bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the most suitable reference gene for gene expression studies with development and abiotic stress response in Bromus sterilis
Authors: Sen Madhab Kumar , Hamouzová Kateřina , Košnarová Pavlina , Roy Amit , Soukup Josef 
Published: June 2021

AbstractBromus sterilis is an annual weedy grass, causing high yield losses in winter cereals. Frequent use of herbicides had led to the evolution of herbicide resistance in this species. Mechanisms underlying herbicide resistance in B. sterilis must be uncovered because this problem is becoming a global threat. qRT-PCR and the next-generation sequencing technologies can elucidate the resistance mechanisms. Although qRT-PCR can calculate precise fold changes, its preciseness depends on the expression of reference genes. Regardless of stable expression in any given condition, no gene can act as a universal reference gene. Hence, it is necessary to identify the suitable reference gene for each species. To our knowledge, there are no reports on the suitable reference gene in any brome species so far. Thus, in this paper, the stability of eight genes was evaluated using qRT-PCR experiments followed by expression stability ranking via five most commonly used software for reference gene selection. Our findings suggest using a combination of 18S rRNA and ACCase to normalise the qRT-PCR data in B. sterilis. Besides, reference genes are also recommended for different experimental conditions. The present study outcomes will facilitate future molecular work in B. sterilis and other related grass species.
Leaf morphology and chlorophyll fluorescence characteristics of mulberry seedlings under waterlogging stress
Authors: Rao Liangyi , Li Siyuan , Cui Xue 
Published: June 2021

AbstractBecause of its high flooding tolerance, in recent years, mulberry has become a tree species that is used in plant restoration in impact zones in reservoir areas. Therefore, 3-year-old potted forage mulberry seedlings were used to investigate the mechanism of mulberry adaptation to flooding stress. An indoor simulated flooding method was adopted to study the morphology of mulberry seedling leaves and the changes in leaf chlorophyll fluorescence parameters and fluorescence imaging under different flooding times and depths. The results showed that the leaves of mulberry seedlings treated with shallow submergence remained healthy during the flooding period, while the leaves of mulberry seedlings treated with half submergence and full submergence showed different degrees of waterlogging symptoms in the middle and late flooding periods and formed adventitious roots at the base of the stem. Most of the chlorophyll fluorescence parameters decreased at the beginning of flooding, but the steady-state degree of closure of PS II reaction centres (1-qP_Lss) increased significantly. In the later stage of flooding, the fluorescence parameters showed relatively stable trends. Based on these results, we conclude that mulberry has high flooding tolerance due to a combination of morphological and physiological responses.
In vivo loading on the hip joint in patients with total hip replacement performing gymnastics and aerobics exercises
Authors: Haffer Henryk , Popovic Srdan , Martin Franziska , Hardt Sebastian , Winkler Tobias , Damm Philipp 
Published: June 2021

AbstractA further increase in the number of total hip arthroplasty (THA) is predicted, in particular the number of young THA patients has raised and with it their demands. There is no standardized evidence-based rehabilitation program and no reliable guidelines for sports activities after THA. Stretching and strengthening gymnastics are routinely performed in rehabilitation and aerobics as a sport after THA. The aim of the investigation was to determine the in vivo force and moments acting on the hip prosthesis during gymnastics and aerobic exercises to provide a source for evidence-based recommendations. Hip joint loads were measured in six patients with instrumented hip implants. The resulting force FRes, bending moment MBendat the neck and torsional moment MTorsat the stem were examined during seven strengthening (with two different resistance bands) and four stretching gymnastic exercises and seven aerobic exercises with and without an aerobic step board compared to the loads during the reference activity walking. The stretching and strengthening gymnastics exercises and the aerobic exercises with and without a board demonstrated in their median peak force and moments mostly lower or similar values compared to walking. Significantly increased loads were recorded for the flexor stretching exercise in monopod stand (Fresand MBend), the strengthening abduction exercise on the chair (MTors) and the strengthening flexion exercise with the stronger resistance band (MTors). We also found a significant increase in median peak values in aerobic exercises with a board for the "Basic Step" (ipsilateral started Fresand MTors; contralateral started MTors), "Kickstep ipsilateral started" (Fresand MTors) and "Over the Top contralateral started" (Fres). The in vivo loads in THA patients during frequently performed stretching, strengthening and aerobic exercises were demonstrated for the first time. It was proved that stretching gymnastic exercises are safe in terms of resulting force, bending and torque moments for THA patients, although an external assistance for stabilization may be considered. Strengthening gymnastics exercises are reliable in terms of Fres, MBendand MTors, but, based on our data, we recommend to adhere to the communicated specific postoperative restrictions and select the resistance bands with lower tension. Aerobic exercises without an aerobic board can be considered as reliable activity in terms of force and moments for THA patients. Aerobic exercises with a board are not recommended for the early postoperative period and in our opinion need to be adapted to the individual muscular and coordinative resources.
The mechanism of increased intestinal palmitic acid absorption and its impact on hepatic stellate cell activation in nonalcoholic steatohepatitis
Authors: Hanayama Masakazu , Yamamoto Yasunori , Utsunomiya Hiroki , Yoshida Osamu , Liu Shuang , Mogi Masaki , Matsuura Bunzo , Takeshita Eiji , Ikeda Yoshiou , Hiasa Yoichi 
Published: June 2021

AbstractDietary palmitic acid (PA) promotes liver fibrosis in patients with nonalcoholic steatohepatitis (NASH). Herein, we clarified the intestinal absorption kinetics of dietary PA and effect of trans-portal PA on the activation of hepatic stellate cells (HSCs) involved in liver fibrosis in NASH. Blood PA levels after meals were significantly increased in patients with NASH compared to those in the control. Expression of genes associated with fat absorption and chylomicron formation, such as CD36 and MTP, was significantly increased in the intestine of NASH model rats compared with that in the controls. Plasma levels of glucagon-like peptide-2, involved in the upregulation of CD36 expression, were elevated in NASH rats compared with those in the controls. Furthermore, portal PA levels after meals in NASH rats were significantly higher than those in control and nonalcoholic fatty liver rats. Moreover, PA injection into the portal vein to the liver in control rats increased the mRNA levels associated with the activation of HSCs. Increased intestinal absorption of diet-derived PA was observed in NASH. Thus, the rapid increase in PA levels via the portal vein to the liver may activate HSCs and affect the development of liver fibrosis in NASH.
Various myosteatosis selection criteria and their value in the assessment of short- and long-term outcomes following liver transplantation
Authors: Meister Franziska Alexandra , Bednarsch Jan , Amygdalos Iakovos , Boecker Joerg , Strnad Pavel , Bruners Philipp , Lang Sven Arke , Ulmer Tom Florian , Heij Lara , Santana Daniel Antonio Morales , Liu Wen-Jia , Lurje Georg , Neumann Ulf Peter , Czigany Zoltan 
Published: June 2021

AbstractBody composition and myosteatosis affect clinical outcomes in orthotopic liver transplantation (OLT). Here we aimed to compare the value and limitations of various selection criteria to define pre-transplant myosteatosis in the assessment of short- and long-term outcomes following OLT. We retrospectively analyzed the data of 264 consecutive recipients who underwent deceased donor OLT at a German university medical centre. Myosteatosis was evaluated by preoperative computed-tomography-based segmentation. Patients were stratified using muscle radiation attenuation of the whole muscle area (L3Muslce-RA), psoas RA (L3Psoas-RA) and intramuscular adipose tissue content (IMAC) values. L3Muslce-RA, L3Psoas-RA and IMAC performed well without major differences and identified patients at risk for inferior outcomes in the group analysis. Quartile-based analyses, receiver operating characteristic curve and correlation analyses showed a superior association of L3Muslce-RA with perioperative outcomes when compared to L3Psoas-RA and L3IMAC. Long-term outcome did not show any major differences between the used selection criteria. This study confirms the prognostic role of myosteatosis in OLT with a particularly strong value in the perioperative phase. Although, based on our data, L3Muscle-RA might be the most suitable and recommended selection criterion to assess CT-based myosteatosis when compared to L3Psoas-RA and L3IMAC, further studies are warranted to validate these findings.
Deep neural network-based classification of cardiotocograms outperformed conventional algorithms
Authors: Ogasawara Jun , Ikenoue Satoru , Yamamoto Hiroko , Sato Motoshige , Kasuga Yoshifumi , Mitsukura Yasue , Ikegaya Yuji , Yasui Masato , Tanaka Mamoru , Ochiai Daigo 
Published: June 2021

AbstractCardiotocography records fetal heart rates and their temporal relationship to uterine contractions. To identify high risk fetuses, obstetricians inspect cardiotocograms (CTGs) by eye. Therefore, CTG traces are often interpreted differently among obstetricians, resulting in inappropriate interventions. However, few studies have focused on quantitative and nonbiased algorithms for CTG evaluation. In this study, we propose a newly constructed deep neural network model (CTG-net) to detect compromised fetal status. CTG-net consists of three convolutional layers that extract temporal patterns and interrelationships between fetal heart rate and uterine contraction signals. We aimed to classify the abnormal group (umbilical artery pH < 7.20 or Apgar score at 1 min < 7) and the normal group from CTG data. We evaluated the performance of the CTG-net with the F1 score and compared it with conventional algorithms, namely, support vector machine and k-means clustering, and another deep neural network model, long short-term memory. CTG-net showed the area under the receiver operating characteristic curve of 0.73 ± 0.04, which was significantly higher than that of long short-term memory. CTG-net, a quantitative and automated diagnostic aid system, enables early intervention for putatively abnormal fetuses, resulting in a reduction in the number of cases of hypoxic injury.
In Silico identification of a common mobile element insertion in exon 4 of RP1
Authors: Won Dongju , Hwang Joo-Yeon , Shim Yeeun , Byeon Suk Ho , Lee Junwon , Lee Christopher Seungkyu , Kim Min , Lim Hyun Taek , Choi Jong Rak , Lee Seung-Tae , Han Jinu 
Published: June 2021

AbstractMobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder Alu insertion in exon 4 of RP1 has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the Alu insertion in exon 4 of RP1 using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating RP1 variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in RP1 exon 4. This AluY insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this AluY insertion in RP1 exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232–0.383), with no false-positive results using 120 control samples. The MEI in RP1 exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1-Alu grep program efficiently detected the AluY insertion, without the preprocessing of raw data or complex installation processes.
Porcine pancreatic ductal epithelial cells transformed with KRASG12D and SV40T are tumorigenic
Authors: Bailey Katie L. , Cartwright Sara B. , Patel Neesha S. , Remmers Neeley , Lazenby Audrey J. , Hollingsworth Michael A. , Carlson Mark A. 
Published: June 2021

AbstractWe describe our initial studies in the development of an orthotopic, genetically defined, large animal model of pancreatic cancer. Primary pancreatic epithelial cells were isolated from pancreatic duct of domestic pigs. A transformed cell line was generated from these primary cells with oncogenic KRAS and SV40T. The transformed cell lines outperformed the primary and SV40T immortalized cells in terms of proliferation, population doubling time, soft agar growth, transwell migration and invasion. The transformed cell line grew tumors when injected subcutaneously in nude mice, forming glandular structures and staining for epithelial markers. Future work will include implantation studies of these tumorigenic porcine pancreatic cell lines into the pancreas of allogeneic and autologous pigs. The resultant large animal model of pancreatic cancer could be utilized for preclinical research on diagnostic, interventional, and therapeutic technologies.
Synthesis and characterization of analcime (ANA) zeolite using a kaolinitic rock
Authors: Novembre Daniela , Gimeno Domingo 
Published: June 2021

AbstractAnalcime is nowadays an important component in dental porcelain systems, in heterogeneous catalysis, in the nanoelectronic field, in selective adsorption and in stomatology (dental filling and prosthesis). Analcime synthesis from an impure, silica-rich kaolinite rock coming from Romana (Sassari, Italy) is here presented. A synthesis protocol is proposed that aims to make an improvement of synthesis conditions compared to the past. The hydrothermal treatment is in fact here achieved without aging times and without the use of sodium silicate or other additional silica source reported in the literature. Lower calcination temperature, synthesis temperature and crystallization time are verified in this work. The kaolin is subjected to calcination at the temperature of 650 °C and then mixed with NaOH. The experiment is performed at ambient pressure and 170 ± 0.1 °C. The degree of purity of analcime is calculated in 97.57% at 10 h. Analcime is characterized by X-ray diffraction, infrared spectroscopy, scanning electron microscopy, inductively coupled plasma optical emission spectrometry and thermal analysis. Density is also calculated. Cell parameters and the amount of amorphous phase in the synthesis powders is estimated with quantitative phase analysis using the combined Rietveld and reference intensity ratio methods. The experimental conditions make the synthesis protocol particularly attractive from an economic point of view. Also this work does not use a commercial kaolin but silica-rich impure kaolinitic rock from a disused quarry. This further reduces the costs of the experimental protocol. It also gives the protocol an added value, as the synthesis of a useful mineral is obtained through the valorization of an otherwise unused georesource. Both chemical and physical characterization of analcime is satisfactory making the experimental protocol very promising for an industrial transfer.
Combination immunotherapy with two attenuated Listeria strains carrying shuffled HPV-16 E6E7 protein causes tumor regression in a mouse tumor model
Authors: Su Lin , Zhang Yunwen , Zhang Xiang , Liu Ting , Liu Sijing , Li Yongyu , Jiang Mingjuan , Tang Tian , Shen Haiqian , Wang Chuan 
Published: June 2021

AbstractCervical cancer continues to impose a heavy burden worldwide, and human papilloma virus (HPV) infection, especially persistent infection with type 16 (HPV-16), is known to be the primary etiological factor. Therapeutic vaccines are urgently needed because prophylactic vaccines are ineffective at clearing pre-existing HPV infection. Here, two recombinant Listeria strains (LMΔ-E6E7 & LIΔ-E6E7) with deletions of the actA and plcB genes, expressing the shuffled HPV-16 E6E7 protein were constructed. The strains were delivered into the spleen and liver by intravenous inoculation, induced antigen-specific cellular immunity and were eliminated completely from the internal organs several days later. Intravenously treating with single strain for three times, or with both strains alternately for three times significantly reduced the tumor size and prolonged the survival time of model mice. Combination immunotherapy with two strains seemed more effective than immunotherapy with single strain in that it enhanced the survival of the mice, and the LMΔ-E6E7-prime-LIΔ-E6E7-boost strategy showed significant stronger efficacy than single treatment with the LIΔ-E6E7 strain. The antitumor effect of this treatment might due to its ability to increase the proportion of CD8+ T cells and reduce the proportion of T regulatory cells (Tregs) in the intratumoral milieu. This is the first report regarding Listeria ivanovii-based therapeutic vaccine candidate against cervical cancer. Most importantly we are the first to confirm that combination therapy with two different recombinant Listeria strains has a more satisfactory antitumor effect than administration of a single strain. Thus, we propose a novel prime-boost treatment strategy.
Biodegradation of Indanthrene Blue RS dye in immobilized continuous upflow packed bed bioreactor using corncob biochar
Authors: Mohanty Swati Sambita , Kumar Arvind 
Published: June 2021

AbstractThe current study describes the aerobic biodegradation of Indanthrene Blue RS dye by a microbial consortium immobilized on corn-cob biochar in a continuous up-flow packed bed bioreactor. The adsorption experiments were performed without microbes to monitor the adsorption effects on initial dye decolorization efficiency. The batch experiments were carried out to estimate the process parameters, and the optimal values of pH, temperature, and inoculum volume were identified as 10.0, 30 °C, and 3.0 × 106 CFU mL−1, respectively. During the continuous operation, the effect of flow rate, initial substrate concentration, inlet loading rate of Indanthrene Blue RS on the elimination capacity, and its removal efficiency in the bioreactor was studied. The continuous up-flow packed bed bioreactor was performed at different flow rates (0.25 to 1.25 L h−1) under the optimal parameters. The maximum removal efficiency of 90% was observed, with the loading rate varying between 100 and 300 mg L−1 day−1. The up-flow packed bed bioreactor used for this study was extremely useful in eliminating Indanthrene Blue RS dye using both the biosorption and biodegradation process. Therefore, it is a potential treatment strategy for detoxifying textile wastewater containing anthraquinone-based dyes.
Spatial organization of FcγR and TLR2/1 on phagosome membranes differentially regulates their synergistic and inhibitory receptor crosstalk
Authors: Li Wenqian , Li Miao , Anthony Stephen M. , Yu Yan 
Published: June 2021

AbstractMany innate immune receptors function collaboratively to detect and elicit immune responses to pathogens, but the physical mechanisms that govern the interaction and signaling crosstalk between the receptors are unclear. In this study, we report that the signaling crosstalk between Fc gamma receptor (FcγR) and Toll-like receptor (TLR)2/1 can be overall synergistic or inhibitory depending on the spatial proximity between the receptor pair on phagosome membranes. Using a geometric manipulation strategy, we physically altered the spatial distribution of FcγR and TLR2 on single phagosomes. We demonstrate that the signaling synergy between FcγR and TLR2/1 depends on the proximity of the receptors and decreases as spatial separation between them increases. However, the inhibitory effect from FcγRIIb on TLR2-dependent signaling is always present and independent of receptor proximity. The overall cell responses are an integration from these two mechanisms. This study presents quantitative evidence that the nanoscale proximity between FcγR and TLR2 functions as a key regulatory mechanism in their signaling crosstalk.
MYD88, NFKB1, and IL6 transcripts overexpression are associated with poor outcomes and short survival in neonatal sepsis
Authors: AbdAllah Nouran B. , Toraih Eman A. , Al Ageeli Essam , Elhagrasy Hala , Gouda Nawal S. , Fawzy Manal S. , Helal Ghada M. 
Published: June 2021

AbstractToll-like receptor (TLR) family signature has been implicated in sepsis etiopathology. We aimed to evaluate the genetic profile of TLR pathway-related key genes; the myeloid differentiation protein 88 (MYD88), IL1 receptor-associated kinase 1 (IRAK1), the nuclear factor kappa-B1 (NFKB1), and interleukin 6 (IL6) in the blood of neonates with sepsis at the time of admission and post-treatment for the available paired-samples. This case–control study included 124 infants with sepsis admitted to the neonatal intensive care unit and 17 controls. The relative gene expressions were quantified by TaqMan Real-Time qPCR and correlated to the clinic-laboratory data. MYD88, NFKB1, and IL6 relative expressions were significantly higher in sepsis cases than controls. Higher levels of MYD88 and IL6 were found in male neonates and contributed to the sex-based separation of the cases by the principal component analysis. ROC analysis revealed MYD88 and NFKB1 transcripts to be good biomarkers for sepsis. Furthermore, patients with high circulatory MYD88 levels were associated with poor survival, as revealed by Kaplan–Meier curves analysis. MYD88, NFKB1, and IL6 transcripts showed association with different poor-outcome manifestations. Clustering analysis split the patient cohort into three distinct groups according to their transcriptomic signature and CRP levels. In conclusion, the study TLR pathway-related transcripts have a gender-specific signature, diagnostic, and prognostic clinical utility in neonatal sepsis.