bluuebunny/crossref_metadata_2025_split huggingface dataset:
An apicoplast-localized deubiquitinase contributes to the cell growth and apicoplast homeostasis of Toxoplasma gondii
Authors: Xia Jie , Yang Yimin , Chen Xueqiu , Song Kaiyue , Ma Guangxu , Yang Yi , Yao Chaoqun , Du Aifang 
Published: January 2024

AbstractToxoplasma gondii is among the most important parasites worldwide. The apicoplast is a unique organelle shared by all Apicomplexan protozoa. Increasing lines of evidence suggest that the apicoplast possesses its own ubiquitination system. Deubiquitination is a crucial step executed by deubiquitinase (DUB) during protein ubiquitination. While multiple components of ubiquitination have been identified in T. gondii, the deubiquitinases involved remain unknown. The aim of the current study was to delineate the localization of TgOTU7 and elucidate its functions. TgOTU7 was specifically localized at the apicoplast, and its expression was largely regulated during the cell cycle. Additionally, TgOTU7 efficiently breaks down ubiquitin chains, exhibits linkage-nonspecific deubiquitinating activity and is critical for the lytic cycle and apicoplast biogenesis, similar to the transcription of the apicoplast genome and the nuclear genes encoding apicoplast-targeted proteins. Taken together, the results indicate that the newly described deubiquitinase TgOTU7 specifically localizes to the apicoplast and affects the cell growth and apicoplast homeostasis of T. gondii.
I-REFF diagrams: enhancing transparency in systematic review through interactive reference flow diagrams
Authors: Walker Vickie R. , Lemeris Courtney R. , Magnuson Kristen , Sibrizzi Christopher A. , Shipkowski Kelly A. , Taylor Kyla W. , Rooney Andrew A. 
Published: January 2024

AbstractSystematic review methods are recognized for their rigor and transparency and are widely adapted to frameworks that cover review types such as systematic reviews, scoping reviews, and systematic evidence maps. Reporting guidelines help promote better systematic review practices and detailed documentation of the review process for different types of health research (e.g., PRISMA—Preferred Reporting Items for Systematic Reviews and Meta-Analyses; CONSORT—Consolidated Standards of Reporting Trials; and STROBE—Strengthening the Reporting of Observational Studies in Epidemiology). Transparency in the systematic review process and reporting of results is one of the key advantages of the methods and particularly important for hazard and risk assessments due to the high level of scrutiny these reviews face from scientific, political, and public communities. Data visualizations are important to clearly convey information from a review by helping readers perceive, understand, and assess the displayed information easily and quickly. The study flow diagram is a required element of a systematic review and maps out the number of included and excluded records identified, and the reasons for exclusion. Static literature flow diagrams help viewers readily understand the general review methodology and summarize the number of records included or excluded at each stage of the review. However, such diagrams can be time-consuming to develop and maintain during a systematic review or scoping review, and they provide limited summary-level information. We explored how the use of online systematic review tools such as DistillerSR coupled with visualization software such as Tableau can efficiently generate an Interactive REFerence Flow (I-REFF) diagram that is linked to the literature screening data, thus requiring minimal preparation, and resulting in a simplified process for updating the diagram. Furthermore, I-REFF diagrams enhance transparency and traceability by not only summarizing the records in the review but also allowing viewers to follow specific records throughout the review process. We present an example I-REFF diagram and discuss recommendations for key interactive elements to include in these diagrams and how this workflow can improve efficiency and result in an accessible and transparent interactive literature flow diagram without advanced programming.
Systematic review using a spiral approach with machine learning
Authors: Saeidmehr Amirhossein , Steel Piers David Gareth , Samavati Faramarz F. 
Published: January 2024

AbstractWith the accelerating growth of the academic corpus, doubling every 9 years, machine learning is a promising avenue to make systematic review manageable. Though several notable advancements have already been made, the incorporation of machine learning is less than optimal, still relying on a sequential, staged process designed to accommodate a purely human approach, exemplified by PRISMA. Here, we test a spiral, alternating or oscillating approach, where full-text screening is done intermittently with title/abstract screening, which we examine in three datasets by simulation under 360 conditions comprised of different algorithmic classifiers, feature extractions, prioritization rules, data types, and information provided (e.g., title/abstract, full-text included). Overwhelmingly, the results favored a spiral processing approach with logistic regression, TF-IDF for vectorization, and maximum probability for prioritization. Results demonstrate up to a 90% improvement over traditional machine learning methodologies, especially for databases with fewer eligible articles. With these advancements, the screening component of most systematic reviews should remain functionally achievable for another one to two decades.
Basic types and evolutionary characteristics of the socialist built heritage in China, 1949–1978: bibliometrics analysis of the People’s Daily
Authors: Ma Xidong , Zhang Yukun , Li Yan , Zhang Mengdi 
Published: January 2024

Abstract
The socialist built heritage (SBH) is a product of the great and typical socialist construction and is considered to be one of the unique contemporary legacies. However, due to political controversy and a shorter history, its conservation status is dire. In order to better understand and promote future conservation, this study explored the typology and evolution of SBH, using representative socialist China as an example. Based on the official People’s Daily, the spatial term database of various socialist construction fields was generated by utilizing Python and Excel software. Through qualitative logical induction and quantitative word frequency statistics, the basic types and evolutionary characteristics of SBH were obtained. It was found that (1) the composite, multiscale, and extensive SBH were identified as twenty-six basic types. It was most widespread in the industry and agroforestry fields, while factories and facilities, collective organization buildings, government agencies, and assembly buildings were the most common basic types. (2) Related to social development, the fastest growth stage for SBH was from 1953 to 1960 and vice versa from 1966 to 1975. The evolution of SBH in technology field shifted from a non-significant increase to a sudden increase, while those in the finance and trade, and diplomacy fields fluctuated. The remaining fields were marked by large fluctuations to smoothness. The nature of SBH has become more modernized over time. These results further illustrated the distinctive value of the SBH, and can provide positive targeted support for their conservation.
Mechanisms involved in plant growth promotion by Enterobacter cloacae DJ under salinity-alkalinity stress
Authors: Fan Yajun , Wang Hanna , Zhang Zhe , Li YuXing , Zhao Ziyi , Ni Xiuzhen 
Published: January 2024

Abstract
Background
Plant-promoting bacteria are safer alternatives to pesticides and fertilizers, reduce environmental pollution, and increase crop yields. We isolated an Enterobacter cloacae strain DJ with plant-promoting effects from the rhizosphere soil of a plant (Leymus chinensis (Trin.) Tzvel) in the western region of Jilin Province of China and investigated the mechanisms underlying the adaptation of the DJ bacteria to salinity-alkalinity environments and the molecular mechanisms of the cross-talk between DJ bacteria and cucumber seedlings.

Results
The average diameter of the colonies on the salinity-alkalinity medium after incubation for 24 h was 3.3 cm, and this was significantly higher than the 1.9 cm diameter in ADF medium (p < 0.01). Comparative proteomic analysis revealed that 188 differentially expressed proteins, comprising 116 upregulated and 72 downregulated proteins, significantly changed in salinity-alkalinity groups compared to the control groups. The top one upregulated pathway of KEGG enrichment was bacterial chemotaxis, DJ bacteria adapted to salinity-alkalinity environments by upregulating the genes associated with bacterial chemotaxis. The contents of putrescine in salinity-alkalinity and control groups were 4.73 μg/mL and 3.02 μg/mL, whereas the contents of spermidine were 46.18 ng/mL and 0.34 ng/mL, respectively. Comparing to the control cohorts, the concentrations of both polyamines in the experimental cohorts exhibited statistically significant increases (p < 0.01). The expression of Pt gene encoding polyamine transporter protein was sharply up-regulated in cucumber roots after treatment with DJ bacteria under salinity-alkalinity stress; the expression was more than tenfold higher than that in the control groups. The enzyme activities of POD, SOD, and CAT in cucumber seedlings were higher compared to those in the control groups (p < 0.01). The stem height, number of lateral roots, and fresh weight of cucumber seedlings in the DJ treatment groups were 6.0 cm, 17 roots, and 0.42 g, respectively, whereas those of the control groups were 3.8 cm, 14 roots, and 0.28 g, respectively, with a notable difference between two cohorts (p < 0.01).

Conclusions
DJ bacteria can live in salinity-alkalinity conditions by upregulating the expression of genes associated with chemotaxis. The resistance of cucumber seedlings under salinity-alkalinity conditions through the antioxidant pathway was increased by polyamines produced by DJ bacteria.

Graphical Abstract
Closure of open window thoracostomy due to MRSA pyothorax by EWS bronchial occlusion and modified extraperiosteal air plombage: a case report
Authors: Kuramochi Masami , Shinonaga Mayumi , Kuraoka Setsuo 
Published: January 2024

Abstract
Background
Refractory pyothorax caused by methicillin-resistant Staphylococcus aureus (MRSA) is a challenging clinical condition; complications such as bronchopleural fistulae can further hinder its treatment. To avoid a fatal state caused by aspirating pneumonia, open window thoracotomy is not only sometimes performed, but subsequent closure of the window can also be difficult. In this report, we describe the case of a patient with MRSA pyothorax with bronchopleural fistula in whom a successful closure of window thoracostomy was achieved by utilizing Endobronchial Watanabe Spigot　(EWS; Novatech, La Ciotat, France) bronchial occlusion and a modified extraperiosteal air plombage technique.

Case presentation
A 66-year-old man underwent an open window thoracotomy for pyothorax with bronchopleural fistula with MRSA infection at the age of 59. After 7 years, he was referred to our department for the closure of the window. Initially, we occluded the right B6a + b by EWS under bronchoscopy. Subsequently, we dissected the intercostal muscles between the 3rd, 4th, 5th, and 6th ribs to collapse the pyothorax cavity and ensure the coverage of the fistula of lung including the hypertrophied parietal pleura and soft tissues of the chest wall. We filled the extrapleosteal space with a pedicled anterior serratus muscle flap to compress the parietal pleura. Postoperatively, lung expansion was satisfactory, and there has been no recurrence for 6 years since the window closure surgery.

Conclusions
We were able to achieve closure and healing in a patient who underwent open window thoracostomy for MRSA bronchopleural fistula by applying EWS and modified extraperiosteal air plombage technique.
A case series of prophylactic negative pressure wound therapy use with purse-string closure in stoma closure wounds in infants
Authors: Kumata Yuka , Ishii Daisuke , Ishii Seiya , Motoki Keita , Ueno Naomi , Hinooka Ranko , Miyagi Hisayuki 
Published: January 2024

Abstract
Background
The study introduces the application of negative pressure wound therapy (NPWT) in pediatric stoma closure, emphasizing the importance of enhancing aesthetics and minimizing surgical site infections (SSI).

Case presentation
The case series involves four infants undergoing non-umbilical stoma closure with a combination of purse-string closure (PSC) and NPWT, focusing on aesthetic outcomes and infection prevention. NPWT was initiated immediately after surgery, and patients were monitored every 3–4 days. Notably, none of the four infants experienced SSI or other complications. The patients adequately tolerated NPWT, with no significant adverse events. Furthermore, Manchester Scar Scale (MSS) was 9 [7–10], and Patient and Observer Scar Assessment Scale (POSAS) (observer) was 12.5 [12–19], POSAS (patient) was 12.5 [11–16] (all median values [minimum–maximum]), indicating that excellent aesthetic outcomes were achieved.

Discussion
We emphasizes the significance of aesthetics in pediatric patients; in addition, our findings demonstrate that four infants who received NPWT combined with PSC achieved superior outcomes that did the most recent four infants who underwent PSC only at our institution. It also addresses the risk of SSI in stoma closure and discusses the pros and potential cons of using NPWT in pediatric cases, underlining the need for further research and the accumulation of additional reports.

Conclusions
This is the inaugural report of prophylactic NPWT for pediatric stoma closure, emphasizing the effectiveness of combining PSC and NPWT for SSI prevention and improved aesthetics. The study calls for additional research and reports on NPWT in pediatric cases to further solidify its benefits in this patient population.
High burden of wasting among children under-five with hydrocephalus receiving care at CURE children’s hospital in Uganda: a cross-sectional study
Authors: Grace Naula , Mbabazi Edith , Mukunya David , Tumuhamye Josephine , Okechi Humphrey , Wegoye Emmanuel , Olupot-Olupot Peter , Matovu Joseph KB , Hopp Leah , Napyo Agnes 
Published: January 2024

Abstract
Background
Hydrocephalus is one of the most common neurological disabilities presenting in children. Although there are limited studies on its association with wasting, neurological comorbidities such as dysphagia have been associated with an increased risk of wasting in children. In this study, we aimed to determine the prevalence and factors associated with wasting in children less than five years with hydrocephalus.

Methods
We conducted a cross-sectional study at various satellite clinics of CURE Children’s Hospital in Uganda between September and November 2021. Children with hydrocephalus were identified at the outpatient departments of the satellite clinics of the Cure Children’s Hospital and these include Mbale, Gulu, Lira, Jinja and Katalemwa. A structured questionnaire was used to collect information on several variables including (1) for the mother: socio-demographic characteristics, partner support, and wealth index (2) for the child: socio-demographic characteristics, clinical symptoms, feeding difficulties and neural comorbidity. Anthropometric measurements were also taken and these included the mid-upper arm circumference. Data were analysed using Stata version 14. We estimated adjusted odds ratios and their corresponding 95% confidence intervals while relying on multivariable logistic regression models.

Results
The prevalence of wasting among children with hydrocephalus was 23.2% (n = 89/384) (95%CI: 19 − 27.7%). Their mean age was 19.5 months (SD 16.8). Most of the children were below 12 months (47.9%) and were male (57.5%). The factors associated with wasting among children with hydrocephalus included: having; difficulty in chewing and swallowing (AOR = 2.6, (95%CI:1.05–3.94), a poor appetite (AOR = 1.74, (95%CI: 1.31–2.32), difficulty in breathing (AOR = 1.9, (95%CI: 1.18–3.16), chocking on food (AOR = 1.42, (95%CI:1.1–1.9) and attending the Mbale satellite clinic (AOR = 2.1 (95% CI 1.19–3.7). Children under 5 years of age with hydrocephalus that were born to women whose highest level of education was 7 to 10 years of formal schooling (AOR = 0.32, 95%CI: (0.12–0.87) were less likely to be wasted.

Conclusions and recommendations
The prevalence of wasting among children with hydrocephalus was high. The factors associated with wasting were mainly feeding challenges. We recommend that children with hydrocephalus should be given greater attention regarding their nutrition especially those with various forms of feeding difficulties. The caregivers of children with hydrocephalus should receive counseling on nutrition and on the best modalities to rely on while feeding their children.
Global shocks and fiscal stimulus: a tale of an oil-dependent-exporting country
Authors: Okorie David Iheke , Lin Boqiang 
Published: January 2024

AbstractGlobal shocks potentially distort economy’s achieved equilibria. Considering the 2020 global crude oil price shock and the 2019 coronavirus disease pandemic, this study proposes an energy and environment integrated general equilibrium model to analyze the economic, energy, and environmental effects of these global shocks on Nigeria, a developing, oil-producing, oil-dependent, and oil-exporting country. Furthermore, the mitigating roles of a fiscal stimulus–response package (palliative) are investigated and analyzed. Generally, the developed model predicts a decline in the level of economic activities. The study results are unsurprising due to Nigeria’s heavy reliance on crude oil. However, sectorial-specific impacts exist as some sectors experience output declines while others do not. Environmental quality is improved since more carbon is abated, nonetheless. Carbon intensities increased given that the price effects outweighed the quantity effects— reduced emission results from reduced economic activities and not from technological progress. The results further show a revenue-abatement paradox; a fixed carbon tax approach minimizes the tax revenue loss but may discourage carbon abatement. Conversely, the ad valorem and specific carbon tax systems encourage carbon abatement but reduce carbon tax revenues. The government’s fiscal policy stimulus–response (palliative) action dampens the impact of these global shocks on both the domestic agents and the overall economy. The results are robust and can be applied to the experiences of other developing oil-producing, oil-exporting, and oil-dependent economies.
Two decades of research on the role of diet in Alzheimer’s disease (2003–2023): a bibliometric and visual analysis based on CiteSpace
Authors: Xu Wanyin , Xu Zhengyanran , Guo Yi , Wu Jing 
Published: January 2024

Abstract
Background
In recent years, the impact of diet on Alzheimer's disease (AD) as a modifiable lifestyle has attracted widespread attention. We aimed to elucidate the current research status, frontiers, and research trends regarding the role of diet in AD over the past two decades through CiteSpace.

Methods
Studies related to AD and diet that were published from January 1, 2003, to June 30, 2023, were retrieved via the Web of Science Core Collection. We imported the study data into CiteSpace for visual analysis of countries, institutions, co-authors, and co-occurring keywords.

Results
A total of 922 relevant studies were included in our analysis, which found Nikolaos Scarmeas was the most prolific author (13 studies, 1.41%). The results also indicated that USA and Columbia University were the country and institution with the highest number of publications, with 209 (22.67%) and 23 (2.49%), respectively. The keywords that had a burst in the past four years were neuroinflammation, AD, tau, association, and beta.

Conclusion
Talent exchange and regional cooperation are recommended in this study field. The results indicate that the effectiveness of various dietary patterns and mechanisms of dietary interventions using biomarkers and supplementation with refined nutrients will be the main research trends in the future.
Sustainable development of inland waterways transport: a review
Authors: Calderón-Rivera N. , Bartusevičienė I. , Ballini F. 
Published: January 2024

AbstractOver the years, the demand for transportation has experienced a consistent rise, which has exacerbated a multitude of issues including environmental, visual, and noise pollution, congestion, land use conflicts, and various other related challenges. In this regard, the pursuit of alternatives aimed at mitigating these adverse effects stands as a priority for governments and policymakers. Consequently, inland waterway transport (IWT) emerges as an appealing solution, due to its advantages across the social, environmental, and economic considerations. However, in relation to IWT the concept of sustainable development is insufficiently investigated. The objective of this paper is to undertake a comprehensive review of how the concept of sustainable development is addressed and applied within the framework of IWT systems. To achieve this goal, a systematic literature review was meticulously conducted, utilizing three academic databases (Scopus, Google Scholar, and EBSCO). The review process yielded a total of 51 papers that proved to be pertinent and relevant to the subject matter. The comprehensive literature review facilitated the delineation of the principal elements, factors, and characteristics of the IWT system, as well as the primary drivers for its sustainable development. However, the implications for further research were identified, such as a comprehensive examination of each case due to the distinct geographical, social, economic, and political conditions inherent to each individual basin. That is essential for understanding the unique barriers present within each context and for formulating viable solutions aimed at fostering and incentivizing the sustainable development of IWT systems.