Chinese tax professionals, and randomly divides the sample equally into two parts, utilizing 500 samples for the initial test and another 500 samples for the robustness test. This research shows that pollutant emission monitoring (correlation coefficient is 0.07), preferential tax policies (correlation coefficient is 0.03) and the quality of tax personnel (correlation coefficient is 0.06) are not conducive to realizing the crowding-out effect of the Environmental Protection Tax Law, while preferential tax policies (correlation coefficient is 0.05), information-sharing platforms (correlation coefficient is 0.06) and the quality of tax personnel (correlation coefficient is 0.05) hinder the incentive effect, and the remaining elements passed the correlation coefficient test within certain confidence intervals. Therefore, the implementation of China's Environmental Protection Tax Law should be improved in the following ways: the accuracy of the environmental protection departments' supervision of pollutant emissions as well as the scientificity and rationality of preferential tax policies should be improved, the construction of environmental protection tax information-sharing platforms should be strengthened, and compound tax collection and management talent should be created.
Assessing the reliability of point mutation as data augmentation for deep learning with genomic data
Authors: Lee Hyunjung , Ozbulak Utku , Park Homin , Depuydt Stephen , De Neve Wesley , Vankerschaver Joris 
Published: April 2024

Abstract
Background
Deep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation of deep neural networks, however, is their high demand for data during training. To overcome this challenge, other fields, such as computer vision, use various data augmentation techniques to artificially increase the available training data for DNNs. Unfortunately, most data augmentation techniques used in other domains do not transfer well to genomic data.

Results
Most genomic data possesses peculiar properties and data augmentations may significantly alter the intrinsic properties of the data. In this work, we propose a novel data augmentation technique for genomic data inspired by biology: point mutations. By employing point mutations as substitutes for codons, we demonstrate that our newly proposed data augmentation technique enhances the performance of DNNs across various genomic tasks that involve coding regions, such as translation initiation and splice site detection.

Conclusion
Silent and missense mutations are found to positively influence effectiveness, while nonsense mutations and random mutations in non-coding regions generally lead to degradation. Overall, point mutation-based augmentations in genomic datasets present valuable opportunities for improving the accuracy and reliability of predictive models for DNA sequences.
Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein–protein interfaces
Authors: Gurusinghe Sagara N. S. , Shifman Julia M. 
Published: April 2024

Abstract
Background
Protein–protein interactions (PPIs) are conveyed through binding interfaces or surface patches on proteins that become buried upon binding. Structural and biophysical analysis of many protein–protein interfaces revealed certain unique features of these surfaces that determine the energetics of interactions and play a critical role in protein evolution. One of the significant aspects of binding interfaces is the presence of binding hot spots, where mutations are highly deleterious for binding. Conversely, binding cold spots are positions occupied by suboptimal amino acids and several mutations in such positions could lead to affinity enhancement. While there are many software programs for identification of hot spot positions, there is currently a lack of software for cold spot detection.

Results
In this paper, we present Cold Spot SCANNER, a Colab Notebook, which scans a PPI binding interface and identifies cold spots resulting from cavities, unfavorable charge-charge, and unfavorable charge-hydrophobic interactions. The software offers a Py3DMOL-based interface that allows users to visualize cold spots in the context of the protein structure and generates a zip file containing the results for easy download.

Conclusions
Cold spot identification is of great importance to protein engineering studies and provides a useful insight into protein evolution. Cold Spot SCANNER is open to all users without login requirements and can be accessible at: https://colab.research.google.com/github/sagagugit/Cold-Spot-Scanner/blob/main/Cold_Spot_Scanner.ipynb.
NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing
Authors: Xie Gengqiang , Toledo Maria Pilar , Hu Xue , Yong Hyo Jeong , Sanchez Pamela Sandoval , Liu Chengyang , Naji Ali , Irianto Jerome , Wang Yue J. 
Published: April 2024

Abstract
Background
Current approaches to profile the single-cell transcriptomics of human pancreatic endocrine cells almost exclusively rely on freshly isolated islets. However, human islets are limited in availability. Furthermore, the extensive processing steps during islet isolation and subsequent single cell dissolution might alter gene expressions. In this work, we report the development of a single-nucleus RNA sequencing (snRNA-seq) approach with targeted islet cell enrichment for endocrine-population focused transcriptomic profiling using frozen archival pancreatic tissues without islet isolation.

Results
We cross-compared five nuclei isolation protocols and selected the citric acid method as the best strategy to isolate nuclei with high RNA integrity and low cytoplasmic contamination from frozen archival human pancreata. We innovated fluorescence-activated nuclei sorting based on the positive signal of NKX2-2 antibody to enrich nuclei of the endocrine population from the entire nuclei pool of the pancreas. Our sample preparation procedure generated high-quality single-nucleus gene-expression libraries while preserving the endocrine population diversity. In comparison with single-cell RNA sequencing (scRNA-seq) library generated with live cells from freshly isolated human islets, the snRNA-seq library displayed comparable endocrine cellular composition and cell type signature gene expression. However, between these two types of libraries, differential enrichments of transcripts belonging to different functional classes could be observed.

Conclusions
Our work fills a technological gap and helps to unleash frozen archival pancreatic tissues for molecular profiling targeting the endocrine population. This study opens doors to retrospective mappings of endocrine cell dynamics in pancreatic tissues of complex histopathology. We expect that our protocol is applicable to enrich nuclei for transcriptomics studies from various populations in different types of frozen archival tissues.