Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cancers-Specific Survival of Metastatic Pulmonary Carcinoids and Sites of Distant Metastasis: A Population-Based Study

Background: Lung cancer is the leading cause of cancer-related deaths and pulmonary carcinoids (PCs) account for almost 2% of all pulmonary malignancies. However, few published articles have reported prognosis and related factors of pulmonary carcinoid patients. Material and Method: The Surveillance, Epidemiology, and End Results (SEER) database was used to collect data of patients diagnosed with metastatic PCs from 2010 to 2016. The prognosis and survival of these patients were compared by employing Cox proportional hazards and the Kaplan-Meier survival analysis. Results: A total of 1763 patients were analyzed. The liver (668, 25.6%) was shown to be the most common metastatic site in the isolated organ metastasis cohort, followed by the lung (636, 24.4%), bone (562, 21.6%), and brain (460, 17.6%). Among the patients, the tumor metastasized to a single distant site included the liver, bone, lung, and brain. Cancer-specific survival (CSS) in metastatic PCs is determined by the site of metastasis and the total number of such sites. Pulmonary carcinoid patients with isolated liver metastasis manifested more favorable survival rates in comparison to patients having isolated metastasis in the lung, brain, or bone. The median CSS was 45, 7, 6, 5 months (P = 0.011). The number of distant metastatic sites and the location of distant metastasis were found to be independent risk factors for CSS. For patients with distant isolated metastasis, liver metastasis (P < 0.0001) had better CSS in comparison to those with bone metastasis. When compared to patients whose carcinoids had metastasized to the bones, patients with a brain (P = 0.273) or lung (P = 0.483) metastasis had the same CSS. Conclusion: Cancer-specific survival in metastatic PCs depends on the site of metastasis and the total number of such locations. PC patients with isolated liver metastasis manifested more favorable survival in comparison to patients with isolated metastasis in the lung, brain, or bone.
Safety and tolerability of a natural supplement containing glucosinolates, phytosterols and citrus flavonoids in adult women: a randomized phase I, placebo-controlled, multi-arm, double-blinded clinical trial

Abstract Objective To evaluate the safety and tolerability of an oral herbal supplement containing glucosinolates, phytosterols, and citrus flavonoids (Warmi®, Lima Perú;) in otherwise healthy adult women. Methods This was a phase-I, randomized parallel three arms, double-blinded, and a placebo-controlled clinical trial. A total of 55 participants aged 18-40 were randomly assigned to one of three groups to receive for three months: (1) an oral herbal supplement of 1650 mg/day; (2) an oral herbal supplement of 3300 mg/day; or (3) an oral placebo 3300 mg/day. The primary endpoints were oral safety and tolerability of the supplement. The secondary endpoint was its effect on vital functions, anthropometrics, and laboratory tests. We used an exploratory approach by covariance analysis (ANCOVA) adjusted for the variables’ baseline value for the secondary outcomes. Results All women completed three months of follow-up, reporting no side effects. Our exploratory analysis revealed that treatment with the herbal supplement of 1650 mg/day was associated with increased glucose and uric acid levels. In comparison, the herbal supplement 3300 mg/day was associated with reduced breathing rate, increased basal temperature, and systolic blood pressure, both compared to the placebo group. However, despite significant differences, none of these was clinically significant. Conclusion The oral herbal supplement had a favorable safety and tolerability profile in studied women. There is a need to study its potential as an option to treat menopausal symptoms.
Identification of the Biosynthetic Gene Cluster for the Organoarsenical Antibiotic Arsinothricin

Antimicrobial resistance is an emerging global public health crisis, calling for urgent development of novel potent antibiotics. We propose that arsinothricin and related arsenic-containing compounds may be the progenitors of a new class of antibiotics to extend our antibiotic era. ABSTRACT The soil bacterium Burkholderia gladioli GSRB05 produces the natural compound arsinothricin [2-amino-4-(hydroxymethylarsinoyl) butanoate] (AST), which has been demonstrated to be a broad-spectrum antibiotic. To identify the genes responsible for AST biosynthesis, a draft genome sequence of B. gladioli GSRB05 was constructed. Three genes, arsQML, in an arsenic resistance operon were found to be a biosynthetic gene cluster responsible for synthesis of AST and its precursor, hydroxyarsinothricin [2-amino-4-(dihydroxyarsinoyl) butanoate] (AST-OH). The arsL gene product is a noncanonical radical S-adenosylmethionine (SAM) enzyme that is predicted to transfer the 3-amino-3-carboxypropyl (ACP) group from SAM to the arsenic atom in inorganic arsenite, forming AST-OH, which is methylated by the arsM gene product, a SAM methyltransferase, to produce AST. Finally, the arsQ gene product is an efflux permease that extrudes AST from the cells, a common final step in antibiotic-producing bacteria. Elucidation of the biosynthetic gene cluster for this novel arsenic-containing antibiotic adds an important new tool for continuation of the antibiotic era. IMPORTANCE Antimicrobial resistance is an emerging global public health crisis, calling for urgent development of novel potent antibiotics. We propose that arsinothricin and related arsenic-containing compounds may be the progenitors of a new class of antibiotics to extend our antibiotic era. Here, we report identification of the biosynthetic gene cluster for arsinothricin and demonstrate that only three genes, two of which are novel, are required for the biosynthesis and transport of arsinothricin, in contrast to the phosphonate counterpart, phosphinothricin, which requires over 20 genes. Our discoveries will provide insight for the development of more effective organoarsenical antibiotics and illustrate the previously unknown complexity of the arsenic biogeochemical cycle, as well as bring new perspective to environmental arsenic biochemistry.
Effects of vitamin D administration on nociception and spinal cord pro-oxidant and antioxidant markers in a rat model of neuropathic pain

Reactive oxygen species (ROS) are involved in neuropathic pain, a complicated condition after nerve tissue lesion. Vitamin D appears to improve symptoms of pain and exhibits antioxidant properties. We investigated the effects of oral administration of vitamin D3, the active form of vitamin D, on nociception, the sciatic functional index (SFI), and spinal cord pro-oxidant and antioxidant markers in rats with chronic constriction injury (CCI) of the sciatic nerve, a model of neuropathic pain. Vitamin D3 (500 IU/kg per day) attenuated the CCI-induced decrease in mechanical withdrawal threshold and thermal withdrawal latency (indicators of antinociception) and SFI. The vitamin prevented increased lipid hydroperoxide levels in injured sciatic nerve without change to total antioxidant capacity (TAC). Vitamin D3 prevented increased lipid hydroperoxide, superoxide anion generation (SAG), and hydrogen peroxide (H2O2) levels in the spinal cord, which were found in rats without treatment at 7 and 28 days post-CCI. A significant negative correlation was found between mechanical threshold and SAG and between mechanical threshold and H2O2 at day 7. Vitamin D3 also prevented decreased spinal cord total thiols content. There was an increase in TAC in the spinal cord of vitamin-treated CCI rats, compared to CCI rats without treatment only at 28 days. No significant changes were found in body weight and blood parameters of hepatic and renal function. These findings demonstrated, for first time, that vitamin D modulated pro-oxidant and antioxidant markers in the spinal cord. Since antinociception occurred in parallel with oxidative changes in the spinal cord, the oxidative changes may have contributed to vitamin D-induced antinociception.
Social dysfunction is transdiagnostically associated with default mode network dysconnectivity in schizophrenia and Alzheimer’s disease

Abstract Objectives Social dysfunction is one of the most common signs of major neuropsychiatric disorders. The Default Mode Network (DMN) is crucially implicated in both psychopathology and social dysfunction, although the transdiagnostic properties of social dysfunction remains unknown. As part of the pan-European PRISM (Psychiatric Ratings using Intermediate Stratified Markers) project, we explored cross-disorder impact of social dysfunction on DMN connectivity. Methods We studied DMN intrinsic functional connectivity in relation to social dysfunction by applying Independent Component Analysis and Dual Regression on resting-state fMRI data, among schizophrenia (SZ; N = 48), Alzheimer disease (AD; N = 47) patients and healthy controls (HC; N = 55). Social dysfunction was operationalised via the Social Functioning Scale (SFS) and De Jong-Gierveld Loneliness Scale (LON). Results Both SFS and LON were independently associated with diminished DMN connectional integrity within rostromedial prefrontal DMN subterritories (pcorrected range = 0.02–0.04). The combined effect of these indicators (Mean.SFS + LON) on diminished DMN connectivity was even more pronounced (both spatially and statistically), independent of diagnostic status, and not confounded by key clinical or sociodemographic effects, comprising large sections of rostromedial and dorsomedial prefrontal cortex (pcorrected =0.01). Conclusions These findings pinpoint DMN connectional alterations as putative transdiagnostic endophenotypes for social dysfunction and could aid personalised care initiatives grounded in social behaviour.
Layer dependent magnetism and topology in monolayer and bilayers ReX 3 (X = Br, I)

The realization of robust intrinsic ferromagnetism in two-dimensional materials with the possibility to support topologically non-trivial states has provided the fertile ground for novel physics and next-generation spintronics and quantum computing applications. In this contribution, we investigated the formation of topological states and magnetism in monolayer and bilayer systems of ReX 3 (X = Br, I), with PBE, ACBN0 (self-consistent Hubbard-U), excluding/including van der Waals (vdW) corrections and/or spin–orbit coupling. Bulk ReX 3 (X = Br, I) is predicted to crystallize in space group R3¯ (#148), similar to CrI3, with monolayer exfoliation energies that are comparable or less than that of graphite. The topological character of the monolayer and bilayer systems of ReX 3 (X = Br, I) is derived from anomalous Hall conductivity computations. Topologically non-trivial states in ReX 3 (X = Br, I) are absent in the Hubbard-U computations if vdW interactions are included, a prediction that is attributed to the large Hubbard-U difference between the chemical constituents, ΔU ∼ 1.5–1.6 eV, and a significant ∼2.0%–3.6% compressive in-plane strain introduced by vdW interactions. In contrast to the fragile and likely absent topological states in ReX 3 (X = Br, I), magnetic properties are robust and independent of the level of theory: ferromagnetic monolayers are coupled antiferromagnetically to bilayers, with an energy separation between ferromagnetic and antiferromagnetic bilayer spin configurations that could be as low as 0.02 meV/Re (f = 4.8 GHz), well within the microwave range. This suggests that layer dependent magnetism in ReX 3 (X = Br, I) may support a microwave controllable magnetic qubit, consisting of a superposition of antiferromagnetic and ferromagnetic bilayer states.
The Effect of Online Low-intensity Exercise Training on Fitness and Cardiovascular Parameters

Abstract Online exercise is undoubtedly useful and important; however, chronic adaptations to online exercise, particularly strength gain, muscle hypertrophy, and cardiovascular parameters, remain unclear. We investigated the effect of online exercise training using Zoom on fitness parameters compared with the same exercises supervised directly. In the present study, 34 subjects (age: 42.9±14.4 years) were included. Twenty-three subjects performed 8 weeks of body mass-based exercise training online using Zoom, and eleven subjects performed the same exercise supervised directly as the control group. The subjects performed low-load resistance exercises twice a week for 8 weeks for a total of 16 sessions. The sessions included 9 exercises: leg raises, squats, rear raises, shoulder presses, rowing, dips, lunges, Romanian dead lifts, and push-ups. Chair-stand, push-up, and sit-and-reach tests were performed on all subjects. Overall, the home exercise program effectively increased strength and muscle mass and decreased blood pressure and arterial stiffness, but there were no differences between the groups. Changes in chair-stand and sit-and-reach test results were higher in the control group than in the online group. Our results show that there is a similar training response to body mass-based training in both groups, even with virtual experiences using Zoom.
Formation and growth of atmospheric nanoparticles in the eastern Mediterranean: results from long-term measurements and process simulations

Abstract. Atmospheric new particle formation (NPF) is a common phenomenon all over the world. In this study we present the longest time series of NPF records in the eastern Mediterranean region by analyzing 10 years of aerosol number size distribution data obtained with a mobility particle sizer. The measurements were performed at the Finokalia environmental research station on Crete, Greece, during the period June 2008–June 2018. We found that NPF took place on 27 % of the available days, undefined days were 23 % and non-event days 50 %. NPF is more frequent in April and May probably due to the terrestrial biogenic activity and is less frequent in August. Throughout the period under study, nucleation was observed also during the night. Nucleation mode particles had the highest concentration in winter and early spring, mainly because of the minimum sinks, and their average contribution to the total particle number concentration was 8 %. Nucleation mode particle concentrations were low outside periods of active NPF and growth, so there are hardly any other local sources of sub-25 nm particles. Additional atmospheric ion size distribution data simultaneously collected for more than 2 years were also analyzed. Classification of NPF events based on ion spectrometer measurements differed from the corresponding classification based on a mobility spectrometer, possibly indicating a different representation of local and regional NPF events between these two measurement data sets. We used the MALTE-Box model for simulating a case study of NPF in the eastern Mediterranean region. Monoterpenes contributing to NPF can explain a large fraction of the observed NPF events according to our model simulations. However the adjusted parameterization resulting from our sensitivity tests was significantly different from the initial one that had been determined for the boreal environment.
Prognostic Analysis of Primary Pulmonary Malignant Mesenchymal Tumors Treated Surgically

Background Primary pulmonary malignant mesenchymal tumors are rare, constituting only 0.4% of all lung cancers. Since sarcomas are chemo/radio-resistant, surgical resection is the optimal treatment choice for patients with suitable medical conditions and tumor stage. In the present study, we analyzed the surgical outcomes and survival of primary pulmonary malignant mesenchymal tumors treated surgically. Methods We retrospectively examined the records of patients with primary pulmonary malignant mesenchymal tumors who underwent surgical resection at our department between January 2010 and December 2020. Patient data were analyzed according to age, sex, tumor grade and stage, resection completeness, surgical type, and tumor histopathology. Results Twenty patients were included in the study. There were 13 men (65%) and 7 women (35%). The median survival rate was 36 months (range, 19–53 months), and the 5-year overall survival rate was 37%. Unfavorable prognostic factors for overall survival included parietal pleural invasion (p=0.02), high tumor grade (p=0.02), advanced tumor stage (p=0.02), and extensive parenchymal resection (pneumonectomy and bilobectomy, p=0.01). The median length of disease-free survival was 31 months (interquartile range, 21–41 months), and the 5-year disease-free survival rate was 32%. The most unfavorable prognostic factors for recurrence were parietal pleural invasion (p=0.02), high tumor grade (p=0.01), and tumors requiring lung resection with chest wall resection (p=0.02). Conclusion Primary malignant mesenchymal lung tumors are aggressive and have a high mortality rate. However, acceptable overall and disease-free survival rates can be obtained with surgical therapy.
Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants.

In nature, single-strand breaks (SSBs) in DNA occur more frequently (by orders of magnitude) than double-strand breaks (DSBs). SSBs induced by the CRISPR/Cas9 nickase at a distance of 50 to 100 bp on opposite strands are highly mutagenic, leading to insertions/deletions (InDels), with insertions mainly occurring as direct tandem duplications. As short tandem repeats are overrepresented in plant genomes, this mechanism seems to be important for genome evolution. We investigated the distance at which paired 5' overhanging SSBs are mutagenic and which DNA repair pathways are essential for insertion formation in Arabidopsis thaliana. We were able to detect InDel formation up to a distance of 250 bp, although with much reduced efficiency. Surprisingly, the loss of the classical non-homologous end joining (NHEJ) pathway factors KU70 or DNA ligase 4 (LIG4) completely abolished tandem repeat formation. The microhomology-mediated NHEJ factor POLQ was required only for patch-like insertions, which are well-known from DSB repair as templated insertions from ectopic sites. As SSBs can also be repaired using homology, we furthermore asked whether the classical homologous recombination pathway is involved in this process in plants. The fact that RAD54 is not required for homology-mediated SSB repair demonstrates that the mechanisms for DSB- and SSB-induced homologous recombination differ in plants.
Anticancer Effects of Combination of Indole-3-Carbinol and Hydroxychloroquine on Ehrlich Ascites Carcinoma via Targeting Autophagy and Apoptosis

Abstract Indole-3-carbinol (I3C) is an active component of cruciferous vegetables which is considered a promising antineoplastic agent. This study aimed to assess I3C antineoplastic activity alone and with hydroxychloroquine (HCQ) on Ehrlich ascites carcinoma (EAC) model. Eighty female mice were divided into six groups wherein all groups except groups I and II received EAC cells (106 cells/mouse i.p.). Group I, served as control; group II served as I3C; group III served as EAC; groups IV and V received I3C (250 mg/kg body weight oral), and HCQ (60 mg/kg body weight i.p.) respectively; GVI received both I3C and HCQ. Antitumor response markers, serum, hepatic and renal biochemical parameters, histopathological changes, as well as autophagy and apoptosis markers in EAC cells were analyzed. The combination of I3C and HCQ showed the best antitumor responses with increased survival time and ameliorated biochemical parameters. Moreover, I3C upregulated LC3B and downregulated p62 gene expression in EAC cells. Furthermore, I3C combined with HCQ induced apoptosis by highly upregulating cleaved caspase-3 and Bax while downregulating Bcl-2 proteins expression in EAC cells in comparison with each drug alone. In conclusion, I3C combined with HCQ exhibited better antitumor activities than each drug alone via targeting autophagy and apoptosis.
Classification of a Violacein-Producing Psychrophilic Group of Isolates Associated with Freshwater in Antarctica and Description of Rugamonas violacea sp. nov.

Our polyphasic approach provides a new understanding of the taxonomy of novel pigmented Rugamonas species isolated from freshwater samples in Antarctica. The isolates showed considerable extracellular bactericidal secretions. ABSTRACT A group of 11 bacterial strains was isolated from streams and lakes located in a deglaciated northern part of James Ross Island, Antarctica. They were rod-shaped, Gram-stain-negative, motile, and catalase-positive and produced blue-violet-pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, automated ribotyping, repetitive element sequence-based PCR (rep-PCR), MALDI-TOF MS, fatty acid profile, chemotaxonomy analyses, and extensive biotyping was applied in order to clarify the taxonomic position of these isolates. Phylogenetic analysis based on the 16S rRNA gene indicated that all the isolates constituted a coherent group belonging to the genus Rugamonas. The closest relatives to the representative isolate P5900T were Rugamonas rubra CCM 3730T, Rugamonas rivuli FT103WT, and Rugamonas aquatica FT29WT, exhibiting 99.2%, 99.1%, and 98.6% 16S rRNA pairwise similarity, respectively. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole-genome sequencing data clearly proved that P5900T represents a distinct Rugamonas species. The G+C content of genomic DNAs was 66.1 mol%. The major components in fatty acid profiles were summed feature 3 (C16:1 ω7c/C16:1 ω6c), C 16:0, and C12:0. The cellular quinone content contained exclusively ubiquinone Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The polyamine pattern was composed of putrescine, 2-hydroxputrescine, and spermidine. IMPORTANCE Our polyphasic approach provides a new understanding of the taxonomy of novel pigmented Rugamonas species isolated from freshwater samples in Antarctica. The isolates showed considerable extracellular bactericidal secretions. The antagonistic activity of studied isolates against selected pathogens was proved by this study and implied the importance of such compounds’ production among aquatic bacteria. The psychrophilic and violacein-producing species Roseomonas violacea may play a role in the diverse consortium among pigmented bacteria in the Antarctic water environment. Based on all the obtained results, we propose a novel species for which the name Rugamonas violacea sp. nov. is suggested, with the type strain P5900T (CCM 8940T; LMG 32105T). Isolates of R. violacea were obtained from different aquatic localities, and they represent the autochthonous part of the water microbiome in Antarctica.
Hedgehog interacting protein–expressing lung fibroblasts suppress lymphocytic inflammation in mice

Chronic obstructive pulmonary disease (COPD) is mainly caused by cigarette smoking and characterized by chronic inflammation in vulnerable individuals. However, it is unknown how genetic factors may shape chronic inflammation in COPD. To understand how hedgehog interacting protein, encoded by HHIP gene identified in the genome-wide association study in COPD, plays a role in inflammation, we utilized Hhip+/– mice that present persistent inflammation and emphysema upon aging similar to that observed in human COPD. By performing single-cell RNA sequencing of the whole lung from mice at different ages, we found that Hhip+/– mice developed a cytotoxic immune response with a specific increase in killer cell lectin-like receptor G1–positive CD8+ T cells with upregulated Ifnγ expression recapitulating human COPD. Hhip expression was restricted to a lung fibroblast subpopulation that had increased interaction with CD8+ T lymphocytes in Hhip+/– compared with Hhip+/+ during aging. Hhip-expressing lung fibroblasts had upregulated IL-18 pathway genes in Hhip+/– lung fibroblasts, which was sufficient to drive increased levels of IFN-γ in CD8+ T cells ex vivo. Our finding provides insight into how a common genetic variation contributes to the amplified lymphocytic inflammation in COPD.