bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and dynamics of endogenous protein complexes in human heart tissue captured by native nanoproteomics
Authors: Ge Ying , Chapman Emily , Roberts David , Tiambeng Timothy , Andrews Jaan , Wang Man-Di , Reasoner Emily , Melby Jake , Li Brad , Kim Donguk , Alpert Andrew , Jin Song 
Published: July 2023

Abstract
Protein complexes are highly dynamic entities that display substantial diversity in their assembly, post-translational modifications, and non-covalent interactions, allowing them to play critical roles in various biological processes. The heterogeneity, dynamic nature, and low abundance of protein complexes in their native states present tremendous challenges to study using conventional structural biology techniques. Here we develop a “native nanoproteomics” strategy for the native enrichment and subsequent native top-down mass spectrometry (nTDMS) of low-abundance protein complexes. Specifically, we demonstrate the first comprehensive characterization of the structure and dynamics of cardiac troponin (cTn) complexes directly from human heart tissue. The endogenous cTn complex is effectively enriched and purified using peptide-functionalized superparamagnetic nanoparticles under non-denaturing conditions to enable the isotopic resolution of cTn complexes, revealing their complex structure and assembly. Moreover, nTDMS elucidates the stoichiometry and composition of the heterotrimeric cTn complex, localizes Ca2+ binding domains (II-IV), defines cTn-Ca2+ binding dynamics, and provides high-resolution mapping of the proteoform landscape. This native nanoproteomics strategy opens a new paradigm for structural characterization of low-abundance native protein complexes.
Meta-analysis of three randomized trials of capecitabine plus cisplatin (XP) versus S-1 plus cisplatin (SP) as first-line treatment for advanced gastric cancer
Authors: Kazuhiro Nishikawa , Kawakami Hisato , Shimokawa Toshio , Fujitani Kazumasa , Tamura Shigeyuki , Endo Shunji , Kobayashi Michiya , Kawada Junji , Kurokawa Yukinori , Tsuburaya Akira , Yoshikawa Takaki , Sakamoto Junichi , Satoh Taroh 
Published: July 2023

Abstract
Background
S-1 plus cisplatin (SP) and capecitabine plus cisplatin (XP) are standard first-line regimens for advanced gastric cancer (AGC) worldwide. We conducted a meta-analysis using individual participant data (IPD) to investigate which is more suitable.
Methods
IPD from three randomized trials were collected. In these trials, patients with AGC were randomly allocated to SP (S-1 80–120 mg for 21 days plus cisplatin 60 mg/m2 (q5w)) or XP (capecitabine 2,000 mg/m2 for 14 days plus cisplatin 80 mg/m2 (q3w)).
Results
In 211 eligible patients, median overall survival (OS) for SP versus XP was 13.5 and 11.7 months (hazard ratio [HR], 0.787; p = 0.114), progression-free survival (PFS) was 6.2 and 5.1 months (HR, 0.767; P = 0.076), and TTF was 5.1 and 4.0 months (HR, 0.611; P = 0.001). The most common grade ≥ 3 adverse events with SP or XP were neutropenia (18% vs. 29%) and anorexia (16% vs.18%). Subgroup analysis demonstrated significant interaction between treatment effect and performance status > 1 (HR, 0.685; P = 0.036), measurable lesion (HR, 0.709; P = 0.049), primary upper third tumor (HR, 0.539; P = 0.040), and differentiated type (HR, 0.549; interaction, 0.236; P = 0.019). For the differentiated type, OS was significantly longer in the SP group (13.2 months) than in the XP group (11.1 months) (HR, 0.549; P = 0.019). For the undifferentiated type, OS was similar in the SP group (14.2 months) and in the XP group (12.4 months) (HR, 0.868; P = 0.476).
Conclusions
SP and XP were both effective and well tolerated. SP might be suitable for the pathological differentiated subtype of AGC.
Phylogeography, character evolution and taxonomy of Scurrulinae (Loranthaceae): New insights into the circumscription of the genus Taxillus
Authors: Le Chi Toan , Lu Limin , Du Nguyen Van , Chen Zhiduan , Omollo Wyckliffe Omondi , Liu Bing 
Published: July 2023

Abstract
Background
Exploring the relationship between parasitic plants and answering taxonomic questions are still challenging. The subtribe Scurrulinae (Loranthaceae), which has a wide distribution in Asia and Africa, provides an excellent example to illuminate this scenario. Using a comprehensive taxon sampling of the subtribe, this study focuses to infer the phylogenetic relationships within Scurrulinae, investigate the phylogeography of the subtribe, and establish a phylogenetically-based classification incorporating both molecular and morphological evidence. We conducted phylogenetic, historical biogeography, and ancestral character state reconstruction analyses of Scurrulinae based on the sequences of 6 DNA regions from 89 individuals to represent all 5 tribes of the Loranthaceae and the dataset from eleven morphological characters.
Results
The results strongly support the non-monophyletic of Scurrulinae, with Phyllodesmis recognized as a separate genus from its allies Taxillus and Scurrula. “Afrotaxillus” is well supported as a new genus from Africa. The mistletoe Scurrulinae originated in Asia during the Oligocene. Scurrulinae was inferred to have been widespread in Asia but did not disperse to other areas. “Afrotaxillus” was confirmed to have originated in Africa from African Loranthaceae ca. 17 Ma, and likely the genus independently evolved from Taxillus in Asia.
Conclusions
This study based on comprehensive taxon sampling of the subtribe Scurrulinae, strongly supports the relationship between genera. The taxonomic treatment for Phyllodesmis, Afrotaxillus were provided. The historical biogeography of mistletoe Scurrulinae was determined with origin in Asia during the Oligocene. Taxillus and Scurrula diverged during the climatic optimum in the middle Miocene. Afrotaxillus originated in Africa from African Loranthaceae. Diversification of Scurrulinae and the development of endemic species in Asia may have been supported by the fast-changing climate, including cooling, drying, and the progressive uplift of the high mountains in central Asia, especially during the late Pliocene and Pleistocene.
Evaluation of urethral traumas in children: A retrospective analysis
Authors: Kaba Mehmet , Kılıç Sinan , Gecit İlhan 
Published: July 2023

Abstract
Objective: The leading cause of child mortality is trauma. Urethral injuries, although rare and with low mortality rates, pose a challenging treatment process. In this study, we conducted a retrospective evaluation of cases from two centers with anterior, posterior urethral, and bladder neck injuries associated with trauma. Our aim was to discuss the obtained results in conjunction with the existing literature.
Materials and Methods: A total of 14 cases with urethral and bladder neck injuries resulting from trauma were retrospectively analyzed. These cases were selected from the period between 2010 and 2015 in the first clinic, and between 2017 and 2022 in the second clinic. Parameters such as age, gender, mechanism of injury, location of urethral injury, presence of additional injuries, surgical interventions performed, and treatment outcomes were retrospectively evaluated.
Results: The average age was 10.2±2.9 years (Range: 4-13 years). Motor vehicle accidents were documented in nine cases, fall down from higher places were in two cases, bicycle accidents in three cases, and injury due to clean intermittent catheterization in one case. Based on the identified localization of urethral injuries, seven cases involved bladder neck injuries, six cases had posterior urethral injuries, and one case had an anterior urethral injury. All patients were observed from their first admission to full recovery.
Conclusion: Urethral injuries in childhood are considered rare traumas that often lack sufficient expertise in a single center. While most mild anterior and posterior urethral injuries in children can be managed with urethral catheterization, advanced strictures may necessitate frequent dilation and anastomotic resection. It is crucial to meticulously plan personalized treatment strategies to ensure voluntary and satisfactory voiding with appropriate calibration.
Effects of Meteorological Variation and Air Pollution on Pediatric Allergic Visits: A retrospective study
Authors: Li Yahui , Gu Yujing , Gu Xiaohong , Zhang jing , Deng Huiwen 
Published: July 2023

Abstract
Background: The health of children can be seriously affected by adverse weather conditions and high levels of air pollution. However, it is not clear how different environmental exposures affect allergic diseases in children in different regions. The objective of this study was to determine the impact of meteorological factors and air pollutants on allergic diseases in children in Wuxi, China.
Objectives: The objective of this research was to measure and compare the influence of meteorological conditions and air pollutants on allergic illnesses among children residing in Wuxi, China.
Methods: The study collected data on children who visited Wuxi Children's Hospital from 2015 to 2023 due to asthma, allergic rhinitis (AR), and atopic dermatitis (AD). Meteorological data, including daily average temperature, air pressure, precipitation, relative humidity, and wind speed, were obtained from the China Meteorological Data website. Air pollution data, such as PM10, PM2.5, NO2, SO2, CO, and O3, were downloaded from China National Environmental Monitoring Station. The paper used a combination of quasi-Poisson regression and distributed lag nonlinear model (DLNM), as well as Poisson regression and generalized linear model, to assess the impact of meteorological factors and air pollutants on allergic diseases among children in Wuxi.
Results: The study reported a total of 10,099 cases of asthma, 15,209 cases of AR, and 59,440 cases of AD. The findings suggest that most environmental factors were significantly associated with childhood allergic diseases. Among them, mean daily temperature (standard β: 0.017 (95% confidence interval (CI): 0.013, 0.021)) and wind speed (standard β: 0.029 (95% CI: 0, 0.058)) were found to play a more important role in the development of these allergic diseases than other environmental factors.
Conclusions: The relationship between climate change and air pollution and their impact on allergic diseases in children has been studied. The research suggests that while both factors are linked to allergic diseases, climate factors have a greater influence on their development. These findings have significant implications for the development of prevention strategies for allergic diseases in children.
Construction of a tree-species classification map using multispectral images of UAVs: A case study of the Dong Rui Commune wetlands, Vietnam
Authors: Ngo Dung Trung , Nguyen Khanh Quoc , Dang Cuong Hung , Dang Ngoc Thi 
Published: July 2023

Abstract
Wetlands provide resources, regulate the environment, and stabilize shorelines; however, they are among the most vulnerable ecosystems in the world. Managing and monitoring wetland ecosystems are important for the development and maintenance of ecosystem services and their sustainable use in the context of climate change. We used Phantom 4 multispectral unmanned aerial vehicles (UAVs) to collect data from wetland areas in the Dong Rui Commune, which is one of the most diverse and valuable wetland ecosystems in northern Vietnam. A tree-species classification map was constructed through a combination of the visual classification method and spectral reflectance values of each plant species, and the characteristic distributions of mangrove plants, including Bruguiera gymnorrhiza, Rhizophora stylosa, and Kandelia obovata, were determined with an overall accuracy of 91.11% and a kappa coefficient (K) of 0.87. Universal reflectance graphs of each mangrove plant species were constructed for five wave channels, including blue, green, red, red edges, and near-infrared and the normalized difference vegetation index (NDVI). An experiment was conducted to map plant taxonomy in the same area based only on a graph of spectral reflectance values at five single-spectral bands and constructed NDVI values, resulting in an overall accuracy of 78.22% and a K of 0.67. The constructed map is useful for classifying, monitoring, and evaluating the structure of each group of mangroves, thereby enabling the efficient management and conservation of the Dong Rui Commune wetlands.
Determining the Intermediate and High Strain Rate Properties of Bar Bending Braking System Material in a Forward Velocity Sled
Authors: Sriniva Sathiya Naarayan , B Nagarajappa , Vorkady Yathish , Kumar Sharad , J Dhayanidhi 
Published: July 2023

Abstract
The Bar Bending Braking System (BBBS) in a forward velocity sled utilizes the plastic deformation of the metallic bars to dissipate the Kinetic energy of impact and generate the required deceleration pulse. The National Aerospace Laboratories forward velocity sled’s BBBS material, Mild steel St37-2, is characterized in compression at room temperature, using the quasi-static tests and the Split Hopkinson Pressure Bar (SHPB) at strain rates ranging from 10− 3/s − 2500/s. Very high strain rate dependence of yield and flow stress was observed from these tests as there was nearly a 100% increase in the yield stress between the highest and lowest strain rates. Thinner samples (L/D < 0.5) were used for the SHPB tests apart from the usual ratio (L/D = 0.5) samples and it was observed that the stress strain curves of these thinner samples were consistent with those of the samples with L/D = 0.5 showing that there was no significant effect of the three-dimensional state of stress on the curves. The Compression stress-strain data for the steel, which has over 12 stress strain curves at different strain rates, is analysed to determine the Viscoplastic Johnson-Cook (JC) model and the Cowper-Symonds (CS) Model. The JC Model was developed over a limited strain rate range (0.001-300/s), as linear dependence of the log(strainrate) to the yield or flow stress was only possible in this range. The CS model was developed for the entire range and effectively models the stress strain curves throughout the range of strain rate. The values of the JC and CS constants are compared with existing literature for St 37 steel and are found similar for strain rate sensitivity though there is considerable difference in the static plasticity constants.
The Red Queen hypothesis from a structural perspective: a case study over 30 years of Dengue virus in Brazil
Authors: Penteado André Bernt , Ribeiro Geovani de Oliveira , Araújo Emerson Luiz Lima , Kato Rodrigo Bentes , Freire Caio Cesar de Melo , de Araújo Joselio Maria Galvão , Wallau Gabriel da Luz , Salvato Richard Steiner , de Jesus Ronaldo , Bosco Geraldine Goés , Franz Helena Ferreira , Silva Pedro Eduardo Almeida da , Leal Elcio de Souza , Trossini Gustavo Henrique Goulart , Neto Daniel Ferreira de Lima 
Published: July 2023

Abstract
The interaction between the dengue virus (DENV) and the human dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) receptor plays a crucial role in viral entry and infection. Understanding the dynamics of this interaction and its evolution over time is essential for comprehending the host-virus relationship and the emergence of viral strains with increased pathogenicity. In this study, we employed phylogenetic filtering to provide a structural approach to investigate the co-evolutionary patterns between DENV envelope (E) protein and human DC-SIGN receptor throughout the evolutionary history of the virus sampling the sequences available in Brazil for the past 30 years. The obtained complexes of DENV E and DC-SIGN were then subjected to molecular dynamics simulations to examine the atomistic interaction using the MM/GBSA methodology. Our results revealed conserved evolutionary patterns of interaction in the DENV E protein We identified specific amino acid residues in the E protein that showed evidence of positive selection and were potentially involved in the interaction with DC-SIGN. This study provides valuable insights into the co-evolutionary dynamics of DENV and the human DC-SIGN receptor. Understanding the evolutionary arms race between viruses and their hosts is critical for developing effective strategies to combat emerging viral pathogens such as DENV. The findings presented here contribute to our knowledge of DENV pathogenesis and may facilitate the design of novel therapeutic interventions targeting the E protein-DC-SIGN interaction by providing a structural perspective on the evolutionary gains this virus must aquire.
Experimental study on the dissolution characteristics of ethane into oil-based mud in complex oil and gas wellbore environments
Authors: Song Xuncheng , Liu Yongwang , Huang Hongqiang , Lin Guojun , Sukari Bernard Francis , Cai Jun , Wang Lei ,   8)	Zhiqiang Jiang
Published: July 2023

Abstract

Accurate determination of ethane solubility in oil-based mud is significant to identify the gas kick severity and implementing proper well control procedures. The main factors affecting the ethane gas solubility in oil-based drilling fluid are base oil content, pressure, temperature, and the drilling fluid viscosity. This work tests the complete series of solubility of high-purity ethane in oil-based mud simulating downhole conditions on a 5000m deep well relative to temperature, pressure, viscosity and base oil content with temperature range 40 ℃ to 140 ℃ and partial pressure range 0.17MPa to 5.92MPa by using PVT autoclave, then the effects of temperature, pressure, base oil content and drilling fluid viscosity on the test target are analyzed by using multiple experimental data processing methods. It is found that the variation of ethane solubility with pressure and temperature are almost linearly under interested ranges, the effects of pressure (1.24 ~ 2.78%/MPa) are almost 50 times higher than that of temperature (-0.013 ~ -0.049%/℃) in oil-based drilling mud, the solubility of ethane decreases as viscosity increases, the ethane solubility in 80% and 90% of oil-based muds are about 1.6 times and 2.0 times higher than that in 70% of oil-based mud under the same test conditions. Models for predicting ethane solubility have been developed using screening procedures and statistics regression, which can be integrated into gas-liquid flow models so as to investigate flow behavior while gas kicking.
Immobilized Enzyme Microreactors for Efficient Analysis of Tryptic Peptides in β-Casein and β-Lactoglobulin
Authors: Rodzik Agnieszka , Railean Viorica , Pomastowski Paweł , Buszewski Bogusław , Szumski Michał 
Published: July 2023

Abstract

In this study, our primary aim was to design and implement a rapid and effective analytical method for the examination of trypsin-digested peptides of two model proteins found in cow's milk: β-casein and β-lactoglobulin. These proteins were selected for their abundant nutrient content and functional attributes, notwithstanding their structural and compositional differences. We employed two methods for this purpose: the traditional in-gel protein digestion method and protein digestion using immobilized enzyme microreactors (μ-IMER). Both techniques made use of ZipTip pipette tips filled with C18 reverse phase media. These tips served to concentrate and purify the peptide samples, with the objective of determining the influence of such sample preparation on the improvement or reduction of sequence coverage results. In the preparation of the microreactor, we utilized a monolithic copolymer synthesized from GMA and EDMA. This was followed by surface modifications to attach the enzyme with the highest efficiency. We then evaluated the efficiency of the prepared microreactor under HPLC chromatographic conditions using a small-molecule trypsin substrate, BAEE. In the final stage, we analyzed the hydrolysates obtained from both the microreactor and the traditional digestion in solution method, with and without the presence of ZipTip pipette tips, using MALDI-TOF MS. This comprehensive approach facilitated a thorough study of peptides in β-casein and β-lactoglobulin, thereby enhancing our understanding of these vital cow's milk proteins.
Two polysaccharides in Zanthoxylum bungeanum Maxim with protective effects against Parkinson's disease
Authors: Huang Jiahui , Hui Haochen , Gao Meng , Zhao Xuerong , Li Kunjie , Luo Ziyi , Song Bo , Yin Lian-hong 
Published: July 2023

Abstract

BackgroundZanthoxylum bungeanumMaxim can alleviate cognitive dysfunction, improve learning and memory impairment in mice. However, there are no reports on structure identification of polysaccharides fromZ. bungeanum, and no data on the effects and possible mechanisms of polysaccharides from the plant against Parkinson's disease (PD). Methods In the present study, crude polysaccharides were obtained by hydroextraction and alcoholic precipitation, DEAE-52 and dextran G-75 chromatographic columns were used for the separation and purification. high-performance gel-permeation chromatography, ion chromatography, GC-MS and NMR were used for structure identification. Activity evaluation was performed by CCK-8, ROS, RT-PCR and Western Blotting experiments. Results Two degraded polysaccharides (WZBP-1-2 and WZBP-2) fromZ. bungeanumwere purified and identified, and their biological activities were evaluated. WZBP-1-2 and WZBP-2 with average molecular weight (Mw) of 10.89 and 18 kDa mainly contained galacturonic acid, and they were homogalacturonans with the main chain of →4)-α-D-GalAp-(1→. Biological investigation showed that WZBP-1-2 and WZBP-2 significantly increased the viabilities of MN9D cells induced by N-methyl-4-phenylpyridinium (MPP+) and reduced ROS levels compared with model groups. Mechanism study showed that WZBP-1-2 and WZBP-2 markedly increased the expression levels of SIRT1 and Nrf2, and inhibited the protein or mRNA levels of NF-κB, TNF-α and IL-6. Conclusion WZBP-1-2 and WZBP-2 fromZ. bungeanummay exhibit protective effects against MPP+-induced neuroinflammation and oxidative stress through activation of SIRT1 signaling and should be considered as candidates for the treatment of PD.
Type 2 diabetes mellitus and post-colonoscopy colorectal cancer: Clinical and molecular characteristics and survival
Authors: Boysen Mette L. , Troelsen Frederikke S. , Sørensen Henrik T. , Erichsen Rune 
Published: July 2023

Abstract
Purpose
Studies suggest that patients with type 2 diabetes mellitus (T2D) may be at increased risk of post-colonoscopy colorectal cancer (PCCRC). We investigated clinical and molecular characteristics and survival of T2D patients with PCCRC to elucidate how T2D-related PCCRC may arise.
Methods
We identified T2D patients with colorectal cancer (CRC) from 1995 to 2015 and computed prevalence ratios (PRs) comparing clinical and molecular characteristics of CRC in T2D patients with PCCRC vs. in T2D patients with colonoscopy-detected CRC (dCRC). We also followed T2D patients from the diagnosis of PCCRC/dCRC until death, emigration, or study end and compared mortality using Cox-proportional hazards regression models adjusted for sex, age, year of CRC diagnosis, and CRC stage.
Results
Compared with dCRC, PCCRC was associated with a higher prevalence of proximal CRCs (54% vs. 40%; PR: 1.43, 95% confidence interval [CI]: 1.27–1.62) in T2D patients. We found no difference between PCCRC vs. dCRC for CRC stage, histology, and mismatch repair status. The proportion of CRCs that could be categorized as PCCRC decreased over time. Within one year after CRC, 63% of PCCRC vs. 78% of dCRC patients were alive (hazard ratio [HR]: 1.85 [95% CI: 1.47–2.31]). Within five years after CRC, 44% of PCCRC vs. 54% of dCRC patients were still alive (HR: 1.44 [95% CI: 1.11–1.87]).
Conclusion
The increased prevalence of proximally located PCCRCs and the poorer survival may suggest overlooked colorectal lesions, as well as changed or rapid tumor progression as explanations for T2D-related PCCRC.