bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reevaluating the splice-altering variant in TECTA as a cause of nonsyndromic hearing loss DFNA8/12 by functional analysis of RNA
Authors: Yang Yan , Luo Haiyan , Pan Lijuan , Feng Chuanxin , Guo Zhen , Zou Yongyi , Zeng Baitao , Huang Shuhui , Yuan Huizhen , Wu Ping , Liu Danping , Dan Yi , Xiao Junfang , Li XinYu , Chen ZhongFa , Zeng Xiao Ni , Jiang XiangLong , Yang Bicheng , Liu Yuhe , Liu Yanqiu 
Published: April 2024

Abstract

Purpose
The aim of this study was to determine the genetic cause of early onset autosomal dominant hearing loss segregating in five-generation kindred of Chinese descent and provide preimplantation genetic testing (PGT)for them.

Methods
Clinical examination, pedigree analysis and exome sequencing were carried out on the family. Minigene-based splicing analysis, in vivo RNA analysis and protein structure prediction by molecular modeling were conducted on the candidate variant. PGT for the causative variation and chromosome aneuploidis based on SNP analysis has been used for avoidance of hearing loss in this family.

Results
All the affected individuals presented with moderate down-sloping hearing loss and whole-exome sequencing identified a novel splice-site variant c.5383+6T&gt;A in the tested subjects within the TECTA locus. Genotyping of all the 32 family members confirmed segregation of this variant and the hearing loss phenotype in the extended family. Functional analysis of RNA and molecular modeling indicates that c.5383+6T&gt;A is a pathogenic splice-site variant and should be considered as genetic cause of the hearing loss. Furthermore, a successful singleton pregnancy with no variation in TECTA c.5383+6 was established and a healthy male child was born by PGT.

Conclusion
We have identified a novel variant c.5383+6T&gt;A in TECTA ZA-ZP inter-domain, which could be attributable to the early-onset autosomal dominant hearing loss. The implications of our study are valuable in elucidating the disrupted RNA splicing and uncovering the genetic cause of hearing loss with TECTA pathogenic variants, as well as providing reproductive approaches to healthy offspring.
The association between low serum calcium level and new-onset atrial fibrillation after coronary artery bypass grafting
Authors: Pan Yilin , Liu Yuhua , Peng Zhan , Yang Yunxiao , Liu Linqi , Yang Xiubin , Hua Kun 
Published: April 2024

Abstract

OBJECTIVES
This study aims to investigate the relationship between serum calcium (SC) levels and the incidence of postoperative atrial fibrillation (POAF) in patients undergoing coronary artery bypass graft surgery.

METHODS
This retrospective, observational cohort study consecutively enrolled patients undergoing isolated coronary artery bypass grafting in Beijing Anzhen Hospital from January 2018 to December 2021. Patients with a previous history of atrial fibrillation or atrial flutter or requiring concomitant cardiac surgery were excluded. A logistic regression model was used to determine predictors of POAF. Multivariable adjustment, inverse probability of treatment weighting and propensity score matching were used to adjust for confounders. Moreover, we conducted univariable and multivariable logistic regression analyses on preoperative and postoperative SC and ionized SC levels.

RESULTS
The analysis encompassed 12 293 patients. The POAF rate was significantly higher in patients with low SC level than those without (1379 [33.9%] vs 2375 [28.9%], P &lt; 0.001). Low SC level was associated with an increased odds ratio of POAF (odds ratio [95% confidence interval]: 1.27 [1.18–1.37], P &lt; 0.001). Inverse probability of treatment weighting and propensity score matching analyses confirmed the results. The increased POAF rate in low SC level group still existed among subgroup analysis based on different age, sex, body mass index, hypertension, hyperlipidaemia, CHA2DS2-VASc and magnesium.

CONCLUSIONS
Low SC level indicates elevated POAF risk in patients undergoing isolated coronary artery bypass graft surgery even after the adjustment for age, sex, cardiovascular risk factors, echocardiographic parameters and laboratory markers.
Pathways to green urbanism: evaluating Jeddah’s environmental sustainability progress and prospects
Authors: Hegazy Ibrahim Rizk , Hammad Hazem Abdelazim , Munshi Ammar Mohammedsaeed , Alqurashi Ahmed Abdulmohsen , Bahreldin Ibrahim Zakaria 
Published: April 2024

Abstract
This research provides a comprehensive analysis of environmental sustainability in Jeddah, focusing on the unique challenges and opportunities it faces as a rapidly urbanizing city in an arid region. The study evaluates Jeddah’s performance across multiple environmental areas, including energy and carbon dioxide emissions, land and building use, transportation, waste management, water use, sanitation and air quality. A detailed SWOT analysis identifies the city’s strengths, weaknesses, opportunities and threats in achieving sustainable urban development. The results reveal high per capita carbon dioxide emissions, energy consumption and waste generation, along with challenges in managing water resources and maintaining air quality. The study highlights Jeddah’s efforts in renewable energy policies, urban mass transportation and waste management strategies. The conclusion provides a set of comprehensive recommendations for policy improvement, focusing on the need for sustainable urban planning, energy conservation, improved waste and water management and public engagement. This research contributes significantly to the understanding of urban sustainability in arid environments, providing a valuable framework for policymakers and urban planners.
Long-term storage and quality stability of biodiesel fuels
Authors: Karchkhadze Kakha , Khetsuriani Natela 
Published: April 2024

Abstract
A special nano-composition of biodiesel was created that can increase the storage capacity and quality stability of the biodiesel fuel. The group compositions of pure nano-biodiesel and its blends with mineral diesel fuel were analyzed using a Fourier Infra Red (IR) spectrometer, and the individual hydrocarbons were identified by a gas chromatograph. The group compositions and physical and chemical parameters of the nano-biodiesel fuel fully met the standards and remained stable from 2018 through 2021, proving that this type of biodiesel can be stored for more than 4 years while maintaining physical and chemical properties and quality parameters.
The Gender- and Sexuality-Based Harms of Refugee Externalization: A Role for Human Rights Due Diligence
Authors: Talbot Anna , Vogl Anthea , Dehm Sara 
Published: April 2024

Abstract
Refugee externalization arrangements are increasingly common in refugee-receiving global North States. Such arrangements have broad-ranging and significant human rights implications, especially (but not only) for refugee women and LGBTQI refugees who may be at increased risk of gender- or sexuality-based harm. This is particularly the case where refugees are placed in situations of risk or harm as a result of a ‘sending’ State’s extraterritorial regime, or where domestic laws in receiving States outlaw certain practices such as pregnancy termination or same-sex sexual activity. There has been limited scholarly analysis of the gendered impacts of externalization policies, and States rarely take into account the gendered implications of externalization when implementing these policies. This article examines the possibilities and limits of international human rights law to protect refugees at risk of gender- and sexuality-based harms through a focus on States’ positive due diligence obligations. While there is limited jurisprudence on the scope of such obligations in the context of refugee externalization, the article emphasizes that due diligence human rights obligations require sending States to adopt effective measures to protect people from unlawful discrimination and from cruel, inhuman or degrading treatment. Due diligence obligations also offer a vital accountability mechanism for violations in extraterritorial settings through their potential preventative, remedial, and visibility functions. Using the case study of Australia’s extraterritorial asylum regime in the Pacific, the article argues that such obligations encompass identifying and addressing foreseeable risks of gender- and sexuality-based harm, both prior to forcibly transferring refugees abroad and on an ongoing basis. Further, it argues that the gender- and sexuality-based human rights impacts of Australia’s externalization regime have immediate and urgent relevance as other States consider or implement similar policies.
Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges
Authors: Glasl Bettina , Luter Heidi M , Damjanovic Katarina , Kitzinger Katharina , Mueller Anna J , Mahler Leonie , Engelberts Joan Pamela , Rix Laura , Osvatic Jay T , Hausmann Bela , Séneca Joana , Daims Holger , Pjevac Petra , Wagner Michael 
Published: April 2024

Abstract
Ammonia-oxidizing archaea and nitrite-oxidizing bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification—the aerobic oxidation of ammonia to nitrite and further to nitrate—and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterize two novel nitrifying symbiont lineages, Candidatus Nitrosokoinonia and Candidatus Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, in situ visualization, and physiological rate measurements. Both represent a new genus in the ammonia-oxidizing archaeal class Nitrososphaeria and the nitrite-oxidizing bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonized by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidizing archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e. ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidizing bacterial symbionts of the genus Ca. Nitrosymbion may reciprocally support the ammonia-oxidizers with ammonia via the utilization of sponge-derived urea and cyanate. Comparative analyses of published environmental 16S rRNA gene amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.
Antimicrobial resistance profiles of Escherichia coli isolated from clinical and environmental samples: findings and implications
Authors: Kasanga Maisa , Shempela Doreen Mainza , Daka Victor , Mwikisa Mark J , Sikalima Jay , Chanda Duncan , Mudenda Steward 
Published: April 2024

Abstract

Background
The overuse and misuse of antimicrobials has worsened the problem of antimicrobial resistance (AMR) globally. This study investigated the AMR profiles of Escherichia coli isolated from clinical and environmental samples in Lusaka, Zambia.

Methods
This was a cross-sectional study conducted from February 2023 to June 2023 using 450 samples. VITEK® 2 Compact was used to identify E. coli and perform antimicrobial susceptibility testing. Data analysis was done using WHONET 2022 and SPSS version 25.0.

Results
Of the 450 samples, 66.7% (n = 300) were clinical samples, whereas 33.3% (n = 150) were environmental samples. Overall, 47.8% (n = 215) (37.8% clinical and 10% environmental) tested positive for E. coli. Of the 215 E. coli isolates, 66.5% were MDR and 42.8% were ESBL-producers. Most isolates were resistant to ampicillin (81.4%), sulfamethoxazole/trimethoprim (70.7%), ciprofloxacin (67.9%), levofloxacin (64.6%), ceftriaxone (62.3%) and cefuroxime (62%). Intriguingly, E. coli isolates were highly susceptible to amikacin (100%), imipenem (99.5%), nitrofurantoin (89.3%), ceftolozane/tazobactam (82%) and gentamicin (72.1%).

Conclusions
This study found a high resistance of E. coli to some antibiotics that are commonly used in humans. The isolation of MDR and ESBL-producing E. coli is a public health concern and requires urgent action. Therefore, there is a need to instigate and strengthen interventional strategies including antimicrobial stewardship programmes to combat AMR in Zambia.
Suspected North Carolina counterfeit pill-involved deaths, 2020–2022
Authors: Friederich Laura W , Cox Mary E , Hyson Brian E , Bishop-Freeman Sandra C 
Published: April 2024

Abstract
The NC Office of the Chief Medical Examiner regularly assumes jurisdiction over deaths that are suspicious, unusual or unattended by a medical professional. In recent years, the presence of counterfeit pills is occasionally suggested by investigatory notes and/or scene findings that document reported consumption of prescription drugs, or prescription drugs on scene, which are not reflected in the final autopsy findings after toxicological analysis of the decedent’s blood samples. Counterfeit pill consumption is a major public health hazard worthy of attention from the forensic toxicology community. Seventy-five cases from January 2020 to December 2022 serve as a convenience sample of cases where prescription pills including formulations of alprazolam, oxycodone and hydrocodone were specifically referenced during the death scene investigation as recently consumed, yet an unexpected substance was found during toxicological analysis rather than the expected pharmaceutical drug. Of note, novel benzodiazepines detected included flualprazolam, etizolam, clonazolam metabolite (8-aminoclonazolam), bromazolam, flubromazolam and desalkylflurazepam. Decedents’ ages ranged from 16 to 69, across 33 different NC counties. Case notes indicated that eight of the decedents obtained pills through direct personal relationships, six decedents obtained them from “the street” and one decedent likely purchased pills online. Pills were largely consumed orally or through insufflation. Seven case reports contained indication that decedents knew or suspected the counterfeit nature of their pills. This study describes the context and characteristics of 2020–2022 suspected counterfeit pill-involved deaths in NC to further the understanding of the forensic science community, law enforcement partners, public health stakeholders and those potentially at risk through the consumption of counterfeit pills.
Private Landowner Willingness to Manage Their Land for Carbon Sequestration in New York State
Authors: Stedman Richard Clark , Armstrong Andrea , Walsh Kathryn Bills , Connelly Nancy 
Published: April 2024

Abstract
Efforts to enhance carbon sequestration, including afforestation and reforestation, are critical strategies to meet the New York State (NYS) climate goals. In NYS, converting underutilized lands to mature forests can mitigate 4.9 million metric tons of CO2 annually, but 97% of suitable lands are privately owned. These mitigation figures do not consider landowner willingness to grow mature forest. Drawing on a survey of 979 NYS landowners, we explored interest in growing mature forest, potential barriers, and how they can be mitigated. Survey results indicate landowners seem reasonably interested (about one-third were “very interested”) in converting at least some of their land to mature forest for carbon sequestration. Respondents were most willing to convert land in young forest and shrubland and least willing to convert fallow fields, grassland, and agricultural land. Key barriers are related to inadequate labor and financial resources. Incentives focused on finances most increase willingness but only modestly so.
Study Implications: Land availability for carbon sequestration can only be realistically understood if we consider private landowner willingness to grow forests. We observed relatively strong enthusiasm for converting young forest and shrubland. Land conversion proponents could tailor management and communication strategies to owners of these land types. Conversion is tied to overcoming negative attitudes about the potential conflict between current management and managing for carbon sequestration and providing resources for conversion. Landowner willingness was less when the agricultural footprint was greater. With much farmland in NYS, the amount of land available for reforestation may be lower than what landcover-based estimates suggest.
SpatialSPM: statistical parametric mapping for the comparison of gene expression pattern images in multiple spatial transcriptomic datasets
Authors: Ohn Jungyoon , Seo Mi-Kyoung , Park Jeongbin , Lee Daeseung , Choi Hongyoon 
Published: April 2024

Abstract
Spatial transcriptomic (ST) techniques help us understand the gene expression levels in specific parts of tissues and organs, providing insights into their biological functions. Even though ST dataset provides information on the gene expression and its location for each sample, it is challenging to compare spatial gene expression patterns across tissue samples with different shapes and coordinates. Here, we propose a method, SpatialSPM, that reconstructs ST data into multi-dimensional image matrices to ensure comparability across different samples through spatial registration process. We demonstrated the applicability of this method by kidney and mouse olfactory bulb datasets as well as mouse brain ST datasets to investigate and directly compare gene expression in a specific anatomical region of interest, pixel by pixel, across various biological statuses. Beyond traditional analyses, SpatialSPM is capable of generating statistical parametric maps, including T-scores and Pearson correlation coefficients. This feature enables the identification of specific regions exhibiting differentially expressed genes across tissue samples, enhancing the depth and specificity of ST studies. Our approach provides an efficient way to analyze ST datasets and may offer detailed insights into various biological conditions.
Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements
Authors: Pham Phuong , Wood Elizabeth A , Dunbar Emma L , Cox Michael M , Goodman Myron F 
Published: April 2024

Abstract
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, $ \le$2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.
Cancer drug sensitivity estimation using modular deep Graph Neural Networks
Authors: Campana Pedro A , Prasse Paul , Lienhard Matthias , Thedinga Kristina , Herwig Ralf , Scheffer Tobias 
Published: April 2024

Abstract
Computational drug sensitivity models have the potential to improve therapeutic outcomes by identifying targeted drugs components that are tailored to the transcriptomic profile of a given primary tumor. The SMILES representation of molecules that is used by state-of-the-art drug-sensitivity models is not conducive for neural networks to generalize to new drugs, in part because the distance between atoms does not generally correspond to the distance between their representation in the SMILES strings. Graph-attention networks, on the other hand, are high-capacity models that require large training-data volumes which are not available for drug-sensitivity estimation. We develop a modular drug-sensitivity graph-attentional neural network. The modular architecture allows us to separately pre-train the graph encoder and graph-attentional pooling layer on related tasks for which more data are available. We observe that this model outperforms reference models for the use cases of precision oncology and drug discovery; in particular, it is better able to predict the specific interaction between drug and cell line that is not explained by the general cytotoxicity of the drug and the overall survivability of the cell line. The complete source code is available at https://zenodo.org/doi/10.5281/zenodo.8020945. All experiments are based on the publicly available GDSC data.
Consensus recommendations on management of selumetinib-associated adverse events in pediatric patients with neurofibromatosis type 1 and plexiform neurofibromas
Authors: Azizi Amedeo A , Hargrave Darren , Passos João , Wolkenstein Pierre , Rosenbaum Thorsten , Santoro Claudia , Rosenmayr Verena , Pletschko Thomas , Ascierto Paolo A , Hernández Héctor Salvador 
Published: April 2024

Abstract

Background
Selumetinib is the first approved treatment for pediatric patients with neurofibromatosis type 1 (NF1) and symptomatic, inoperable plexiform neurofibromas (PN) in the EU and US, as well as in multiple other countries. Evidence for the management of selumetinib-associated adverse events (AEs) is mostly limited to clinical trials and expanded-access programs. We gathered a panel of European healthcare practitioners with clinical experience prescribing selumetinib and/or managing pediatric patients with NF1-PN to provide recommendations on the prevention and management of AEs.

Methods
A modified Delphi approach was used to develop the recommendations among the group of experts. Initial statements were developed from a literature review of current management recommendations and regulatory reports. The panel refined the statements and rated the extent to which they agreed with them in 2 sessions and a follow-up survey. The panel comprised 2 pediatric neuro-oncologists, 1 pediatric oncologist, 1 pediatrician, 1 neuropediatrician, 1 oncologist, 1 neurologist, 2 psychologists, and 1 dermatologist.

Results
The experts agreed on the relative frequency and impact of AEs potentially associated with selumetinib. Consensus-level agreement was reached for 36 statements regarding the prevention and management of AEs potentially associated with selumetinib. Experts recommended treatments for AEs based on their experience.

Conclusions
The development of a variety of consensus statements indicates expert agreement on best practices for the prevention and management of AEs potentially associated with selumetinib in pediatric patients with NF1-PN. These events are generally manageable and should be considered alongside treatment benefit. Information sharing is warranted as further experience is gained.