bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of Intra-Abdominal Pressure to Trunk Rotation Torque Generation and an Examination of Its Role
Authors: Kimura Asuka , Hakozaki Taisei , Yasuda Yohei , Shimizu Takuya 
Published: January 2025

Abstract

Purpose While the dynamics of intra-abdominal pressure (IAP) during high-intensity resistance exercises are well-documented, its dynamics and role in trunk rotation remain unclear. This study aimed to clarify the actual situation of torque and IAP during trunk rotation torque exertion and to examine the role of IAP in trunk rotation.Methods Eighteen male participants aged 22.2 ± 1.2 years, with a height of 170.9 ± 4.8 cm and weight of 67.3 ± 7.0 kg, demonstrated trunk rotation torque while IAP was measured, and the temporal variation and maximum values of both were measured. Maximum IAP values were also measured during the Valsalva maneuvers (VM); IAPRMAX indicates IAP when maximum trunk rotation torque was recorded, and IAPVM indicates maximum IAP recorded during VM.Results In all participants, significant positive correlations with large effect sizes were found between trunk rotation torque and IAP variation over time (P < 0.01, rs = 0.924), between maximum trunk rotation torque and IAPRMAX (P < 0.01, r = 0.594), and between maximum trunk rotation torque and IAPVM (P < 0.05, r = 0.542).Conclusion The temporal variability of trunk rotation torque and IAP was nearly synchronized. Furthermore, greater torque exertion tended to be associated with higher IAPRMAX and IAPVM values. IAP during trunk rotation during torque exertion is believed to enhance the mechanical efficiency of abdominal wall muscle contraction through the “muscle length–tension relationship,” thereby supporting optimal torque generation.
Ecological and phenological study of native flora in dynamic habitats of semi-arid subtropical region, district Mandi Baha Uddin of Punjab, Pakistan
Authors: Jamil Muhammad Danish , Ali Muhammad Azhar 
Published: January 2025

Abstract

Documentation of ecological traits of vegetation and its distribution among various geographical locations is a fundamental criterion for conservation and management of ecosystem. For this, present research was conducted during 2021 to 2023 to explore native vegetation and record their eco-functional traits in district Mandi Baha Uddin (MB Din) of Punjab, Pakistan. Plant species were collected from various microhabitats by applying random stratified sampling method from 90 sampling points having 270 quadrates. Canoco and R packages were practiced to link vegetation and environmental factors. A total of 133 native species linked to 32 families were recorded. Distribution of native species among the dissimilar families was very uneven with the prominent families recorded were Poaceae (38 species) and Leguminosae (16 species). The dominant habit form was herbaceous, which contributed 68 herbs (51%) and 38 (29%) grasses. A total of 77 (58%) annual and 56 (42%) perennial native plants were identified in relation to life form. In relation to biological spectrum of native plants, leading life form spectra was of therophytes with 73 (54%) species followed by chamaeophytes with 29 (21%) species and leading leaf size spectra was of nanophylls with 53 (40%) and microphyll 38 (29%). Phenological pattern uncovered that maximum flowering response was exposed during the months of Aug-Sep (70 species) and Mar-Apr (39 species). Temporal analysis depicted that monsoon (70 species) and spring (41 species) seasons favored the flowering of flora compared to summer (18) and winter (4 species) seasons in the research area and that was greatly influenced by change in temperature among various climatic variables. Vegetation link with different habitats designed 5 vegetation groups in various microhabitats among which grassland, forest land and road side habitats favored maximum native flora whereas barrage land and dry land show minimum diversity.
A translational protocol optimizes the isolation of plasma-derived extracellular vesicle proteomics
Authors: Reséndiz Jussara Ríos de los Ríos , Herrmann-Sim Freya , Wilkesmann Liliana , Helm Dominic , Schneider Martin , Campione Giorgia , Plügge Klara , Greiner Giovanni , García Leonie Lazaro , Berker Julia , Zielske Lin , Richter Karsten , Hofmann Wolf-Karsten , von Hohenberg Katharina Clemm 
Published: January 2025

Abstract

In translational research and clinical routine, liquid biopsy is a promising tool to direct individually targeted treatments. Among the components of liquid biopsy, extracellular vesicles (EVs) carry manyfold molecular cargo and are increasingly being studied for biomarker identification. In order to identify potential confounding factors and determine optimal conditions when studying blood-derived EV proteins, the impact of pre-analytical variables needs to be assessed. Here we establish an EV enrichment for proteomic analysis workflow in a real world clinical setting in which we evaluate variables from blood collection through protein preparation and storage for mass spectrometry (MS). We assess hemolysis, particle concentration and size, protein quantity, protein markers and comprehensive proteomic analysis using mass spectrometry to assess the influence of different pre-analytical variables like blood collection tubes, transportation of blood samples and delayed processing. Under these conditions, density gradient and size exclusion chromatography using Sepharose CL-4B show good EV enrichment. For MS, lysis with increased protease inhibitors shows high protein yields while TCA protein precipitation results in high numbers of identified proteins. In summary, we develop here an optimized protocol for the analysis of plasma EV-derived proteomics, evaluating pre-analytical variables relevant for implementation in a clinical setting.
Exploring Natural Analgesics for Chronic Pain Management: Cannabinoids and Other Phytoconstituents
Authors: Bjørklund Geir , Oleshchuk Oleksandra , Gontova Tetiana , Klantsa Mykola , Lukanyuk Mariana , Denefil Olha , Koshovyi Оleh , Shanaida Volodymyr , Shanaida Mariia 
Published: January 2025

Abstract:
Chronic pain lasting more than three months or persisting after normal healing
is a significant global health issue. In a healthcare system, it is crucial to ensure proper
chronic pain management. Traditional pharmacological and non-pharmacological
pain management techniques may not fully meet the requirements of physicians regarding
effectiveness and safety. Therefore, researchers are exploring natural analgesics.
Plant-based phytoconstituents show promise in relieving chronic pain associated with
various diseases. This study aims to review the latest advances in discovering natural
bioactive compounds that can help alleviate chronic pain. It discusses the pathways of
chronic pain and a multifactorial treatment strategy. It also organizes data on using plant-
derived substances, such as cannabinoids, terpenoids, phenolics, and crude extracts.
Additionally, it delves into the pharmacodynamics of cannabinoids, including their route
of administration and elimination. The review presents the results of 22 clinical trials on
various cannabinoids for pain relief. It is important to note that opioids and other alkaloids
from plants are not covered in this article due to their primary use in controlling
acute rather than chronic pain.
Unveiling the Role of SLC6A17 in Lung Adenocarcinoma: Prognosis,
Pathways, and Therapeutic Implications
Authors: Chen Ping , Li Jingbo , Wen JiFan , Li Dongbing , Li Yingjie 
Published: January 2025

Background:
The role of solute carrier family 6 member 17 (SLC6A17) in
lung adenocarcinoma (LUAD) is unclear.

Objectives:
To address this gap in knowledge, we employed bioinformatics analysis and
experimental validation.

Methods:
This research aimed to scrutinize the expression patterns of the SLC6A17
gene across a spectrum of cancers and specifically within LUAD, utilizing data extracted from The Cancer Genome Atlas (TCGA). The correlation between SLC6A17 expression and LUAD prognosis was investigated to assess its diagnostic relevance. The study
delved into the possible regulatory mechanisms of SLC6A17, focusing on its links to immune cell infiltration and drug response in LUAD. The examination of SLC6A17 expression was extended to single-cell sequencing data in LUAD, alongside an evaluation of
the gene's genomic alterations and clinical implications within this disease context. Validation of SLC6A17 expression levels was conducted using datasets from GSE87340 and
various cell lines, employing quantitative real-time polymerase chain reaction (qRTPCR) techniques.

Results:
SLC6A17 exhibited aberrant expression in both pan-cancer and LUAD. Increased expression of SLC6A17 in LUAD patients was significantly associated with
poorer overall survival (p = 0.008), progress-free survival (p = 0.019), and disease specific survival (p = 0.030). In LUAD patients, the levels of SLC6A17 expression were
found to be a significant standalone indicator of prognosis, with a p-value of 0.031. SLC6A17 exhibited associations with various pathways, including focal adhesion, ECM receptor interaction, cell cycle, linoleic acid metabolism, pathways in cancer, and more.
SLC6A17 expression demonstrated correlations with immune infiltration in LUAD. SLC6A17 expression revealed a notably inverse relationship with several substances, including AR-42, T0901317, tubastatin A, SB52334, and amuvatinib, within the context
of LUAD. SLC6A17 was found to be significantly positively regulated in LUAD cell
lines.

Conclusions:
These findings suggest that SLC6A17 indicates the potential of a potential
prognostic biomarker and immunotherapeutic target for patients with LUAD.
Investigation of the Potential Pharmacological Substance Basis and Mechanism of Action of Xuantu Granules in Treating Diabetic Kidney Disease Based on UHPLC-Q-Exactive-HRMS and Bioinformatics
Authors: Fan Jingna , Kong Chang , Yu Bin , Wang Rong , Qi Zhenqiang 
Published: January 2025

Objective:
The objective of this study is to analyze and identify the main chemical
components and blood-absorbed components of Xuantu Granules and predict their pharmacological
substance basis and mechanism in the treatment of DKD.

Methods:
A DKD rat model was established by feeding SD rats a high-fat and high-sugar diet
and administering intraperitoneal injections of streptozotocin (STZ). The therapeutic effect of
Xuantu granules was evaluated. Drug-containing serum was prepared after gavage, and the major
chemical components of Xuantu Granules and the drug-containing serum were detected using
UHPLC-Q-Exactive-HRMS. Blood-absorbed components were identified based on retention
time, mass-to-charge ratio, and MS/MS spectrum. Blood-absorbed components’ target proteins
were searched using the CTD, SwissTarget, BindingDB, and TargetNet databases. DKD disease
target genes were screened from the GEO database using WGCNA. A “bioactive blood-absorbed
component-target-disease” PPI network was constructed using Cytoscape software, and the key
clustering subnetworks were identified by MCODE plugin. GO functional analysis and KEGG
pathway enrichment analysis were performed on subnetworks.

Results:
Xuantu Granules lowered fasting blood glucose, improved renal function, reduced proteinuria,
and improved renal tissue pathological changes in DKD rats. 36 chemical components
were identified, among which 12 compounds, including β -Carboline-1-propionic acid, Morin,
Afzelin, Schizandrin, Gomisin A were identified as blood-absorbed components. Bioinformatics
analysis indicated that AKT1, TNF, TP53, IL6, SRC, IL1B, EGFR, JUN, BCL2, and CASP3
might be the main therapeutic targets. The involved pathways included the IL-17 signaling
pathway, PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic complications
and so on.

Conclusion:
Xuantu Granules may exert therapeutic effects on DKD through multiple targets
and pathways.
Identification of the Metabolic Characteristic of Organ Fibrosis Using
Microbial Analysis on RNA-seq Data
Authors: Wang Zitong , Wang Ping , He Guoyou , Cheng Liang , Li Tianyu , Wang Yan , Li Hong 
Published: January 2025

Background::
Fibrosis refers to abnormal deposition of extracellular matrix, which
leads to organ dysfunction. Metabolic alterations, especially enhanced glycolysis and suppressed
fatty acid oxidation, are recognized as an essential pathogenic process of fibrosis. Recently, several
reports indicate that the changes in microbiota composition are associated with metabolic disorders,
suggesting microbes may contribute to organ fibrosis by regulating metabolic processes.

Method::
In this study, microbial reannotation was carried out on the RNA-seq data of fibrotic organs.
Then, the microbial composition differences among healthy and fibrotic organ samples were
determined by alpha and beta diversity analysis. Common and specific microbial markers of fibrosis
were also identified by LEfSe. After that, the correlation analysis of the characteristic microbe--
gene-functional pathway was conducted to confirm the effects of microbes on host metabolism.

Result::
The results showed that the microbial composition significantly differed between healthy
and diseased organs. Besides, the common characteristic microbes interacted closely with each
other and contributed to fibrosis through symbiosis or inhibition. The largest proportion in fibrosis
organs was Proteobacteria, which was the main source of pathogenic microbes.

Conclusion::
Further study found that the metabolic alteration driven by common and special characteristic
microbes in fibrotic organs focused on the processes related to glycolysis and fatty acid
metabolism.
Ionizing Radiation Combined with Gold Complex Compounds Causes Apoptosis in Colorectal Cancer Cells by Increasing the Level of Caspase-3
Authors: Sano Naoyuki , Yoshino Hironori , Sato Yoshiaki , Honma Hideo , Cordonier Christopher E. J. , Kashiwakura Ikuo 
Published: January 2025

Background:
The anticancer activity and radiosensitizing effect of
Auranofin, an an-tirheumatic and an approved gold metallic drug, have been
investigated from multiple perspectives. In this study, the action of the new gold
complex compound TPN-Au(I)-MM4 was compared with that of auranofin.

Methods:
The inhibitory effect of 10 μM and 50 μM concentrations on cell proliferation
was investigated using the human colon cancer cell lines HCT116 and SW480. The
radiosensitizing effect of HCT116 cells was evaluated by measuring the ability to
induce apoptotic cell death. The mechanism of action was qualitatively determined via
western blotting analysis of the level of cleaved caspase-3 protein.

Results:
Auranofin completely inhibited cell proliferation in both cell lines at both
concentrations. In contrast, only 50 μM of TPN-Au(I)-MM4 significantly inhibited the
proliferation of SW480 cells, but did not affect the proliferation of HCT116 cells. On the
other hand, both compounds effectively increased the apoptotic cell death rate when
combined with 4 Gy of X-ray irradiation. This mechanism was caused by a significant
increase in the level of caspase-3, which is an apoptosis execution factor, by the
combination of these two treatments.

Conclusion:
Both compounds promoted the significant expression of caspase-3, an
apoptosis execution factor, and exhibited radio-sensitizing effects. In particular, TPNAu(
I)-MM4 showed no inhibitory effect on cell proliferation alone, but had a significant
radiosensitising effect on HCT116 cells. Therefore, TPN-Au(I)-MM4 has the potential
for use as a new radiosensitizer.
Agar-Agar Matrix-Mediated Immobilization for Enhanced Catalytic
Behavior and Stability of 1,4-α-D-Glucan Glucanohydrolase Obtained
from Halotolerant Micrococcus spp. K11
Authors: Aman Ullah Ayisha , Jamaluddin Aysha , Zohra Raheela Rahmat , Siddiqui Ayesha , Naheed Suad 
Published: January 2025

Background::
Entrapment is supposed to be the most effective and simple method
among various strategies of enzyme immobilization as it preserves the original conformation and
biological activity of the enzyme with greater immobilization yield. A suitable and cost-effective
protocol for the entrapment of 1,4-α-D-glucan glucanohydrolase obtained from halotolerant Micrococcus
spp., K11 has been developed.

Objective::
The major objective of the present study was to explore halotolerant bacteria as potential
producer of 1, 4-α-D-glucan glucanohydrolase from salt mines.

Method::
A total of 11 bacterial strains were isolated and purified using the halophilic medium.
Strain K11 was selected on the basis of a large zone of starch hydrolysis. The crude enzyme extract
was utilized to entrap in agar-agar scaffolds. Kinetic studies of agar-agar entrapped 1,4-α-Dglucan
glucanohydrolase were assessed and compared with the properties of soluble enzyme.

Results::
It was observed that optimum immobilization of 1,4-α-D-glucan glucanohydrolase was attained
at 4% concentration of agar-agar. Maximum entrapped enzyme activity was noticed after
15 minutes, highlighting the 5-minute increase in free enzyme. Moreover, temperature maxima for
optimal enzyme substrate reaction were recorded to be 30°C for both immobilized and soluble
1,4-α-D-glucan glucanohydrolase, whereas pH maxima of 1,4-α-D-glucan glucanohydrolase were
shifted from 6.5 to 7.0 after entrapment. The need for optimum substrate concentration for entrapped
amylase activity was recorded to be 3% (gm), and for soluble 1,4-α-D-glucan glucanohydrolase,
2% (gm) starch was required for improved enzymatic efficacy. The reusability studies
showed that agar-agar immobilized 1,4-α-D-glucan glucanohydrolase could be consumed up to 6
repeated cycles.

Conclusion::
It is concluded that exploited features of immobilized 1,4-α-D-glucan glucanohydrolase
enhance its applicability in several industrial processes.
Study on the Role of Human Gut Microbiome in Controlling MRSA-Induced Sepsis Using Proteomics Tool
Authors: Giriraj Aditi , Bhat Apoorva , Sabat Sasmita 
Published: January 2025

Background:
Sepsis is defined as the extreme response of a body to an infection, leading
to untimely death if left untreated. The human gut microbiome is characterized by the presence of
several microorganisms in the gastrointestinal tract. This study provides insight into the potential
therapeutic effects of a peptide present in the human gut microbiome that helps control sepsis.

Aim:
This study aimed to explore the therapeutic application of a peptide from Lactobacillus sp. in
the human gut microbiome as an alternative to MRSA, which causes severe, fatal diseases like sepsis.
It also elucidates the peptide-protein interactions that enhance the efficacy of infection control
and treatment.

Objectives:
We aimed to investigate the interactions between protein-peptide and protein-drug complexes
through in silico analyses.

Methods:
Molecular docking was performed using PyRx and HADDOCK tools. Next, we performed
molecular simulation studies using GROMACS v2020.6 at different physiological pH values
of 4, 6, and 7.4. Stability, compactness, and binding energies were analyzed using parameters such as RMSD, Rg, and MMPBSA, among other parameters.

Results:
We observed stability on docking between Plantaricin KL-1Y, an effective bacteriocin
from Lactobacillus plantarum (organism from gut microbiome), and PBP2a from Staphylococcus
aureus (causative organism of sepsis). This was indicated by a binding affinity of -13.4 kcal/mol,
higher than that of PBP2a-FDA-approved drug (-8 kcal/mol). The MMPBSA results of the PBP2a-
Plantaricin KL-1Y complex showed a significantly higher binding affinity at pH 7.4 of -228.451
kcal/mol in comparison to -69.5747 kcal/mol for the PBP2a-Ceftaroline fosamil complex.

Conclusion:
These results indicate the possible use of a peptide from the human gut as a potential
therapeutic agent against S. aureus infection.
Integrated Analysis of the Proteome Datasets Using the Assembled
Genome Sequence Provides New Insights into the Specialization of Shoots,
Stolons, and Rhizomes in Bermudagrass (Cynodon dactylon L.)
Authors: Zhang Bing , Yuan Shuai 
Published: January 2025

Introduction::
Bermudagrass (Cynodon dactylon L.) simultaneously has three types of
stems: shoots, stolons, and rhizomes, which lays the basis for the fast clonal growth of this important
warm-season turfgrass species. However, the mechanisms underlying the differentiation,
growth, and development of the three types of stems remain unclear.

Methods::
In this study, the annotation information of the assembled bermudagrass genome was
used to reanalyze the mass spectrometry raw data generated in the comparative proteomics analysis
of bermudagrass shoots and stolons as well as stolons and rhizomes. One-way analysis of variance
and the Student-Newman-Keuls test was performed to identify the Differentially Expressed Proteins
(DEPs) in paired comparison of shoots versus stolons, shoots versus rhizomes, and stolons versus
rhizomes.

Results::
A total of 3190 proteins were simultaneously expressed in the three types of stems, whereas
135, 1012, and 876 DEPs were identified between shoots and stolons, shoots and rhizomes, and
stolons and rhizomes, respectively. Venn diagram analysis indicated that 23 DEPs were simultaneously
identified in the three paired comparisons. Functional enrichment analysis indicated endocytosis
and terpenoid backbone biosynthesis to be the most significantly DEP-enriched biochemical
pathways among the three types of stems.

Conclusion::
The results of this study not only provided new insights into the specialization of
shoots, stolons, and rhizomes in bermudagrass, but also pointed out the importance of high-quality
genome assembly and annotation in proteomics research.