bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification, characterization, and prognosis investigation of pivotal genes shared in different stages of breast cancer
Authors: Rommasi Foad 
Published: May 2023

AbstractOne of the leading causes of death (20.1 per 100,000 women per year), breast cancer is the most prevalent cancer in females. Statistically, 95% of breast cancer are categorized as adenocarcinomas, and 55% of all patients may go into invasive phases; however, it can be successfully treated in approximately 70–80% of cases if diagnosed in the nascent stages. The emergence of breast tumor cells which are intensely resistant to conventional therapies, along with the high rate of metastasis occurrence, has highlighted the importance of finding novel strategies and treatments. One of the most advantageous schemes to alleviate this complication is to identify the common differentially expressed genes (DEGs) among primary and metastatic cancerous cells to use resultants for designing new therapeutic agents which are able to target both primary and metastatic breast tumor cells. In this study, the gene expression dataset with accession number GSE55715 was analyzed containing two primary tumor samples, three bone-metastatic samples, and three normal samples to distinguish the up- and down regulated genes in each stage compared to normal cells as control. In the next step, the common upregulated genes between the two experimental groups were detected by Venny online tool. Moreover, gene ontology, functions and pathways, gene-targeting microRNA, and influential metabolites were determined using EnrichR 2021 GO, KEGG pathways miRTarbase 2017, and HMDB 2021, respectively. Furthermore, elicited from STRING protein–protein interaction networks were imported to Cytoscape software to identify the hub genes. Then, identified hub genes were checked to validate the study using oncological databases. The results of the present article disclosed 1263 critical common DEGs (573 upregulated + 690 downregulated), including 35 hub genes that can be broadly used as new targets for cancer treatment and as biomarkers for cancer detection by evaluation of expression level. Besides, this study opens a new horizon to reveal unknown aspects of cancer signaling pathways by providing raw data evoked from in silico experiments. This study’s outcomes can also be widely utilized in further lab research since it contains diverse information on common DEGs of varied stages and metastases of breast cancer, their functions, structures, interactions, and associations.
Prediction and experimental evidence of different growth phases of the Podospora anserina hyphal network
Authors: Ledoux Clara , Chapeland-Leclerc Florence , Ruprich-Robert Gwenaël , Bobée Cécilia , Lalanne Christophe , Herbert Éric , David Pascal 
Published: May 2023

AbstractUnder ideal conditions, the growth of the mycelial network of a filamentous fungus is monotonous, showing an ever increasing complexity with time. The components of the network growth are very simple and based on two mechanisms: the elongation of each hypha, and their multiplication by successive branching. These two mechanisms are sufficient to produce a complex network, and could be localized only at the tips of hyphae. However, branching can be of two types, apical or lateral, depending on its location on the hyphae, therefore imposing the redistribution of the necessary material in the whole mycelium. From an evolutionary point of view, maintaining different branching processes, with additional energy needs for structure and metabolism, is intriguing. We propose in this work to discuss the advantages of each branching type using a new observable for the network growth, allowing us to compare growth configurations. For this purpose, we build on experimental observations of the Podospora anserina mycelium growth, enabling us to feed and constrain a lattice-free modeling of this network based on a binary tree. First, we report the set of statistics related to the branches of P. anserina that we have implemented into the model. Then, we build the density observable, allowing us to discuss the succession of growth phases. We predict that density over time is not monotonic, but shows a decay growth phase, clearly separated from an other one by a stationary phase. The time of appearance of this stable region appears to be driven solely by the growth rate. Finally, we show that density is an appropriate observable to differentiate growth stress.
Effects of energy drinks on myogenic differentiation of murine C2C12 myoblasts
Authors: Park Sun Young , Karantenislis Georgia , Rosen Hannah T. , Sun Hong 
Published: May 2023

AbstractEnergy drinks, often advertised as dietary supplements that enhance physical and mental performance, have gained increasing popularity among adolescents and athletes. Several studies on individual ingredients such as caffeine or taurine have reported either adverse or favorable influences on myogenic differentiation, a key process in muscle regeneration to repair microtears after an intense workout session. However, the impact of different energy drinks with various formulas on muscle differentiation has never been reported. This study aims to examine the in vitro effects of various energy drink brands on myogenic differentiation. Murine C2C12 myoblast cells were induced to differentiate into myotubes in the presence of one of eight energy drinks at varying dilutions. A dose-dependent inhibition of myotube formation was observed for all energy drinks, supported by reduced percentage of MHC-positive nuclei and fusion index. Moreover, expression of myogenic regulatory factor MyoG and differentiation marker MCK were also decreased. Furthermore, given the variation in formulas of different energy drinks, there were remarkable differences in the differentiation and fusion of myotubes between energy drinks. This is the first study to investigate the impact of various energy drinks on myogenic differentiation and our results suggest an inhibitory effect of energy drinks in muscle regeneration.
Ikaros expression is associated with an increased risk of chronic graft-versus-host disease
Authors: Pereira A. D. , de Molla V. C. , Fonseca A. R. B. M. , Tucunduva L. , Novis Y. , Pires M. S. , Popi A. F. , Arrais-Rodrigues C. A. 
Published: May 2023

AbstractImmune reconstitution after hematopoietic stem cell transplantation (HSCT) is a complex and extremely variable process. TheIkarostranscription factor plays an important role in hematopoiesis in several cell lines, especially in the lymphoid lineage. We hypothesized thatIkarosmight influence immune reconstitution, and consequently, the risk of opportunistic infections, relapse, and graft versus host disease (GVHD). Samples were collected from the graft and from the peripheral blood (PB) of the recipients 3 weeks after neutrophil recovery. Real-time polymerase chain reaction (RT-PCR) was performed to analyze the absolute and relativeIkarosexpression. Patients were divided into two groups, according toIkarosexpression in the graft and in the recipients’ PB based on the ROC curves for moderate/severe cGVHD. A cutoff of 1.48 was used forIkarosexpression in the graft, and a cutoff of 0.79 was used forIkarosexpression in the recipients’ PB. Sixty-six patients were included in this study. Median age of patients was 52 years (range 16–80 years), 55% of them were male, and 58% of them had acute leukemia. Median follow-up period was 18 months (range 10–43 months). There was no association betweenIkarosexpression and the risk of acute GVHD, relapse, or mortality. However, a significant association was observed with the risk of chronic GVHD. HigherIkarosexpression in the graft was associated with a significantly higher cumulative incidence (CI) of moderate/severe chronic GVHD according to the National Institute of Health (NIH) classification at two years (54% vs. 15% for patients with lower expression, P = 0.03). A higherIkarosexpression in the recipients’ PB 3 weeks after engraftment was also associated with a significantly higher risk of moderate/severe chronic GVHD (65% vs. 11%, respectively, P = 0.005). In conclusion,Ikarosexpression in the graft and in the recipients’ PB after transplantation was associated with a higher risk of moderate/severe chronic GVHD.Ikarosexpression should be evaluated in larger prospective trials as a potential biomarker for chronic GVHD.
RETRACTED ARTICLE: The application of non-uniform magnetic field for thermal enhancement of the nanofluid flow inside the U-turn pipe at solar collectors
Authors: Li Sida , Mao Liudan , Alizadeh As’ad , Zhang Xin , Mousavi S. Valiallah 
Published: May 2023

AbstractThe improvement of heat transfer inside the solar heat exchangers is important for the development of solar energy in an urban area. In this study, the usage of a non-uniform magnetic field on the thermal efficiency of the nanofluid (Fe3O4) streaming inside the U-turn pipe of solar heat exchangers is examined. Computational fluid dynamic is applied to visualize the nanofluid flow inside the solar heat exchanger. The role of magnetic intensity and Reynolds number on thermal efficiency are fully investigated. The effect of single and triple sources of the magnetic field is also studied in our research. Obtained results indicate that the usage of the magnetic field results in the production of vortex in the base fluid and heat transfer improves inside the domain. Our finding indicates that the usage of the magnetic field with Mn = 25 K would improve the average heat transfer by about 21% along the U-turn pipe of solar heat exchangers.
Entomotoxic efficacy of fungus-synthesized nanoparticles against immature stages of stored bean pests
Authors: Helmy Eman Ahmed Mohamed , San Phyu Phyu , Zhang Yao Zhuo , Adarkwah Charles , Tuda Midori 
Published: May 2023

AbstractNanopesticides, particularly biosynthesized ones using organic reductants, hold great promise as a cost-effective and eco-friendly alternative to chemical pesticides. However, their efficacy on stored product pests, which can cause damage to dried grains, has not been extensively tested, especially on immature stages. Here, we biosynthesized six types of nanoparticles (NPs) using extracts from the fungus Fusarium solani: silver (AgNPs), selenium (SeNPs), silicon dioxide (SiO2NPs), copper oxide (CuONPs), titanium dioxide (TiO2NPs) and zinc oxide (ZnONPs) ranging in size from 8 to 33 nm. To test their efficacy on stored bean pests, they were applied to the eggs and larvae of pest beetles Callosobruchus chinensis and Callosobruchus maculatus (Coleoptera: Chrysomelidae: Bruchinae), which burrow into seeds as larvae. Susceptibility to the NPs was species-dependent and differed between developmental stages; eggs were more susceptible than larvae inhabiting in seeds. SeNPs and TiO2NPs reduced the hatchability of C. chinensis eggs by 23% and 18% compared to the control, respectively, leading to an 18% reduction in egg-to-adult survival by SeNPs. In C. maculatus, TiO2NPs applied to eggs reduced larva-to-adult survivorship by 11%, resulting in a 15% reduction in egg-to-adult survival. The egg mass of C. chinensis was 23% smaller than that of C. maculatus: the higher surface-area-to-volume ratio of the C. chinensis eggs could explain their higher acute mortality caused by the NPs compared to C. maculatus eggs. The biosynthesized SeNPs and TiO2NPs have potential for controlling major stored bean pests when applied to their eggs. This is the first to show the efficacy of biosynthesized SeNPs and TiO2NPs on stored product pests and the efficacy of Fusarium-synthesized NPs on insects.
Alteration in molecular properties during establishment and passaging of endometrial carcinoma patient-derived xenografts
Authors: Imai Toshio , Yoshida Hiroshi , Machida Yukino , Kuramochi Mizuki , Ichikawa Hitoshi , Kubo Takashi , Takahashi Mami , Kato Tomoyasu 
Published: May 2023

AbstractPatient-derived xenograft (PDX) tumor models are known to maintain the genomic and phenotypic profiles, including the histopathological structures, of the parental tumors. On the other hand, unique enrichment of single-nucleotide variants or copy number aberrations has been reported in several types of tumors. However, an understanding of endometrial carcinoma PDXs is limited. The purpose of the present study was to clarify the presence or absence of the molecular properties of endometrial carcinomas in PDXs passaged up to eight times. Established PDXs of endometrioid carcinomas maintained their histopathological characteristics, but those of carcinosarcomas predominantly consisted of sarcomatous components when compared to the parental tumors. Alterations in the proportion of cells with positive/negative immunohistochemical staining for estrogen receptor, PTEN, PAX8, and PAX2 were observed, whereas the proportions of cells with AE1/AE3, TP53, ARID1A, PMS2, and MSH6 staining were unchanged. Variants of cancer-associated genes were compared between PDXs and parental tumors. Mutations in POLE and a frameshift deletion in BRCA1 were observed in the parental tumor tissue in each of the six cases, and additional genomic alterations, which were not apparently related to histopathological and immunohistochemical alterations, were found in the PDXs of these cases. The genomic and phenotypic alterations observed between endometrial carcinoma PDXs and parental tumors were partly associated with endometrial cancer-specific characteristics related to cellular differentiation and gene mutations.
Two step I to II type transitions in layered Weyl semi-metals and their impact on superconductivity
Authors: Rosenstein Baruch , Shapiro B. Ya. 
Published: May 2023

AbstractNovel “quasi two dimensional” typically layered (semi) metals offer a unique opportunity to control the density and even the topology of the electronic matter. Along with doping and gate voltage, a robust tuning is achieved by application of the hydrostatic pressure. In Weyl semi-metals the tilt of the dispersion relation cones, $$\kappa ,$$

κ
,

increases with pressure, so that one is able to reach type II ($$\kappa >1$$

κ
>
1

starting from the more conventional type I Weyl semi-metals $$\kappa <1$$

κ
<
1

. The microscopic theory of such a transition is constructed. It is found that upon increasing pressure the I to II transition occurs in two continuous steps. In the first step the cones of opposite chirality coalesce so that the chiral symmetry is restored, while the second transition to the Fermi surface extending throughout the Brillouin zone occurs at higher pressures. Flattening of the band leads to profound changes in Coulomb screening. Superconductivity observed recently in wide range of pressure and chemical composition in Weyl semi-metals of both types. The phonon theory of pairing including the Coulomb repulsion for a layered material is constructed and applied to recent extensive experiments on $$HfTe_{5}$$

H
f
T

e
5

.
GO nanoparticles mitigate the negative effects of salt and alkalinity stress by enhancing gas exchange and photosynthetic efficiency of strawberry plants
Authors: Malekzadeh Mohammad Reza , Roosta Hamid Reza , Kalaji Hazem M. 
Published: May 2023

AbstractConsidering the potential use of nanomaterials, particularly carbon-based nanostructures, in agriculture, we conducted a study to investigate the effect of graphene oxide (GO) on strawberry plants under salinity and alkalinity stress conditions. We used GO concentrations of 0, 2.5, 5, 10, and 50 mg/L, and applied stress treatments at three levels: without stress, salinity (80 mM NaCl), and alkalinity (40 mM NaHCO3). Our results indicate that both salinity and alkalinity stress negatively impacted the gas exchange parameters of the strawberry plants. However, the application of GO significantly improved these parameters. Specifically, GO increased PI, Fv, Fm, and RE0/RC parameters, as well as chlorophyll and carotenoid contents in the plants. Moreover, the use of GO significantly increased the early yield and dry weight of leaves and roots. Therefore, it can be concluded that the application of GO can enhance the photosynthetic performance of strawberry plants, and improve their resistance to stress conditions.
Survival of patients with cancers of the female genital organs in Poland, 2000–2019
Authors: Caetano dos Santos Florentino Luciano , Wojciechowska Urszula , Michalek Irmina Maria , Didkowska Joanna 
Published: May 2023

AbstractThe purpose of this study was to estimate cancer survival in Poland between 2000 and 2019 for malignant neoplasms of female genital organs (FGO). We calculated survival in cancer of vulva, vagina, cervix uteri, corpus uteri, ovary, and other unspecified female genital organs. Data were obtained from the Polish National Cancer Registry. We estimated age-standardized 5- and 10-year net survival (NS) with the life table method and the Pohar-Perme estimator using the International Cancer Survival Standard weights. Overall, 231,925 FGO cancer cases were included in the study. The overall FGO age-standardized 5-year NS was 58.2% (95% confidence interval (CI) 57.9–58.5%) and the 10-year NS 51.5% (51.5–52.3%). Between 2000 and 2004 and 2015–2018, the highest statistically significant increase in age-standardized 5-year survival was noted for ovarian cancer at + 5.6% (P < 0.001). The FGO cancer median survival time was 8.8 years (8.6–8.9 years), with a standardized mortality rate of 6.1 (6.0–6.1), and with cause-specific years of life lost at 7.8 years (7.7–7.8 years). Hazard ratios (HR) increased with age at diagnosis (HR = 1.02, 95% CI 1.01–1.03, P = 0.001). Although FGO cancer survivorship has been consistently improving during the last twenty years, additional efforts need to be undertaken to improve survivorship in several FGO cancers.
Multi biomarker approach to assess manganese and manganese nanoparticles toxicity in Pangasianodon hypophthalmus
Authors: Kumar Neeraj , Thorat Supriya Tukaram , Reddy Kotha Sammi 
Published: May 2023

AbstractManganese (Mn) is an essential element for humans and animals including, fish. It is a still poorly studied in aquatic organisms, where it can be noticeably useful for dietary components and also found pollutant in aquatic environment at high concentrations. On the above information, an experiment was delineated to determine the lethal concentration of manganese (Mn) and manganese nanoparticles (Mn-NPs) alone and with high temperature (34 °C) and its effect on various biochemical markers in Pangasianodon hypophthalmus. The median lethal concentration (96-LC50) of Mn alone (111.75 mg L−1) and along with high temperature (110.76 mg L−1), Mn-NPs alone (93.81 mg L−1) and with high temperature (34 °C) (92.39 mg L−1) was determined in P. hypophthalmus. The length and weight of the fish were 6.32 ± 0.23 cm and 7.57 ± 1.35 g. The present investigation used five hundred forty-six fish, including range finding (216 fish) and definitive test (330 fish). The acute definitive doses were applied to assess the effect of oxidative stress, glycolytic biomarkers, protein biomarkers, fish immunity, neurotransmitter, energy level, stress hormone and histopathology. Oxidative stress (catalase, superoxide dismutase, glutathione-s-transferase and glutathione peroxidase), stress biomarkers (lipid peroxidation, cortisol, heat shock protein, and blood glucose), lactate and malate dehydrogenase, alanine and aspartate aminotransferase, a neurotransmitter, glucose-6-phosphate dehydrogenase (G6PDH), ATPase, immune system biomarkers (NBT, total protein, albumin, globulin and A:G ratio) were altered with exposure to Mn and Mn-NPs. The histopathology of the liver and gill were also changed due to exposure to Mn and Mn-NPs. The bioaccumulation of Mn in the liver, gill, kidney, brain and muscle tissues, and experimental water at different intervals of 24, 48, 72 and 96 h were determined. Based on the present results, it is strongly suggested that Mn and Mn-NPs exposure alone and with high temperature (34 °C) enhanced toxicity and altered biochemical and morphological attributes. This study also suggested that essential elements in both forms (inorganic and nano) at higher concentrations of Mn and Mn-NPs lead to pronounced deleterious alteration in cellular and metabolic activities and histopathology of P. hypophthalmus.
Coincidence measurements of two quantum-correlated photon pairs widely separated in the frequency domain
Authors: Hojo Masayuki , Tani Shuntaro , Kobayashi Yohei , Tanaka Koichiro 
Published: May 2023

AbstractQuantum correlation is a key concept characterizing the properties of quantum light sources and is important for developing quantum applications with superior performance. In particular, it enables photon pairs that are widely separated in the frequency domain, one in the visible region, the other in the infrared region, to be used for quantum infrared sensing without direct detection of infrared photons. Here, simultaneous multiwavelength and broadband phase matching in a nonlinear crystal could provide versatile photon-pairs source for broadband infrared quantum sensing. This paper describes direct generation and detection of two quantum-correlated photon pairs produced via simultaneous phase-matched processes in periodic crystals. These simultaneous photon pairs provide a correlated state with two frequency modes in a single pass. To confirm the correlation, we constructed an infrared-photon counting system with two repetition-synchronized fiber lasers. We performed coincidence measurements between two pairs, 980 nm and 3810 nm, and 1013 nm and 3390 nm, which yielded coincidence-to-accidental ratios of 6.2 and 6.5, respectively. We believe that our novel correlated light source with two separate pairs in the visible and infrared region complements a wide-range of multi-dimensional quantum infrared processing applications.
Induction of a torpor-like hypothermic and hypometabolic state in rodents by ultrasound
Authors: Yang Yaoheng , Yuan Jinyun , Field Rachael L. , Ye Dezhuang , Hu Zhongtao , Xu Kevin , Xu Lu , Gong Yan , Yue Yimei , Kravitz Alexxai V. , Bruchas Michael R. , Cui Jianmin , Brestoff Jonathan R. , Chen Hong 
Published: May 2023

AbstractTorpor is an energy-conserving state in which animals dramatically decrease their metabolic rate and body temperature to survive harsh environmental conditions. Here, we report the noninvasive, precise and safe induction of a torpor-like hypothermic and hypometabolic state in rodents by remote transcranial ultrasound stimulation at the hypothalamus preoptic area (POA). We achieve a long-lasting (>24 h) torpor-like state in mice via closed-loop feedback control of ultrasound stimulation with automated detection of body temperature. Ultrasound-induced hypothermia and hypometabolism (UIH) is triggered by activation of POA neurons, involves the dorsomedial hypothalamus as a downstream brain region and subsequent inhibition of thermogenic brown adipose tissue. Single-nucleus RNA-sequencing of POA neurons reveals TRPM2 as an ultrasound-sensitive ion channel, the knockdown of which suppresses UIH. We also demonstrate that UIH is feasible in a non-torpid animal, the rat. Our findings establish UIH as a promising technology for the noninvasive and safe induction of a torpor-like state.