bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Respiratory Factor 1 Promotes The Growth of Liver Hepatocellular Carcinoma Cells Via E2F1 Transcriptional Activation
Authors: Wang Dan , Wan Baolan , Zhang Xiaojing , Sun Pingping , Lu Shu , Liu Chenxu , Zhu Li 
Published: September 2021

Abstract
Background Recent studies have shown that functional mitochondria are essential for cancer cells. Nuclear respiratory factor 1 (NRF1) is a transcription factor that activates mitochondrial biogenesis and the expression of the respiratory chain, but little is known about its role and underlying mechanism in liver hepatocellular carcinoma (LIHC). Methods NRF1 expression was analyzed via public databases and 24 paired LIHC samples. Clinical-pathological information and follow-up data were collected from 165 patients with LIHC or online datasets. Furthermore, cellular proliferation and the cell cycle were analyzed by MTT, Clone-forming assay and flow cytometric analyses. NRF1 target genes were analyzed by Chromatin immunoprecipitation sequencing (ChIP-Seq). PCR and WB analysis was performed to detect the expression of related genes. ChIP and luciferase activity assays were used to identify NRF1 binding sites.Results Our results showed that NRF1 expression was upregulated in LIHC compared to normal tissues. NRF1 expression was associated with tumour size and poor prognosis in patients. Knockdown of NRF1 repressed cell proliferation, and overexpression of NRF1 accelerated the G1/S phase transition. Additionally, data from ChIP-seq pointed out that some NRF1 target genes are involved in the cell cycle. Our findings indicated that NRF1 directly binds to the E2F1 promoter as a transcription factor and regulates its gene expression. Conclusion Therefore, this study revealed that NRF1 promotes cancer cell growth via the indirect transcriptional activation of E2F1 and is a potential biomarker in LIHC.
Effect of Cerebrospinal Fluid Area Mask Correction on 123I-FP-CIT SPECT Images in Idiopathic Normal Pressure Hydrocephalus
Authors: Ohba Makoto , Kobayashi Ryota , Iseki Chifumi , Kirii Kazukuni , Morioka Daichi , Otani Koichi , Ohta Yasuyuki , Sonoda Yukihiko , Suzuki Koji , Kanoto Masafumi 
Published: September 2021

Abstract
Cerebrospinal fluid (CSF) mask correction has been developed to reduce the influence by CSF area dilatation for 123I-FP-CIT accumulation. In this study, we assessed the effect of CSF mask correction on the specific binding ratio (SBR) for 25 patients with idiopathic normal pressure hydrocephalus (iNPH). The SBRs with and without CSF mask correction were calculated, and changes in quantitative values were verified. Additionally, the volume removed from striatal and background (BG) volume of interest (VOI) by the CSF mask correction was calculated, the volumes removed were compared to verify their effect on SBR. Twenty and five patients had low and high SBRs, respectively, after CSF mask correction. The images of 20 and 5 patients with SBRs that were decreased and increased, respectively, by CSF mask correction showed that the volumes removed from the BG region VOI were higher and lower, respectively, than those in the striatal region. In conclusion, the SBR before and after CSF mask correction was associated with the ratio of the volume removed from the striatal and BG VOIs, and the SBR was high or low according to the ratio. The results may indicate that CSF mask correction is effective in patients with iNPH. This study was registered in the UMIN Clinical Trials Registry (UMIN-CTR) as UMIN study ID: UMIN000044826.
Effect of N-acyl-homoserine lactones（AHL) on biogenic amine formation by Pantoea agglomerans
Authors: Lu Jing , Li Ziqin , Yang Hui , Zhang Qiang , Jia wenting 
Published: September 2021

Abstract
The effect of N-acyl-homoserine lactone (AHL)-based quorum sensing (QS) on biogenic amine (BA) formation by Pantoea agglomerans was studied. Agrobacterium tumefaciens A136 and KYC55-based bioassays confirmed AHLs production by Pantoea agglomerans. The production ability of AHLs was quantified on the basis of β-galactosidase activity. The influence of temperature (10°C and 20°C) and pH (5.5 and 6.5) on β-galactosidase activity and BAs production by Pantoea agglomerans was determined. Acidification of the environment adversely affected the growth and β-galactosidase activity of Pantoea agglomerans, and AHLs production and BAs accumulation by Pantoea agglomerans was inhibited at low temperature. A significant correlation between β-galactosidase activity and BAs (putrescine, histamine, putrescine and tryptamine) was identified (P < 0.01). Based on the results of this study, the AHL-based QS system influences the concentrations and types of BAs produced by Pantoea agglomerans.
Opinions About the Most Appropriate Surgical Management of Diabetes-Related Foot Infection: A Cross-Sectional Survey
Authors: Seng Leonard , Drovandi Aaron , Fernando Malindu E , Golledge Jonathan 
Published: September 2021

Abstract
Background: There is a lack of high quality evidence to guide the optimal management of diabetes-related foot infection, particularly in severe cases of diabetes-related foot infection and diabetes-related foot osteomyelitis. This study examined the opinions of surgeons about the best management of severe diabetes-related foot infection. Methods: Vascular and orthopaedic surgeons in Australia and New Zealand were invited to complete an online survey via email. The survey included multi-choice and open-ended questions on clinical management of diabetes-related foot infection. Responses of vascular surgeons and orthopaedic surgeons were compared using non-parametric statistical tests. Open-text responses were examined using inductive content analysis. Results: 29 vascular and 20 orthopaedic surgeons completed the survey. One-third (28.6%) used best-practice guidelines to assist in decisions about foot infection management. Areas for guideline improvement identified included more specific advice regarding the indications for available treatments, more information about the overall non-surgical patient management and advice on how management can be varied in regions with limited health service resource. The probe-to-bone test and magnetic resonance imaging were the preferred methods of diagnosing osteomyelitis. Approximately half (51.2%) of respondents indicated piperacillin combined with Tazobactam as the preferred antibiotic choice for empirical treatment of severe diabetes-related foot infection. Negative pressure wound therapy was the most common way of managing a wound following debridement. All vascular surgeons (100%) made revascularisation decisions based the severity of ischemia while most orthopaedic surgeons (66.7%) were likely to refer to vascular surgeons to make revascularisation decisions. Vascular surgeons preferred using wound swabs while orthopaedic surgeons favoured tissue or bone biopsies to determine the choice of antibiotic. Respondents perceived a moderate variation in management decisions between specialists and supported the need for further trials to test different management pathways. Conclusions: Most vascular and orthopaedic surgeons do not use best-practice guidelines to assist in decisions about management of diabetes-related foot infection. Vascular and orthopaedic surgeons appear to have different preferences for wound sampling to determine choice of antibiotic. There is a need to advance available evidence supporting different treatments and the related guidelines for the surgical managing of diabetes-related foot infection.
3C based DNA hybridization method for chromosomal translocation screening
Authors: Absalan Moloud , Jabbarpour Zahra , Ghahremani Mohammad Hossein , Motevaseli Elahe , Mahmoudian Fatemeh , Karimi Roya , Tavoosidana Gholamreza 
Published: September 2021

Abstract
Background

DNA probes have been widely used as diagnostic tools for chromosomal translocations in malignancies. PCR-based methods often fail to detect translocations such as MYC/TRD in chronic lymphocytic leukemia. In addition, microscopic techniques cannot be helpful due to size detection limitations. This study sought to design a screening tool using immobilized ssDNA probes on a nitrocellulose membrane followed by 3C library fragments hybridization.
Results

Hence, we focused on developing a suitable 27 bp specific probe for the juxtaposed region of MYC and TRD. Colloidal gold nanoparticles (AuNP) functionalized translocation fragments of the MYC gene with a thiol group (MYC-AuNP-probe). Then TRD-probes were immobilized on nitrocellulose surface to detect TRD/MYC translocation in the SKW3 cells. Hybridization between DNA probes and 3C-library fragments of SKW3 cells was determined by color intensity. Optimal hybridization of the 3C library sample of the cell line to TRD-probe and MYC-AuNP-probe showed higher color intensity due to their convenient proximity to the juxtaposed region compare with normal cells.
Conclusions

Our results demonstrated that DNA hybridization colorimetric assay could be a helpful technique in chromosomal rearrangements screening. Accordingly, the combination of 3C based techniques and DNA-DNA hybridization can identify cancer cells with high specificity and sensitivity.
Fibrinogen, a Promising Marker to Evaluate Severity and Prognosis of Acute Exacerbation of Chronic Obstructive Pulmonary Disease: A Retrospective Observational Study.
Authors: Sun Wei , Cao Zhixin , Ma Yingmin , Wang Jing , Zhang Liming , Luo Zujin 
Published: September 2021

Abstract
Background: Fibrinogen is increasingly studied as an inflammatory biomarker in chronic obstructive pulmonary disease (COPD), and there are limited data about the role of fibrinogen to assess the severity of acute exacerbation of COPD. This study aimed to explore whether circulating fibrinogen could be used as a surrogate to measure the severity and predict the prognosis of acute exacerbation of chronic obstructive pulmonary disease (AECOPD).Methods: A total of 523 AECOPD patients diagnosed at our center from January 2016 to June 2021 were retrospectively enrolled in this study. Electronic medical record of each patient was retrieved to collect data regarding baseline characteristics and laboratory parameters, as well as the use of noninvasive positive pressure ventilation (NPPV) and patients’ prognosis. Multiple linear regression analyses were used to identify the independent factors that associated with fibrinogen values. Receiver-operating characteristic (ROC) curve and multivariate logistic regression analysis were applied to further verify the use of fibrinogen to predict NPPV failure. Results: Compared to patients with low levels of fibrinogen (≤3.5g/L), patients with increased fibrinogen levels (>3.5g/L) were associated with increased CRP expression, leukocyte, neutrophil counts and more frequent antibiotics use. In addition, the average fibrinogen level among patients with NPPV failure was significantly increased compared to non-NPPV patients and NPPV success patients. The presence of emphysema, pneumonia, history of long-term oxygen therapy (LTOT) and the CRP value were independent risk factors associated with increased fibrinogen levels in AECOPD. Furthermore, our data indicated that fibrinogen could be considered as an reliable biomarker to predict NPPV failure (AUC, 0.890; 95% CI 0.832–0.947) with an odds ratio of 6.1 (95% CI, 1.86-19.98; P=0.03). Conclusions: The level of fibrinogen could be used as a surrogate to measure severity, and among AECOPD patients who required NPPV, higher fibrinogen could independently predict NPPV failure.
Comparative Actualistic Study Hints at Origins of Intriguing Miocene “Coprolites” of Poland
Authors: Brachaniec Tomasz , Środek Dorota , Surmik Dawid , Niedźwiedzki Robert , Georgalis Georgios L. , Płachno Bartosz J. , Duda Piotr , Lukeneder Alexander , Gorzelak Przemysław , Salamon Mariusz A. 
Published: September 2021

Abstract
Excrement-shaped siderite masses have been the subject of much controversy. They have been variously interpreted either as being coprolites, cololites or pseudofossils created by mechanical deformation of plastic sediment. Here we report excrement-shaped ferruginous masses recovered from the Miocene of the Turów mine in south-western Poland.
Mineralogical, geochemical, petrographic and microtomographical analyses indicate that these masses consist of siderite and iron oxide rather than phosphate, and rarely contain recognizable food residues, which may suggest abiotic origins of these structures. On the other hand, evidence in support of a faecal origin include: (i) the presence of two distinct morphotypes differing in size and shape, (ii) the limited quantity of specimens, (iii) the presence of rare hair-like structures or coalified inclusions and (iv) the presence of fine striations on the surface. Importantly, comparative actualistic studies of Recent vertebrate feces show overall resemblance of the first morphotype (sausage-shaped with rare coalified debris) to excrements of testudinoid turtles (Testudinoidea), whose shell fragment was found in the investigated locality. The second morphotype (rounded to oval-shaped with hair-like structures), in turn, is similar to the feces of some snakes (Serpentes), the remains of which were noted in the Miocene of the neighborhood areas.
Transcriptome and proteomics analysis revealed key genes in rabbit skeletal muscle after weight loss
Authors: Wang Jie , Li YanHong , Elzo Mauricio A. , Xia Siqi , Fan Huimei , Tang Tao , Shao Jiahao , Jia Xianbo , Chen Shiyi , Lai Songjia 
Published: September 2021

Abstract
Skeletal muscle is one of the important organs of energy metabolism and is closely related to insulin secretion. Its metabolic characteristics have a major influence on fat distribution in various body tissues. However, rabbit skeletal muscle has lower intramuscular fat content, and its metabolic mechanism is still unclear. We investigated skeletal muscle growth and metabolic differences among rabbits using a comparative multi-omics approach after a 14-day weight loss by a restricted diet. Rabbit body weight and perirenal fat were significantly reduced after the weight loss. Transcriptomics data revealed 917 differentially expressed genes in skeletal muscle primarily enriched in the FOXO signaling, Glutathione metabolism, and AMPK signaling pathways. Proteomics data found 127 differential proteins concentrated in protein metabolism and immunoinflammatory pathways. Conbined analysis demonstrated that eight genes (ATP2A2, PDLIM3, GPX7, FKBP5, MYL3, COL5A2, UCHL1, and COL3A1) were strongly correlated at the transcriptional and translational levels. These results provide a good reference for further revealing the mechanism of skeletal muscle metabolism in rabbits.
Comparative Analysis of Whole Blood Ionised Calcium, Lactate and Chloride Concentrations by Gem Premier 3000 and Edan I15 Vet and the Effect of Parity and Postpartum Blood Collection Time on Blood Calcium Status in Holstein With and Without Subclinical Hypocalcemia - Part 1
Authors: Deniz Abdulkerim , AKSOY Kemal , Metin Mert , Pekmezci Aytaç 
Published: September 2021

Abstract
Lactating Holstein (n=125) were enrolled randomly for the coccygeal whole blood analysis by blood gas devices GEM Premier 3000 (GEM) and Edan i15 Vet (EDAN) between calving to postpartum day 3 (G1) and postpartum day 4 to 27 (G2). Blood pH, ionised calcium (ICA7.4) and lactate analysis were significantly correlated between GEM and EDAN (r=0.86, 0.94, 0.87 respectively). The bias for ICA7.4, lactate and pH analysis was -0.054, -0.344 mmol/L and +0.009 respectively. ICA7.4 was correlated negatively with parity and chloride, but positively with lactate. The averages of ICA7.4 and serum total calcium (TC) was significantly lower in G1 than G2. Chloride and lactate were significantly higher in G1 than G2. Subclinical hypocalcemia prevalence (SCH) (serum TC<2.15 mmol/L, as reference) was 52.9% in G1 and 21.1% in G2. Cows with SCH had frequently over 50% ICA7.4/TC ratio. Sensitivity analysis provided a sensitivity of 57.4% for ICA7.4 cut-points of 1.02 (GEM) and 1.05 (EDAN) mmol/L to detect SCH based on reference serum TC. Primiparous (PRP) with and without SCH in G1 had significantly higher ICA7.4 than multiparous (MUL). Cows with SCH had significantly higher chloride in G1 than G2. MUL had significantly higher lactate and chloride in G1 than G2. Conclusively, ICA7.4 and pH analysis between GEM and EDAN were correlated well with acceptable biases, but high differences occurred in lactate analysis. MUL was at risk in G1 due to lower ICA7.4 and TC over PRP. Higher ICA7.4 of PRP can reduce the risk and frequency of clinical hypocalcemia. SCH correlated negatively with Cl concentration in G1, but not lactate.
The Plasma Proteome
Authors: Chen Zhuo Zhen , Wang Wei-Cheih , Johnson Lloyd , Dufresne Jaimie , Bowden Peter , Trahtemberg Uriel , DosSantos Claudia , Ho Hsin-Yu , Ho Ja-An , Hsu Cheng-Chih Richard , Marshall John 
Published: September 2021

Abstract
The authors have requested that this preprint be removed from Research Square.
Machine-learning analysis for discriminating radial pulse-waveform quality by applying different contact pressures
Authors: OuYoung Te , Weng Wan-Ling , Hu Ting-Yu , Lee Chia-Chien , Wu Li-Wei , Hsiu Hsin 
Published: September 2021

Abstract
Pulse measurements made using wearable devices can aid the monitoring of the human physiological condition. However, accurate estimation of waveforms is often difficult for nonexperts and motion artifacts may occur during tonometry measurements when the skin-sensor contact pressure is insufficient. An alternative approach is to extract only high-quality pulses for use in index calculations. The present study aimed to determine the effectiveness of using machine-learning analysis in discriminating between high-quality and low-quality pulse waveforms induced by applying different contact pressures. Radial blood pressure waveform (BPW) signals were measured noninvasively in healthy young subjects using a strain-gauge transducer. One-minute-long trains of pulse data were measured when applying the appropriate contact pressure (67.80±1.55 mmHg) and a higher contact pressure (151.80±3.19 mmHg). Eight machine-learning algorithms were employed to evaluate the following 40 harmonic pulse indices: amplitude proportions and their coefficients of variation, and phase angles and their standard deviations. Significant differences were noted in BPW indices between applying appropriate and higher skin-surface contact pressures. The present appropriate contact pressure could not only provide a suitable holding force for the wearable device, but also helped to maintain the physiological stability of the underlying tissues. Machine-learning analysis provides an effective method for distinguishing between the high-quality and low-quality pulses with excellent discrimination performance (leave-one-out test: random-forest AUC=0.96). This approach will aid the development of an automatic screening method for waveform quality, and thereby improve the reliability of pulse waveforms acquired by wearable devices. The effects of other possible interfering factors in practical wearable applications can also be systematically studied using a similar procedure.
Mechanical properties and acoustic emission characteristics of coal samples with different fissure angle
Authors: Gu Xuebin , Zhao Tongbin , Guo Weiyao , Gong Xufei , Zhao Yongqiang , Chen Yang , Xu Ninghui 
Published: September 2021

Abstract
To study the influence of fissure angle on the failure mechanism of coal mass, uniaxial compression tests were conducted on coal specimens with different fissure angles. The failure process and acoustic emission characteristics during loading were obtained. The mechanical properties and failure mode were further analyzed. The results showed that (1) The stress-strain behavior of specimens with different fissure angles can be divided into four typical stages, compaction, elastic deformation, crack growth and propagation, and strain-softening. The existence of pre-existing fissures reduces the duration of the elastic stage with an obvious influence on the crack growth and propagation stage, and strain-softening stage. (2) The uniaxial compressive strength, elastic modulus of the specimens containing pre-existing fissure are all lower than those of the unfissured. The strength and elastic modulus do not change significantly with fissure angle, which is closely related to the primary fracture of the coal. (3) With the increase of the fissure angle, the crack initiation location moves from the center of the pre-existing fissure to the tip. While fissure angle has no obvious effect on the crack propagation direction, the cracks develop along the loading direction. (4) The AE characteristics can be divided into three typical periods, quiet period, active period, and remission period. With the increase of the fissure angle, the duration proportion of the quiet period increases, indicating that the energy storage time of coal increases. With the increase of the fissure angle, the occurrence time of low frequency and high energy signal is delayed, indicating that the large-size rupture gradually concentrates in the late loading period. (5) Compared with rock samples containing pre-existing fissure, coal specimens have more primary fractures, and the failure mechanism of coal is dominated by the non-uniform primary fractures.
Bilateral Helicoid Peri-papillary Sub-retinal Fibrosis Due to a Biallelic NR2E3 Mutation: Describing Variable Expressivity of a Single Genetic Mutation
Authors: Hassanpoor Narges , Ebrahimiadib Nazanin , Riazi-Esfahani Hamid , Moghaddasi Afrooz , Suri Fatemeh 
Published: September 2021

Abstract
Background: To describe different clinical presentations of NR2E3 (nuclear receptor subfamily 2, group E, member 3; OMIM 604485) recessive mutation in two families and within one family. Design: Interventional family study. Results: Our first case was a one-year-old male child with high hyperopia and refractive accommodative esotropia. In retinal examination, peri-papillary sub-retinal fibrosis with a helicoid configuration was observed in both eyes. Parents and the only sibling had no pathologic finding in the eyes. The child showed to have severely reduced responses in both photopic and scotopic electroretinogram components. In genetic investigation, a homozygous autosomal recessive mutation in NR2E3 gene was discovered in the affected child, while the other family members were heterozygous for this mutation. We followed up the patient for 3 years and no new lesion developed during this time period. The second case was a 13-year-old male child who was referred to retina clinic for decreased vision in the right eye. In retina examination, there were nummular pigmentary changes at the level of retinal pigment epithelium and along the vascular arcades with foveo-schitic changes in both eyes. A choroidal neovascularization (CNV) was noticed in macula of his right eye. Genetic evaluation proved the same mutation in NR2E3 gene. Family history was remarkable for an uncle, an aunt and two cousins with night blindness. In retina examination, asymptomatic father of proband showed to have slight pallor of optic nerve head and arterial narrowing in both eyes. Conclusion: NR2E3 gene mutation can cause heterogeneous clinical manifestations such as slight retinal changes in the absence of any visual symptoms to high hyperopia associated with helicoid peri-papillary sub-retinal fibrosis.