Miracle-dz/UniFAR-FTUs huggingface dataset:
The association between circulating levels of vitamin D and inflammatory markers in the first 2 years after colorectal cancer diagnosis

Background: Calcitriol, the active form of vitamin D, may inhibit colorectal cancer (CRC) progression, which has been mechanistically linked to an attenuation of a pro-inflammatory state. The present study investigated the associations between circulating 25 hydroxy vitamin D3 (25(OH)D3) levels and inflammatory markers (IL10, IL8, IL6, TNFα and hsCRP) in the 2 years following CRC diagnosis. Methods: Circulating 25(OH)D3 levels and inflammatory markers were assessed at diagnosis, after 6, 12 and 24 months from 798 patients with sporadic CRC participating in two prospective cohort studies. Associations between 25(OH)D3 levels and individual inflammatory markers as well as a summary inflammatory z-score were assessed at each time point by multiple linear regression analyses. To assess the association between 25(OH)D3 and inflammatory markers over the course of 2 years, linear mixed model regression analyses were conducted. Results: Higher 25(OH)D3 levels were associated with lower IL6 levels at diagnosis, at 6 months after diagnosis and over the course of 2 years (β −0.06, 95% CI −0.08 to −0.04). In addition, 25(OH)D3 levels were inversely associated with the summary inflammatory z-score at diagnosis and over the course of 2 years (β −0.17, 95% CI −0.25 to −0.08). In addition, a significant inverse association between 25(OH)D3 levels and IL10 was found over the course of 2 years. Intra-individual analyses showed an inverse association between 25(OH)D3 and IL10, IL6 and TNFα. No statistically significant associations between 25(OH)D3 and IL8 and hsCRP levels were observed. Conclusions: Serum 25(OH)D3 levels were inversely associated with the summary inflammatory z-score and in particular with IL6 in the years following CRC diagnosis. This is of potential clinical relevance as IL6 has an important role in chronic inflammation and is also suggested to stimulate cancer progression. Further observational studies should investigate whether a possible 25(OH)D3-associated reduction of inflammatory mediators influences treatment efficacy and CRC recurrence.
Comparative Analysis of Sample Extraction and Library Construction for Shotgun Metagenomics

Human fecal specimens, serve as important materials, are widely used in the field of microbiome research, in which inconsistent results have been a pressing issue. The possible attribute factors have been proposed including the specimen status after preservation, extracted DNA quality, library preparation protocol, and sample DNA input. In this study, quality comparisons for shotgun metagenomics sequencing were performed between 2 DNA extraction methods for fresh and freeze-thaw samples, 2 library preparation protocols, and various sample inputs. The results indicate that Mag-Bind® Universal Metagenomics Kit (OM) outperformed DNeasy PowerSoil Kit (QP) with a higher DNA quantity. Controlling on library preparation protocol, OM detected on-average more genes than QP. For library construction comparison by controlling on the same DNA sample, KAPA Hyper Prep Kit (KH) outperformed the TruePrep DNA Library Prep Kit V2 (TP) with the higher number of detected genes number and Shannon index. No significant differences were found in taxonomy between 2 library preparation protocols using the fresh, freeze-thaw and mock community samples. No significant difference was observed between 250 and 50 ng DNA inputs for library preparation on both fresh and freeze-thaw samples. Through the preliminary study, a combined protocol is recommended for performing metagenomics studies, by using OM method plus KH protocol as well as suitable DNA quantity on either fresh or freeze-thaw samples. Our findings provide clues for potential variations from various DNA extraction methods, library protocols, and sample DNA inputs, which are critical for consistent and comprehensive profiling of the human gut microbiome.
A case of cervical myelopathy following chronic hypertrophic non-union type 2 odontoid fracture managed with posterior C1 decompression and C1-3 instrumentation: Case report and brief review of literature

Background: Type 2 odontoid fractures are the most common type of fracture of the axis. In rare cases, nonunion of a type 2 odontoid fracture can be hypertrophic resulting in myelopathy due to cervical cord compression. Case Description: A 48-year-old male presented with hypertrophic nonunion of a chronic type 2 odontoid fracture resulting in cord compression/myelopathy. This was adequately treated utilizing a C1 decompression and C1-3 instrumented fusion; no anterior procedure was necessary. Conclusion: Here, we successfully treated a patient with a hypertrophic nonunion of a chronic type 2 odontoid fracture utilizing a posterior only approach consisting of a C1 laminectomy with C1-C3 fusion.
Intrasession Reliability of Arterial Spin-Labeled MRI–Measured Noncontrast Perfusion in Glioblastoma at 3 T

Arterial spin-labeled magnetic resonance imaging can provide quantitative perfusion measurements in the brain and can be potentially used to evaluate therapy response assessment in glioblastoma (GBM). The reliability and reproducibility of this method to measure noncontrast perfusion in GBM, however, are lacking. We evaluated the intrasession reliability of brain and tumor perfusion in both healthy volunteers and patients with GBM at 3 T using pseudocontinuous labeling (pCASL) and 3D turbo spin echo (TSE) using Cartesian acquisition with spiral profile reordering (CASPR). Two healthy volunteers at a single time point and 6 newly diagnosed patients with GBM at multiple time points (before, during, and after chemoradiation) underwent scanning (total, 14 sessions). Compared with 3D GraSE, 3D TSE-CASPR generated cerebral blood flow maps with better tumor-to-normal background tissue contrast and reduced image distortions. The intraclass correlation coefficient between the 2 runs of 3D pCASL with TSE-CASPR was consistently high (≥0.90) across all normal-appearing gray matter (NAGM) regions of interest (ROIs), and was particularly high in tumors (0.98 with 95% confidence interval [CI]: 0.97–0.99). The within-subject coefficients of variation were relatively low in all normal-appearing gray matter regions of interest (3.40%–7.12%), and in tumors (4.91%). Noncontrast perfusion measured using 3D pCASL with TSE-CASPR provided robust cerebral blood flow maps in both healthy volunteers and patients with GBM with high intrasession repeatability at 3 T. This approach can be an appropriate noncontrast and noninvasive quantitative perfusion imaging method for longitudinal assessment of therapy response and management of patients with GBM.
Prostate cancer patients can benefit from 5-alpha-reductase inhibitor treatment: a meta-analysis

Background The efficacy and safety of 5α-reductase inhibitors (5ARIs) in treating prostate cancer (PCa) have not been fully determined. We performed a meta-analysis to evaluate the effectiveness and safety of 5ARIs for PCa patients. Methods A comprehensive literature search of online databases was conducted to obtain comparative studies exploring the effectiveness and safety of 5ARIs in treating PCa up to October 2019. Summarized odds ratio s (OR s) or hazard ratio s (HR s) were calculated to compare the outcomes between 5ARI and control groups. Our meta-analysis was registered in PROSPERO under number CRD42018109809. Results A total of 2,277 patients from 10 studies were included. No significant difference was found in prostate-specific antigen progression between two groups (OR = 0.82, 95% CI [0.52–1.29], P = 0.40). However, 5ARI treatment significantly reduced the total progression of PCa (OR = 0.61, 95% CI [0.48–0.77], P < 0.0001), especially for patients with local (OR = 0.56, 95% CI [0.44–0.73], P < 0.00001) and low-Gleason score (≤7) PCa (OR = 0.63, 95% CI [0.48–0.84], P = 0.002). Additionally, 5ARIs also significantly prolonged the progression-free survival time (HR = 0.57, 95% CI [0.34–0.96], P = 0.04) for PCa patients. No significant difference was found in the occurrence of PCa recurrence, metastasis, biopsy reclassification, and side-effects between two groups. Conclusions Our study suggests that 5ARI treatment can benefit patients with local and low Gleason score (≤7) PCa, especially in delaying the disease progression. More studies with larger sample size and comprehensive study design are still needed to verify our outcomes.
Roles of Fungal Volatiles from Perspective of Distinct Lifestyles in Filamentous Fungi

Volatile compounds (VOCs) are not only media for communication within a species but also effective tools for sender to manipulate behavior and physiology of receiver species. Although the influence of VOCs on the interactions among organisms is evident, types of VOCs and specific mechanisms through which VOCs work during such interactions are only beginning to become clear. Here, we review the fungal volatile compounds (FVOCs) and their impacts on different recipient organisms from perspective of distinct lifestyles of the filamentous fungi. Particularly, we discuss the possibility that different lifestyles are intimately associated with an ability to produce a repertoire of FVOCs in fungi. The FVOCs discussed here have been identified and analyzed as relevant signals under a range of experimental settings. However, mechanistic insight into how specific interactions are mediated by such FVOCs at the molecular levels, amidst complex community of microbes and plants, requires further testing. Experimental designs and advanced technologies that attempt to address this question will facilitate our understanding and applications of FVOCs to agriculture and ecosystem management.
Simultaneous determination of phenolic metabolites in Chinese citrus and grape cultivars

Background As the major bioactive compounds in citrus and grape, it is significant to use the contents of flavonoids and phenolic acids as quality evaluation criteria to provide a better view of classifying the quality and understanding the potential health benefits of each fruit variety. Methods A total of 15 varieties of citrus and 12 varieties of grapes were collected from Fujian, China. High-performance liquid chromatography method was used for the simultaneous determination of 17 phenolic compounds, including gallic acid, chlorogenic acid, caffeic acid, syringic acid, ρ-coumaric acid, ferulic acid, benzoic acid, salicylic acid, catechin, epicatechin, resveratrol, rutin, naringin, hesperidin, quercetin, nobiletin and tangeritin in the peels of citrus and grape cultivars. Further, the cultivars of citrus and grape were classified using principal component analysis (PCA) and hierarchical cluster analysis (HCA). Results A thorough separation of the 17 compounds was achieved within 100 min. The tested method exhibited good linearity (the limits of detection and limits of quantification were in the range of 0.03–1.83 µg/mL and 0.09–5.55 µg/mL, respectively), precision (the relative standard deviations of repeatability were 1.02–1.97%), and recovery (92.2–102.82%) for all the compounds, which could be used for the simultaneous determination of phenolic compounds in citrus and grape. Hesperidin (12.93–26,160.98 µg/g DW) and salicylic acid (5.35–751.02 µg/g DW) were the main flavonoids and phenolic acids in 15 citrus varieties, respectively. Besides, the hesperidin (ND to 605.48 µg/g DW) and salicylic acid (ND to 1,461.79 µg/g DW) were found as the highest flavonoid and the most abundant phenolic acid in grapes, respectively. A total of 15 citrus and 12 grape samples were classified into two main groups by PCA and HCA with strong consistency.
Misuse of Tramadol in the United States: An Analysis of the National Survey of Drug Use and Health 2002-2017

Objective: To analyze the rates of misuse - that is, use in any way not directed by a doctor - of products containing oral tramadol, a Schedule IV opioid, from the National Survey of Drug Use and Health (NSDUH), as compared to comparator Schedule II opioids (morphine, oxycodone, and hydrocodone) and alprazolam, a commonly prescribed Schedule IV controlled substance in the U.S. Methods: The NSDUH is a congressionally mandated household survey that collects information on tobacco, alcohol, and drug use, mental health and other health-related issues in the US. A cross-sectional surveillance study design was used to examine lifetime and past year misuse of oral tramadol and comparators of interest among NSHUH respondents aged 12 years or older. Based on when particular data were available, the past-year misuse analysis includes NSDUH data from 2015 to 2017, and the lifetime misuse analysis includes NSDUH data from 2002 to 2014. Results: In 2015 to 2017, past-year misuse of oral tramadol was approximately 4% of the total number of prescriptions, versus 7% to 8% for all of the comparators when adjusted for drug availability. In 2002 to 2014, lifetime misuse of oral tramadol remained at 1.5% or less over the 13-year period, and was lower than reported for hydrocodone (6%) and oxycodone (4%), respectively. Comparison of oral tramadol and alprazolam showed misuse of tramadol was also much lower than alprazolam. Too few reports of tramadol misuse by injection (n = 7) were reported, versus 570, 1096, and 32 reports of injection of morphine, oxycodone, and hydrocodone, respectively, during the 16-year analysis period to allow for any population-based estimation. Only morphine has an intravenous formulation available and tramadol was not available as an intravenous formulation in the U.S. during that time period. Conclusions: This analysis shows a low prevalence of oral tramadol misuse, relative to other commonly prescribed opioids, in a nationally representative sample of noninstitutionalized US residents. Estimates of reported oral tramadol misuse have remained relatively stable over time and are substantially lower than those reported for comparators when adjusted for prescription volume. Reports of oral tramadol misuse are also much less than alprazolam, another Schedule IV drug.
Trametenolic Acid B Triggers HSP90AA4P and Autophagy in HepG2/2.2.15 Cells by Proteomic Analysis

Our previous studies have demonstrated that trametenolic acid B (TAB) extracted from the Laetiporus sulphureus (Fr.) Murrill owned effective anti-proliferation of HepG2/2.215 cells and induced autophagy activity. The present aim was to further investigate its mechanisms involved by proteomic analysis. The iTRAQ of TAB on HepG2/2.215 was carried out and the western blot was used to verify the results of the proteomics analysis. According to the peptide segment quantitative standard (FDR ≤ 1%), a total of 5324 proteins were identified in HepG2/2.215 by proteomic analysis. The results identified that the major up-regulated proteins were HSP90AA4P, MYB, SERPINE1, and down-regulated proteins were Rho C, SERPINA1, and PIK3R4, which were related to PI3K/Akt signaling pathway, cell metastasis, and autophagy. HSP90AA4P and Rho C’s proteomics analysis were further confirmed by the western blot. The proteomic results demonstrated that the anti-hematoma effect of TAB was closely related to the increase of HSP90AA4P protein expressions and autophagy, which may be a critical target of TAB, which was expected to be a candidate drug for the treatment liver cancer.
Bone Crushing in Infected Pseudarthrosis – An Extraordinary Way to Treat Osteomyelitis Caused by Resistant Bacteria

Introduction Osteomyelitis with multiresistant bacteria in non-union following fracture treated with osteosynthesis requires complete removal of infected sequestrum and dead bone. For consecutive bone defects, it is frequently necessary to bridge with a fixator external. The treatment is not only challenging due to reduced bone stock but also characterized by decreased bioavailability of antibiotics. Case Report We report a two-step-surgery approach to preserve the bone stock using autologous cancellous bone in a bacterial infected non-union for subsequently leg length reconstruction. The 24-year-old male patient from Belarus was admitted to our department with persistent wound secretion and subsequent osteomyelitis of the right femur 3 years after initial surgery, several revisions, and several different antibiotic therapies. Biopsy revealed methicillin-resistant and borderline oxacillin-resistant Staphylococcus aureus. Firstly, the Ilizarov ring fixator was removed and a vigorous debridement was performed by refreshing the pseudarthrosis, removing of sequestrum, and dead bone. Finally, an AO fixator external was applied for 10 weeks combined with appropriate antibiotic treatment followed by 5 weeks antibiotic-free window. The bone defect was stabilized by a long gamma trochanteric nail after removal of the AO fixateurexterne. A wide resection of the fragments was performed and the resected bone tissue was crushed and placed adjacent to the nail. Noteworthy, the biopsies of both re-section sides revealed same germs as detected in initial biopsies. Thus, antibiotics were administered for additional 3 months. Frequent radiographic and clinical controls showed a remodeling of the femur during a period of 3 years and no signs of infection. Subsequently, we restored leg length of 4 cm using a fully implantable motorized lengthening nail. In the end, the patient achieved full weight-bearing with unlimited range of motion in hip and knee. No further germ could be revealed in biopsies. Conclusion In this case report, we used autologous bone from the infected side, crushed, and placed it adjacent to an intramedullary nail. Crushed bone tissue might improve bioavailability of antibiotics when dealing with multiresistant bacteria in non-union healed fracture side. Furthermore, this approach was able to provide new bone formation in a limb resulting in full weight-bearing.
Genetic, Antigenic, and Pathogenic Characteristics of Infectious Bronchitis Virus GI-7/TW-II in China

SUMMARY. Nine infectious bronchitis virus (IBV) strains belonging to the GI-7 lineage were isolated between 2009 and 2017 in China. Phylogenetic analysis and comparisons of full-length sequences of the S1 gene suggested that the GI-7 lineage should be further classified as Taiwan (TW)-I and TW-II sublineages, which correspond to the previous TW-I and TW-II genotypes. The nine IBV strains were clustered in the TW-II sublineage. Further investigation revealed that viruses in the TW-I and TW-II were not only genetically but also antigenically different. Moreover, the TW-II sublineage contained various clades and recombinants. A recombinant was found to originate from recombination events between field strains (TW-II ck/CH/LJL/090608- and GI-19 ck/ CH/LDL/091022-like viruses) in which the recombination in the S1 subunit coding sequences had led to changes in antigenicity of the viruses. A more in-depth investigation demonstrated that TW-II viruses appear to have undergone a significant evolution following introduction in mainland China, which resulted in the viruses diverging into different clades. The viruses between the different clades in TW-II sublineage exhibited a significant change in genetic and antigenic characteristics. In addition, the five TW-II viruses selected on the basis of the results of S1 nucleotide sequence phylogenetic trees showed different pathogenicity to specific-pathogen-free chickens, although they could induce nephritis in the infected chickens and thus were identified as nephropathogenic strains.
Isolation and Characterization of Novel Trichomonas gallinae Ribotypes Infecting Domestic and Wild Birds in Riyadh, Saudi Arabia

SUMMARY. Trichomonas gallinae, a single-celled protozoan parasite, is a causative agent of the disease trichomonosis, which is distributed worldwide and has recently been highlighted as a pandemic threat to several wild bird species. The aim of this study was to determine the prevalence and genotypic diversity of T. gallinae in Riyadh, Saudi Arabia. For this purpose, 273 oral swab samples from different bird species (feral pigeon Columba livia, common mynah Acridotheres tristis, chicken Gallus gallus domesticus, turkey Meleagris gallopavo, and ducks Anatidae) were collected and tested for T. gallinae infection with InPouch™ TV culture kits. The results showed that the overall prevalence of T. gallinae in these samples was 26.4% (n = 72). The PCRs were used to detect the internal transcribed spacer (ITS) region of T. gallinae, and the results of the sequence analysis indicated genetic variation. Among 48 sequences, we found 15 different ribotypes, of which 12 were novel. Three had been previously described as ribotypes A, C, and II. To our knowledge, this study demonstrated the presence of T. gallinae strain diversity in Saudi Arabian birds for the first time and revealed that ribotypes A and C are predominant among Riyadh birds.
Chapter 1 Introduction to New Caledonia: geology, geodynamic evolution and mineral resources

Supplementary material: List and content of the GIS files (ESRI format) corresponding to the geological map (Fig. 1.2) and the database structure of Figure 1.3 are available at https://doi.org/10.6084/m9.figshare. c.4984385 New Caledonia is a French overseas territory in the SW Pacific, located in the southern tropical zone between 19 and 24° S. The country consists of several islands that are the emergent parts of two parallel submarine ridges: the Norfolk Ridge to the SW and the Loyalty Ridge to the NE (Fig. 1.1). The total area of the country is 18 350 km2. Grande Terre, the largest and main island, is mountainous, c. 400 km long and c. 50 km wide. The highest points are Mont Panie (1628 m) in the north and Mont Humboldt (1618 m) in the south. Grande Terre is surrounded by a 1500 km long barrier reef complex, the second longest in the world, with parts listed as a UNESCO World Heritage site. By contrast, the Loyalty Islands have a low elevation (127 m maximum height on Mare). As well as Grand Terre and the Loyalty Islands, the New Caledonia archipelago includes the isolated and uninhabited Matthew and Hunter islands to the east and the sandy Chesterfield islets to the west. The New Caledonia Exclusive Economic Zone covers an area of 1 360 000 km2. Fig. 1.1. ( a ) New Caledonia in the SW Pacific. ( b ) New Caledonia archipelago. ( c ) Map of New Caledonia with 1:50 000 scale geological map series (grey rectangle) and index numbers. 1, Iles Belep; 2, Poum–Yande; 3, Paagoumene; 4, Pam-Ouegoa; 5, Pouebo; 6, Koumac, 7, Paimboas; 8, Hienghene; 9, Ouaco-Voh; 10, Goyeta-Pana; 11, 12, Touho-Poindimie; 13, Pouembout; 14, Paeoua; 15, Ponerihouen; 16, Baie Lebris; 17, Poya-Plaine des Gayacs; 18, Me Maoya; 19, Houailou; 20, Kouaoua; 21, Bourail; 22, Moindou; 23, Canala-La …