bluuebunny/crossref_metadata_2025_split huggingface dataset:
The development of a hiPSC-based platform to identify tissue-dependencies of IDH1 R132H
Authors: Kahlert Ulf , Mehjardi Nargis , Sanin Ahmed , Picard Daniel , Westhoff Philipp , Nickel Ann-Christin , Uhlmann Constanze , Shi Wenjie , Steiger Hans-Jacob , Remke Marc , Keitel-Anselmino Verena , Fischer Igor , Croner Roland 
Published: August 2023

Abstract
Hotspot mutations in the DNA encoding for the R132 codon of the enzyme isocitrate dehydrogenase 1 (IDH1) is a common molecular feature of different tumors. The oncogenic potential of IDH1R132 and its clinical prognostic value however, varies strongly between tumors of different tissues. Technologies to conduct functional investigations of isogentic controlled IDH1R132 in dependency of differentiation status offers a chance to understand underlying mechanisms of this heterogeneity or identify new tissue-dependent features of IDH1 mutation. Here we genetically engineered the first IDH1MUT model using human induced pluripotent stem cells (hiPSC) for inducible overexpression of IDH1R132H or its wildtype paralog. Confirming the known relevance of IDH1R132H, we identified a transcriptomic switch of hiPSC cells towards pro-angiogenetic program meanwhile suppression of p53 signaling upon oncogene induction. We chose neural differentiation of the cells and drug sensitivity testing to compare the influence of IDH1R132H on functional properties of the cells in tissue-specific context. Our results reveal the augmentation of drug resistance levels to clinical approved kinase inhibitors in induced neural stem cells, which was not observed in the pluripotent counterpart. Applying our technology in follow-up projects, such as comparing isogenic progenitor cells of different differentiation lineages, might help to understand a variety of tissue-related functions of IDH1 mutations. Moreover, given the fact that patient-derived human neuronal in vitro models with constitutive active IDH1R132H are challenging to establish, the presented work supports to overcome this limitation.
Comparative Analysis of End Device and Field Test Device Measurements for RSSI, SNR and SF Performance Parameters in an Indoor LoRaWAN Network
Authors: Aksoy Ataberk , Yıldız Ömer , Karlık Associate Professor Sait Eser 
Published: August 2023

Abstract
Internet of things (IoT) phenomenon has brought up distinctive technologies that are using wireless communication and appearing in smart city applications. Long range (LoRa) modulation technique has pulled up the market and forced the announcement of LoRa wide area network (LoRaWAN) standard in 2021 by ITU-T with Y.4480 standard code. LoRaWAN is a medium access control protocol using low power wide area network approaches with the aim of long-range coverage and management of many edge devices. LoRaWAN networks are emerging all over the world with some existing optimization, planning and network allocation problems that need to be overcome. This paper focuses on comparative analysis and interpretation of measurements performed in a LoRaWAN network deployed in an 18-floor building with a LoRaWAN gateway on the roof. The research covers results of comparative measurements between end device and Adeunis field test device (AFTD) for received signal strength indicator (RSSI), signal-to-noise ratio (SNR) and spreading factor (SF). End devices have been randomly selected from 18th, 12th, 6th and 1st floors and their daily performance data have been gathered through the network server. AFTD has been used to get 10 sample measurements for each floor in the same day. Minimum RSSI values measured by end devices are better than the ones measured with AFTD except the case in 1st floor. All SNR values measured with end devices are better than measurements performed with AFTD. SF measurements show that SF differs with increasing distances from 7 to 12 in order as expected with theoretical computations.
Advances in diffusion barrier coatings for high-temperature applications
Authors: Narita Toshio , Kato Yasumichi , Narita Takuro , Ara Mayumi 
Published: August 2023

Abstract
Diffusion barrier coating (DBC) systems on heat resistant alloys consist of a multi-layer structure: an outer Al-reservoir layer and an inner diffusion barrier layer. The outer Al-reservoir layer forms a protective Al2O3 scale and the inner layer acts as a barrier layer against alloy interdiffusion. Three kinds of diffusion barrier layers (DBL) were developed, containing Re on Ni-based super alloys, W on stainless steels, and Cr on Ni-Cr alloys. It was found that DBC systems have excellent mechanical properties (creep and fatigue), improving alloy substrate performance, and enhance the anti-exfoliation properties of YSZ in thermal barrier coatings (TBC) in addition to providing excellent oxidation resistance. At temperatures higher than 1,300℃, however, the DBC design based on kinetics (diffusion) is insufficient to form and maintain a protective Al2O3 scale. In this case a self-maintaining coating (SMC) system designed on the basis of thermodynamics (phase stability) is required. The SMC system formed on Nb-Hf (C-103) alloy consists of a multi-layer structure: an outer Re (Al, Si)1.8 and inner NbSi2 layers, plus a transient Nb5Si3 layer formed during oxidation. At temperatures higher than 1,300℃ the Al2O3 can be formed by changing the Al/Si ratio in the Re (Al, Si)1.8 in which Si was supplied from the decomposition reaction of NbSi2 to Si + Nb5Si3 during selective oxidation of Al. It is proposed that coatings alloy should be designed for not only high temperature oxidation, but also alloy substrate mechanical properties and anti-exfoliation of oxide scales, based on both kinetic principles (DBC system) and thermodynamics (SMC system).
Identification of a novel gene signature related to prognosis and metastasis in gastric cancer
Authors: Matheu Ander , Elizazu Joseba , Otaegi-Ugartemendia Maddalen , Moncho-Amor Veronica , Artetxe-Zurutuza Aizpea , Carrasco-García Estefania 
Published: August 2023

Abstract
Background: Gastric Cancer (GC) presents poor outcome, which is consequence of the high incidence of recurrence and metastasis at early stages. GC patients presenting recurrent or metastatic disease display a median life expectancy of only 8 months. The mechanisms underlying GC progression remain poorly understood.
Methods: We took advantage of public available GC datasets from TCGA using GEPIA, and identified the matched genes among the 100 genes most significantly associated with overall survival (OS) and disease free survival (DFS). Results were confirmed in ACRG cohort and in over 2,000 GC cases obtained from several cohorts integrated using our own analysis pipeline. The Kaplan-Meier method and multivariate Cox regression analyses were used for prognostic significance and linear modelling and correlation analyses for association with clinic-pathological parameters and biological hallmarks. In vitro and in vivo functional studies were performed in GC cells with candidate genes and the related molecular pathways were studied by RNA sequencing.
Results: High expression of ANKRD6, ITIH3, SORCS3, NPY1R and CCDC178 individually and as a signature was associated with poor prognosis and recurrent disease in GC. Among the 5 genes, ANKRD6, ITIH3 and NPY1R represented independent prognostic factors determined through multivariate Cox regression analyses. Moreover, the expression of ANKRD6 and ITIH3 was significantly higher in metastasis and its levels associated to EMT and stemness markers. Moreover, ANKRD6 silencing in GC metastatic cells showed impairment in GC tumorigenic activity and EMT in functional studies in vivo and in molecular pathways in transcriptomic studies.
Conclusions: Our study identified a novel signature involved in GC malignancy and prognosis, and revealed a novel pro-metastatic role of ANKRD6 in GC.
Personalized mRNA Vaccine Combined with PD-1 Inhibitor Therapy in a Patient with Advanced Esophageal Squamous Cell Carcinoma
Authors: Wang Bin , Peng Xiao-Bo , Li Jie , Wang Yi-Ran , Chen Long-Pei , Wu Mei-Hong , Zhang Ying-Yi , Wang Wei , Feng Dan , Tang Shu-Hui , Zhang Lin-Li , Zhan Xianbao 
Published: August 2023

Abstract
Background Therapeutic cancer vaccines serve as a valuable tool to educate the immune system to fight tumors precisely. Cancer cells have characteristics of genetic instability and rapidly accumulate somatic mutations rapidly, which can result in the production of tumour-specific antigens (TSAs) called neoantigens. The main goal of neoantigen-based cancer vaccines is to activate the immune system and effective tumor-specific T-cell responses against cancer cells. Patients with advanced esophageal squamous cell carcinoma (ESCC) who achieved partial remission after personalized mRNA vaccine treatment have not been reported. As personalized neoantigen-based immunotherapies are emerging, we report a case in which mRNA vaccines were used to treat advanced ESCC firstly.Methods Samples of tissues from the recurrence focus in the esophagus were subjected to whole transcriptome sequencing. The neoantigens were identified by bioinformatics analyses and the top 20 neoantigens were selected. These 20 neoantigens, composing the polyneoantigen vaccine, were administered at 1 mg every 3 weeks for 4 cycles in combination with a PD-1 inhibitor, and the patient was boosted with a single dose of the PD-1 inhibitor 8 weeks after the 4th cycle. In addition, immune responses were evaluated before and after the 4 cycles of vaccine therapy. The lesions were evaluated by imaging examination.Results Our results revealed that neoantigen-based vaccines significantly activated the tumour-specific immune response. TCR V-J pairing analysis showed that the abundance of oligoclonal TCRs was increased, that is, the homogeneity was improved. No other grade 3 or higher drug-related adverse events were observed, except for grade 4 thrombocytopenia, which was caused by PD-1 inhibitor treatment. The patient reported here achieved a partial response (PR).Conclusions Our report showed that combining the personalized mRNA vaccine therapy with PD-1 blockade therapy may be an effective treatment strategy for this patient with advanced esophageal cancer. However, further study should be performed in clinical trials to confirm the efficacy and safety of personalized neoantigen-based immunotherapies in the treatment of advanced ESCC .
Effect L-fucose on the metabolism of peritoneal macrophages of Muc2 −/− mice in vitro
Authors: Arzhanova Elena L. , Makusheva Yulia S. , Pershina Elena G. , Medvedeva Snezhanna S. , Litvinova Ekaterina A. 
Published: August 2023

Abstract
In the development of inflammatory bowel disease (IBD), macrophages play a huge role. A widely used experimental model of IBD is Muc2 −/− mice. L-fucose is one of monosaccharides present in a variety of glycolipids and glycoproteins produced by mammalian and bacterial cells. It can participate in signaling processes as epithelial and immune cells. Macrophages and dendritic cells have a receptor for fucose recognition (DC-SIGN, also known as CD209). It was shown that peroral treatment of L-fucose had immunomodulatory effect and repolarized mouse peritoneal macrophages in vivo. Activation of macrophages by L-fucose treatment could be mediated through changes in gut microbiota composition and activation due to microbe-associated molecular patterns containing monosaccharides. Also, L-fucose-and fucose-containing glycans of mammalian and bacterial origin could interact with receptors on macrophages and dendritic cells and activate other immune cells by cytokine and chemokine release. We found a decrease in the amount of CD209 + peritoneal macrophages and an increase in the amount of M1-like peritoneal macrophages of Muc2 −/− mice. We investigated the effect of L-fucose on the metabolic and morphological characteristics of peritoneal macrophages in vitro. It was found that L-fucose treatment enhanced the level of ATP and Ca 2+ production and reduced Parp1, Mt-Nd2, and Mt-Nd6 gene expression level, that may be an evidence for a decreased production of pro-inflammatory factors and differentiation of peritoneal macrophages to the M2 type.
The complete chloroplast genome of Meconopsis simplicifolia and its genetic comparison to other Meconopsis species
Authors: Yang Yixi , Li Rui , Zhu Zhidan , Huang Peng 
Published: August 2023

Abstract
M. simplicifolia, an endangered Chinese herb, possesses medicinal properties used in the treatment of various disorders. Despite its importance, there is a lack of genomic information available for M. simplicifolia, hindering our understanding of its molecular biology. Therefore, this study aimed to assemble and compare the chloroplast (cp) genome of M. simplicifolia with other reported Meconopsis cp genomes. The assembled M. simplicifoliaplastome spanned 152,772 bp and exhibited the typical quadripartite structure comprising large (LSC, 83,824 bp) and small (SSC, 17,646 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,651 bp). Overall, 131 genes were predicted, including 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. Additionally, 33 SSRs and 27 long repeat sequences were identified. The seven Meconopsis species shared conserved genomic features in terms of gene structure and gene order. However, a comparison of the IR boundaries of the seven Meconopsis cp genomes revealed minor differences at the IR/SC boundary regions. Interestingly, M. simplicifolia exhibited the loss of the rpl2 gene in the IRb region, which could be valuable for future plant classification research. A phylogenetic analysis including M. simplicifolia and eight other Meconopsis species indicated that M. simplicifolia clustered together with M. betonicifolia. The availability of the cp genome sequence ofM. simplicifolia is of utmost importance for understanding phylogenetic and evolutionary aspects at or above the Meconopsislevel. Comparative analysis of the cp genomes of Meconopsis species will facilitate species identification and enable selective breeding studies of these medicinal plants.
A New Approach for Detecting Process Injection Attacks Using Memory Analysis
Authors: Nasereddin Mohammed , Al-Qassas Raad 
Published: August 2023

Abstract
This paper introduces a new approach for examining and analyzing fileless malware artifacts in computer memory. The proposed approach offers the distinct advantage of conducting a comprehensive live analysis of memory without the need for periodic memory dumping. Once a new process arrives, log files are collected by monitoring the Event Tracing for Windows facility as well as listing the executables of the active process for violation detection. The proposed approach significantly reduces detection time and minimizes resource consumption by adopting parallel computing (programming), where the main software (Master) divides the work, organizes the process of searching for artifacts, and distributes tasks to several agents (Slaves). A dataset of 17411 malware samples is used in the assessment of the new approach. It provided satisfactory and reliable results in dealing with at least six different process injection techniques including classic DLL injection, reflective DLL injection, process hollowing, hook injection, registry modifications, and .NET DLL injection. The detection accuracy rate has reached 99.93% with a false-positive rate of 0.068%. Moreover, the accuracy was monitored in the case of launching several malwares using different process injection techniques simultaneously, and the detector was able to detect them efficiently. Also, it achieved a detection time with an average of 0.052 msec per detected malware.
The Association Between Glaucoma Treatment Adherence with Disease Progression and Loss to Follow-Up
Authors: Oltramari Laura , Mansberger Steven L. , Souza Júlia Mendonça Ponte , Souza Luciene Barbosa , Azevedo Sarah Fumian Milward , Abe Ricardo Yuji 
Published: August 2023

Abstract
Prospective cohort study from Brazil to evaluate glaucoma treatment adherence using a medication event monitoring system (MEMS) device and correlate with glaucoma progression and loss to follow-up (LTF) after one year of follow up. We included glaucoma patients treated with at least one ocular hypotensive eye drop. MEMS devices was used to monitor adherence for 60 days and evaluate the percentage of doses prescribed taken within the 60-day period. We classified patients according to rates of adherence: low adherence (less than 80% from MEMS measurements) and high adherence (more than 80% from MEMS measurements). We applied a questionnaire to investigated self-reported behavior towards treatment behaviors (glaucoma treatment compliance assessment tool, GTCAT). We also correlated rates of treatment adherence with clinical, demographical variables and the occurrence of glaucoma progression or LTF after one year of observation. We included 110 glaucoma patients and found that 28.18% of them were considered low adherent. We identify several variables associated with poor adherence such as glaucoma progression, LTF, younger age, low educational and income levels, absence of health insurance, years of disease and peak intraocular pressure. Several constructs from the self-reported GTCAT were also correlated with the rates of treatment adherence. To date, this is the first study in Latin America to evaluate glaucoma treatment adherence with MEMS devices and correlate adherence rates with glaucoma progression and LTF. We found a low-adherence rate of 28.18% and several additional risk factors were statistically associated with poor adherence.
A Systematic Review and Meta-Analysis on the Effectiveness of Aerobic Exercise and Diet for Individuals with Type 2 Diabetes and Obesity
Authors: AL-Mhanna Samer Badri , Rocha-Rodriguesc Sílvia , Mohamed Mahaneem , Aldhahi Monira I. , Afolabi Hafeez Abiola , Yagin Fatma Hilal , Alhussain Maha H. , Gülü Mehmet , Abubakar Bishir Daku , Ghazali Wan Syaheedah Wan , Alghannam Abdullah F. , Badicu Georgian 
Published: August 2023

Abstract
Background
Lifestyle changes involving diet and exercise are recommended for patients diagnosed with obesity and type 2 diabetes mellitus (T2DM). However, the effectiveness of combining aerobic exercise and diet (AEDT) in obese T2DM patients has not been studied in a systematic review and meta-analysis. Therefore, the purpose of this review was to systematically evaluate the effects of AEDT on individuals with obesity and T2DM. Methodology: A comprehensive search of the PubMed, Web of Science, Scopus, Science Direct, Cochrane, and Google Scholar databases was conducted for this meta-analysis. Statistical analysis was performed using the random effects model for continuous variables, and the results were presented as mean differences (MD) or standardized mean difference (SMD) with 95% confidence intervals (CI).
Results
Out of the 16,129 studies identified, 15 trials involving a total of 2,454 patients were included in the meta-analysis. The findings revealed significant reductions in body mass index, body weight, waist circumference, systolic blood pressure (SBP), diastolic blood pressure (DBP), total cholesterol (TC), triglyceride levels, glycated hemoglobin (HbA1c), fasting blood glucose, fasting plasma insulin, leptin, interleukin-6 (IL-6), and C-reactive protein (CRP) (p < 0.005) compared to the standard treatment (ST) group. On the other hand, there was a significant increase in adiponectin levels in response to AEDT (p < 0.005). However, when evaluating obesity-related factors, no significant differences were observed between the AEDT and ST groups for parameters such as fat mass, hip circumference, waist-to-hip ratio, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and tumor necrosis factor-alpha (TNF-α) (p > 0.05).
Conclusions
AEDT could be considered an additional therapy in conjunction with conventional clinical treatments due to its significant positive impact on obese T2DM patients. Nevertheless, further robust evidence is necessary to determine whether AEDT is an effective intervention for reducing the need for aggressive pharmacological approaches in individuals with obesity and T2DM.
Acute Ischemic Stroke in Tsutsugamushi: Understanding the Underlying Mechanisms and Risk Factors
Authors: Kim Dain , Cho Yeon Hee , Bong Jeong Bin , Kim Young Seo , Shin Byoung-Soo , Kang Hyun Goo 
Published: August 2023

Abstract
Background: Tsutsugamushi (scrub typhus) is an acute infectious febrile disease common in the Asia-Pacific region. Common symptoms of tsutsugamushi include lymphadenopathy, fever, and myalgia, and it rarely causes acute ischemic stroke (AIS). However, we hypothesized that tsutsugamushi infection could trigger AIS.
Method: We retrospectively examined patients diagnosed with AIS within 2 weeks of tsutsugamushi diagnosis at three hospitals over a 15-year period. We categorized patients who developed AIS while being treated for tsutsugamushi as the case group and those (of similar age and sex) who did not develop AIS as the control group. The case and control groups consisted of 22 and 66 participants, respectively. When a scattered pattern was observed or lesions were found in two or more vascular territories on diffusion-weighted imaging, the pattern was defined as embolic. Other patterns were defined as nonembolic.
Results: Among the 19 patients, excluding three with transient ischemic stroke, 15 (78.9%) showed an embolic pattern. Although fever was common in the control group, it was less common in the case group. A higher D-dimer level at the time of hospitalization was associated with the development of AIS in patients with tsutsugamushi.
Conclusions: AIS in patients with tsutsugamushi showed an embolic rather than a non-embolic pattern on brain magnetic resonance imaging. It was more likely to occur in patients with risk factors for stroke. Tsutsugamushi patients with AIS were likely to have no fever or high D-dimer levels. We hypothesized that D-dimers play an important role in the pathophysiology, where tsutsugamushi infection increases the likelihood of AIS.
Research on rockburst prevention systems based on the attenuation law of coal and rock vibration wave energy
Authors: Rong Hai , Wang Zijian , Konicek Petr , Pan Liting , Tang Guoshui , Kajzar Vlastimil , Wang Yadi 
Published: August 2023

Abstract
During the coal and rock mass fracture process, elastic properties are released and vibration waves are radiated outward. The energy attenuation characteristics of these waves can describe the cumulative damage and elastic energy accumulation of the mass. To investigate coal and rock mass failure characteristics and energy attenuation rules during rockburst, numerical simulation and laboratory testing were utilized to study the energy transfer laws under various parameters. Six variables, including elastic modulus, Poisson's ratio, bulk density, cohesion, internal friction angle, and porosity, were selected to simulate the rockburst energy release process under different parameter combinations by adding surface pressure to the model. The coal and rock mass energy attenuation coefficient was obtained by fitting the node energy straight line using the least squares method. The above six variable’s influence weights on the vibration wave energy transfer were obtained using the analytic hierarchy process program written in MATLAB, and a comprehensive calculation formula was proposed. Using the energy attenuation coefficient, the rock layer energy diffusion distance was calculated and compared with the roof collapse rock layer step distance, resulting in the roof rock layer cutting distance determination. By roof rock strata precutting, rockburst occurrence can be prevented, ensuring safe and efficient coal mine production.