bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to avoid harm with feeding critically ill patients: a synthesis of viewpoints of a basic scientist, dietitian and intensivist
Authors: Reintam Blaser Annika , Rooyackers Olav , Bear Danielle E. 
Published: July 2023

AbstractThe optimal feeding strategy in critically ill patients is a matter of debate, with current guidelines recommending different strategies regarding energy and protein targets. Several recent trials have added to the debate and question our previous understanding of the provision of nutrition during critical illness. This narrative review aims to provide a summary of interpretation of recent evidence from the view of basic scientist, critical care dietitian and intensivist, resulting in joined suggestions for both clinical practice and future research. In the most recent randomised controlled trial (RCT), patients receiving 6 versus 25 kcal/kg/day by any route achieved readiness for ICU discharge earlier and had fewer GI complications. A second showed that high protein dosage may be harmful in patients with baseline acute kidney injury and more severe illness. Lastly, a prospective observational study using propensity score matched analysis suggested that early full feeding, especially enteral, compared to delayed feeding is associated with a higher 28-day mortality. Viewpoints from all three professionals point to the agreement that early full feeding is likely harmful, whereas important questions regarding the mechanisms of harm as well as on timing and optimal dose of nutrition for individual patients remain unanswered and warrant future studies. For now, we suggest giving low dose of energy and protein during the first few days in the ICU and apply individualised approach based on assumed metabolic state according to the trajectory of illness thereafter. At the same time, we encourage research to develop better tools to monitor metabolism and the nutritional needs for the individual patient accurately and continuously.
The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus
Authors: Cunningham Christopher B. , Shelby Emily A. , McKinney Elizabeth C. , Schmitz Robert J. , Moore Allen J. , Moore Patricia J. 
Published: July 2023

AbstractBackgroundThe function of DNA methyltransferase genes of insects is a puzzle, because an association between gene expression and methylation is not universal for insects. If the genes normally involved in cytosine methylation are not influencing gene expression, what might be their role? We previously demonstrated that gametogenesis ofOncopeltus fasciatusis interrupted at meiosis following knockdown ofDNA methyltransferase 1(Dnmt1) and this is unrelated to changes in levels of cytosine methylation. Here, using transcriptomics, we tested the hypothesis thatDmnt1is a part of the meiotic gene pathway. Testes, which almost exclusively contain gametes at varying stages of development, were sampled at 7 days and 14 days following knockdown ofDmnt1using RNAi.ResultsUsing microscopy, we found actively dividing spermatocysts were reduced at both timepoints. However, as with other studies, we sawDnmt1knockdown resulted in condensed nuclei after mitosis–meiosis transition, and then cellular arrest. We found limited support for a functional role forDnmt1in our predicted cell cycle and meiotic pathways. An examination of a priori Gene Ontology terms showed no enrichment for meiosis. We then used the full data set to reveal further candidate pathways influenced byDnmt1for further hypotheses. Very few genes were differentially expressed at 7 days, but nearly half of all transcribed genes were differentially expressed at 14 days. We found no strong candidate pathways for howDnmt1knockdown was achieving its effect through Gene Ontology term overrepresentation analysis.ConclusionsWe, therefore, suggest thatDmnt1plays a role in chromosome dynamics based on our observations of condensed nuclei and cellular arrest with no specific molecular pathways disrupted.
Islet transplantation: overcoming the organ shortage
Authors: Mantovani Marluce da Cunha , Gabanyi Ilana , Pantanali Carlos Andrés , Santos Vinícius Rocha , Corrêa-Giannella Maria Lúcia Cardillo , Sogayar Mari Cleide 
Published: July 2023

AbstractBackgroundType 1 diabetesmellitus(T1D) is a condition resulting from autoimmune destruction of pancreatic β cells, leading patients to require lifelong insulin therapy, which, most often, does not avoid the most common complications of this disease. Transplantation of isolated pancreatic islets from heart-beating organ donors is a promising alternative treatment for T1D, however, this approach is severely limited by the shortage of pancreata maintained under adequate conditions.MethodsIn order to analyze whether and how this problem could be overcome, we undertook a retrospective study from January 2007 to January 2010, evaluating the profile of brain-dead human pancreas donors offered to our Cell and Molecular Therapy NUCEL Center (www.usp.br/nucel) and the basis for organ refusal.ResultsDuring this time period, 558 pancreata were offered by the São Paulo State Transplantation Central, 512 of which were refused and 46 were accepted for islet isolation and transplantation. Due to the elevated number of refused organs, we decided to analyze the main reasons for refusal in order to evaluate the possibility of improving the organ acceptance rate. The data indicate that hyperglycemia, technical issues, age, positive serology and hyperamylasemia are the top five main causes for declination of a pancreas offer.ConclusionsThis study underlines the main reasons to decline a pancreas offer in Sao Paulo—Brazil and provides some guidance to ameliorate the rate of eligible pancreas donors, aiming at improving the islet isolation and transplantation outcome.Trial registration: Protocol CAPPesq number 0742/02/CONEP 9230.
Diabetes duration or age at onset and mortality in insulin-dependent diabetics: a systematic review and meta-analysis
Authors: Wang Xing-mu , Zhong Shu-ping , Li Gang-feng , Zhuge Fu-yuan 
Published: July 2023

Abstract
Background
This meta-analysis was conducted given the contradictory findings from studies on the influence of diabetes duration or age at onset on mortality in patients with insulin-dependent diabetes mellitus (IDDM).

Methods
Electronic databases (PubMed, Embase, Cochrane, Web of Knowledge, Scopus, and CINHAL) were comprehensively searched to identify relevant studies until October 31, 2022. All of the selected articles contained statistics on hazard ratios, relative risks (RRs), or odds ratios, or data for estimating the association between diabetes duration or age at onset and total mortality in IDDM patients. Regardless the heterogeneity assessed by the I2 statistic, pooled RRs and 95% confidence intervals (CI) for total mortality were acquired via random effect meta-analysis with inverse variance weighting.

Results
This meta-analysis finally included 19 studies involving 122, 842 individuals. Both age at onset and diabetes duration were positively associated with an increased mortality rate in IDDM patients. Specifically, the pooled RRs for age at onset and diabetes duration were 1.89 (95%CI 1.43–2.50) and 1.89 (95%CI 1.16–3.09) respectively. Subgroup analyses revealed that only prepubertal onset was associated with a greater survival advantage than pubertal or postpubertal onset.

Conclusions
The findings of this meta-analysis and systematic review suggest that a later age at onset or longer diabetes duration is associated with increased risk of total mortality in IDDM patients. However, this conclusion shall be interpreted with caution due to the possibility of residual confounding and be confirmed in the future by well-designed studies.
Integrated biomarker profiling of the metabolome associated with type 2 diabetes mellitus among Tibetan in China
Authors: Meng Jinli , Huang Fangfang , Shi Jing , Zhang Chenghui , Feng Li , Wang Suyuan , Li Hengyan , Guo Yongyue , Hu Xin , Li Xiaomei , He Wanlin , Cheng Jian , Wu Yunhong 
Published: July 2023

Abstract
Introduction
Metabolomic signatures of type 2 diabetes mellitus (T2DM) in Tibetan Chinese population, a group with high diabetes burden, remain largely unclear. Identifying the serum metabolite profile of Tibetan T2DM (T-T2DM) individuals may provide novel insights into early T2DM diagnosis and intervention.

Methods
Hence, we conducted untargeted metabolomics analysis of plasma samples from a retrospective cohort study with 100 healthy controls and 100 T-T2DM patients by using liquid chromatography–mass spectrometry.

Results
The T-T2DM group had significant metabolic alterations that are distinct from known diabetes risk indicators, such as body mass index, fasting plasma glucose, and glycosylated hemoglobin levels. The optimal metabolite panels for predicting T-T2DM were selected using a tenfold cross-validation random forest classification model. Compared with the clinical features, the metabolite prediction model provided a better predictive value. We also analyzed the correlation of metabolites with clinical indices and found 10 metabolites that were independently predictive of T-T2DM.

Conclusion
By using the metabolites identified in this study, we may provide stable and accurate biomarkers for early T-T2DM warning and diagnosis. Our study also provides a rich and open-access data resource for optimizing T-T2DM management.
A case report of acute food protein-induced enterocolitis syndrome to walnut
Authors: Zhu Wen Zheng , Perkins Siobhan 
Published: July 2023

Abstract
Background
Food protein-induced enterocolitis syndrome (FPIES) is a delayed, non-IgE-mediated food allergy. This syndrome was once thought to be rare, but emerging literature suggests an increasing incidence along with more foods being implicated. Also, with the introduction of guidelines on early peanut introduction, peanut-induced FPIES seems to be increasing in Australia and USA. Although most patients are diagnosed with FPIES within the first year of life, most commonly with food triggers to cow’s milk or soy, other phenotypes exist in comparison to this classic presentation. In this case report, we present a patient with late onset of acute FPIES at age 3 to walnut.

Case Presentation
We describe a case of FPIES in a 12-year-old boy who had recurrent episodes of repetitive emesis, that began at age 3, each time after consuming walnuts. Mom does not give a history of intentional feeding (or avoidance) of walnut and/ or pecans. She also described possible reactions with pine nuts and macadamia. He was assessed with an oral food challenge to walnut, which triggered an episode of acute FPIES. He developed vomiting with onset 2 h post-ingestion, pallor, lethargy, and required an emergency department visit for anti-emetic medications and oral rehydration therapy. He improved on the therapy and now avoids cashew, pistachio, hazelnuts, walnuts, pecans, pine nuts, and macadamia nuts.

Conclusions
This case report adds to the limited literature that exists on culprit food allergens in FPIES. We present an acute FPIES triggered by the ingestion of walnuts. The diagnosis, common food triggers, and natural history of FPIES are described. There remains a lack of information on the natural history of FPIES, especially towards uncommon food triggers and on FPIES that present beyond infancy.
Tetra-block: ultrasound femoral, lateral femoral-cutaneous, obturator, and sciatic nerve blocks in lower limb anesthesia: a case series
Authors: Coviello Antonio , Iacovazzo Carmine , Cirillo Dario , Diglio Pasquale , Bernasconi Alessio , Cozzolino Andrea , Izzo Antonio , Marra Annachiara , Servillo Giuseppe , Vargas Maria 
Published: July 2023

Abstract
Background
The gold standard anesthesiologic procedure for urgent femur fracture surgery is Spinal Anesthesia. It is not always feasible because of patients' severe comorbidities and difficulties in optimizing drug therapy in the appropriate time frame such as discontinuation of anticoagulant drugs. The use of four peripheral nerve blocks (tetra-block) can be a winning weapon when all seems lost.

Case presentation
We present, in this case series, three Caucasian adult femur fractures (an 83-year-old woman, a 73-year-old man, and a 68-year-old woman) with different and major comorbidities (cardiac or circulatory disorders on anticoagulants therapy that were not discontinued on time; breast cancer and others) underwent the same anesthesiologic approach in the urgent setting. Ultrasound peripheral nerve blocks, that is femoral, lateral femoral cutaneous, obturator, and sciatic with parasacral approach were successfully performed in all patients who underwent intramedullary nailing for intertrochanteric fracture. We evaluated the adequacy of the anesthesia plane, postoperative pain control with the VAS scale, and the incidence of postoperative side effects.

Conclusions
Four peripheral nerve blocks (Tetra-block) can be alternative anesthesiologic management in urgent settings, in patients where drug therapy cannot be optimized, as in antiplatelet and anticoagulant therapy.
FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards
Authors: Gaignard Alban , Rosnet Thomas , De Lamotte Frédéric , Lefort Vincent , Devignes Marie-Dominique 
Published: July 2023

AbstractThe current rise of Open Science and Reproducibility in the Life Sciences requires the creation of rich, machine-actionable metadata in order to better share and reuse biological digital resources such as datasets, bioinformatics tools, training materials, etc. For this purpose, FAIR principles have been defined for both data and metadata and adopted by large communities, leading to the definition of specific metrics. However, automatic FAIRness assessment is still difficult because computational evaluations frequently require technical expertise and can be time-consuming. As a first step to address these issues, we propose FAIR-Checker, a web-based tool to assess the FAIRness of metadata presented by digital resources. FAIR-Checker offers two main facets: a “Check” module providing a thorough metadata evaluation and recommendations, and an “Inspect” module which assists users in improving metadata quality and therefore the FAIRness of their resource. FAIR-Checker leverages Semantic Web standards and technologies such as SPARQL queries and SHACL constraints to automatically assess FAIR metrics. Users are notified of missing, necessary, or recommended metadata for various resource categories. We evaluate FAIR-Checker in the context of improving the FAIRification of individual resources, through better metadata, as well as analyzing the FAIRness of more than 25 thousand bioinformatics software descriptions.
Differential impact of BRAFV600E isoforms on tumorigenesis in a zebrafish model of melanoma
Authors: De Paolo Raffaella , Sarti Samanta , Bernardi Sara , Cucco Francesco , Tavosanis Andrea , Pitto Letizia , Poliseno Laura 
Published: July 2023

AbstractBRAFV600E comes as two main splicing variants. The well-studied ref isoform and the recently discovered X1 isoform are co-expressed in cancer cells and differ in terms of 3’UTR length and sequence, as well as C-term protein sequence. Here, we use a melanoma model in zebrafish to study the role played by each isoform in larval pigmentation, nevi formation, and their progression into melanoma tumours. We show that both BRAFV600E-ref and BRAFV600E-X1 proteins promote larval pigmentation and nevi formation, while melanoma-free survival curves performed in adult fish indicate that BRAFV600E-ref protein is a much stronger melanoma driver that BRAFV600E-X1 protein. Crucially, we also show that the presence of the 3’UTR suppresses the effect of ref protein. Our data highlight the necessity to undertake a systematic study of BRAFV600E isoforms, in order to uncover the full spectrum of their kinase-(in)dependent and coding-(in)dependent functions, hence to develop more informed strategies for therapeutic targeting.
Extracellular matrix remodelling and stiffening contributes to tumorigenesis of salivary carcinoma ex pleomorphic adenoma——A study based on patient-derived organoids
Authors: Chen Wanling , Gu Ting , Chen Qianqian , Qu Chuxiang , Zhang Chunye , Hu Yuhua , Xia Ronghui , Zhang Ying , Wang Min , Huang Xinyi , Li Jiang , Shi Chaoji , Tian Zhen 
Published: July 2023

Abstract
Background
Salivary carcinoma ex pleomorphic adenoma (CXPA) is defined as a carcinoma that develops from benign pleomorphic adenoma (PA). Abnormally activated Androgen signaling pathway and amplification of HER-2/neu(ERBB-2) gene are known to be involved in CXPA tumorigenesis. Recent progress in tumour microenvironment research has led to identification that extracellular matrix (ECM) remodelling and increased stiffness act as critical contributing role in tumour carcinogenesis. This study examined ECM modifications to elucidate the mechanism underlying CXPA tumorigenesis.

Results
PA and CXPA organoids were successfully established. Histological observation, immunohistochemistry (IHC), and whole-exome sequencing demonstrated that organoids recapitulated phenotypic and molecular characteristics of their parental tumours. RNA-sequencing and bioinformatic analysis of organoids showed that differentially expressed genes are highly enriched in ECM-associated terms, implying that ECM alternations may be involved in carcinogenesis. Microscopical examination for surgical samples revealed that excessive hyalinized tissues were deposited in tumour during CXPA tumorigenesis. Transmission electron microscopy confirmed that these hyalinized tissues were tumour ECM in nature. Subsequently, examination by picrosirius red staining, liquid chromatography with tandem mass spectrometry, and cross-linking analysis indicated that tumour ECM was predominantly composed of type I collagen fibers, with dense collagen alignment and an increased level of collagen cross-linking. IHC revealed the overexpression of COL1A1 protein and collagen-synthesis-related genes, DCN and IGFBP5 (p < 0.05). Higher stiffness of CXPA than PA was demonstrated by atomic force microscopy and elastic imaging analysis. We utilized hydrogels to mimic ECM with varying stiffness degrees in vitro. Compared with softer matrices (5Kpa), CXPA cell line and PA primary cells exhibited more proliferative and invasive phenotypes in stiffer matrices (50Kpa, p < 0.01). Protein-protein interaction (PPI) analysis of RNA-sequencing data revealed that AR and ERBB-2 expression was associated with TWIST1. Moreover, surgical specimens demonstrated a higher TWIST1 expression in CXPA over PA. After knocking down TWIST1 in CXPA cells, cell proliferation, migration, and invasiveness were significantly inhibited (p < 0.01).

Conclusion
Developing CXPA organoids provides a useful model for cancer biology research and drug screening. ECM remodelling, attributed to overproduction of collagen, alternation of collagen alignment, and increased cross-linking, leads to increased ECM stiffness. ECM modification is an important contributor in CXPA tumorigenesis.
Comparison of the new version of DEEC protocol to extend WSN lifetime
Authors: El-Sayed Hamdy H. , Hashem Zainab Mostafa 
Published: July 2023

AbstractWireless sensor networks (WSNs) are used in many different fields. One of the most recent and rapidly expanding applications is the Internet of Things (IoT), which enables the connectivity of numerous objects or devices over the Internet. However, WSNs have a bigger concern about battery power than mobile ad hoc networks, which shortens the network's lifetime. As a result, extensive research has been done on lowering WSNs' energy usage. Designing a hierarchical clustering algorithm is one of many methods for lowering the energy consumption of WSNs. Given the restricted hardware capabilities of the sensor nodes, modeling and building energy-efficient routing solutions to enhance the overall network lifetime has emerged as one of the most crucial approaches in wireless sensor networks. Cluster-based heterogeneous routing protocols, a typical feature of routing technology, have demonstrated efficacy in managing topology, energy consumption, data collection or fusion, dependability, or stability in distributed sensor networks. The existing Distributed Energy-Efficient Clustering (DEEC) clustering protocol is changed in this study by switching the power level between the nodes and adding a threshold limit for cluster head selection. The number of packets sent to a base station increases by 843% when comparing the proposed improved DEEC protocol to the existing DEEC protocol, increasing the number of living nodes to more than 10,000 rounds, or over 30,000 rounds, which can be used to extend the WSN lifetime. The suggested algorithm outperforms alternative energy-efficient protocols in terms of stability period and network lifetime under various scenarios of area, energy, and node density.
Trajectory optimization for UAV-assisted relay over 5G networks based on reinforcement learning framework
Authors: Abohashish Sara M. M. , Rizk Rawya Y. , Elsedimy E. I. 
Published: July 2023

AbstractWith the integration of unmanned aerial vehicles (UAVs) into fifth generation (5G) networks, UAVs are used in many applications since they enhance coverage and capacity. To increase wireless communication resources, it is crucial to study the trajectory of UAV-assisted relay. In this paper, an energy-efficient UAV trajectory for uplink communication is studied, where a UAV serves as a mobile relay to maintain the communication between ground user equipment (UE) and a macro base station. This paper proposes a UAV Trajectory Optimization (UAV-TO) scheme for load balancing based on Reinforcement Learning (RL). The proposed scheme utilizes load balancing to maximize energy efficiency for multiple UEs in order to increase network resource utilization. To deal with nonconvex optimization, the RL framework is used to optimize the trajectory UAV. Both model-based and model-free approaches of RL are utilized to solve the optimization problem, considering line of sight and non-line of sight channel models. In addition, the network load distribution is calculated. The simulation results demonstrate the effectiveness of the proposed scheme under different path losses and different flight durations. The results show a significant improvement in performance compared to the existing methods.
Abnormal expression of fission and fusion genes and the morphology of mitochondria in eutopic and ectopic endometrium
Authors: Ye Chaoshuang , Chen Pei , Xu Bingning , Jin Yang , Pan Yongchao , Wu Tianyu , Du Yongjiang , Mao Jingxia , Wu Ruijin 
Published: July 2023

AbstractMitochondria play a pivotal role in physiological and metabolic function of the cell. Mitochondrial dynamics orchestrate mitochondrial function and morphology, involving fission and fusion as well as ultrastructural remodeling. Mounting evidence unravels the close link between mitochondria and endometriosis. However, how mitochondrial architecture changes through fission and fusion in eutopic and ectopic tissues of women with ovarian endometriosis remains unknown. We detected the expression of fission and fusion genes and the morphology of mitochondria in eutopic and ectopic endometrium in ovarian endometriosis. The results showed that the expression of DRP1 and LCLAT1 was upregulated in eutopic endometrial stromal cells (ESCs), and the expression of DRP1, OPA1, MFN1, MFN2, and LCLAT1 was significantly downregulated in ectopic ESCs, and reduced number of mitochondria, wider cristae width and narrower cristae junction width was observed, but there was no difference in cell survival rate. The altered mitochondrial dynamics and morphology might, respectively, provide an advantage for migration and adhesion in eutopic ESCs and be the adaptive response in ectopic endometrial cells to survive under hypoxic and oxidative stress environment.