Miracle-dz/UniFAR-FTUs huggingface dataset:
Cannabis use and episodic memory performance among adolescents: Moderating effects of depression symptoms and sex

Abstract Objective: Cannabis use has been linked to poorer episodic memory. However, little is known about whether depression and sex may interact as potential moderators of this association, particularly among adolescents. The current study addresses this by examining interactions between depression symptoms and sex on the association between cannabis use and episodic memory in a large sample of adolescents. Method: Cross-sectional data from 360 adolescents (M age = 17.38, SD = .75) were analyzed at the final assessment wave of a two-year longitudinal study. We used the Drug Use History Questionnaire to assess for lifetime cannabis use, and the Computerized Diagnostic Interview Schedule for Children, Fourth edition to assess the number of depression symptoms in the past year. Subtests from the Wechsler Memory Scale, Fourth Edition and the California Verbal Learning Test, Second Edition were used to assess episodic memory performance. Results: The effect of the three-way interaction among cannabis use, depression symptoms, and sex did not have a significant impact on episodic memory performance. However, follow-up analyses revealed a significant effect of the two-way interaction of cannabis use and depression symptoms on episodic memory, such that associations between cannabis use and episodic memory were only significant at lower and average levels of depression symptoms. Conclusions: Contrary to our hypotheses, we found that as depression symptoms increased, the negative association between cannabis use and episodic memory diminished. Given the use of a predominantly subsyndromic sample, future studies should attempt to replicate findings among individuals with more severe depression.
Overlap Integral in Abnormal Guided Acousto-Optic Interaction

A computer model of overlap integral is presented in abnormal guided acoustooptic interaction using mode conversion. Overlap integral of LiNbO3 is analyzed for TE↔TM polarized light in abnormal acoustooptic interaction with different penetration depths. Some valuable results are obtained for design of acoustooptic devices.
Nosology of genetic skeletal disorders: 2023 revision

The “Nosology of genetic skeletal disorders” has undergone its 11th revision and now contains 771 entries associated with 552 genes reflecting advances in molecular delineation of new disorders thanks to advances in DNA sequencing technology. The most significant change as compared to previous versions is the adoption of the dyadic naming system, systematically associating a phenotypic entity with the gene it arises from. We consider this a significant step forward as dyadic naming is more informative and less prone to errors than the traditional use of list numberings and eponyms. Despite the adoption of dyadic naming, efforts have been made to maintain strong ties to the MIM catalog and its historical data. As with the previous versions, the list of disorders and genes in the Nosology may be useful in considering the differential diagnosis in the clinic, directing bioinformatic analysis of next‐generation sequencing results, and providing a basis for novel advances in biology and medicine.
Combined proliferation and apoptosis index provides better risk stratification in breast cancer

Breast cancer (BC) risk stratification is critical for predicting behaviour and guiding management decision‐making. Despite the well‐established prognostic value of cellular proliferation in BC, the interplay between proliferation and apoptosis remains to be defined. In this study, we hypothesised that the combined proliferation and apoptosis indices can provide a more accurate in‐vivo growth rate measure and a precise prognostic predictor.
Active vibration absorber design for mechanical systems with frequency-varying excitations

A conventional vibration absorber is valid when the external excitation frequency falls into the neighborhood of a specific value. It is not feasible for vibration suppression applications subject to frequency-varying excitations. In this paper, an adaptive controller is proposed to learn the disturbance spectrum in real time so that output vibration suppression can be achieved regardless of the variations in the excitation frequency. The Lyapunov-like analysis is used to verify the closed-loop stability and ensure boundedness of internal signals. Simulation cases show that the proposed strategy can give satisfactory performance.
The effects of age, genotype and diet on hippocampal subfield iron dysregulation and Alzheimer's disease biomarkers in an ApoE mouse model

Current theories regarding accumulation of Alzheimer's disease‐related deposits of abnormal intra‐ and extracellular proteins include reactions to inflammation and mitochondrial dysfunction. In this study, we explored whether age, genotype and inflammation via diet have a greater effect on dysregulatory protein accumulation in any particular subfield of the hippocampus. We stained for ferritin, ferroportin, hyperphosphorylated tau and β‐amyloid proteins in the hippocampal region of Apolipoprotein E2 (ApoE2), ApoE3 or ApoE4 mice fed a control diet or a hypothesized inflammation‐inducing methionine diet and euthanized at 3, 6, 9 or 12 months. We analysed stains based on hippocampal subfield and compared the protein accumulation levels within each group. We found significantly decreased ferritin expression in ApoE4 mice in the CA1 and Hi regions and decreased ferroportin expression in ApoE4 mice in the Hi region. There was also a significant effect on hyperphosphorylated tau protein levels based upon a given mouse genotype and diet interaction. Additionally, there were nonsignificant trends in each hippocampal subfield of increasing ferroportin and hyperphosphorylated tau after 6 months of age and decreasing β‐amyloid and ferritin with age. This study identified that there are changes in iron regulatory molecules based on genotype in the Hi and CA1 regions. Our findings also suggest a diet‐genotype interaction, which affects levels of specific Alzheimer's disease biomarkers in the hippocampus. Additionally, we identified a trend toward increased ability to clear β‐amyloid and decreased ability to clear hyperphosphorylated tau with age in all subfields, in addition to evidence of increasing iron load with time.
Global Transcriptional Response of Escherichia coli Exposed In Situ to Different Low-Dose Ionizing Radiation Sources

Escherichia coli strain DH10β, a well-characterized model bacterium, was subjected to short-term (1-day) and long-term (15-day) exposures to three different in situ radiation sources comprised of radionuclides relevant to nuclear activities to induce a measurable and identifiable genetic response. We found E. coli had both common and unique responses to the three exposures studied, suggesting both dose rate- and radionuclide-specific effects. ABSTRACT Characterization of biological and chemical responses to ionizing radiation by various organisms is essential for potential applications in bioremediation, alternative modes of detecting nuclear material, and national security. Escherichia coli DH10β is an optimal system to study the microbial response to low-dose ionizing radiation at the transcriptional level because it is a well-characterized model bacterium and its responses to other environmental stressors, including those to higher radiation doses, have been elucidated in prior studies. In this study, RNA sequencing with downstream transcriptomic analysis (RNA-seq) was employed to characterize the global transcriptional response of stationary-phase E. coli subjected to 239Pu, 3H (tritium), and 55Fe, at an approximate absorbed dose rate of 10 mGy day−1 for 1 day and 15 days. Differential expression analysis identified significant changes in gene expression of E. coli for both short- and long-term exposures. Radionuclide source exposure induced differential expression in E. coli of genes involved in biosynthesis pathways of nuclear envelope components, amino acids, and siderophores, transport systems such as ABC transporters and type II secretion proteins, and initiation of stress response and regulatory systems of temperature stress, the RpoS regulon, and oxidative stress. These findings provide a basic understanding of the relationship between low-dose exposure and biological effect of a model bacterium that is critical for applications in alternative nuclear material detection and bioremediation. IMPORTANCE Escherichia coli strain DH10β, a well-characterized model bacterium, was subjected to short-term (1-day) and long-term (15-day) exposures to three different in situ radiation sources comprised of radionuclides relevant to nuclear activities to induce a measurable and identifiable genetic response. We found E. coli had both common and unique responses to the three exposures studied, suggesting both dose rate- and radionuclide-specific effects. This study is the first to provide insights into the transcriptional response of a microorganism in short- and long-term exposure to continuous low-dose ionizing radiation with multiple in situ radionuclide sources and the first to examine microbial transcriptional response in stationary phase. Moreover, this work provides a basis for the development of biosensors and informing more robust dose-response relationships to support ecological risk assessment.
Analysis of Genetic Ancestry from NGS Data Using EthSEQ

Next‐generation sequencing (NGS) is widely utilized both in translational cancer genomics studies and in the setting of precision medicine. Identification and stratification of an individual's ancestry is fundamental for the correct interpretation of genetic and genomic profiling. EthSEQ provides an easy and effective computational workflow to determine the ancestry of individuals, exploiting single nucleotide polymorphism genotypes computed from NGS data of whole‐exome and targeted sequencing experiments. Genotypes are determined by EthSEQ from sequencing alignment files (BAM files) or can be provided as input in Variant Call Format (VCF) or CoreArray Genomic Data Structure (GDS) format. Ancestry is determined and assigned to individuals by EthSEQ exploiting a reference model and a standard or multi‐step refinement approach based on Principal Component Analysis (PCA). A complete and detailed set of textual and graphical output files are generated by EthSEQ as result. EthSEQ is easy to use and can be integrated into any NGS‐based processing pipeline also exploiting multi‐core capabilities. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
On the regularization of the ill-posed logarithmic kernel integral equation of the first kind

The logarithmic kernel integral equation of the first kind is investigated as an improperly posed problem by considering its right-hand side as an observed quantity in a suitable space with a weaker norm. The improperly posed problem is decomposed into a well-posed one, extensively studied in the literature, and an ill-posed imbedding problem. For regularizing the ill-posed part a modified truncated singular value decomposition method is proposed that allows an easily performable a posteriori parameter choice. Then the whole problem is solved by combining the regularization method with a numerical procedure for the well-posed part. Finally, an error estimate is given to reveal the influence of the observation error on the approximation error of the numerical procedure. If the discretization parameter is specified as a known function of the noise level only, the optimal convergence order is achieved.
A carbonate corrosion experiment at a marine methane seep: The role of aerobic methanotrophic bacteria

Methane seeps are typified by the formation of authigenic carbonates, many of which exhibit corrosion surfaces and secondary porosity believed to be caused by microbial carbonate dissolution. Aerobic methane oxidation and sulfur oxidation are two processes capable of inducing carbonate corrosion at methane seeps. Although the potential of aerobic methanotrophy to dissolve carbonate was confirmed in laboratory experiments, this process has not been studied in the environment to date. Here, we report on a carbonate corrosion experiment carried out in the REGAB Pockmark, Gabon‐Congo‐Angola passive margin, in which marble cubes were deployed for 2.5 years at two sites (CAB‐B and CAB‐C) with apparent active methane seepage and one site (CAB‐D) without methane seepage. Marble cubes exposed to active seepage (experiment CAB‐C) were found to be affected by a new type of microbioerosion. Based on 16S rRNA gene analysis, the biofilms adhering to the bioeroded marble mostly consisted of aerobic methanotrophic bacteria, predominantly belonging to the uncultured Hyd24‐01 clade. The presence of abundant 13C‐depleted lipid biomarkers including fatty acids (n‐C16:1ω8c, n‐C18:1ω8c, n‐C16:1ω5t), various 4‐mono‐ and 4,4‐dimethyl sterols, and diplopterol agrees with the dominance of aerobic methanotrophs in the CAB‐C biofilms. Among the lipids of aerobic methanotrophs, the uncommon 4α‐methylcholest‐8(14)‐en‐3β,25‐diol is interpreted to be a specific biomarker for the Hyd24‐01 clade. The combination of textural, genetic, and organic geochemical evidence suggests that aerobic methanotrophs are the main drivers of carbonate dissolution observed in the CAB‐C experiment at the REGAB pockmark.
Structure-Aided Identification of an Inhibitor Targets Mps1 for the Management of Plant-Pathogenic Fungi

M. oryzae is the causal agent of rice blast, one of the most devastating diseases of cultivated rice. Chemical control is still the main strategy for its management, and the identification of novel fungicide targets is indispensable for overcoming existing problems such as drug resistance and food safety. ABSTRACT Blast disease caused by Magnaporthe oryzae threatens rice production worldwide, and chemical control is one of the main methods of its management. The high mutation rate of the M. oryzae genome results in drug resistance, which calls for novel fungicide targets. Fungal proteins that function during the infection process might be potential candidates, and Mps1 (M. oryzae mitogen-activated protein kinase 1) is such a protein that plays a critical role in appressorium penetration of the plant cell wall. Here, we report the structure-aided identification of a small-molecule inhibitor of Mps1. High-throughput screening was performed with Mps1 against a DNA-encoded compound library, and one compound, named A378-0, with the best performance was selected for further verification. A378-0 exhibits a higher binding affinity than the kinase cosubstrate ATP and can inhibit the enzyme activity of Mps1. Cocrystallization of A378-0 with Mps1 revealed that A378-0 binds to the catalytic pocket of Mps1, while the three ring-type substructures of A378-0 constitute a triangle that squeezes into the pocket. In planta assays showed that A378-0 could inhibit both the appressorium penetration and invasive growth but not the appressorium development of M. oryzae, which is consistent with the biological function of Mps1. Furthermore, A378-0 exhibits binding and activity inhibition abilities against Mpk1, the Mps1 ortholog of the soilborne fungal pathogen Fusarium oxysporum. Collectively, these results show that Mps1 as well as its orthologs can be regarded as fungicide targets, and A378-0 might be used as a hit compound for the development of a broad-spectrum fungicide. IMPORTANCE M. oryzae is the causal agent of rice blast, one of the most devastating diseases of cultivated rice. Chemical control is still the main strategy for its management, and the identification of novel fungicide targets is indispensable for overcoming existing problems such as drug resistance and food safety. With a combination of structural, biochemical, and in planta assays, our research shows that Mps1 may serve as a fungicide target and confirms that compound A378-0 binds to Mps1 and possesses bioactivity in inhibiting M. oryzae virulence. As fungal orthologs of Mps1 are conserved, A378-0 may serve as a hit for broad-spectrum fungicide development, as evidenced with Mpk1, the Mps1 ortholog of F. oxysporum. Additionally, A378-0 contains a novel chemical scaffold that has not been reported in approved kinase inhibitors, suggesting its potential to be considered the basis for the development of other kinase inhibitors.
GEOMETRY MODIFICATIONS AND ALIGNMENT OF H2O IN AN INTENSE FEMTOSECOND LASER PULSE

The Coulomb explosion of H2O in laser pulses of 50 fs and intensity of 3 X 10(16) W/cm(2) has been investigated using an ion momentum-imaging technique to determine the shape of the exploding molecule. The molecule is found to straighten substantially during the ionization process with the bend distribution at a maximum between 130 degrees and 180 degrees. [S1050-2947(99)50904-9].
Recombineering: Genetic Engineering in Escherichia coli Using Homologous Recombination

The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using either PCR products or synthetic double‐stranded DNA (dsDNA) or single‐stranded DNA as substrates. Multiple linear dsDNA molecules can be assembled into an intact plasmid. The technology of recombineering is possible because bacteriophage‐encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to the location of restriction sites and can also be used in combination with CRISPR/Cas targeting systems. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
Authors' reply to the comment by Sabour

We appreciate the constructive discussion of our recent publication (Sabour, 2023; Wandrey et al., 2022). In response to the points raised regarding our statistical methods, we agree that alternative models are available to evaluate score validity and interrater reliability. In our study, we calculated an interrater reliability of BPSNI and PAINADG using Cohen's Kappa resulting in substantial congruence for BPSNI (CohensKappa 0.71) and moderate congruence (CohensKappa 0.48) for PAINADG, respectively (Cohen, 1992; McHugh, 2012; Wandrey et al., 2022). As proposed, we analysed data with an additional Bland– Altman plot (Martin Bland & Altman, 1986) (Figure 1a,b). In line with our results of substantial congruence in interrater reliability, most of the values of the BPSNI lie within the 95% confidence interval relatively close to the mean (Figure 1a). Regarding the PAINADG, the results appear similar, though there are more differences in the values and more single values are outside the 95% confidence interval (Figure 1b). This goes in line with our results stating the moderate congruence of interrater reliability presented in our manuscript. This methodological triangulation further underscores the quality of our results. Independent from the statistical approach, clinical assessment and interpretation of both scores was an important aspect of our multiprofessional study. BPSNI appeared
Double‐reporter‐guided targeted activation of the oxytetracycline silent gene cluster in Streptomyces rimosus M527

In Streptomyces rimosus M527, the oxytetracycline (OTC) biosynthetic gene cluster is not expressed under laboratory conditions. In this study a reported‐guided mutant selection (RGMS) procedure was used to activate the cluster. The double‐reporter plasmid pAGT was constructed in which gusA encoding a β‐glucuronidase and tsr encoding a thiostrepton resistance methyltransferase were placed under the control of the native promoter of oxyA gene (PoxyA). Plasmid pAGT was introduced and integrated into the chromosome of S. rimosus M527 by conjugation, yielding initial strain M527‐pAGT. Subsequently, mutants of M527‐pAGT were generated by using ribosome engineering technology. The mutants harboring activated OTC gene cluster were selected based on visual observation of GUS activity and thiostrepton resistance. Finally, mutant M527‐pAGT‐R7 was selected producing OTC in a concentration of 235.2 mg/L. In this mutant transcriptional levels of oxysr genes especial oxyAsr gene were increased compared to wild‐type strain S. rimosus M527. The mutant M527‐pAGT‐R7 showed antagonistic activities against Gram‐negative and Gram‐positive strains. All data indicate that the OTC gene cluster was successfully activated using the RGMS method.
Calibration of the static aberrations in an MCAO system

The ESO Multi-conjugate Adaptive optics Demonstrator (MAD) is a prototype intended to be tested at the VLT Nasmyth focus. With its development raises the problem of calibration of an AO system composed of several correcting devices and wave front sensors. One part of this process is the calibration of the static aberrations of the system, always present in spite of the best efforts made during the design, the manufacturing of the optics and their alignment. In this paper we present a study to find an optimized way to correct for the static aberrations in the scientific FoV of an MCAO system. Thanks to images from the camera, the WF error in the FoV is computed, the contribution of several altitudes reconstructed, and finally projected on the deformable mirrors in order to compensate for the measured aberrations. This technique, inspired from the calibration of the static aberration of the system NAOS-CONICA, allows bringing the best quality to the scientific instrument fed by an MCAO system, by taking the most of the presence of correcting devices in the optical path.
Bayesian Analysis of Structural Equation Model With Fixed Covariates

This article extends the LISREL model to incorporate fixed covariates at both the measurement and the structural equations of the model. A Bayesian procedure with conjugate type prior distributions is established. The joint Bayesian estimates of the latent variables and the structural parameters that involve the regression coefficients of the covariates, the variances, covariances and causations among the manifest and latent variables are obtained via the Gibbs sampler algorithm. It is shown that the conditional distributions required in the Gibbs sampler are familiar distributions, hence the algorithm is very efficient. A goodness of fit statistic for assessing the proposed model is presented. An illustrative example with some real data is presented.
High-energy transversely pumped alkali vapor laser

We report on the results from our transversely pumped alkali laser. This system uses an Alexandrite laser to pump a stainless steel laser head. The system uses methane and helium as buffer gasses. Using rubidium, the system produced up to 40 mJ of output energy when pumped with 63 mJ. Slope efficiency was 75%. Using potassium as the lasing species the system produced 32 mJ and a 53% slope efficiency.
Increased IFN‐γ+ and TNF‐α+ mucosal‐associated invariant T cells in patients with aplastic anemia

Aplastic anemia (AA) is known as an autoimmune disease in which T cell activation is aberrant. It has been reported that unconventional T cells, mucosal‐associated invariant T (MAIT) cells, play an important role in several autoimmune diseases, but it is unclear if they are involved in AA.
Effects of well number in 1.3-/spl mu/m GaInAsP/InP GRIN-SCH strained-layer quantum-well lasers

Effects of well number in 1.3-/spl mu/m GaInAsP/InP GRIN-SCH compressively strained-layer quantum-well lasers were investigated from the viewpoint of the crystal quality of the strained-layer quantum wells and low threshold current operation at high temperature. As a result, we find that the optimum well number that gives the minimum threshold current increases with operating temperature and it was limited to the degradation of crystal quality of the quantum wells due to the critical thickness. A very high CW operating temperature of 170/spl deg/C was obtained. A very high output power of over 300 mW was also achieved. >