bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical studies on low-strain integrity testing of cast-in-place pile
Authors: Ma Lemin , Duan Zhiqiang , Guo Wei , Ren Yuxiao
Published: July 2024

A series of in situ tests were conducted using the low-strain integrity testing method to detect the defects of cast-in-place concrete piles. Numerical studies were conducted to observe the time-domain waveform along cast-in-place concrete piles with diameter expansion, diameter reduction and segregation defects. It is found the time-domain waveforms of the pile with the diameter expansion defects have second wave troughs after the first wavelength while those with diameter reduction and segregation defects have second wave crests. However, it is difficult to use amplitudes to directly determine the length, diameter and segregation degree of the defects. The second wavelengths could be used to identify the lengths of diameter reduction and segregation defects but it is hard to identify those of diameter expansion defects. The locations of diameter reduction and segregation defects could be determined through the time of second wave crests using the linear interpolation method, and those of diameter expansion defects could be determined through the time of second wave trough.
Manganese(II) and Zinc(II) metal complexes of novel bidentate formamide-based Schiff base ligand: synthesis, structural characterization, antioxidant, antibacterial, and in-silico molecular docking study
Authors: Juyal Vijay Kumar , Thakuri Shweta Chand , Panwar Mohit , Rashmi  , Prakash Om , Perveen Kahkashan , Bukhari Najat A. , Nand Viveka
Published: July 2024

A new bidentate Schiff base ligand (C16H16Cl2N4), condensation product of ethylene diamine and 4-chloro N-phenyl formamide, and its metal complexes [M(C16H16Cl2N4)2(OAc)2] (where M = Mn(II) and Zn(II)) were synthesized and characterized using various analytical and spectral techniques, including high-resolution mass spectrometry (HRMS), elemental analysis, ultraviolet–visible (UV–vis), Fourier-transform infrared (FTIR) spectroscopy, AAS, molar conductance, 1H NMR, and powder XRD. All the compounds were non-electrolytes and nanocrystalline. The synthesized compounds were assessed for antioxidant potential by DPPH radical scavenging and FRAP assay, with BHT serving as the positive control. Inhibitory concentration at 50% inhibition (IC50) values were calculated and used for comparative analysis. Furthermore, the prepared compounds were screened for antibacterial activity against two Gram-negative bacteria (Staphylococcus aureus and Bacillus subtilis) and two Gram-positive bacteria (Escherichia coli and Salmonella typhi) using disk-diffusion methods, with amikacin employed as the standard reference. The comparison of inhibition zones revealed that the complexes showed better antibacterial activity than the ligand. To gain insights into the molecular interactions underlying the antibacterial activity, the ligand and complexes were analyzed for their binding affinity with S. aureus tyrosyl–tRNA synthetase (PDB ID: 1JIL) and S. typhi cell membrane protein OmpF complex (PDB ID: 4KR4). These analyses revealed robust interactions, validating the observed antibacterial effects against the tested bacterial strains.
Low-carbon economic dispatch strategy for integrated electrical and gas system with GCCP based on multi-agent deep reinforcement learning
Authors: Feng Wentao , Deng Bingyan , Zhang Ziwen , Jiang He , Zheng Yanxi , Peng Xinran , Zhang Le , Jing Zhiyuan
Published: July 2024

With the growing concern for the environment, sustainable development centred on a low-carbon economy has become a unifying pursuit for the energy industry. Integrated energy systems (IES) that combine multiple energy sources such as electricity, heat and gas are essential to facilitate the consumption of renewable energy and the reduction of carbon emission. In this paper, gas turbine (GT), carbon capture and storage (CCS) and power-to-gas (P2G) device are introduced to construct a new carbon capture coupling device model, GT-CCS-P2G (GCCP), which is applied to the integrated electrical and gas system (IEGS). Multi-agent soft actor critic (MASAC) applies historical trajectory representations, parameter spatial techniques and deep densification frameworks to reinforcement learning for reducing the detrimental effects of time-series data on the decisional procedure. The energy scheduling problem of IEGS is redefined as a Markov game, which is addressed by adopting a low carbon economic control framework based on MASAC with minimum operating cost and minimum carbon emission as the optimization objectives. To validate the rationality and effectiveness of the proposed low-carbon economy scheduling model of IEGS based on MASAC, this paper simulates and analyses in integrated PJM-5 node system and seven nodes natural gas system.
Land-use and habitat quality prediction in the Fen River Basin based on PLUS and InVEST models
Authors: Hou Yanjun , Wu Juemei
Published: July 2024

Assessment and prediction analyses of the ecological environmental quality of river basins are pivotal to realize ecological protection and high-quality coordinated development. Methods: The PLUS and InVEST models were used to analyze the spatiotemporal evolution characteristics of land-use in the Fen River Basin and simulate the spatial pattern of land-use under natural development (ND), ecological protection (EC), and economic development (ED) scenarios in 2030, as well as evaluate habitat quality (HQ) and its spatiotemporal variation characteristics from 2000 to 2030. From 2000 to 2020, the Fen River Basin consisted primarily of cultivated land, followed by forests, and then unused land. Habitat quality in the Fen River Basin showed a downward trend from 2000 to 2020. Between 2010 and 2020, the rate of decline decreased, and by 2030, the HQ in the EC scenario exhibited improvement compared to 2020. However, there was a reduction in HQ in the natural development and economic development scenarios and there was obvious heterogeneity in spatial distribution, showing the characteristics of “low middle and high edge”. The cultivated land was converted into forests, construction land, and grasslands, and the conversion of construction land and forests to cultivated land dominated the changes in HQ in the Fen River Basin.
The impact of land use change on carbon storage and multi-scenario prediction in Hainan Island using InVEST and CA-Markov models
Authors: Lei Jinrui , Zhang Le , Chen Zongzhu , Wu Tingtian , Chen Xiaohua , Li Yuanling
Published: July 2024

As a fundamental element of global carbon storage, the storage carbon in terrestrial ecosystem is significant for climate change mitigation. Land use/cover change (LUCC) is a main impact element of ecosystems’ carbon storage. Evaluating the relation between land use change and carbon storage is vital for lowering global carbon emissions. Taking Hainan Island as an example, this paper employs the InVEST as well as the CA-Markov models to assess and predict how different land use affects carbon storage in various situations from 2000 to 2020 and from 2030 to 2050 on Hainan Island. The influence factors, together with driving mechanisms of carbon storage spatial distribution are quantitatively analyzed as well in this paper. The results demonstrate that, from 2000 to 2020, Hainan Island’s net increase in built land was 605.49 km2, representing a growth rate of 77.05%. Over the last 20 years, Hainan Island’s carbon storage and density have decreased by 5.90 Tg and 1.75 Mg/hm2, respectively. The sharp rise in built land mainly makes the carbon storage decline. From 2030 to 2050, land use changes on Hainan Island are expected to result in differing degrees of carbon storage loss in various scenarios. In 2050, Hainan Island’s carbon storage will decline by 17.36 Tg in the Natural Development Scenario (NDS), 13.61 Tg in the Farmland Protection Scenario (FPS), and 8.06 Tg in the Ecological Protection Scenario (EPS) compared to 2020. The EPS can efficiently maintain carbon sequestration capability, but it cannot effectively prevent cropland area loss. Regarding the carbon storage’s spatial distribution, Hainan Island generally exhibits a pattern of high carbon storages in the low and middle carbon storages in the surrounding areas. Areas with high value are primarily located in Hainan Island’s central and southern mountainous areas, whereas areas with low value are primarily located in surrounding areas with lower elevations, primarily encompassing built land and cropland. Geographic detection presented the spatial differentiation of carbon storage in Hainan Island is mainly influenced by factors like slope, land use intensity, and DEM, as well as its interaction with other factors is significantly strengthened (p < 0.05). Under the strategic framework of the “carbon peaking and carbon neutrality” goal and the national ecological civilization pilot zone, it is imperative to carefully consider scenarios for ecological protection and farmland protection, adopt ecological regulation models with spatial differentiation, and implement land use policies to improve ecosystem stability, which will contribute to carbon storage loss reduction and ensure food and ecological security.
TRIM28 in cancer and cancer therapy
Authors: Li Kailang , Wang Haifeng , Jiang Bitao , Jin Xiaofeng
Published: July 2024

TRIM28 (tripartite motif protein 28) was initially believed to be a transcription inhibitor that plays an important role in DNA damage repair (DDR) and in maintaining cancer cellular stemness. As research has continued to deepen, several studies have found that TRIM28 not only has ubiquitin E3 ligase activity to promote degradation of substrates, but also can promote SUMOylation of substrates. Although TRIM28 is highly expressed in various cancer tissues and has oncogenic effects, there are still a few studies indicating that TRIM28 has certain anticancer effects. Additionally, TRIM28 is subject to complex upstream regulation. In this review, we have elaborated on the structure and regulation of TRIM28. At the same time, highlighting the functional role of TRIM28 in tumor development and emphasizing its impact on cancer treatment provides a new direction for future clinical antitumor treatment.
E-selectin in vascular pathophysiology
Authors: Zhang Jinjin , Huang Shengshi , Zhu Zhiying , Gatt Alex , Liu Ju
Published: July 2024

Selectins are a group of Ca2+-dependent, transmembrane type I glycoproteins which attract cell adhesion and migration. E-selectin is exclusively expressed in endothelial cells, and its expression is strongly enhanced upon activation by pro-inflammatory cytokines. The interaction of E-selectin with its ligands on circulating leukocytes captures and slows them down, further facilitating integrin activation, firm adhesion to endothelial cells and transmigration to tissues. Oxidative stress induces endothelial cell injury, leading to aberrant expression of E-selectin. In addition, the elevated level of E-selectin is positively related to high risk of inflammation. Dysregulation of E-selectin has been found in several pathological conditions including acute kidney injury (AKI), pulmonary diseases, hepatic pathology, Venous thromboembolism (VTE). Deletion of the E-selectin gene in mice somewhat ameliorates these complications. In this review, we describe the mechanisms regulating E-selectin expression, the interaction of E-selectin with its ligands, the E-selectin physiological and pathophysiological roles, and the therapeutical potential of targeting E-selectin.
Comparing 2-day vs 3-day flu-CY lymphodepleting regimens for CD19 CAR T-cell therapy in patients with non-hodgkin’s lymphoma
Authors: Frame David G. , Geer Marcus , Kasha Salena , Markstrom Denise , Scappaticci Gianni , Feeney Tate , Hayduk Andrew , Mansoor Hilary M. , Oberfeld Avery , D’Antonio Hannah , Anand Sarah , Choi Sung Won , Maciejewski John , Pawarode Attaphol , Riwes Mary Mansour , Tewari Muneesh , Magenau John , Ghosh Monalisa
Published: July 2024

Introduction

Lymphodepleting chemotherapy (LDC) is critical to CAR T-cell expansion and efficacy. Despite this, there is not a consensus in the literature regarding the optimal LDC regimen, including dose and frequency.

Methods

We retrospectively reviewed consecutive patients at a single institution that received LDC prior to treatment with the CD19 directed CAR T-cell products axicabtagene ciloleucel and tisagenlecleucel. Patients treated at our center received fludarabine 30 mg/m2 and cyclophosphamide 500 mg/m2 for 3 consecutive days prior to May 2019. After this timepoint patients routinely received fludarabine 40 mg/m2 and cyclophosphamide 500 mg/m2 for 2 consecutive days. Clinical data from each cohort were obtained from the electronic medical record and compared for differences in CAR T-cell efficacy and toxicity.

Results

From June 2018 to August 2023, LDC was given to 92 patients prior to CD19 directed CAR T-cell therapy for relapsed non-Hodgkin’s lymphoma. Twenty-eight patients received a 3-day regimen, and 64 patients received a 2-day regimen. In the total cohort, 75% of patients received axicabtagene ciloleucel and 25% received tisagenlecleucel. The overall response rates in both the 2-day regimen group and the 3-day regimen group were similar (69% vs 75%, p= 0.21) as were the complete response rates (50% vs 54%, p=0.82). There were no significant differences between the 2-day and 3-day regimens for grade 2–4 cytokine release syndrome (55% vs 50%, p=0.82), grade 2–4 immune effector cell associated-neurotoxicity syndrome (42% vs 29%, p=0.25), or time to resolution of neutropenia or thrombocytopenia. The rate of prolonged platelet recovery lasting greater than 60 days was higher with the 3-day regimen (9% vs 27%, p=0.026).

Discussion

As the number of patients eligible for CAR T-cell therapy continues to increase, optimizing each component of therapy is necessary. We show that a 2-day regimen of LDC with fludarabine and cyclophosphamide is feasible without significant impact on CAR T-cell efficacy or toxicity. Prospective studies are necessary to further determine the most effective LDC regimen.
Construction of an IFNAR1 knockout MDBK cell line using CRISPR/Cas9 and its effect on bovine virus replication
Authors: Geng Yuanchen , Jiang Chuanwen , Yang Hao , Xia Qing , Xu Xiaowen , Yang Kaihui , Yuan Xinwei , Chen Jianguo , Chen Yingyu , Chen Xi , Zhang Lei , Hu Changmin , Guo Aizhen
Published: July 2024

The type I interferon (IFN) pathway is important for eukaryotic cells to resist viral infection, as well as an impediment to efficient virus replication. Therefore, this study aims to create an IFNAR1 knockout (KO) Madin-Darby bovine kidney (MDBK) cell line using CRISPR/Cas9 and investigate its application and potential mechanism in increasing viral replication of bovines. The IFNAR1 KO cells showed increased titers of bovine viral diarrhea virus (BVDV) (1.5 log10), with bovine enterovirus and bovine parainfluenza virus type 3 (0.5–0.8 log10). RNA-seq revealed reduced expression of the genes related IFN-I pathways including IFNAR1, STAT3, IRF9, and SOCS3 in IFNAR1 KO cells compared with WT cells. In WT cells, 306 differentially expressed genes (DEGs) were identified between BVDV-infected and -uninfected cells. Of these, 128 up- and 178 down-regulated genes were mainly associated with growth cycle and biosynthesis, respectively. In IFNAR1 KO cells, 286 DEGs were identified, with 82 up-regulated genes were associated with signaling pathways, and 204 down-regulated genes. Further, 92 DEGs were overlapped between WT and IFNAR1 KO cells including ESM1, IL13RA2, and SLC25A34. Unique DEGs in WT cells were related to inflammation and immune regulation, whereas those unique in IFNAR1 KO cells involved in cell cycle regulation through pathways such as MAPK. Knocking down SLC25A34 and IL13RA2 in IFNAR1 KO cells increased BVDV replication by 0.3 log10 and 0.4 log10, respectively. Additionally, we constructed an IFNAR1/IFNAR2 double-knockout MDBK cell line, which further increased BVDV viral titers compared with IFNAR1 KO cells (0.6 log10). Overall, the IFNAR1 KO MDBK cell line can support better replication of bovine viruses and therefore provides a valuable tool for bovine virus research on viral pathogenesis and host innate immune response.
Experimental study on mechanical properties of basalt fiber reinforced nano-SiO2 concrete after high temperature
Authors: Yang Weidong , Liu Huaxin , Wang Hesong
Published: July 2024

In enhancing the high-temperature resistance of concrete, incorporating fiber materials was established as an effective approach. This study focused on evaluating the cubic compressive strength, splitting tensile strength, prism compressive strength, and flexural strength of plain concrete, nano-SiO2 concrete, and basalt fiber nano-SiO2 concrete when subjected to elevated temperatures. Subsequently, a concrete strength prediction model was established, and a microstructure analysis of the specimens was conducted. The results indicated that after exposure to 800°C, the cubic compressive strength, splitting tensile strength, prism compressive strength, and flexural strength of basalt fiber-reinforced nano-SiO₂ concrete increased by 33.7%, 15.6%, 10.4%, and 17.2%, respectively, compared to plain concrete. Furthermore, the fitting values of the strength prediction model were all above 0.9. Microstructure analysis revealed that the filling effect of nano-SiO₂ made the concrete matrix denser, while the basalt fiber effectively restrained the formation of cracks in the concrete matrix. Additionally, nano-SiO₂ promoted the formation of hydrated calcium silicate from Ca(OH)₂(CH) and adhered to the basalt fiber, enhancing bonding and reducing the risk of concrete spalling.
Case report and review of literature: IgG4-gastroduodenitis in upper GI Crohn’s disease: two separate entities or just a marker of disease severity?
Authors: Desmedt Valérie , Geldof Jeroen , Hoorens Anne , Lobaton Triana
Published: July 2024

A 20-year-old man was presented with ulcerative gastritis and duodenitis complicated by pyloric stenosis. Helicobacter pylori infection was excluded, and the lesions did not respond to treatment with proton pump inhibitors. No other parts of the intestinal tract showed signs of inflammation. Histopathological review showed signs of chronic inflammation with granuloma formation. A tentative diagnosis of isolated upper gastrointestinal (UGI) Crohn’s disease was performed. However, additional work-up revealed significantly positive IgG4 staining as well as elevated IgG4 serum levels. Since granulomatous disease is unlikely in IgG4-related disease, an eventual diagnosis of overlapping IgG4-related disease and Crohn’s disease (CD) was performed. Treatment with systemic steroids and anti-TNF in combination with azathioprine led to rapid symptomatic improvement. In this article, we review the available literature on IgG4-related gastroduodenitis, granulomatous gastritis, and upper GI CD. We suggest the possibility that IgG4-infiltration may be a marker of severely active inflammatory bowel disease rather than a separate disease entity.
Multivariate pattern analysis of medical imaging-based Alzheimer's disease
Authors: Alarjani Maitha , Almarri Badar
Published: July 2024

Alzheimer's disease (AD) is a devastating brain disorder that steadily worsens over time. It is marked by a relentless decline in memory and cognitive abilities. As the disease progresses, it leads to a significant loss of mental function. Early detection of AD is essential to starting treatments that can mitigate the progression of this disease and enhance patients' quality of life. This study aims to observe AD's brain functional connectivity pattern to extract essential patterns through multivariate pattern analysis (MVPA) and analyze activity patterns across multiple brain voxels. The optimized feature extraction techniques are used to obtain the important features for performing the training on the models using several hybrid machine learning classifiers for performing binary classification and multi-class classification. The proposed approach using hybrid machine learning classification has been applied to two public datasets named the Open Access Series of Imaging Studies (OASIS) and the AD Neuroimaging Initiative (ADNI). The results are evaluated using performance metrics, and comparisons have been made to differentiate between different stages of AD using visualization tools.
Development and evaluation of a triplex droplet digital PCR method for differentiation of M. tuberculosis, M. bovis and BCG
Authors: Qu Yao , Liu Mengda , Sun Xiangxiang , Liu Yongxia , Liu Jianzhu , Hu Liping , Jiang Zhiqiang , Qi Fei , Nan Wenlong , Yan Xin , Sun Mingjun , Shao Weixing , Li Jiaqi , Sun Shufang , Zhang Haobo , Fan Xiaoxu
Published: July 2024

Introduction

Tuberculosis, caused by Mycobacterium tuberculosis complex (MTBC), remains a global health concern in both human and animals. However, the absence of rapid, accurate, and highly sensitive detection methods to differentiate the major pathogens of MTBC, including M. tuberculosis, M. bovis, and BCG, poses a potential challenge.

Methods

In this study, we have established a triplex droplet digital polymerase chain reaction (ddPCR) method employing three types of probe fluorophores, with targets M. tuberculosis (targeting CFP-10-ESAT-6 gene of RD1 and Rv0222 genes of RD4), M. bovis (targeting CFP-10-ESATs-6 gene of RD1), and BCG (targeting Rv3871 and Rv3879c genes of ΔRD1), respectively.

Results

Based on optimization of annealing temperature, sensitivity and repeatability, this method demonstrates a lower limit of detection (LOD) as 3.08 copies/reaction for M. tuberculosis, 4.47 copies/reaction for M. bovis and 3.59 copies/reaction for BCG, without cross-reaction to Mannheimia haemolytica, Mycoplasma bovis, Haemophilus parasuis, Escherichia coli, Pasteurella multocida, Ochrobactrum anthropi, Salmonella choleraesuis, Brucella melitensis, and Staphylococcus aureus, and showed repeatability with coefficients of variation (CV) lower than 10%. The method exhibits strong milk sample tolerance, the LOD of detecting in spike milk was 5 × 103 CFU/mL, which sensitivity is ten times higher than the triplex qPCR. 60 clinical DNA samples, including 20 milk, 20 tissue and 20 swab samples, were kept in China Animal Health and Epidemiology Center were tested by the triplex ddPCR and triplex qPCR. The triplex ddPCR presented a higher sensitivity (11.67%, 7/60) than that of the triplex qPCR method (8.33%, 5/60). The positive rates of M. tuberculosis, M. bovis, and BCG were 1.67, 10, and 0% by triplex ddPCR, and 1.67, 6.67, and 0% by triplex qPCR, with coincidence rates of 100, 96.7, and 100%, respectively.

Discussion

Our data demonstrate that the established triplex ddPCR method is a sensitive, specific and rapid method for differentiation and identification of M. tuberculosis, M. bovis, and BCG.
Causal associations of gut microbiota and pulmonary tuberculosis: a two-sample Mendelian randomization study
Authors: Lu Zhongkui , Xu Weiping , Guo Yidi , He Fang , Zhang Guoying
Published: July 2024

Background

The prevalence of pulmonary tuberculosis (PTB) as an infectious disease continues to contribute significantly to global mortality. According to recent studies, the gut microbiota of PTB patients and healthy controls (HCs) show significant disparities. However, the causal relationship between them has yet to be elucidated.

Methods

We conducted a study using Mendelian Randomization (MR) to explore the potential causal link between gut microbiota and pulmonary tuberculosis (PTB). The summary statistics of the gut microbiota were acquired from the MiBioGen consortium, while data on PTB were sourced from pheweb.jp. A range of statistical methodologies were employed to evaluate causality, encompassing inverse variance weighting (IVW), MR-Egger, weighted median (WM), weighted model, and simple model. We utilized instrumental variables (IVs) that have a direct causal relationship with PTB to annotate SNPs, aiming to discover the genes harboring these genetic variants and uncover potential associations between host genes and the microbiome in patients with PTB.

Results

Among the 196 bacterial traits in the gut microbiome, we have identified a total of three microbiomes that exhibit a significant association with PTB. The occurrence of Dorea (P = 0.0458, FDR-adjusted P = 0.0458) and Parasutterella (P = 0.0056, FDR-adjusted P = 0.0168) was linked to an elevated risk of PTB, while the presence of Lachnoclostridium (P = 0.0347, FDR-adjusted P = 0.0520) demonstrated a protective effect against PTB. Our reverse Two-Sample Mendelian Randomization (TSMR) analysis did not yield any evidence supporting the hypothesis of reverse causality from PTB to alterations in the intestinal flora.

Conclusion

We have established a connection between the gut microbiota and PTB through gene prediction analysis, supporting the use of gut microecological therapy in managing PTB and paving the way for further understanding of how gut microbiota contributes to PTB’s development.
Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs
Authors: Banović Đeri Bojana , Nešić Sofija , Vićić Ivan , Samardžić Jelena , Nikolić Dragana
Published: July 2024

Advances in small RNAs (sRNAs)-related studies have posed a challenge for NGS-related bioinformatics, especially regarding the correct mapping of sRNAs. Depending on the algorithms and scoring matrices on which they are based, aligners are influenced by the characteristics of the dataset and the reference genome. These influences have been studied mainly in eukaryotes and to some extent in prokaryotes. However, in bacteria, the selection of aligners depending on sRNA-seq data associated with outer membrane vesicles (OMVs) and the features of the corresponding bacterial reference genome has not yet been investigated. We selected five aligners: BBmap, Bowtie2, BWA, Minimap2 and Segemehl, known for their generally good performance, to test them in mapping OMV-associated sRNAs from Aliivibrio fischeri to the bacterial reference genome. Significant differences in the performance of the five aligners were observed, resulting in differential recognition of OMV-associated sRNA biotypes in A. fischeri. Our results suggest that aligner(s) should not be arbitrarily selected for this task, which is often done, as this can be detrimental to the biological interpretation of NGS analysis results. Since each aligner has specific advantages and disadvantages, these need to be considered depending on the characteristics of the input OMV sRNAs dataset and the corresponding bacterial reference genome to improve the detection of existing, biologically important OMV sRNAs. Until we learn more about these dependencies, we recommend using at least two, preferably three, aligners that have good metrics for the given dataset/bacterial reference genome. The overlapping results should be considered trustworthy, yet their differences should not be dismissed lightly, but treated carefully in order not to overlook any biologically important OMV sRNA. This can be achieved by applying the intersect-then-combine approach. For the mapping of OMV-associated sRNAs of A. fischeri to the reference genome organized into two circular chromosomes and one circular plasmid, containing copies of sequences with rRNA- and tRNA-related features and no copies of sequences with protein-encoding features, if the aligners are used with their default parameters, we advise avoiding Segemehl, and recommend using the intersect-then-combine approach with BBmap, BWA and Minimap2 to improve the potential for discovery of biologically important OMV-associated sRNAs.
Biomimetic learning of hand gestures in a humanoid robot
Authors: Olikkal Parthan , Pei Dingyi , Karri Bharat Kashyap , Satyanarayana Ashwin , Kakoty Nayan M. , Vinjamuri Ramana
Published: July 2024

Hand gestures are a natural and intuitive form of communication, and integrating this communication method into robotic systems presents significant potential to improve human-robot collaboration. Recent advances in motor neuroscience have focused on replicating human hand movements from synergies also known as movement primitives. Synergies, fundamental building blocks of movement, serve as a potential strategy adapted by the central nervous system to generate and control movements. Identifying how synergies contribute to movement can help in dexterous control of robotics, exoskeletons, prosthetics and extend its applications to rehabilitation. In this paper, 33 static hand gestures were recorded through a single RGB camera and identified in real-time through the MediaPipe framework as participants made various postures with their dominant hand. Assuming an open palm as initial posture, uniform joint angular velocities were obtained from all these gestures. By applying a dimensionality reduction method, kinematic synergies were obtained from these joint angular velocities. Kinematic synergies that explain 98% of variance of movements were utilized to reconstruct new hand gestures using convex optimization. Reconstructed hand gestures and selected kinematic synergies were translated onto a humanoid robot, Mitra, in real-time, as the participants demonstrated various hand gestures. The results showed that by using only few kinematic synergies it is possible to generate various hand gestures, with 95.7% accuracy. Furthermore, utilizing low-dimensional synergies in control of high dimensional end effectors holds promise to enable near-natural human-robot collaboration.
Whole-brain inputs and outputs of Phox2b and GABAergic neurons in the nucleus tractus solitarii
Authors: Shao Liuqi , Kong Fanrao , Tian Xiaochen , Deng Tianjiao , Wang Yakun , Ji Yake , Wang Xiaoyi , Yu Hongxiao , Yuan Fang , Fu Congrui , Wang Sheng
Published: July 2024

The nucleus tractus solitarii (NTS) plays a critical role in the homeostatic regulation of respiration, blood pressure, sodium consumption and metabolic processes. Despite their significance, the circuitry mechanisms facilitating these diverse physiological functions remain incompletely understood. In this study, we present a whole-brain mapping of both the afferent and efferent connections of Phox2b-expressing and GABAergic neurons within the NTS. Our findings reveal that these neuronal populations not only receive monosynaptic inputs primarily from the medulla oblongata, pons, midbrain, supra-midbrain and cortical areas, but also mutually project their axons to these same locales. Moreover, intense monosynaptic inputs are received from the central amygdala, the paraventricular nucleus of the hypothalamus, the parasubthalamic nucleus and the intermediate reticular nucleus, along with brainstem nuclei explicitly engaged in respiratory regulation. In contrast, both neuronal groups extensively innervate brainstem nuclei associated with respiratory functions, although their projections to regions above the midbrain are comparatively limited. These anatomical findings provide a foundational platform for delineating an anatomical framework essential for dissecting the specific functional mechanisms of these circuits.
High charge of cerebroid nests in nodular melanomas predicts tumor aggressiveness and high mutational tumoral burden: a pilot study
Authors: Caramaschi Stefania , Mangogna Alessandro , Bertoni Laura , Manfredini Marco , Farnetani Francesca , Parente Paola , Attino Vito , Cazzato Gerardo , Salviato Tiziana , Pellacani Giovanni , Reggiani Bonetti Luca
Published: July 2024

Purpose

Even today, melanoma is a highly aggressive neoplasm with a high mortality rate. The nodular type is very aggressive and has cerebroid nests of melanocytes (CNMs) at the growth edge, morphologically similar to the poorly differentiated neoplastic epithelial cell clusters described in colorectal, breast, and endometrioid endometrial cancers.

Patients and methods

We selected 25 nodular melanomas (NMs) with known molecular profiles, of which the entire paraffin-embedded lesion was available. We counted CNMs under a microscopic at a magnification of 20x (i.e., a microscopic field with a major axis of 1 mm). Based on the number of CNMs in the area, melanomas were classified into three groups: G1 (CNMs ranging from 0 to 4), G2 (CNMs ranging from 5 to 9), and G3 (CNMs ≥ 10). The presence of CNMs and their counts were compared with molecular and histopathological data.

Results

Seventeen (NMs) were grouped as G1 (68%), 5 as G2 (20%), and 3 as G3 (12%) based on CNMs count. The presence of CNMs correlated with epithelioid cell morphology (p < 0.05), Clark IV and V levels (p < 0.05), vascular invasion (p < 0.05), and biological mutants (p < 0.05). Melanomas with ≥ 10 CNMs more frequently show ulceration (p < 0.02) and the BRAF V600E mutation (p < 0.02).

Conclusion

CNMs count has a predictive role regardless of tumor size; their association with the BRAF V600E mutation suggests their predictive significance in response to biologics. However, further investigations are needed to strengthen this hypothesis.
Effect of resistance exercise on physical fitness, quality of life, and fatigue in patients with cancer: a systematic review
Authors: Zhang Qiuhua , Gao Yanan , Wang Wenjun , Zhao Xiaoguang , Yu Jiabin , Huang Huiming
Published: July 2024

Objective

The purpose of this study is to conduct a systematic review to assess the effects of different forms of resistance exercises (resistance exercise, resistance exercise combined with aerobic exercise, and resistance exercise combined with other exercises) on physical fitness, quality of life (QOL), and fatigue of patients with cancer.

Methods

We conducted a systematic review using the Cochrane Handbook for Systematic Reviews of Interventions guidelines. We searched PubMed, Web of Science, and Scopus databases for the studies from the establishment of the database to September 2023, including randomized controlled trials and clinical trials that evaluated the effects of different resistance exercise on physical fitness, QOL, and fatigue in all patients with cancer. Two reviewers independently assessed the quality of all the included studies using the Cochrane Handbook for Systematic Reviews of Interventions and MINORS scale. We divided the intervention into three types: resistance exercise, resistance exercise combined with aerobic exercise, and resistance exercise combined with other exercises.

Results

In total, 48 studies (3,843 participants) met the inclusion criteria. The three exercise intervention forms have significant effects on physical fitness and QOL, but the improvement effect on fatigue is not clear. A total of 34 studies reported significant and beneficial effects of resistance exercise on physical fitness across all types of cancer. There were 28 studies that reported significant or borderline improvement effects of resistance on QOL, and only 10 studies reported significant effects of resistance exercise interventions on fatigue improvement in patients with cancer.

Conclusions

Resistance exercise, resistance exercise combined with aerobic exercise, and resistance exercise combined with other exercises all have a positive effect on improving fitness and QOL in patients with cancer. Resistance exercise has an advantage in improving muscle strength, while combined resistance exercise has an advantage in improving QOL; however, there are no consistent findings in improving fatigue, although low-intensity resistance exercise is effective.

Systematic review registration

www.inplasy.com, identifier INPLASY2023110034.
The significance of growth shells in development of symmetry, transparency, and refraction of the human lens
Authors: Greiling Teri M. , Clark Judy M. , Clark John I.
Published: July 2024

Human visual function depends on the biological lens, a biconvex optical element formed by coordinated, synchronous generation of growth shells produced from ordered cells at the lens equator, the distal edge of the epithelium. Growth shells are comprised of straight (St) and S-shaped (SSh) lens fibers organized in highly symmetric, sinusoidal pattern which optimizes both the refractile, transparent structure and the unique microcirculation that regulates hydration and nutrition over the lifetime of an individual. The fiber cells are characterized by diversity in composition and age. All fiber cells remain interconnected in their growth shells throughout the life of the adult lens. As an optical element, cellular differentiation is constrained by the physical properties of light and its special development accounts for its characteristic symmetry, gradient of refractive index (GRIN), short range transparent order (SRO), and functional longevity. The complex sinusoidal structure is the basis for the lens microcirculation required for the establishment and maintenance of image formation.
Revealing the role of metformin in gastric intestinal metaplasia treatment
Authors: Hu Ruoyu , Xue Xia , Sun Xiangdong , Mi Yang , Wen Huijuan , Xi Huayuan , Li Fuhao , Zheng Pengyuan , Liu Simeng
Published: July 2024

Objective

Gastric intestinal metaplasia (IM) is a precancerous stage associated with gastric cancer. Despite the observed beneficial effects of metformin on IM, its molecular mechanism remains not fully elucidated. This study aims to reveal the effects and potential mechanisms of metformin in treating IM based on both bioinformatics and in vivo investigations.

Methods

The seven public databases (GeneCards, DisGeNET, OMIM, SuperPred, Pharm Mapper, Swiss Target Prediction, TargetNet) were used in this work to identify targeted genes related to intestinal metaplasia (IM) and metformin. The shared targeted genes between metformin and IM were further analyzed by network pharmacology, while the interactions in-between were investigated by molecular docking. In parallel, the therapeutic effect of metformin was evaluated in IM mice model, while the core targets and pathways effected by metformin were verified in vivo.

Results

We screened out 1,751 IM-related genes and 318 metformin-targeted genes, 99 common genes identified in between were visualized by constructing the protein-protein interaction (PPI) network. The top ten core targeted genes were EGFR, MMP9, HIF1A, HSP90AA1, SIRT1, IL2, MAPK8, STAT1, PIK3CA, and ICAM1. The functional enrichment analysis confirmed that carcinogenesis and HIF-1 signaling pathways were primarily involved in the metformin treatment of IM. Based on molecular docking and dynamics, we found metformin affected the function of its targets by inhibiting receptor binding. Furthermore, metformin administration reduced the progression of IM lesions in Atp4a−/− mice model significantly. Notably, metformin enhanced the expression level of MUC5AC, while inhibited the expression level of CDX2. Our results also showed that metformin modulated the expression of core targets in vivo by reducing the activity of NF-κB and the PI3K/AKT/mTOR/HIF-1α signaling pathway.

Conclusion

This study confirms that metformin improves the efficacy of IM treatment by regulating a complex molecular network. Metformin plays a functional role in inhibiting inflammation/apoptosis-related pathways of further IM progression. Our work provides a molecular foundation for understanding metformin and other guanidine medicines in IM treatment.
Ethnobotanical study of traditional medicinal plants used to treat human ailments in West Shewa community, Oromia, Ethiopia
Authors: Beressa Tamirat Bekele , Gadisa Diriba Alemayehu , Mammo Siraj , Umeta Gurmu Tesfaye , Meskele Lemma Bose , Gudeta Biruk Mosisa , Taye Getu Melesie
Published: July 2024

Introduction: Plants have formed the basis of traditional medicine (TM) systems, which have been used for thousands of years. According to reports, one-quarter of the commonly used medicines contain compounds isolated from plants. This study aims to identify and document the plants for ethno-pharmacological use by the indigenous communities of West Shoa Zone, Oromia region, Ethiopia.

Methods: The cross-sectional study was conducted from November 2020 to November 2021 in West Shewa Zone, Oromia Region, Ethiopia. The ethnobotanical data was collected from Ejere District, Ada Berga District, Dandi District, Ambo District, Ambo Town, Toke Kutaye District, and Bako Tibe District. A descriptive statistical method (percentage and/or frequency) was employed to summarize ethnobotanical data. Moreover, the informant consensus factor was computed. Microsoft Excel spreadsheet software (Microsoft Corporation, 2016) and SPSS (version 25) were used to organize and analyze the data.

Result: In the study area, a total of 51 families of medicinal plants with 108 Species were identified. Fabaceae 8 species, Asteraceae, Solanaceae and Lamiaceae each with 6 species and Cucurubitacieae 5 species were the frequently reported medicinal plants. The leaf (57.2%) was the most widely used medicinal plant parts, and oral administration (56.5%) was the most cited route of administration. In the present study, most of the medicinal plants were used fresh, which was (75%) and the most common disease the healers treated was gastrointestinal disease, followed by skin disease and febrile illness. The major threat to medicinal plants in the study area was agricultural expansion, which was reported by 30.6% of the respondents. The study area was rich in medicinal plants, Fabaceae which commonly used family.

Conclusion: Most of the medication prepared by the traditional healers was taken orally and derived from the leaf part of the medicinal plant. Since this research is a preliminary study which will be used as a base for further study. The efficacy and safety of the medicinal plant claim should be studied in the future.
The impact of sarcopenia on the efficacy of PD-1 inhibitors in non-small cell lung cancer and potential strategies to overcome resistance
Authors: Liu Zhenchao , Lei Tianxiang , Guo Yunliang , Zheng Chongwen
Published: July 2024

Recent studies have revealed that sarcopenia can adversely affect the efficacy of PD-1 inhibitors in the treatment of non-small cell lung cancer (NSCLC). PD-1 inhibitors are immune checkpoint inhibitors widely used in the treatment of various cancers. However, NSCLC patients may have poorer outcomes when receiving PD-1 inhibitor treatment, and sarcopenia may affect the efficacy of PD-1 inhibitors through immune and metabolic mechanisms. In this article, we summarize the reported negative impact of sarcopenia on the effectiveness of PD-1 inhibitors in the treatment of NSCLC in recent years. Based on existing research results, we analyze the possible mechanisms by which sarcopenia affects the efficacy of PD-1 inhibitors and discuss possible strategies to address this issue. This could help to understand the impact of sarcopenia on the treatment of PD-1 inhibitors and provide more accurate expectations of treatment outcomes for clinicians and patients. Additionally, we present tailored intervention strategies for sarcopenic patients undergoing PD-1 inhibitor therapy, aiming to optimize treatment efficacy and enhance patient quality of life. Nevertheless, further research is warranted to elucidate the mechanisms through which sarcopenia impacts PD-1 inhibitors and to identify more efficacious intervention approaches for improving the effectiveness of PD-1 inhibitor treatment in sarcopenic patients.
Trait divergence and opposite above- and below-ground strategies facilitate moso bamboo invasion into subtropical evergreen broadleaf forest
Authors: Yu Hua , Le Xingui , Peñuelas Josep , Sardans Jordi , Xu Chaobin , Zou Yuxing , Zhang Xue , Li Conghui , Mao Zhenwei , Cheng Dongliang , Zhong Quanlin
Published: July 2024

Understanding the invasion of moso bamboo (Phyllostachys edulis) into adjacent evergreen broadleaf forest based on functional traits is crucial due to its significant influence on ecosystem processes. However, existing research has primarily focused on above- or below-ground traits in isolation, lacking a comprehensive integration of both. In this study, we conducted a trait-based analysis including 23 leaf traits and 11 root traits in three forest types - bamboo forest, mixed bamboo and broadleaf forest, and evergreen broadleaf forest - to investigate trait differences, phenotypic integration, and above- and below-ground resource strategies in bamboo and broadleaf species. Our findings demonstrated significant differences in leaf and root key traits between bamboo and broadleaf species, strongly supporting the “phenotypic divergence hypothesis”. Bamboo exhibited stronger trait correlations compared to broadleaf species, indicating higher phenotypic integration. Above- and below-ground strategies were characterized by trade-offs rather than coordination, resulting in a multi-dimensional trait syndrome. Specifically, a unidimensional leaf economics spectrum revealed that bamboo with higher leaf N concentrations (LNC), P concentrations (LPC), and specific leaf area (SLA) adopted a “fast acquisitive” above-ground strategy, while broadleaf species with thicker leaves employed a “slow conservative” above-ground strategy. A two-dimensional root trait syndrome indicated a “conservation” gradient with bamboo adopting a “slow conservative” below-ground strategy associated with higher root tissue density (RTD), and broadleaf species exhibiting a “fast acquisitive” below-ground strategy linked to higher root N concentrations (RNC) and P concentrations (RPC), and a “collaboration” gradient probably ranging from broadleaf species with a “do-it-yourself” strategy characterized by high specific root length (SRL), to bamboo adopting an “outsourcing” strategy with thicker roots. In conclusion, key trait divergence from coexisting broadleaf species, higher phenotypic integration, and multi-dimensional opposite above- and below-ground resource strategies confer competitive advantages to moso bamboo, shedding light on the mechanistic understanding of its invasion into subtropical evergreen broadleaf forest and providing theoretical guidance for maintaining the stability of subtropical forest ecosystem.
Microbial mediated remediation of heavy metals toxicity: mechanisms and future prospects
Authors: Tang Haiying , Xiang Guohong , Xiao Wen , Yang Zeliang , Zhao Baoyi
Published: July 2024

Heavy metal pollution has become a serious concern across the globe due to their persistent nature, higher toxicity, and recalcitrance. These toxic metals threaten the stability of the environment and the health of all living beings. Heavy metals also enter the human food chain by eating contaminated foods and cause toxic effects on human health. Thus, remediation of HMs polluted soils is mandatory and it needs to be addressed at higher priority. The use of microbes is considered as a promising approach to combat the adverse impacts of HMs. Microbes aided in the restoration of deteriorated environments to their natural condition, with long-term environmental effects. Microbial remediation prevents the leaching and mobilization of HMs and they also make the extraction of HMs simple. Therefore, in this context recent technological advancement allowed to use of bioremediation as an imperative approach to remediate polluted soils. Microbes use different mechanisms including bio-sorption, bioaccumulation, bioleaching, bio-transformation, bio-volatilization and bio-mineralization to mitigate toxic the effects of HMs. Thus, keeping in the view toxic HMs here in this review explores the role of bacteria, fungi and algae in bioremediation of polluted soils. This review also discusses the various approaches that can be used to improve the efficiency of microbes to remediate HMs polluted soils. It also highlights different research gaps that must be solved in future study programs to improve bioremediation efficency.