bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond climate villains: Estimating carbon storage in urban parks using high-resolution imagery combined with field sampling
Authors: Ribeiro Rômulo José da Costa , Goulart Fernando Figueiredo , Jacobson Tamiel Khan Baiocchi , Rocha Dulce Maria Sucena da , Jaloretto Daniel , Gonçalves Bruno Eduardo Ferreira , Gerber Dionatan 
Published: January 2024

Abstract

Urban areas are responsible for 80% of GHG emissions, leading scientists and policymakers to act towards city greening. The contribution of these urban green spaces to storing carbon and climate change mitigation is unknown, particularly in the tropics. Here, we present a methodology that combines high-resolution satellite images (3 x 3 m) with biomass sampling in Brasilia, Brazil's capital. The phytosociological parameters of the woody vegetation and the total aerial biomass of the grass layer were calculated. Our model used a CO2 flux index calibrated with field data. The CO2 flux index was produced by the Planet satellite constellation. The woody plant community had 59 individuals (21 species), and the average biomass of the grass layer varied between 8,915.68 and 11,545.12 kg.ha− 1. The CO2 flux reveals areas with higher carbon flow, indicating greater carbon sequestration due to more expressive photosynthetic activity. Linear regression (R2 = 1) was used to estimate total carbon storage in eight urban parks, and cerrado areas exhibit higher values, while degraded or constructed areas show the lowest values. Our simple and low-cost method using field data with remote sense imagery produces precise biomass estimations at regional levels, which greatly apply to tropical landscapes. By enhancing knowledge about the urban positive and negative influence on the carbon cycle, our method could support scientists and policymakers in targeting climate and biodiversity-friendly agendas.
Exploratory Studies on Amide Bond Replacement of a SARS-CoV-2 Main Protease Inhibitor Utilizing a Chloroalkene Dipeptide Isostere
Authors: Kobayakawa Takuya , Azuma Chika , Higashi-Kuwata Nobuyo , Tsuji Kohei , Ishii Takahiro , Shinohara Kouki , Bolah Peter , Mitsuya Hiroaki , Tamamura Hirokazu 
Published: January 2024

Abstract
The development of peptidomimetics such as alkene dipeptide isosteres, which are designed as structures that mimic the ground states of amide bonds, plays an important role in the discovery of peptide-lead drugs. In this study, as a model of peptides, an inhibitor against the main protease (Mpro) of SARS-CoV-2, compound 4, which has an N- benzyloxycarbonyl (Cbz) protected Val moiety at the P3 site, was adopted. A chloroalkene dipeptide isostere (CADI) was then incorporated as an amide bond surrogate between the P2-P3 sites of compound 4 in order to increase its biological stability and disclose the contribution of the amide bond between the P2-P3 sites on the expression of antiviral activity. Although the synthesized derivative (5) failed to show significant antiviral activity below 100 M, it was found that the amide bond between the P2-P3 sites of this type of Mpro inhibitors is critical for the expression of inhibitory activity of compounds. According to this information, NH or CO of the amide bond between the P2-P3 sites might form a hydrogen bond with the active site of Mpro. The present results suggest that CADI functions as a chemical probe, allowing us to examine the significance of the peptide backbone structure.
Keywords
amide bond surrogate, chloroalkene dipeptide isostere (CADI), coronavirus disease of 2019 (COVID-19), main protease (Mpro) inhibitor, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Knowledge graph-derived feed efficiency analysis via pig intestinal microbiota
Authors: Zhang Junmei , Jiang Qin , Du Zhihong , Geng Yilin , Hu Yuren , Tong Qichang , Song Yunfeng , Zhang Hong-Yu , Yan Xianghua , Feng Zaiwen 
Published: January 2024

Abstract
Feed efficiency (FE) is essential for pig production, has been reported to be partially explained by gut microbiota. Despite an extensive body of research literature to this topic, studies regarding the regulation of feed efficiency by intestinal microbiota remain fragmented and mostly confined to disorganized or semi-structured unrestricted texts. Meanwhile, structured databases for microbiota analysis are available, yet they often lack a comprehensive understanding of the associated biological processes. Therefore, we have devised an approach to construct a comprehensive knowledge graph by combining unstructured textual intelligence with structured database information and applied it to investigate the relationship between pig intestinal microbes and FE. Firstly, we created the pimReading knowledge base and the domain ontology of pig gut microbiota by annotating, extracting, and integrating semantic information from 157 scientific publications. Secondly, we created the pimPubtator by utilizing PubTator to expand the semantic information related to microbiota. Thirdly, we created the pimDatabase by mapping and combining the ADDAGMA, gutMGene, and KEGG databases based on the ontology. These three knowledge bases were integrated to form the Pig Intestinal Microbial Knowledge Graph (PIMKG). Additionally, we created three biological query cases to validate the performance of PIMKG. These cases not only allow us to identify microbes with the most significant impact on FE but also provide insights into the metabolites produced by these microbes and the associated metabolic pathways. This study introduces PIMKG, mapping key microbes in pig feed efficiency and guiding microbiota-targeted optimization.
Bioinformatics-based Investigation of Autophagy-Related Biomarkers in Heritable Ovarian Carcinoma
Authors: Wang Zhi-min , Liu Jia Ning , Sun Nan-xiang , Han Xiao-yu , Chen Xin , Sha Ri-na , Dai Bai 
Published: January 2024

Abstract
Objective
To investigate the role of autophagy-related genes (ARGs) in Heritable Ovarian Carcinoma (HOC) and identify potential biomarkers and therapeutic targets.
Methods
We conducted a comprehensive bioinformatics-based analysis of gene expression patterns in 420 HOC samples and 7 normal tissues. Differential expression of 17 ARGs out of 232 candidate genes was identified. Functional annotation and pathway enrichment analyses were performed to explore the biological functions of these ARGs. A prognostic model based on 11 survival-associated ARGs was established and validated.
Results
Our analysis revealed differentially expressed ARGs in HOC and normal tissues, suggesting their potential as diagnostic biomarkers. GO and KEGG analyses indicated the involvement of these genes in critical biological processes and signaling pathways. The prognostic model demonstrated promising predictive capabilities for patient outcomes in HOC.
Conclusion
Our findings shed light on the significance of ARGs in HOC and provide potential biomarkers and therapeutic targets for improved patient outcomes in this heritable ovarian carcinoma.
Investigation On Ce3+ Doped Barium Tin Boro-Phosphate Glass for White LED And Nuclear Radiation Shielding Applications
Authors: A Paul Dhinakaran , Vinothkumar P. , Praveenkumar S. , Harirajan M. 
Published: January 2024

Abstract
The Ce3+ Doped Barium Tin Boro-phosphate glass was produced according to earlier research, melt quenching method. The amorphous nature of Ce3+ Doped Barium Tin Boro-phosphate glass was verified by powder X-ray diffraction investigation. The Ce3+ Doped Barium Tin Boro-phosphate glass's functional groups were determined using Fourier transform-RAMAN and Fourier transform infrared spectroscopy. Using Ultraviolet-Visible spectroscopy, the linear optical properties of the Ce3+ Doped Barium Tin Boro-phosphate glass were examined. These properties included its optical band gap, extinction coefficient, optical conductivity, and refractive index. Using EDAX and SEM analyses, the chemical compositions and surface morphology of the Ce3+ Doped Barium Tin Boro-phosphate glass were examined. Ce3+ doped barium tin Boro-phosphate glass was studied in terms of its excitation and emission spectra using the photoluminescence technique. The glass's CIE coordinates were also looked at. Additionally, the mass attenuation coefficient, half-value layer, mean free path, tenth value layer, and EABF were studied concerning the glass's gamma-ray shielding qualities using the Phy-X software.
Accuracy of AlphaFold models: Comparison with short N ... O contacts in atomic resolution protein crystal structures
Authors: Carugo Oliviero 
Published: January 2024

Abstract
Artificial intelligence (AI) has revolutionized structural biology by predicting protein 3D structures with near-experimental accuracy. Here, short backbone N-O distances in high-resolution crystal structures were compared to those in three-dimensional models based on AI AlphaFold/ColabFold, specifically considering their estimated standard errors. Experimental and computationally modeled distances very often differ significantly, showing that these models' precision is inadequate to reproduce experimental results at high resolution. T-tests and normal probability plots showed that these computational methods predict atomic position standard errors 3.5–6 times bigger than experimental errors.
Comparison of optical coherence tomography in patients with Wilson's disease of different types
Authors: Liu guizhang , Fang Xiang , Jin Shan , Mei Deng , Tan Lu , Qin Yu , Yuan Feiyan , Zheng Xiaoyu 
Published: January 2024

Abstract

Background: Previous studies have found that changes in Macular and Retinal nerve fiber layer (RNFL) thickness in patients with Neurological forms of Wilson's disease (NWD) are related to clinical symptoms. It is unclear whether this change is similar in other WD patients.
Objective: To study the parameters of the macular center of the inner retina and RNFL thickness in OCT of WD patients with different disease types.
Methods: We recruit 30 patients with NWD and 30 patients with Hepatic Forms Wilson 'sdisease (HWD), respectively, to score the nerve function and liver function of the NWD and HWD patients according to the Unified Wilson Disease Rating Scale (UWDRS). Healthy volunteers in the same period were included AS the standard control group. Anterior segment coherent optical tomography (OCT) was used to scan the macular subfoveal retina and RNFL thickness of all tested eyes, and the differences and changes of macular and RNFL parameters in WD patients with different disease types were analyzed.
Results: The macular and RNFL thickness of the NWD groups were significantly lower than those of the HWD and the standard control groups. The macular and RNFL thickness of the NWD group was negatively correlated with the nervous system score. In contrast, the macular and RNFL thickness of the HWD group had no significant difference from the healthy group.
Conclusion: There are significant differences between macular and RNFL in NWD patients and HWD patients. There was a negative correlation between the change of inner retinal thickness and nerve function defect in NWD patients and no correlation between retinal thickness and clinical symptoms in HWD patients.
Diagnostic Utilities of Washout CYFRA 21-1 combined with Washout Thyroglobulin for Metastatic Lymph Nodes in Thyroid Cancer: A Prospective Study
Authors: Park Joonseon , An Solji , Kim Kwangsoon , Kim Jeong Soo , Jung Chan Kwon , Bae Ja Seong 
Published: January 2024

Abstract
Cervical lymph node (LN) metastasis is common in differentiated thyroid cancer (DTC). This study evaluated the utility of the washout CYFRA 21 − 1 level, combined with the thyroglobulin (Tg) concentration, in terms of diagnosis of LN metastasis. We prospectively enrolled 53 patients who underwent thyroid surgery to treat DTC with lateral cervical LN metastases. Preoperative ultrasound guided needle localization was used to surgical sampling of specific LNs during the operation. The intraoperative washout Tg and CYFRA 21 − 1 levels were measured in such LNs. The Tg and CYFRA 21 − 1 levels differed significantly between metastatic and benign LNs. The cutoff values were 2.63 ng/mL for washout CYFRA 21 − 1 and 22.62 ng/mL for Tg. Combined use of the washout Tg and CYFRA 21 − 1 levels afforded the highest diagnostic accuracy (92.5%), better than that of individual markers. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) were 94.6%, 90.0%, 91.4%, 93.8%, respectively. The conjunction of the washout CYFRA21-1 and Tg levels enhances the diagnostic accuracy of LN metastasis in DTC patients. The washout CYFRA 21 − 1 level may be useful when malignancy is suspected, especially in cases where the cytology and washout Tg findings do not provide definitive results.
The seasonal influence on TMD prevalence in South Korea which has four seasons
Authors: Lee Yeon-Hee , Chung Jin-Woo 
Published: January 2024

Abstract
Aim
This study aimed to explore seasonal variations in temporomandibular disorder (TMD) prevalence in South Korea, utilizing nationwide population-based big data.
Method
Data from the Korean Meteorological Administration combined with big data from the Health Insurance Review and Assessment Service (HIRA) (2010–2022), identified as TMD (K07.6) through a 4-digit disease code search, were used. TMD patient data for the past 13 years were statistically processed every month, and prevalence by season was analyzed.
Results
In 2022, 484,241 individuals sought treatment for TMD in hospitals with an increase of 97.89% from 244,708 cases in 2010. The onset of TMD showed no sex differences in those under 10 years of age. However, a distinct female predominance emerged after 10 years of age, with an average female-to-male ratio of 1.84:1. The peak prevalence was observed in the 20–24 age group. TMD patient numbers across seasons showed no significant increase in winter compared with spring or summer. However, there was a significant correlation between the maximum and minimum temperatures and the number of patients with TMD. A higher temperature difference correlated with a higher TMD patient count. The strongest correlation between TMD patient numbers and temperature differences was observed in winter (r = 0.480, p < 0.01), followed by summer (r = 0.443, p < 0.05), and spring (r = 0.366, p < 0.01). The highest number of patients with TMD were distributed in Seoul and Gyeonggi-do, with metropolitan areas accounting for 50% of the total patient count.
Conclusions
Diurnal temperature fluctuations showed a significantly stronger correlation with the increase in the number of TMD patients than absolute climate temperatures. This aspect should be a key consideration when examining trends in patients with TMD across distinct seasons in South Korea.
Efficient electrochemical oxidation of the biomass platform compound furfural on a Ni 0.48 Co 0.36 O 0.16 electrode
Authors: Zhang Yanru , Wang Xinyue , Wu Pengpeng , Zhang Xiliang , Zhou Qian , Xing Liang , Fan Yongming 
Published: January 2024

Abstract

The use of electrocatalytic technology to replace traditional harsh thermocatalysis in the process of biomass utilization has undoubtedly been an effective means to achieve green and sustainable development. The use of the environmentally friendly method of synthesizing furoic acid (FA) from the biomass platform compound furfural (FF) by electrooxidation was investigated. The surface of the Ni–Co oxide electrode with a Ni content of 0.48 (Ni0.48Co0.36O0.16) obtained by a simple electrodeposition method was covered by a layer of flower-like porous structure, while NiO and Co3O4 coexisted. Moreover, the Ni0.48Co0.36O0.16 electrode exhibited 95.4% FA faraday efficiency and 99.6% selectivity with a substrate concentration of 20 mM at 1.0 V vs. Hg/HgO and 50°C. In addition, a mechanism for electrooxidation of FF into FA over a Ni-Co oxide electrode was proposed.
Fecal Coprococcus, Hidden behind Abdominal Symptoms in Patients with Small Intestinal Bacterial Overgrowth
Authors: Guo Huaizhu , Chen Yuzhu , Dong Wenxin , Lu Siqi , Du Yanlin , Duan Liping 
Published: January 2024

Abstract
Background: Small intestinal bacterial overgrowth (SIBO) is the presence of an abnormally excessive amount of bacterial colonization in the small bowel. Hydrogen and methane breath test has been widely applied as a non-invasive method for SIBO. However, the positive breath test representative of bacterial overgrowth could also be detected in asymptomatic individuals.
Methods: To explore the relationship between clinical symptoms and gut dysbiosis, and find potential fecal biomarkers for SIBO, we compared the microbial profiles between SIBO subjects with positive breath test but without abdominal symptoms (PBT) and healthy controls (HC).
Results: Fecal samples were collected from 63 SIBO who complained of diarrhea, distension, constipation or abdominal pain, 36 PBT and 55 HC. Increased taxonomic diversity and decreased functional diversity were consistent with the progression of SIBO. At the genus level, significantly decreased Bacteroidesand increased Coprococcus_2 were observed, and unique Butyrivibrio could ferment multiple carbohydrates producing hydrogen and hydrogen sulfide. There was a significant correlation between Coprococcus_2 and the severity of abdominal symptoms. Differently, The unique Veillonella, Escherichia-Shigella, Barnesiella and Tyzzerella_3 in PBT group were related to amino acid fermentation. Interestingly, the co-occurrence network density of PBT is the largest indicating a complicated interaction of genera. The Euclidean distance between paired networks using either the betweenness centrality or the degree distribution showed that PBT is closer to SIBO.
Conclusions: Increased taxonomic diversity and decreased functional diversity were consistent with the progression of SIBO. Butyrivibrio and Coprococcus_2 abundance along with lower Bacteroides contributed to more noticeable discomfort of SIBO patients. The enriched Coprococcus may be one of the potential biomarkers of SIBO. Represented by Veillonella, asymptomatic PBT objects exhibited a different microbiome spectrum associated with the fermentation of amino acids and peptides rather than carbohydrates. The network of PBT was more stable which may play a protective role, but it deserved further attention in view of the shared essential “bridged” genera with SIBO.
Development of a novel ultrasound Vacuum -assisted headspace solid phase microextraction approach for determination of solvent residual's in pharmaceuticals and comparison with traditional headspace solid phase microextraction method
Authors: Hajipour Somayeh , Ghiasvand Alireza 
Published: January 2024

Abstract
In this report, an ultrasonication and vacuum assisted headspace solid-phase microextraction procedure followed by gas chromatography-flame ionization detection (UVA-HS-SPME-GC-FID) was proposed for direct extraction of solvent residuals, including benzene, toluene, ethyl benzene, m,p-xylene and o-xylene, in pharmaceutical matrices. A novel robust, reliable and durable nanocomposite solid-phase microextraction (SPME) fiber was prepared by layer-by-layer coating of 3-aminopropyltriethoxysilane-functionalized graphene (APTES) on a stainless-steel wire. Then, the proposed fiber was used for headspace SPME (HS-SPME) and trapping of toluene as a residual solvent in solid penicillin, Ampicillin, and Cefazolin vials followed by gas chromatography-flame ionization detection (GC-FID). UVA-HS-SPME-GC-FID achieves better validation parameters, including limit of detection, limit of quantification, linearity, recovery and repeatability, in comparison with conventional HS-SPME-GC-FID. The UVA-HS-SPME-GC-FID strategy is very effective for quantitative tracing of volatile and semivolatile solvent residuals in various pharmaceutical drugs.
Immune reconstitution after hematopoietic stem cell transplantation with reduced intensity conditioning for inborn errors of immunity
Authors: Shahraki Zahra , Behfar Maryam , Gharagozlou Saber , Mohammadi Shiva , Mahmoudi Shima , Parvaneh Nima , Hamidieh Amir Ali 
Published: January 2024

Abstract
Purpose
Hematopoietic stem cell transplantation (HSCT) is the only curative treatment for many inborn errors of immunity (IEI). Reduced-intensity conditioning (RIC) is used in this setting because of low mortality and morbidity. However, the timely reconstitution of the immune system is essential for long-term survival.
Methods
We included forty-one IEI patients transplanted from September 2016 to September 2019 using fludarabine-based RIC protocol. Lymphocyte reconstitution was evaluated by flow cytometry of CD3, CD4, and CD8 for T lymphocytes, CD19 for B lymphocytes, and CD56 for NK cells in + 3, +6, + 9, and + 12 months after HSCT. We analyzed the effect of different factors on the duration of immune cell reconstitution.
Results
By the third month, 68% of total T cells and 78% of NK cells had returned to normal. However, 73% of B cells, 29% of CD4+ T cells, and 83% of CD8+ T cells were normalized 12 months after HSCT. The absence of acute graft-versus-host disease (aGVHD) was associated with earlier CD3+ T cell and B cell recovery. Absence of chronic GVHD (cGVHD) and cytomegalovirus (CMV) infection was associated with early CD4+ T cell recovery.
Conclusion
With the fludarabine-based RIC protocol, CD4+ T cells showed slow and poor recovery during follow-up. However, this poor recovery did not lead to increased rates of infections. In addition, CMV infection and the development of acute and chronic GVHD negatively affected immune cell recovery. Using an appropriate GVHD prophylaxis regimen and adequate treatment of CMV may improve the immune reconstitution post-HSCT.
The Response Mechanism of COVID-19 spatial global distribution to Eco-geographic Factors
Authors: Pan Jing , Villalan Arivizhivendhan Kannan , Ni GuanYing , Wu RenNa , Sui ShiFeng , Wu XiaoDong , Wang XiaoLong 
Published: January 2024

Abstract
COVID-19 has been massively transmitted for almost three years, and its multiple variants have caused serious health problems and an economic crisis. Our goal was to identify the influencing factors that reduce the threshold of disease transmission and to analyze the epidemiological patterns of COVID-19. This study served as an early assessment of the epidemiological characteristics of COVID-19 using the MaxEnt species distribution algorithm using the maximum entropy model. The transmission of COVID-19 was evaluated based on human factors and environmental variables, including climatic, terrain and vegetation, along with COVID-19 daily confirmed case location data. The results of the SDM model indicate that population density was the major factor influencing the spread of COVID-19. Altitude, land cover and climatic factor showed low impact. We identified a set of practical, high-resolution, multi-factor-based maximum entropy ecological niche risk prediction systems to assess the transmission risk of the COVID-19 epidemic globally. This study provided a comprehensive analysis of various factors influencing the transmission of COVID-19, incorporating both human and environmental variables. These findings emphasize the role of different types of influencing variables in disease transmission, which could have implications for global health regulations and preparedness strategies for future outbreaks.