Miracle-dz/UniFAR-FTUs huggingface dataset:
Overall survival and second primary malignancies in men with metastatic prostate cancer

Background Among prostate cancer (PC) patients, over 90% of distant metastases occur in the bone. PC treatments may be associated with side effects, including second primary malignancies (SPM). There is limited information on the incidence of SPM among men with bone metastatic PC (mPC) and among men with bone metastatic castration-resistant PC (mCRPC). We estimated overall survival and the incidence of SPM in men with mPC and mCRPC. Methods In the Prostate Cancer data Base Sweden, the National Prostate Cancer Register was linked to other national health care registers, 15,953 men with mPC in 1999–2011 were identified. Further, 693 men with mCRPC were identified. Outcomes were evaluated using stratified incidence rates, Kaplan-Meier estimators and Cox models. Results The mean age among men with mPC was 73.9 years and in men with mCRPC 70.0 years. The median respective survivals were 1.5 (13,965 deaths) and 1.14 years (599 deaths), and average times since PC diagnosis 1.8 and 4.7 years. We observed 2,669 SPMs in men with mPC and 100 SPMs in men with mCRPC. The incidence rate of SPM per 1,000 person-years was 81.8 (78.8–85.0) for mPC and 115.6 (95.1–140.7) for mCRPC. High age, prior neoplasms, urinary tract infection, congestive heart failure, diabetes and renal disease were most strongly associated with increased mortality risk. Prior neoplasms and prior use of antineoplastic agents were most strongly associated with increased SPM risk. Several factors associated with increased mortality and SPM risks were more prevalent in the mCRPC cohort. Conclusions Our results on mortality for men with mPC and mCRPC are in line with previous studies from the same time period. Investigation of factors associated with mortality and SPM in men with mPC and mCRPC can help to further understand these outcomes in the era prior to several new treatments have come available.
Freedom of Information (FOI) as a data collection tool for social scientists

This paper evaluates a method of generating a unique dataset that has been underused—a Freedom of Information (FOI) request. The UK’s FOI Act came into force in 2005, allowing the public to make requests of publicly held data. We set out to understand the determinants of the quality responses to FOI requests. We also explain how requests can be made and provide suggestions to construct effective data-driven requests. We applied for data on hate crime from all police forces and on uptake of maternity leave from all universities. We find that observable characteristics of the local area, police force and universities neither determine whether the request was fulfilled, nor the speed of response, suggesting that the data from these FOI requests are representative of the institutions from which they were requested.
2α-Hydroxyeudesma-4,11(13)-Dien-8β,12-Olide Isolated from Inula britannica Induces Apoptosis in Diffuse Large B-cell Lymphoma Cells

2α-Hydroxyeudesma-4,11(13)-dien-8β,12-olide (HEDO), a eudesmane-type sesquiterpene lactone belonging to large group of plant terpenoids isolated from Inula britannica, displays cytotoxic activity against diffuse large B cell lymphoma cells in vitro. However, the molecular mechanism of the anticancer effect remains unclear. In this study, we showed that HEDO inhibits cell growth by inducing apoptosis in lymphoma cell lines through its antiproliferative activity. HEDO increases the depolarization of mitochondrial membrane potential and upregulated intracellular reactive oxygen species (ROS). Furthermore, we examined the cell cycle effect, and our results provided evidence that the arrest of the cell cycle at the SubG0/G1 phase plays an important role in the ability of HEDO to inhibit cell growth in Ontario Cancer Institute (OCI)-LY3 lymphoma cells by preventing nuclear factor-kappa B (NF-κB) signaling. In addition, HEDO induced apoptosis by instigating the activation of Bcl-2-associated X (BAX) and cleaved caspase-3, decreasing B-cell lymphoma 2 (BCL2), B-cell lymphoma-extra large (BCL-XL), and procaspase 3 expression levels. Based on these findings, we suggest that HEDO has potential as an anticancer drug of lymphoma by inducing ROS-dependent accumulation of SubG0/G1 arrest and apoptosis in OCI-LY3 cells.
Genetic associations between serum low LDL-cholesterol levels and variants in LDLR, APOB, PCSK9 and LDLRAP1 in African populations

Non-communicable diseases, including cardiovascular diseases (CVDs), are increasing in African populations. High serum low density lipoprotein cholesterol (LDL-cholesterol) levels are a known risk factor for CVDs in European populations, but the link remains poorly understood among Africans. This study investigated the associations between serum LDL-cholesterol levels and selected variants in the low density lipoprotein receptor (LDLR), apolipoprotein B (APOB), proprotein convertase subtilisin/kexin type 9 (PCSK9) and low density lipoprotein receptor adaptor protein 1 (LDLRAP1) genes in some selected African populations. Nineteen SNPs were selected from publicly available African whole genome sequence data based on functional prediction and allele frequency. SNPs were genotyped in 1000 participants from the AWI-Gen, study selected from the extremes of LDL-cholesterol level distribution (500 with LDL-cholesterol>3.5 mmol/L and 500 with LDL-cholesterol<1.1 mmol/L). The minor alleles at five of the six associated SNPs were significantly associated (P<0.05) with lower LDL-cholesterol levels: LDLRAP1 rs12071264 (OR 0.56, 95% CI: 0.39–0.75, P = 2.73x10-4) and rs35910270 (OR 0.78, 95% CI: 0.64–0.94, P = 0.008); APOB rs6752026 (OR 0. 55, 95% CI: 0.41–0.72, P = 2.82x10-5); LDLR: rs72568855 (OR 0.47, 95% CI: 0.27–0.82, P = 0.008); and PCSK9 rs45613943 (OR = 0.72, 95% CI: 0.58–0.88, P = 0.001). The minor allele of the sixth variant was associated with higher LDL-cholesterol levels: APOB rs679899 (OR 1.41, 95% CI: 1.06–1.86, P = 0.016). A replication analysis in the Africa America Diabetes Mellitus (AADM) study found the PCSK9 variant to be significantly associated with low LDL-cholesterol levels (Beta = -0.10). Since Africans generally have lower LDL-cholesterol levels, these LDL-cholesterol associated variants may be involved in adaptation due to unique gene-environment interactions. In conclusion, using a limited number of potentially functional variants in four genes, we identified significant associations with lower LDL-cholesterol levels in sub-Saharan Africans.
High-Precision Acceleration Measurement System Based on Tunnel Magneto-Resistance Effect †

A high-precision acceleration measurement system based on an ultra-sensitive tunnel magneto-resistance (TMR) sensor is presented in this paper. A “force–magnetic–electric” coupling structure that converts an input acceleration into a change in magnetic field around the TMR sensor is designed. In such a structure, a micro-cantilever is integrated with a magnetic field source on its tip. Under an acceleration, the mechanical displacement of the cantilever causes a change in the spatial magnetic field sensed by the TMR sensor. The TMR sensor is constructed with a Wheatstone bridge structure to achieve an enhanced sensitivity. Meanwhile, a low-noise differential circuit is developed for the proposed system to further improve the precision of the measured acceleration. The experimental results show that the micro-system achieves a measurement resolution of 19 μg/√Hz at 1 Hz, a scale factor of 191 mV/g within a range of ± 2 g, and a bias instability of 38 μg (Allan variance). The noise sources of the proposed system are thoroughly investigated, which shows that low-frequency 1/f noise is the dominant noise source. We propose to use a high-frequency modulation technique to suppress the 1/f noise effectively. Measurement results show that the 1/f noise is suppressed about 8.6-fold at 1 Hz and the proposed system resolution can be improved to 2.2 μg/√Hz theoretically with this high-frequency modulation technique.
Deconvolution of RNA-Seq Analysis of Hyperbaric Oxygen-Treated Mice Lungs Reveals Mesenchymal Cell Subtype Changes

Hyperbaric oxygen (HBO) is widely applied to treat several hypoxia-related diseases. Previous studies have focused on the immediate effect of HBO-exposure induced oxidative stress on the lungs, but knowledge regarding the chronic effects from repetitive HBO exposure is limited, especially at the gene expression level. We found that repetitive HBO exposure did not alter the morphology of murine lungs. However, by deconvolution of RNA-seq from those mice lungs using CIBERSORTx and the expression profile matrices of 8 mesenchymal cell subtypes obtained from bleomycin-treated mouse lungs, we identify several mesenchymal cell subtype changes. These include increases in Col13a1 matrix fibroblasts, mesenchymal progenitors and mesothelial cell populations and decreases in lipofibroblasts, endothelial and Pdgfrb high cell populations. Our data suggest that repetitive HBO exposure may affect biological processes in the lungs such as response to wounding, extracellular matrix, vasculature development and immune response.
Mural Cell SDF1 Signaling is Associated with the Pathogenesis of Pulmonary Arterial Hypertension.

BACKGROUND Pulmonary artery smooth muscle cells (PASMCs) and pericytes are NG2+ mural cells that provide structural support to pulmonary arteries and capillaries. In pulmonary arterial hypertension (PAH), both mural cell types contribute to PA muscularization but whether similar mechanisms are responsible for their behavior is unknown. METHODS RNA-Seq was used to compare the gene profile of pericytes and PASMCs from PAH and healthy lungs. NG2-Cre-ER mice were used to generate NG2-selective reporter mice (NG2tdT) for cell lineage identification and tamoxifen-inducible mice for NG2-selective SDF1 knockout (SDF1NG2-KO). RESULTS Hierarchical clustering of RNA-seq data demonstrated that the genetic profile of PAH pericytes and PASMCs is highly similar. Cellular lineage staining studies on NG2tdT mice in chronic hypoxia showed that similar to PAH, tdT+ cells accumulate in muscularized microvessels and demonstrate significant upregulation of SDF1, a chemokine involved in chemotaxis and angiogenesis. Compared to controls, SDF1NG2-KO mice in chronic hypoxia had reduced muscularization and lower abundance of NG2+ cells around microvessels. SDF1 stimulation in healthy pericytes induced greater contractility and impaired their capacity to establish endothelial-pericyte communications. In contrast, SDF1 knockdown reduced PAH pericyte contractility and improved their capacity to associate with vascular tubes in co-culture. CONCLUSION SDF1 is upregulated in NG2+ mural cells and is associated with PA muscularization. Targeting SDF1 could help prevent and/or reverse muscularization in PAH.
The effect of adjuvant therapy for patients with intrahepatic cholangiocarcinoma after surgical resection: A systematic review and meta-analysis

Backgroud Resection is still the only potentially curative treatment for patients with intrahepatic cholangiocarcinoma (ICC), but the prognosis remains far from satisfactory. However, the benefit of adjuvant therapy (AT) remains controversial, although it has been conducted prevalently. Hence, a meta-analysis was warranted to evaluate the effect of AT for patients with ICC after resection. Patients and methods PubMed, MedLine, Embase, the Cochrane Library, Web of Science were used to identify potentially eligible studies from Jan.1st 1990 to Aug. 31st 2019, investigating the effect of AT for patients with ICC after resection. Primary endpoint was overall survival (OS), and secondary endpoints was recurrence-free survival (RFS). Hazard ratio (HR) with 95% confidence interval (CI) was used to determine the effect size. Results 22 studies with 10181 patients were enrolled in this meta-analysis, including 832 patients in the chemotherapy group, 309 patients in the transarterial chemoembolization (TACE) group, 1192 patients in the radiotherapy group, 235 patients in the chemoradiotherapy group, and 6424 patients in the non-AT group. The pooled HR for the OS rate and RFS rate in the AT group were 0.63 (95%CI 0.52~0.74), 0.74 (95%CI 0.58~0.90), compared with the non-AT group. Subgroup analysis showed that the pooled HR for the OS rate in the AT group compared with non-AT group were as follows: chemotherapy group was 0.57 (95%CI = 0.44~0.70), TACE group was 0.56 (95%CI = 0.31~0.82), radiotherapy group was 0.71 (95%CI = 0.39~1.03), chemoradiotherapy group was 0.73 (95%CI = 0.57~0.89), positive resection margin group was 0.60 (95%CI = 0.51~0.69), and lymph node metastasis (LNM) group was 0.67 (95%CI = 0.57~0.76). Conclusion With the current data, we concluded that AT such as chemotherapy, TACE and chemoradiotherapy could benefit patients with ICC after resection, especially those with positive resection margin and LNM, but the conclusion needed to be furtherly confirmed.
Analysis of EPI phase correction with low flip‐angle excitation to reduce the required minimum TE: Application to whole‐brain, submillimeter‐resolution fMRI at 3 T

Echo planar imaging is used widely for its imaging speed. However, its applications often suffer from ghost artifacts. In the community, an approach using three navigator echoes is used commonly for the artifact correction. Although this scheme is effective, as the matrix size increases for high‐resolution imaging, the navigator echoes can contribute significantly to increasing the “required minimum TE. ” To overcome this issue, this work proposes the use of an alternative navigator echo scheme called the “TR‐external” scheme.
Structures of Mycobacterium tuberculosis Penicillin-Binding Protein 3 in Complex with Five β-Lactam Antibiotics Reveal Mechanism of Inactivation

Because of β-lactamase–mediated resistance, β-lactam antibiotics were long considered ineffective drugs for tuberculosis (TB) treatment. However, some β-lactams, including meropenem and faropenem, are being re-evaluated in patients infected with TB. Penicillin-binding protein (PBP) 3, or ftsI, is an essential transpeptidase in Mycobacterium tuberculosis (Mtb) required for cell division, and thus it is an important drug target. Structures of apo MtbPBP3 and of complexes with five β-lactams, including meropenem and faropenem, reveal how they cause inactivation via formation of hydrolytically stable acyl-enzyme complexes. The structures reveal unique features of the antibiotic interactions, both in terms of differences in their binding to MtbPBP3 and in comparison with structures of other PBPs and serine β-lactamases, including the tautomerization status of the carbapenem-derived acyl-enzyme complexes. The results suggest that rather than hoping PBP inhibitors developed for other infections will work against TB, work should focus on developing PBP inhibitors specialized for treating TB. SIGNIFICANCE STATEMENT The structures of Mycobacterium tuberculosis penicillin-binding protein 3, an essential protein in M. tuberculosis, in complex with a number of widely used β-lactam antibiotics (e.g., meropenem, aztreonam, and amoxicillin) were solved. These data provide new insights for next-generation rational approaches to design tuberculosis (TB)-specific β-lactam or nonlactam antibiotics. This manuscript is a seminal article in the field of anti-TB drug discovery and suitable for the broad readership.
How Different Substitution Positions of F, Cl Atoms in Benzene Ring of 5-Methylpyrimidine Pyridine Derivatives Affect the Inhibition Ability of EGFRL858R/T790M/C797S Inhibitors: A Molecular Dynamics Simulation Study

Lung cancer is the most frequent cause of cancer-related deaths worldwide, and mutations in the kinase domain of the epidermal growth factor receptor (EGFR) are a common cause of non-small-cell lung cancers, which is a major subtype of lung cancers. Recently, a series of 5-methylpyrimidine-pyridinone derivatives have been designed and synthesized as novel selective inhibitors of EGFR and EGFR mutants. However, the binding-based inhibition mechanism has not yet been determined. In this study, we carried out molecular dynamic simulations and free-energy calculations for EGFR derivatives to fill this gap. Based on the investigation, the three factors that influence the inhibitory effect of inhibitors are as follows: (1) The substitution site of the Cl atom is the main factor influencing the activity through steric effect; (2) The secondary factors are repulsion between the F atom (present in the inhibitor) and Glu762, and the blocking effect of Lys745 on the phenyl ring of the inhibitor. (3) The two factors function synergistically to influence the inhibitory capacity of the inhibitor. The theoretical results of this study can provide further insights that will aid the design of oncogenic EGFR inhibitors with high selectivity.
Arabidopsis KETCH1 Is Critical for the Nuclear Accumulation of Ribosomal Proteins and Gametogenesis

Arabidopsis KETCH1, an importin β, promotes the nuclear accumulation of ribosomal proteins and contributes to both male and female gametogenesis, likely by maintaining translational efficiency. Male and female gametophytes are generated from micro- or megaspore mother cells through consecutive meiotic and mitotic cell divisions. Defects in these divisions often result in gametophytic lethality. Gametophytic lethality was also reported when genes encoding ribosome-related proteins were mutated. Although numerous ribosomal proteins (RPs) have been identified in plants based on homology with their yeast and metazoan counterparts, how RPs are regulated, e.g., through dynamic subcellular targeting, is unknown. We report here that an Arabidopsis (Arabidopsis thaliana) importin β, KETCH1 (karyopherin enabling the transport of the cytoplasmic HYL1), is critical for gametogenesis. Karyopherins are molecular chaperones mediating nucleocytoplasmic protein transport. However, the role of KETCH1 during gametogenesis is independent of HYPONASTIC LEAVES 1 (HYL1), a previously reported KETCH1 cargo. Instead, KETCH1 interacts with several RPs and is critical for the nuclear accumulation of RPL27a, whose mutations caused similar gametophytic defects. We further showed that knocking down KETCH1 caused reduced ribosome biogenesis and translational capacity, which may trigger the arrest of mitotic cell cycle progression and lead to gametophytic lethality.
Risk factors and spatial relative risk assessment for influenza A virus in poultry and swine in backyard production systems of central Chile

Abstract Backyard production systems (BPS) are a common form of poultry and swine production worldwide. The limited implementation of biosecurity standards in these operations makes BPS a potential source for the emergence of pathogens that have an impact on both animal and public health. Information regarding circulation of influenza A virus (IAV) in poultry and swine raised in BPS is scarce; particularly in South American countries. The objective of this study was to estimate prevalence and seroprevalence of IAV in BPS in central Chile, identify subtype diversity, evaluate risk factors and spatial relative risk for IAV. Samples were collected from 329 BPS from central Chile. Seroprevalence at BPS level was 34.7% (95% CI: 23.1%–46.2%), 19.7% (95% CI: 9.9%–30.6%) and 11.7% (95% CI: 7.2%–16.4%), whereas prevalence at BPS level was 4.2% (95% CI: 0.0%–8.8%), 8.2% (95% CI: 0.8%–14.0%) and 9.2% (95% CI: 4.8%–13.1%), for the Metropolitan, Valparaiso and LGB O’Higgins regions, respectively. Spatial analysis revealed that central‐western area of Metropolitan region and the southern province of Valparaiso region could be considered as high‐risk areas for IAV (spatial relative risk = 2.2, p < .05). Logistic regression models identified the practice of breeding both poultry and pigs at the BPS as a risk factor (95% CI 1.06–3.75). From 75 IAV ELISA‐positive sera, 20 chicken sera had haemagglutination inhibition titres ranging from 20 to 160, and of these, 11 had microneutralization titres ranging from 40 to 960 for one or more IAV subtypes. Identified subtypes were H1, H3, H4, H9, H10 and H12. Results from this study highlight the need for further IAV surveillance programmes in BPS in Chile. Early detection of IAV strains circulating in backyard animals, especially in regions with large human populations, could have an enormous impact on animal and public health.
Investigation of the Interaction Mechanism of Perfluoroalkyl Carboxylic Acids with Human Serum Albumin by Spectroscopic Methods

Perfluoroalkyl carboxylic acids (PFCAs) are some of the most significant pollutants in human serum, and are reported to be potentially toxic to humans. In this study, the binding mechanism of PFCAs with different carbon lengths to human serum albumin (HSA) was studied at the molecular level by means of fluorescence spectroscopy under simulated physiological conditions and molecular modeling. Fluorescence data indicate that PFCAs with a longer carbon chain have a stronger fluorescence quenching ability. Perfluorobutanoic acid (PFBA) and perfluorohexanoic acid (PFHxA) had little effect on HSA. Fluorescence quenching of HSA by perfluorooctanoic acid (PFOA) and perfluorodecanoic acid (PFDA) was a static process that formed a PFCA–HSA complex. Electrostatic interactions were the main intermolecular forces between PFOA and HSA, while hydrogen bonding and van der Waals interactions played important roles in the combination of PFDA and HSA. In fact, the binding of PFDA to HSA was stronger than that of PFOA as supported by fluorescence quenching and molecular docking. In addition, infrared spectroscopy demonstrated that the binding of PFOA/PFDA resulted in a sharp decrease in the β-sheet and α-helix conformations of HSA. Our results indicated that the carbon chain length of PFCAs had a great impact on its binding affinity, and that PFCAs with longer carbon chains bound more strongly.
Cancer Patients and Anxiety: A Gender Perspective

The complexity of the diagnosis and treatment of cancer means that it is often associated with anxiety symptoms. The aim of our study was to further our understanding of the oncological process and the presence of anxiety symptoms, from a gender perspective. A cross-sectional study was performed, examining 402 medical records obtained by simple random sampling of oncology patients at a hospital in northern Spain from July 2012 to July 2014. Data collection took place between February and May 2015. Psychiatric and sociodemographic variables were gathered, as well as pain variables and information regarding the oncological process. The data analysis included a descriptive univariate analysis and a bivariate analysis, and a logistic regression model was performed. Our results suggest that women with cancer suffer more anxiety symptoms than men with cancer. Women with anxiety symptoms represented 76.5% of all patients with anxiety. The OR of suffering anxiety symptoms between women and men was 2.43 (95% CI 1.05–5.63) (p = 0.04). A greater incidence of anxiety symptoms was found in patients with cancer pain and oncological treatment with biological therapy. Our results suggest that the gender perspective is necessary in the management of mental health in patients with cancer. Nonetheless, further studies are necessary to confirm our findings.