bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fucoidan modulates SIRT1 and NLRP3 to alleviate hypertensive retinopathy: in vivo and in vitro insights
Authors: Li Jing , Wang Xiaochen , Bai Jie , Wei Huangzhao , Wang Wenbo , Wang Shuai 
Published: February 2024

Abstract
Background
Hypertension influences the inflammatory pathological changes in the retina. The function of the inflammasomes is significant. To see if Sirtuin 1 (SIRT1) regulates angiotensin II (Ang II)-induced hypertensive retinopathy and inflammation by modulating NOD-like receptor thermal protein domain associated protein 3 (NLRP3) inflammasome activation and the potential protective effects of fucoidan (FO) in mouse retinal vascular endothelial cells (mRECs) and mice retina.

Methods
The diagnosis of hypertensive retinopathy was made after three weeks of Ang II infusion (3000 ng/kg/min). One day prior to the commencement of Ang II infusion, the mice were treatment with NLRP3 inhibitor MCC950 (10 mg/kg/day, intraperitoneal injections) or FO (300 mg/kg/day, oral gavage). A blood pressure was recorded. Hematoxylin and eosin (H&E) staining was used to conduct pathological alterations, dihydroethidium bromide (DHE) was utilized to assess oxidative stress damage in the retina, and fluorescence angiography was used to identify vascular disorders in the eye. Using immunohistochemical labeling, NLRP3 expression was found. Reactive protein and mRNA expression levels in mouse retina and cells were assessed using Western blot and real-time quantitative polymerase chain reaction (RT-qPCR).

Results
NLRP3 inflammasome activation and SIRT1 decrease were brought about by Ang II infusion. Retinopathy and dysfunction were lessened by MCC950 target-induced NLRP3 inflammasome activation, while overexpression of SIRT1 had the opposite impact on NLRP3 inflammasome activation, indicating that SIRT1 functions as an upstream regulator of NLRP3 activity. FO may improve SIRT1 expression and decrease NLRP3 activation in retinopathy and dysfunction brought on by Ang II, and the effects were consistent across both in vivo and in vitro models.

Conclusions
SIRT1 adversely regulates the NLRP3 inflammasome pathway, which in turn increases Ang II-induced inflammation and hypertensive retinopathy. FO may mitigate Ang II-induced retinopathy and dysfunction via modulating the expression of SIRT1/NLRP3. This implies practical approaches to the management of hypertensive retinopathy.
PlantNh-Kcr: a deep learning model for predicting non-histone crotonylation sites in plants
Authors: Jiang Yanming , Yan Renxiang , Wang Xiaofeng 
Published: February 2024

Abstract
Background
Lysine crotonylation (Kcr) is a crucial protein post-translational modification found in histone and non-histone proteins. It plays a pivotal role in regulating diverse biological processes in both animals and plants, including gene transcription and replication, cell metabolism and differentiation, as well as photosynthesis. Despite the significance of Kcr, detection of Kcr sites through biological experiments is often time-consuming, expensive, and only a fraction of crotonylated peptides can be identified. This reality highlights the need for efficient and rapid prediction of Kcr sites through computational methods. Currently, several machine learning models exist for predicting Kcr sites in humans, yet models tailored for plants are rare. Furthermore, no downloadable Kcr site predictors or datasets have been developed specifically for plants. To address this gap, it is imperative to integrate existing Kcr sites detected in plant experiments and establish a dedicated computational model for plants.

Results
Most plant Kcr sites are located on non-histones. In this study, we collected non-histone Kcr sites from five plants, including wheat, tabacum, rice, peanut, and papaya. We then conducted a comprehensive analysis of the amino acid distribution surrounding these sites. To develop a predictive model for plant non-histone Kcr sites, we combined a convolutional neural network (CNN), a bidirectional long short-term memory network (BiLSTM), and attention mechanism to build a deep learning model called PlantNh-Kcr. On both five-fold cross-validation and independent tests, PlantNh-Kcr outperformed multiple conventional machine learning models and other deep learning models. Furthermore, we conducted an analysis of species-specific effect on the PlantNh-Kcr model and found that a general model trained using data from multiple species outperforms species-specific models.

Conclusion
PlantNh-Kcr represents a valuable tool for predicting plant non-histone Kcr sites. We expect that this model will aid in addressing key challenges and tasks in the study of plant crotonylation sites.
The association of ICUC trauma score and quick DASH in a distal radius fracture cohort
Authors: Liu Wen-Chih , Hartwich Magdalena , Locascio Joseph J. , Regazzoni Pietro , Jupiter Jesse B. , Fernandez Dell’Oca Alberto 
Published: February 2024

Abstract
Background
This study evaluates the association between ICUC trauma and short-form Disabilities of the Arm, Shoulder, and Hand Questionnaire (Quick DASH) scores among patients who underwent surgery for distal radius fractures.

Methods
This research gathered patient-reported outcomes (PROs) from patients registered in the ICUC database at a single trauma center. The study involved 76 adult patients who underwent surgical treatment for distal radius fractures before 2023. These patients received a volar locking plate for their distal radius fracture. The research utilized two different PROs to evaluate the patients’ conditions. The ICUC trauma score measures functional impairment and pain through two 5-point scale questions, allowing patients to self-assess these aspects. The Quick DASH, comprising 11 questions, was used to evaluate symptoms and functionality of the upper extremity.

Results
For patients aged 55.9 ± 15.3 years and 4.6 ± 3.9 years post-op follow-up, the ICUC trauma score was 0.70 ± 0.95, and Quick DASH was 6.07 ± 10.35. A strong correlation between ICUC and Quick DASH was identified (r = 0.71, P < 0.01). The interaction between the ICUC trauma score and age at the surgery to Quick DASH revealed a significant unstandardized partial regression coefficient of 0.19 (95% confidence interval 0.08–0.31; P < 0.01).

Conclusion
This study demonstrated a strong correlation between the ICUC trauma score and the Quick DASH among patients, especially the elderly. It was noted that an elevation in the ICUC trauma score is linked to a more marked increase in the Quick DASH score, particularly in older patients. Given its simplicity and efficacy, the ICUC trauma score may be a viable alternative to the Quick DASH for assessing the patient’s clinical outcomes.
Genome-scale transcriptional activation by non-homologous end joining-mediated integration in Yarrowia lipolytica
Authors: Liu Xiaoqin , Deng Jingyu , Zhang Jinhong , Cui Zhiyong , Qi Qingsheng , Hou Jin 
Published: February 2024

Abstract
Background
Genome-scale screening can be applied to efficiently mine for unknown genes with phenotypes of interest or special functions. It is also useful to identify new targets for engineering desirable properties of cell factories.

Results
Here, we designed a new approach for genome-scale transcription activation using non-homologous end joining (NHEJ)-mediated integration in Yarrowia lipolytica. We utilized this approach to screen for genes that, upon activation, confer phenotypes including improved acetic acid tolerance and xylose metabolism. The candidates were validated using gene overexpression, and functional changes including improved growth performance under multiple stressors and activated pentose metabolism were identified.

Conclusions
This study provides a simple and effective approach to randomly activate endogenous genes and mine for key targets associated with phenotypes of interest. The specific gene targets identified here will be useful for cell factory construction and biorefining lignocellulose.
Stable expression of mucin glycoproteins GP40 and GP15 of Cryptosporidium parvum in Toxoplasma gondii
Authors: Li Muxiao , Sun Xiaohua , Chen Haoyu , Li Na , Feng Yaoyu , Xiao Lihua , Guo Yaqiong 
Published: February 2024

Abstract
Background
Cryptosporidium spp. are common protozoa causing diarrhea in humans and animals. There are currently only one FDA-approved drug and no vaccines for cryptosporidiosis, largely due to the limited knowledge of the molecular mechanisms involved in the invasion of the pathogens. Previous studies have shown that GP60, which is cleaved into GP40 and GP15 after expression, is an immunodominant mucin protein involved in the invasion of Cryptosporidium. The protein is highly O-glycosylated, and recombinant proteins expressed in prokaryotic systems are non-functional. Therefore, few studies have investigated the function of GP40 and GP15.

Methods
To obtain recombinant GP40 with correct post-translational modifications, we used CRISPR/Cas9 technology to insert GP40 and GP15 into the UPRT locus of Toxoplasma gondii, allowing heterologous expression of Cryptosporidium proteins. In addition, the Twin-Strep tag was inserted after GP40 for efficient purification of GP40.

Results
Western blotting and immunofluorescent microscopic analyses both indicated that GP40 and GP15 were stably expressed in T. gondii mutants. GP40 localized not only in the cytoplasm of tachyzoites but also in the parasitophorous vacuoles, while GP15 without the GPI anchor was expressed only in the cytoplasm. In addition, a large amount of recTgGP40 was purified using Strep-TactinXT supported by a visible band of ~ 50 kDa in SDS-PAGE.

Conclusions
The establishment of a robust and efficient heterologous expression system of GP40 in T. gondii represents a novel approach and concept for investigating Cryptosporidium mucins, overcoming the limitations of previous studies that relied on unstable transient transfection, which involved complex steps and high costs.

Graphical Abstract
Relationships of change in Clinical Dementia Rating (CDR) on patient outcomes and probability of progression: observational analysis
Authors: Tariot Pierre N. , Boada Mercè , Lanctôt Krista L. , Hahn-Pedersen Julie , Dabbous Firas , Udayachalerm Sariya , Raket Lars Lau , Halchenko Yuliya , Michalak Wojciech , Weidner Wendy , Cummings Jeffrey 
Published: February 2024

Abstract
Background
Understanding the relationship among changes in Clinical Dementia Rating (CDR), patient outcomes, and probability of progression is crucial for evaluating the long-term benefits of disease-modifying treatments. We examined associations among changes in Alzheimer’s disease (AD) stages and outcomes that are important to patients and their care partners including activities of daily living (ADLs), geriatric depression, neuropsychiatric features, cognitive impairment, and the probabilities of being transitioned to a long-term care facility (i.e., institutionalization). We also estimated the total time spent at each stage and annual transition probabilities in AD.

Methods
The study included participants with unimpaired cognition, mild cognitive impairment (MCI) due to AD, and mild, moderate, and severe AD dementia in the National Alzheimer’s Coordinating Center (NACC) Uniform Data Set (UDS) database. The associations among change in AD stages and change in relevant outcomes were estimated using linear mixed models with random intercepts. The probability of transitioning to long-term care facilities was modeled using generalized estimating equations. The total length of time spent at AD stages and annual transition probabilities were estimated with multistate Markov models.

Results
The estimated average time spent in each stage was 3.2 years in MCI due to AD and 2.2, 2.0, and 2.8 years for mild, moderate, and severe AD dementia, respectively. The annual probabilities of progressing from MCI to mild, moderate, and severe AD dementia were 20, 4, and 0.7%, respectively. The incremental change to the next stage of participants with unimpaired cognition, MCI, and mild, moderate, and severe AD dementia (to death) was 3.2, 20, 26.6, 31, and 25.3%, respectively. Changes in ADLs, neuropsychiatric features, and cognitive measures were greatest among participants who transitioned from MCI and mild AD dementia to more advanced stages. Participants with MCI and mild and moderate AD dementia had increasing odds of being transitioned to long-term care facilities over time during the follow-up period.

Conclusions
The findings demonstrated that participants with early stages AD (MCI or mild dementia) were associated with the largest changes in clinical scale scores. Early detection, diagnosis, and intervention by disease-modifying therapies are required for delaying AD progression. Additionally, estimates of transition probabilities can inform future studies and health economic modeling.
Improvement of ribonucleic acid production in Cyberlindnera jadinii and optimization of fermentation medium
Authors: Li Mengting , Gao Shuhong , Yang Pengcheng , Li Hejin 
Published: February 2024

AbstractTo enhance the ribonucleic acid (RNA) productivity for industrial applications, this study employed strain screening and medium optimization to improve the content of RNA in Cyberlindnera jadinii. A rapid screening method, combining atmospheric and room temperature plasma mutagenesis, 48-deep-well plates fermentation, and microplate reader detection, was developed. A mutant strain named WB15 with high RNA content was successfully obtained, exhibiting the RNA content of 156 ± 4.5 mg/g DCW, 1.4 times of the starting strain CCTCC AY 92020. Furthermore, Plackett–Burman design and response surface methodology were employed to identify three significant factors (yeast extract, soybean peptone, and KH2PO4) affecting the RNA content. By utilizing the optimal medium composed of 13.43 g/L yeast extract, 12.12 g/L soybean peptone and 2.78 g/L KH2PO4, the RNA content of WB15 further increased to 184 ± 4.9 mg/g DCW. Additionally, the mutant strain WB15 exhibited a greater cellular width compared to AY 92020, along with increased growth rate and single-cell RNA content by 22% and 48.9%, respectively. Perturbations in ribosome assembly, specifically a reduction in the ratio of ribosomal proteins to ribosomal RNA of the large subunit, might indirectly contribute to the higher RNA content in the WB15 strain. Overall, the combination of rapid screening with fermentation medium optimization proved to be an effective approach for improving the RNA content of C. jadinii, thus facilitating the industrial production of RNA.
Lava flow impacts on the built environment: insights from a new global dataset
Authors: Meredith Elinor S. , Jenkins Susanna F. , Hayes Josh L. , Lallemant David , Deligne Natalia I. , Teng Natalie R. X. 
Published: February 2024

AbstractThe recent destruction of thousands of homes by lava flows from La Palma volcano, Canary Islands, and Nyiragongo volcano, Democratic Republic of Congo, serves as a reminder of the devastating impact that lava flows can have on communities living in volcanically active regions. Damage to buildings and infrastructure can have widespread and long-lasting effects on rehabilitation and livelihoods. Our understanding of how lava flows interact with buildings is limited and based upon sparse empirical data. Often a binary impact is assumed (destroyed when in contact with the flow and intact when not in contact with the flow), although previous events have shown this to be an oversimplification. Empirical damage data collected after past events provide an evidence base from which to better understand lava flow impacts across a range of building types, environments, and eruption styles, as well as to explore the temporal and spatial trends in these impacts. However, information on lava flow impacts is scattered across literature, reports, and maps; no comprehensive dataset of lava flow impacts exists. In this study, we compile and standardise lava flow impact information from previously compiled data, eruption records, and published literature to create the first comprehensive global dataset of impacts on the built environment from lava flows. We found that since the first recorded event between 5494 yr B.P. and 5387 yr B.P., lava flows from at least 155 events have impacted buildings or infrastructure (e.g., roads, electricity pylons, ski-lifts), with most (47%, n = 73) recorded as located in Europe. Over the last century, there have been approximately seven lava flow impact events per decade (n = 71 total). This greatly expands on the past compilations of lava flow impact events. Since ca. 1800 CE, impacts have been consistently documented for less than 14% of recorded eruptions with lava flows globally; prior to 1800 CE, impacts were recorded much more variably (between 0 and 70% of lava flows in any 10-year time bin). The most destructive recorded events were the 1669 CE lava flows at Etna volcano, Italy, which destroyed up to 12 villages and part of the city of Catania, and the 2002 CE lava flows at Nyiragongo volcano, Democratic Republic of Congo, which destroyed up to 14,000 buildings. We found that few studies in the dataset report building typology, damage severity, or hazard intensity at the building-level scale, limiting our ability to assess past building-lava interactions. Future collection of building-level hazard and impact data, supplemented with non-English language records, can be used to inform models that forecast future impacts, support lava flow risk assessments, and develop potential mitigation measures.
Clinical effect of different concentrations of ropivacaine in the labor analgesia of dural puncture epidural technique for obese puerperae
Authors: Shi Liping , Zhang Difei , Ye Pengfei , Peng Weihua , Yin Yan , Zhang Ye 
Published: February 2024

Abstract
Background
This study was performed to analyze the clinical effect of different concentrations of ropivacaine in the labor analgesia of the dural puncture epidural (DPE) technique for obese puerperae.

Methods
One hundred and fifty first-term obese women who received vaginal delivery and required labor analgesia in our hospital were selected prospectively for this study, and divided into groups A, B, and C. The three groups of puerpera were given epidurals with different concentrations of ropivacaine (0.075%, 0.10%, and 0.125%) with sufentanil (0.5 μg/ml) for the labor analgesia regimen. The visual analog scale (VAS), Ramsay scale, and Bromage scale of puerperae before analgesia and at different time points after anesthesia, and analgesic onset time, analgesia time, first PCEA time, PCEA pressing time, ropivacaine consumption, labor time, maternal blood pressure and heart rate, maternal adverse reactions, blood gas analysis in the neonatal umbilical artery, and Apgar score were observed.

Results
The analgesia onset time, PCEA pressing time, and ropivacaine consumption in group C were lower and the analgesia time and the first PCEA time were longer than those in groups A and B. At T1-T3 and T5, VAS scores of group A were higher than those in groups B and C, Ramsay score of group A was lower than that of groups B and C at T2–T3, and Bromage score of group C at any time point was higher than other two groups. The time of the second stage of labor in groups B and C was longer than that in group A, which in group C was longer than that in group B. Compared with groups A and C, the blood pressure and heart rate of puerperae in group B were closer to normal values. Three different concentrations of ropivacaine had no significant effect on the umbilical artery blood gas analysis indices and Apgar scores at 1st minute and 5th minute in neonates. The incidence of maternal adverse reactions in group C was lower than those in groups A and B.

Conclusion
0.1% ropivacaine combined with 0.5 μg/ml sufentanil through DPE technique has good analgesic efficacy and few adverse effects in obese puerperae.
Existing evidence on the use of environmental DNA as an operational method for studying rivers: a systematic map and thematic synthesis
Authors: Cruz-Cano R. , Kolb M. , Saldaña-Vázquez R. A. , Bretón-Deval L. , Cruz-Cano N. , Aldama-Cervantes A. 
Published: February 2024

Abstract
Background
Environmental DNA (eDNA) is the DNA that can be extracted from an environmental sample, enabling the monitoring of whole biological communities across a large number of samples, at a potentially lower cost, which can significantly benefit river conservation. A systematic mapping protocol was designed to investigate the use of eDNA in rivers, specifically in terms of research topics, geographic and taxonomic biases, as well as information gaps. Furthermore, the potential research opportunities of eDNA in rivers and possible paths to find this kind of information on available platforms are identified.

Methods
A published systematic map protocol was applied, consisting of a search for published articles and gray literature in two bibliographic databases and one search engine. All search results were submitted to a 2-stage screening for relevance and pertinence in accordance with pre-defined eligibility criteria. Data extraction and codification regarding country of study, year, taxonomic group, sequencing platform, and type of technique employed resulted in a publicly available database.

Results
From 7372 studies initially obtained by the search, 545 met the inclusion criteria spanning a period from 2003 to 2022. The five countries with most studies are: USA (134), Japan (61), China (54), Brazil (29) and the UK (25). The most used fragments to analyze DNA are 16S and COI, whilst 26S and 23S are the least used. Only 84 (15%) of the studies reported hypervariable regions, among which the most used are V4 and V5. Regarding taxonomic groups, fishes are most often studied (176), followed by bacteria (138) and virus (52), while fungi is the least studied group (3). Concerning data availability, 229 (42%) studies provided access to sequencing data.

Conclusions
This study presents a comprehensive analysis of the available evidence regarding the implementation of the eDNA methods in rivers. The findings indicate that since the year 2003, this approach has been applied to aquatic lotic systems, and their recent increase can be attributed to the development of Next-Generation-Sequencing technologies and their reduced costs. However, there is a bias towards high-income countries, particularly USA and Europe. Widespread use and applications of this approach at a global level would allow for the generation of a large amount of information that can be compared between countries to understand if responses of aquatic systems follow similar patterns worldwide.