Miracle-dz/UniFAR-FTUs huggingface dataset:
Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus

Background Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. Principal Findings Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. Significance For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.
Two new polyketides from the fungus Penicillium oxalicum MHZ153

Abstract Two new polyketides, penicilloxalones A (1) and B (2), together with 13 known compounds (3–15), were isolated from the ethyl acetate extract of the solid substrate fermentation cultures of the fungus Penicillium oxalicum MHZ153. The structures of the isolates were determined by spectroscopic analysis and comparison of their spectroscopic and physicochemical data with the literature values. Compounds 7 and 11 showed inhibition of nitric oxide production in lipopolysaccharide-stimulated BV-2 microglial cells with IC50 values of 0.9 ± 0.2 μM and 87.9 ± 0.7 μM, respectively.
VICTOR: genome-based phylogeny and classification of prokaryotic viruses

Bacterial and archaeal viruses (“phages”) play an enormous role in global life cycles and have recently regained importance as therapeutic agents to fight serious infections by multi-resistant bacterial strains. Nevertheless, taxonomic classification of phages is up to now only insufficiently informed by genome sequencing. Despite thousands of publicly available phage genomes, it still needs to be investigated how this wealth of information can be used for the fast, universal and accurate classification of phages. The Genome BLAST Distance Phylogeny (GBDP) approach is a truly whole-genome method currently used for in silico DNA: DNA hybridization and phylogenetic inference from prokaryotic genomes. Based on the principles of phylogenetic systematics, we here established GBDP for phage phylogeny and classification, using the common subset of genome-sequenced and officially classified phages. Trees inferred with the best GBDP variants showed only few deviations from the official phage classification, which were uniformly due to incorrectly annotated GenBank entries. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clustering genome sequences with distance thresholds optimized for the agreement with the classification turned out to be phylogenetically reasonable. Accordingly modifying genera and species is taxonomically optional but would yield more uniform sequence divergence as well as stronger branch support. Analysing an expanded data set containing > 4000 phage genomes from public databases allowed for extrapolating regarding the number, composition and host specificity of future phage taxa. The selected methods are implemented in an easy-to-use web service “VICTOR” freely available at http://ggdc.dsmz. de/victor.php.
Observation of nanoscopic charge-transfer region at metal/MoS2 interface

2D materials are promising for next-generation device applications, such as flexible transistors. However, the devices using 2D materials as active layers cannot exhibit good performance. One of the causes is that electronic properties are influential to the interface with, for instance, metal contact due to an ultra-thinness of the 2D materials. We have, therefore, performed core-level photoelectron microscopy measurements to investigate the local electronic states at interfaces in a MoS2 field-effect transistor (FET). We detect a charge-transfer region (CTR) at the MoS2/metal-electrode interface, which expands over ∼500 nm with the electrostatic potential (energy shift) variation of ∼70 meV, which causes band bending in the MoS2 electronic structure with a Fermi level shift. The observed potential variation of the CTR is well reproduced by a simple calculation using Poisson’s approximation. Our results point to a potential way of understanding the interfacial effect of the MOS2/metal electrode on the device characteristics and performance.
Antibacterial Activity of Onopordum Espinae: Identification of Hispidulin and Dehydromelitensin-8-(4ꞌ-Hydroxy-Methacrylate)

Hexane, ethyl acetate and methanol extracts of Onopordum espinae leaves were investigated for their antibacterial activities against Bacillus cereus, Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Salmonella enteritidis. Hexane and ethyl acetate extracts were toxic to Gram-positive bacteria with inhibition zone diameters ranging between 12 and 30 mm. Two products, hispidulin 1, and dehydromelitensin-8-(4ꞌ-hydroxy-methacrylate) 2 were isolated from the ethyl acetate extract of leaves and identified by 2D-NMR for the first time from this species. Ethyl acetate extractꞌs total flavonoid content was the highest, as 78.73 mg quercetin equivalents (QE)/g. The methanol extract showed the highest total phenolic content as 243.43 mg gallic acid equivalents (GAE)/g and gave the most important 2,2-diphenyl-1-picrylhydrazyl (DPPH)scavenging activity (EC50 = 86 µg/mL).
Breakfast at the Desk : The Impact of Universal Breakfast Programs on Academic Performance

Between 12 and 30 percent of school-aged children reportedly skip breakfast on a given weekday. To mitigate any impacts on health and academic performance, many schools implement universally free breakfast programs for students. This paper exploits the staggered implementation of an in-classroom breakfast program in San Diego elementary schools, which provides meals to all students during class time, to determine the impacts of universally free school breakfasts on student attendance rates, classroom behavior and academic performance. Introducing universally free breakfasts increases math and reading test score gains by roughly 15 and 10 percent of a standard deviation on average, respectively. Gains are higher in schools where fewer students were previously participating in school breakfasts. Moreover, these effects persist in later years of treatment. Moving breakfast into the classroom does not significantly impact academic achievements in schools with pre-existing universal breakfast programs, but does increase student behavior evaluation scores in such schools, particularly student preparedness. The results suggest that offering universally free breakfasts increases participation–perhaps by reducing associated social stigmas–and that the resulting positive impacts on academic achievement are at least partly driven by year round benefits rather than only consumption at the time of testing. Universally free breakfasts appear to be a relatively inexpensive way to achieve significant student gains in low-income schools. ∗This paper was supported by fellowship funding from the Spencer Foundation. I would like to thank Julian Betts for guidance on this project. I am grateful to Julie Cullen, Gordon Dahl, Bridget Long, Leah Nelson, and Prashant Bharadwaj for insightful comments and suggestions. I also thank participants of the UCSD applied microeconomics seminars for useful feedback, as well as Andrew Zau and SDUSD faculty for their assistance with data availability and collection. Any errors are solely those of the author.
Overexpressed circPVT1, a potential new circular RNA biomarker, contributes to doxorubicin and cisplatin resistance of osteosarcoma cells by regulating ABCB1

Circular RNAs (circRNAs) represent a widespread class of non-coding RNAs generated from back-splicing, with a circular loop structure. Many circRNAs have been reported to play essential roles in cancer development and have the potential to serve as a novel class of biomarkers for clinical diagnosis. However, the role of circRNA in osteosarcoma (OS) remains largely unknown. In the current study, we examined the expression level of circular RNA PVT1 (circPVT1), previously screened and identified the oncogenic role in gastric cancer, in OS and found that circPVT1 was significantly up-regulated in the OS tissues, serums and chemoresistant cell lines, correlated with poor prognosis of OS patients. Besides, ROC curve demonstrated that circPVT1 may be a better diagnostic biomarker than alkaline phosphatase (ALP) in OS with more sensitivity and specificity. In addition, functional assays revealed that circPVT1 knockdown by siRNA could weaken the resistance to doxorubicin and cisplatin of OS cells through decreasing the expression of classical drug resistance-related gene ABCB1. These findings may provide a new insight into the role of circPVT1 as a biomarker for the diagnosis and treatment target of OS.
Exploring Factors Associated with Citizens’ Perception of Their Political Environment: Evidence from Palestine

This study explores factors associated with citizens’ perception of their political environment in Palestine (N = 1270). Understanding these factors in this context has potential to enhance knowledge in relation to features that may be associated with dissatisfaction and civil unrest. This knowledge may help inform development of policies with greater potential to improve welfare. Overall, results of this study suggested that gender, government anti-corruption initiatives, and the country’s economic condition are important in explaining appraisal of the political environment as stable or unstable. Implications for welfare and scholarship are discussed.
The rs12917707 polymorphism at the UMOD locus and glomerular filtration rate in individuals with type 2 diabetes: evidence of heterogeneity across two different European populations

Background UMOD variability has been associated at a genome-wide level of statistical significance with glomerular filtration rate (GFR) in Swedish individuals with type 2 diabetes (T2D; n = 4888). Whether this finding is extensible also to diabetic patients from other populations deserves further study. Our aim was to investigate the relationship between UMOD variability and GFR in patients with T2D from Italy. Methods Genotyping of the single nucleotide polymorphism (SNP) rs12917707 at the UMOD locus has been carried out in 3087 individuals from four independent Italian cohorts of patients with T2D by TaqMan allele discrimination. Results In none of the four study cohorts was rs12917707 significantly associated with GFR (P > 0.05 for all). Similar results were obtained when the four samples were pooled and analyzed together (β = 0.83, P = 0.19). Such effect was strikingly smaller than that previously reported in Swedish patients (P for heterogeneity = 1.21 × 10-7). Conclusions The previously reported strong association between rs12917707 and GFR in diabetic patients from Sweden is not observed in Italian diabetic patients, thus clearly pointing to a heterogeneous effect across the two different samples. This suggests that UMOD is a strong genetic determinant of kidney function in patients with T2D in some, but not all, populations.
Hemophagocytic Lymphohistiocytosis Due to Acute Myeloid Leukemia Relapse: A Very Unusual Association

Hemophagocytic lymphohistiocytosis (HLH) diagnosed in the course of acute myeloid leukemia (AML) is generally triggered by treatment-induced infections. AML-induced HLH is a very rare situation for which no diagnostic or therapeutic guidelines are available. We report the occurrence of HLH in an AML5 post-transplant relapse. In our case, the absence of detectable pathogen and the parallel evolution between HLH and leukemia burden suggested a direct link between AML and HLH. We suggest that the diagnostic of AML-related HLH should be promptly considered in front of unexplained fever, cytopenia, liver dysfunction or neurological symptoms as therapeutic intervention is urgent in this life-threatening situation.
Design and control of a prosthetic leg for above-knee amputees operated in semi-active and active modes

This paper proposes a new prosthesis operated in two different modes; the semi-active and active modes. The semi-active mode is achieved from a flow mode magneto-rheological (MR) damper, while the active mode is obtained from an electronically commutated (EC) motor. The knee joint part of the above knee prosthesis is equipped with the MR damper and EC motor. The MR damper generates reaction force by controlling the field-dependent yield stress of the MR fluid, while the EC motor actively controls the knee joint angle during gait cycle. In this work, the MR damper is designed as a two-end type flow mode mechanism without air chamber for compact size. On other hand, in order to predict desired knee joint angle to be controlled by EC motor, a polynomial prediction function using a statistical method is used. A nonlinear proportional-derivative controller integrated with the computed torque method is then designed and applied to both MR damper and EC motor to control the knee joint angle. It is demonstrated that the desired knee joint angle is well achieved in different walking velocities on the ground ground.
Poor sleep is associated with CSF biomarkers of amyloid pathology in cognitively normal adults

Objective: To determine the relationship between sleep quality and CSF markers of Alzheimer disease (AD) pathology in late midlife. Methods: We investigated the relationship between sleep quality and CSF AD biomarkers in a cohort enriched for parental history of sporadic AD, the Wisconsin Registry for Alzheimer's Prevention. A total of 101 participants (mean age 62.9 ± 6.2 years, 65.3% female) completed sleep assessments and CSF collection and were cognitively normal. Sleep quality was measured with the Medical Outcomes Study Sleep Scale. CSF was assayed for biomarkers of amyloid metabolism and plaques (β-amyloid 42 [Aβ42]), tau pathology (phosphorylated tau [p-tau] 181), neuronal/axonal degeneration (total tau [t-tau], neurofilament light [NFL]), neuroinflammation/astroglial activation (monocyte chemoattractant protein–1 [MCP-1], chitinase-3-like protein 1 [YKL-40]), and synaptic dysfunction/degeneration (neurogranin). To adjust for individual differences in total amyloid production, Aβ42 was expressed relative to Aβ40. To assess cumulative pathology, CSF biomarkers were expressed in ratio to Aβ42. Relationships among sleep scores and CSF biomarkers were assessed with multiple regression, controlling for age, sex, time between sleep and CSF measurements, and CSF assay batch. Results: Worse subjective sleep quality, more sleep problems, and daytime somnolence were associated with greater AD pathology, indicated by lower CSF Aβ42/Aβ40 and higher t-tau/Aβ42, p-tau/Aβ42, MCP-1/Aβ42, and YKL-40/Aβ42. There were no significant associations between sleep and NFL or neurogranin. Conclusions: Self-report of poor sleep was associated with greater AD-related pathology in cognitively healthy adults at risk for AD. Effective strategies exist for improving sleep; therefore sleep health may be a tractable target for early intervention to attenuate AD pathogenesis.
Effects of Testing Variables on the Strength of High-Strength (90 Mpa) Concrete Cylinders

Synopsis: A full factorial experimental design was used to investigate the effects of the following variables on cylinder strength: end preparation (sulfur capping versus grinding), cylinder size (100 versus 150 mm diameter), type of testing machine (1.33-MN capacity versus a 4.45-MN capacity), and nominal stress rate (0.14 versus 0.34 MPa/s). Two levels of strength were used (45 and 90 MPa), and three replicates were tested for each run. Specific gravities were measured to check on the consistency of cylinder fabrication. Statistical analyses indicated that all the factors had significant effects on the measured compressive strength. On average, the 1 00-mm cylinders resulted in about 1.3% greater strength, the faster stress rate produced about 2.6% greater strength, the ground cylinders were 2.1% stronger, and the 1.33-MN testing machine resulted in about 2.3% greater strength. There were significant interactions among the factors, so that the effects were greater than the average values for particular factor settings. For example, the effect of end preparation depended on the strength level. For the 45-MPa concrete, there was no strength difference due to the method of end preparation, but for the 90-MPa concrete, grinding resulted in as much as 6% greater strength in certain cases. Analysis of dispersion indicated that the 1 00-mm cylinders had higher within-test variability, but the differences were not statistically significant. Recommendations for modifications to testing standards are provided. to examine the provide a to establish the significance of on the
AIM2-Like Receptors Positively and Negatively Regulate the Interferon Response Induced by Cytosolic DNA

ABSTRACT Cytosolic DNAs derived from retrotransposons serve as pathogen-associated molecular patterns for pattern recognition receptors (PRRs) that stimulate the induction of interferons (IFNs) and other cytokines, leading to autoimmune disease. Cyclic GMP-AMP synthase is one PRR that senses retrotransposon DNA, activating type I IFN responses through the stimulator of IFN genes (STING). Absent in melanoma 2 (AIM2)-like receptors (ALRs) have also been implicated in these pathways. Here we show that the mouse ALR IFI205 senses cytosolic retrotransposon DNA independently of cyclic GMP-AMP production. AIM2 antagonizes IFI205-mediated IFN induction activity by sequestering it from STING. We also found that the complement of genes located in the ALR locus in C57BL/6 and AIM2 knockout mice are different and unique, which has implications for interpretation of the sensing of pathogens in different mouse strains. Our data suggest that members of the ALR family are critical to the host IFN response to endogenous DNA. IMPORTANCE Autoimmune diseases like Aicardi-Goutières syndrome and lupus erythematosus arise when cells of the immune system become activated and attack host cells and tissues. We found that DNA generated by endogenous retroviruses and retroelements in inbred mice and mouse cells is recognized by several host proteins found in macrophages that are members of the ALR family and that these proteins both suppress and activate the pathways leading to the generation of cytokines and IFNs. We also show that there is great genetic diversity between different inbred mouse strains in the ALR genes, which might contribute to differential susceptibility to autoimmunity. Understanding how immune cells become activated is important to the control of disease. Autoimmune diseases like Aicardi-Goutières syndrome and lupus erythematosus arise when cells of the immune system become activated and attack host cells and tissues. We found that DNA generated by endogenous retroviruses and retroelements in inbred mice and mouse cells is recognized by several host proteins found in macrophages that are members of the ALR family and that these proteins both suppress and activate the pathways leading to the generation of cytokines and IFNs. We also show that there is great genetic diversity between different inbred mouse strains in the ALR genes, which might contribute to differential susceptibility to autoimmunity. Understanding how immune cells become activated is important to the control of disease.
Hopping and Landing Performance in Male Youth Soccer Players: Effects of Age and Maturation

Abstract Quantifying hopping and landing performances can assist coaches in identifying young male soccer players who may be at increased risk of injury. The influence of chronological age and maturation on these measures in this population is unknown. Single leg hop for distance (SLHD) and 75% horizontal hop and stick landing force (75%Hop) were examined in a cross-sectional sample (N=400) of elite male youth soccer players. Between-group differences for both chronological age (U11–U18) and stage of maturation (pre-, circa- or post-peak height velocity (PHV)) were analyzed. Absolute 75%Hop increased with both age and maturation. Apart from the U18s, pre-PHV and U11–U12 players displayed the greatest relative landing forces compared to all other groups (p<0.001; d=0.56–0.93). Absolute and relative SLHD were greatest in the U18s and post-PHV players (p<0.001; d=0.35–2.04). A trend showed increased SLHD with each consecutive age group although a reduction in performance was identified in the U13s (d=0.50–0.59). High volumes of accumulated soccer participation in the U18s may lead to altered landing strategies indicative of high injury risk. A temporary reduction in hop performance in the U13s may also be linked to a period of adolescent awkwardness.