Miracle-dz/UniFAR-FTUs huggingface dataset:
Epithelial cell invasion by salmonella typhimurium induces modulation of genes controlled by aryl hydrocarbon receptor signaling and involved in extracellular matrix biogenesis

ABSTRACT Salmonella is the only bacterium able to enter a host cell by the two known mechanisms: trigger and zipper. The trigger mechanism relies on the injection of bacterial effectors into the host cell through the Salmonella type III secretion system 1. In the zipper mechanism, mediated by the invasins Rck and PagN, the bacterium takes advantage of a cellular receptor for invasion. This study describes the transcriptomic reprogramming of the IEC-6 intestinal epithelial cell line to Salmonella Typhimurium strains that invaded cells by a trigger, a zipper, or both mechanisms. Using S. Typhimurium strains invalidated for one or other entry mechanism, we have shown that IEC-6 cells could support both entries. Comparison of the gene expression profiles of exposed cells showed that irrespective of the mechanism used for entry, the transcriptomic reprogramming of the cell was nearly the same. On the other hand, when gene expression was compared between cells unexposed or exposed to the bacterium, the transcriptomic reprogramming of exposed cells was significantly different. It is particularly interesting to note the modulation of expression of numerous target genes of the aryl hydrocarbon receptor showing that this transcription factor was activated by S. Typhimurium infection. Numerous genes associated with the extracellular matrix were also modified. This was confirmed at the protein level by western-blotting showing a dramatic modification in some extracellular matrix proteins. Analysis of a selected set of modulated genes showed that the expression of the majority of these genes was modulated during the intracellular life of S. Typhimurium.
Solution X‐ray scattering highlights discrepancies in Plasmodium multi‐aminoacyl‐tRNA synthetase complexes

tRip is a tRNA import protein specific to Plasmodium, the causative agent of malaria. In addition to its membrane localization and tRNA trafficking properties, tRip has the capacity to associate with three aminoacyl‐tRNA synthetases (aaRS), the glutamyl‐ (ERS), glutaminyl‐ (QRS), and methionyl‐ (MRS) tRNA synthetases. In eukaryotes, such multi‐aaRSs complexes (MSC) regulate the moonlighting activities of aaRSs. In Plasmodium, tRip and the three aaRSs all contain an N‐terminal GST‐like domain involved in the assembly of two independent complexes: the Q‐complex (tRip:ERS:QRS) and the M‐complex (tRip:ERS:MRS) with a 2:2:2 stoichiometry and in which the association of the GST‐like domains of tRip and ERS (tRip‐N:ERS‐N) is central. In this study, the crystal structure of the N‐terminal GST‐like domain of ERS was solved and made possible further investigation of the solution architecture of the Q‐ and M‐complexes by small‐angle x‐ray scattering (SAXS). This strategy relied on the engineering of a tRip‐N‐ERS‐N chimeric protein to study the structural scaffold of both Plasmodium MSCs and confirm the unique homodimerization pattern of tRip in solution. The biological impact of these structural arrangements is discussed.
Advances in Record-Linkage Methodology as Applied to Matching the 1985 Census of Tampa, Florida

Abstract A test census of Tampa, Florida and an independent postenumeration survey (PES) were conducted by the U.S. Census Bureau in 1985. The PES was a stratified block sample with heavy emphasis placed on hard-to-count population groups. Matching the individuals in the census to the individuals in the PES is an important aspect of census coverage evaluation and consequently a very important process for any census adjustment operations that might be planned. For such an adjustment to be feasible, record-linkage software had to be developed that could perform matches with a high degree of accuracy and that was based on an underlying mathematical theory. A principal purpose of the PES was to provide an opportunity to evaluate the newly implemented record-linkage system and associated methodology. This article discusses the theoretical and practical issues encountered in conducting the matching operation and presents the results of that operation. A review of the theoretical background of the record-linkage.
Multimodal physical training combined with tDCS improves physical fitness components in people after stroke: a double-blind randomized controlled trial

ABSTRACT Background Transcranial direct current stimulation (tDCS) seems to be a potential tool to optimize the long-term effects of multimodal physical training (MPT) on fitness components in post-stroke patients. Objective We investigated the effects of cortical tDCS combined with MPT on motor function reflected by strength, motor performance, and cardiorespiratory capacity in chronic stroke patients. Methods This double-blind randomized controlled trial included 18 volunteers (55 ± 10 y, 72 ± 13 kg), who underwent MPT preceded by either sham stimulation (SHAM) or 2 mA bi-hemispheric tDCS. MPT consisted of 24 sessions of 60–70 min performed 2 d/wk within 12–16 weeks, with individualized intensity. Outcomes were Fugl-Meyer scores for lower limbs (FM-LL), and total (FM-Total); speed in the 10-m walk test (10MWT); oxygen uptake and work output at maximal effort (VO2max and Wmax), and gas exchange threshold (VO2-GET and W-GET); peak torque of isokinetic knee extension (PT-EXT) and flexion (PT-FLEX) of paretic and non-paretic limbs; bilateral strength deficit during knee extension (DS-EXT) and flexion (DS-FLEX). Results Pre- vs. post-intervention improvements were detected in tDCS vs. SHAM (p < 0.05) for FM-total (29.6% vs. 15.9%; effect size [ES] = 0.78), FM-LL (35.9% vs. 9.0%; ES = 1.23), 10MWT (10.6% vs. 3.8%; ES = 0.67), Wmax (75.0% vs. 4.3%; ES = 1.68), W-GET (91.6% vs. 12.4%; ES = 1.62), PT-EXT (25.6% vs. −6.5%; ES = 1.94) and PT-FLEX (26.3% vs. 9.8%; ES = 0.65) of the paretic limb, and DS-EXT (−13.7% vs. 2.5; ES = 1.43). Conclusion Bi-hemispheric cortical tDCS optimized the effects of MPT performed with moderate volume and intensity upon muscle strength, motor function, and cardiorespiratory performance in stroke hemiparetic survivors. (Registration number RBR-22rh3p).
Greenspan acoustic viscometer for gases

Double Helmholtz acoustic resonators, first proposed by Greenspan for measuring the viscosity of gases, were tested with helium, argon, and propane. Two different resonators were tested extensively with all three gases. For each of these instruments, the results for the viscosities of the three gases were consistent within ±0.5% at pressures spanning the range 25–1000 kPa. Without calibration, the viscosities deduced from one viscometer were systematically 1% larger than data from the literature; the viscosities from the second viscometer were systematically 3% larger than data from the literature. If the systematic differences were removed for each viscometer by calibration with a single gas at a single temperature and pressure, then nearly all the results for both instruments would have fallen within ±0.5% of the data from the literature. In these viscometers, the test gases are in contact with robust metal parts only; thus, these instruments are applicable to a very wide variety of gases over a very wide range of temperatures.
Adaptive prediction of human eye pupil position and effects on wavefront errors

The effects of pupil motion on retinal imaging are studied in this paper. Involuntary eye or head movements are always present in the imaging procedure, decreasing the output quality and preventing a more detailed diagnostics. When the image acquisition is performed using an adaptive optics (AO) system, substantial gain is foreseen if pupil motion is accounted for. This can be achieved using a pupil tracker as the one developed by Imagine Eyes R®, which provides pupil position measurements at a 80Hz sampling rate. In any AO loop, there is inevitably a delay between the wavefront measurement and the correction applied to the deformable mirror, meaning that an optimal compensation requires prediction. We investigate several ways of predicting pupil movement, either by retaining the last value given by the pupil tracker, which is close to the optimal solution in the case of a pure random walk, or by performing position prediction thanks to auto-regressive (AR) models with parameters updated in real time. We show that a small improvement in prediction with respect to predicting with the latest measured value is obtained through adaptive AR modeling. We evaluate the wavefront errors obtained by computing the root mean square of the difference between a wavefront displaced by the assumed true position and the predicted one, as seen by the imaging system. The results confirm that pupil movements have to be compensated in order to minimize wavefront errors.
Nano‐RECall provides an integrated pipeline for HIV‐1 drug resistance testing from Oxford Nanopore sequence data

Low‐capital‐layout sequencing options from Oxford Nanopore Technologies (ONT) could assist in expanding HIV drug resistance testing to resource‐limited settings. HIV drug resistance mutations often occur as mixtures, but current ONT pipelines provide a consensus sequence only. Moreover, there is no integrated pipeline that provides a drug resistance report from an ONT sequence file without intervention from skilled bioinformaticists. We therefore investigated Nano‐RECall, which provides seamless drug resistance interpretation while requiring low‐read coverage ONT sequence data from affordable Flongle or MinION flow cells and which provides mutation mixtures similar to Sanger Sequencing.
Transport Properties of YBa2Cu3O7: Resistivity, Thermal Conductivity, Thermopower and Hall Effect

For the high-Tc superconductor YBa2Cu3O7, we present results on the resistivity, Hall effect, and thermopower for temperatures up to 350 K as well as on the thermal conductivity in the range 0.2 K ≤ T ≤ 120 K. The Hall coefficient is positive and varies approximately with T-1. The thermopower is very small and sample dependent. These results suggest transport in more than one band. The thermal conductivity indicates dominant phonon heat transport. For the residual resistivity an upper bound, ρ0 ≤ 250 μΩ cm, is deduced. Combining this with published results for the slope of the upper critical field and the penetration depth, we estimate the specific-heat coefficient, 5 ≤ γ < 9 mJ/K2 mole-Cu, and the effective carrier density, 1.1 1022 cm-3.
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active

The modern ribosome catalyzes all coded protein synthesis in extant organisms. It is likely that its core structure is a direct descendant from the ribosome present in the last common ancestor (LCA). Hence, its earliest origins likely predate the LCA and therefore date further back in time. Of special interest is the pseudosymmetrical region (SymR) that lies deep within the large subunit (LSU) where the peptidyl transfer reaction takes place. It was previously proposed that two RNA oligomers, representing the P- and A-regions of extant ribosomes dimerized to create a pore-like structure, which hosted the necessary properties that facilitate peptide bond formation. However, recent experimental studies show that this may not be the case. Instead, several RNA constructs derived exclusively from the P-region were shown to form a homodimer capable of peptide bond synthesis. Of special interest will be the origin issues because the homodimer would have allowed a pre-LCA ribosome that was significantly smaller than previously proposed. For the A-region, the immediate issue will likely be its origin and whether it enhances ribosome performance. Here, we reanalyze the RNA/RNA interaction regions that most likely lead to SymR formation in light of these recent findings. Further, it has been suggested that the ability of these RNA constructs to dimerize and enhance peptide bond formation is sequence-dependent. We have analyzed the implications of sequence variations as parts of functional and nonfunctional constructs.
Direct detection of WIMP dark matter

The question of the nature of dark matter in the universe is perhaps the greatest problem facing cosmology and particle physics at present. New observations of the cosmic microwave background radiation and distant supernovae show that more that 90% of the mass in the universe is in the form of some unknown matter. Many lines of evidence from cosmology and particle physics suggest that the best candidate for this dark matter is a weakly interacting massive particle, or WIMP. Such particles are predicted by supersymmetry, a theory extending the Standard Model of particle physics, and many experiments around the world are now trying to directly detect these WIMPs. This article reviews the reasons for believing WIMPs to be the dark matter, and considers the challenges involved in detecting their rare low-energy interactions with normal matter. Current experimental searches are reviewed with regard to the claimed detection of WIMPs by the DAMA group. These experiments are just beginning to reach the sensitivity needed to detect, or rule out, supersymmetric WIMPs, and higher sensitivity future experiments are also discussed.
Analysis of fecal microbial profiles in dogs with intestinal lymphangiectasia

Intestinal lymphangiectasia (IL) is a common complication in dogs. This study analyzed intestinal microbiota using 16S rRNA amplicon analysis as candidate factors that strongly influence the small intestinal lymphatic vessels in dogs with and without IL. Twelve dogs were included, of which six were diagnosed with lymphoplasmacytic enteritis, four with small-cell lymphoma, and two with large-cell lymphoma. Seven of these dogs had IL, whereas five did not. First, the microbial diversity analyzed by Faith pd index was significantly decreased in dogs with IL compared to dogs without IL. Then, the relative amounts of each bacterial taxa were compared between dogs with and without IL using Linear discriminant analysis effect size analysis. At the genus level, the Ruminococcus gnavus group significantly increased in dogs with IL compared to dogs without IL. A total of four genera, including Ruminococcus torques group and Faecalibacterium, which produce butyrate, significantly decreased in dogs with IL. This study showed decreased intestinal bacterial diversity and several alterations of intestinal microbiota, including a decrease in butyrate-producing bacteria in dogs with IL, compared to dogs without IL.
Thermal optimum of photosynthesis is controlled by stomatal conductance and does not acclimate across an urban thermal gradient in six subtropical tree species.

Modeling the response of plants to climate change is limited by our incomplete understanding of the component processes of photosynthesis and their temperature responses within and among species. For ≥20 individuals each of six common subtropical tree species occurring across steep urban thermal gradients in Miami, Florida (USA) we determined rates of net photosynthesis (Anet ), maximum RuBP carboxylation, maximum RuBP regeneration, and stomatal conductance, and modeled the optimum temperature (Topt ) and process rate of each parameter to address two questions: (1) Do the Topt of Anet (ToptA ) and the maximum Anet (Aopt ) of subtropical trees reflect acclimation to elevated growth temperatures? And (2) What limits Anet in subtropical trees? Against expectations, we did not find significant acclimation of ToptA , Aopt , or the Topt of any of the underlying photosynthetic parameters to growth temperature in any of the focal species. Model selection for the single best predictor of Anet both across leaf temperatures and at ToptA revealed that the Anet of most trees was best predicted by stomatal conductance. Our findings are in accord with those of previous studies, especially in the tropics, that have identified stomatal conductance to be the most important factor limiting Anet , rather than biochemical thermal responses. This article is protected by copyright. All rights reserved.
The Effect of Living Environmental Factors on Cardiovascular Diseases in Chinese Adults: Results from a Cross-sectional and Longitudinal Study.

AIMS This study aimed to investigate the association between multiple living environmental factors and cardiovascular diseases (CVDs). METHODS This study was conducted on the China Health and Retirement Longitudinal Study (CHARLS), with 12,489 subjects in the cross-sectional study and 7,932 subjects in the seven-year follow-up. Living environmental factors included ambient fine particulate matter (PM2.5), indoor fuel use, tap water use, and residence type. Logistic regression and Cox proportional hazard regression models were applied to explore the association between living environmental risk factors and CVD events in a cross-sectional and a cohort analysis, respectively. RESULTS Compared with subjects in the low-risk groups, those in the middle-risk (odd ratio [OR], 95% confidence interval [CI]: 1.203, 0.943-1.534) and high-risk groups (OR, 95% CI: 1.616, 1.259-2.074) showed increased risks of CVD prevalence when considering the combined effects of their living environment. During the follow-up, similar associations were observed (hazard ratio [HR], 1.541, 95% CI [1.142-2.080] for the high-risk group; HR 1.296, 95% CI [0.968-1.736] for the middle-risk group); P for trend = 0.003). CONCLUSION An overall poor living environmental quality is a potential risk factor for CVD. Future studies should focus more on the effects of exposure to multiple factors.
A Simplified Radiative-Dynamical Model for the Static Stability of Rotating Atmospheres

Abstract In order to obtain estimates of the static stability in rotating atmospheres without performing numerical integrations of the equations of motion, a simple model is developed in which the radiative flux of heat is assumed to be balanced by the fluxes of sensible beat and potential energy due to large-scale eddies. The radiative flux divergence is modeled by a linearization about the radiative equilibrium state and the dynamical fluxes are modeled by calculating correlations from stability theory and by assuming that the amplitudes are limited by nonlinear effects. From the energy equation a single algebraic equation is derived for the mean equilibrium value of the Richardson number, Ri, in the troposphere. The radiative equilibrium state is assumed to be known. Once the solution for RI is found, the mean vertical and meridional gradients of potential temperature, 〈∂θ/∂z〉 and 〈∂θ/∂y〉, and the main properties of the mean zonal wind and eddies can be easily calculated. Even though many important flu.
Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion

Abstract Chromosomal translocations in cancer genomes, key players in many types of cancers, generate chimeric proteins that drive oncogenesis. Genomes with chromosomal rearrangements can also produce fusion circular RNAs (f-circRNAs) by backsplicing of chimeric transcripts, as first shown in leukemias with PML::RARα and KMT2A::MLLT3 translocations and later in solid cancers. F-circRNAs contribute to the oncogenic processes and reinforce the oncogenic activity of chimeric proteins. In leukemia with KMT2A::AFF1 (MLL::AF4) fusions, we previously reported specific alterations of circRNA expression, but nothing was known about f-circRNAs. Due to the presence of two chimeric sequences, fusion and backsplice junctions, the identification of f-circRNAs with available tools is challenging, possibly resulting in the underestimation of this RNA species, especially when the breakpoint is not known. We developed CircFusion, a new software tool to detect linear fusion transcripts and f-circRNAs from RNA-seq data, both in samples for which the breakpoints are known and when the information about the joined exons is missing. CircFusion can detect linear and circular chimeric transcripts deriving from the main and reciprocal translocations also in the presence of multiple breakpoints, which are common in malignant cells. Benchmarking tests on simulated and real datasets of cancer samples with previously experimentally determined f-circRNAs showed that CircFusion provides reliable predictions and outperforms available methods for f-circRNA detection. We discovered and validated novel f-circRNAs in acute leukemia harboring KMT2A::AFF1 rearrangements, leading the way to future functional studies aimed to unveil their role in this malignancy.
Dysregulated cholesterol metabolism, aberrant excitability and altered cell cycle of astrocytes in fragile X syndrome

Fragile X syndrome (FXS), the most prevalent heritable form of intellectual disability, is caused by the transcriptional silencing of the FMR1 gene. While neuronal contribution to FXS has been extensively studied in both animal and human‐based models of FXS, the roles of astrocytes, a type of glial cells in the brain, are largely unknown. Here, we generated a human‐based FXS model via differentiation of astrocytes from human‐induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) and characterized their development, function, and proteomic profiles. We identified shortened cell cycle, enhanced Ca2+ signaling, impaired sterol biosynthesis, and pervasive alterations in the proteome of FXS astrocytes. Our work identified astrocytic impairments that could contribute to the pathogenesis of FXS and highlight astrocytes as a novel therapeutic target for FXS treatment.
Genetic defects in peroxisome morphogenesis (Pex11β, dynamin‐like protein 1, and nucleoside diphosphate kinase 3) affect docosahexaenoic acid‐phospholipid metabolism

Peroxisomes are essential organelles involved in lipid metabolisms including plasmalogen biosynthesis and β‐oxidation of very long‐chain fatty acids. Peroxisomes proliferate by the growth and division of pre‐existing peroxisomes. The peroxisomal membrane is elongated by Pex11β and then divided by the dynamin‐like GTPase, DLP1 (also known as DRP1 encoded by DNM1L gene), which also functions as a fission factor for mitochondria. Nucleoside diphosphate kinase 3 (NME3) localized in both peroxisomes and mitochondria generates GTP for DLP1 activity. Deficiencies of either of these factors induce abnormal morphology of peroxisomes and/or mitochondria, and are associated with central nervous system dysfunction. To investigate whether the impaired division of peroxisomes affects lipid metabolisms, we assessed the phospholipid composition of cells lacking each of the different division factors. In fibroblasts from the patients deficient in DLP1, NME3, or Pex11β, docosahexaenoic acid (DHA, C22:6)‐containing phospholipids were found to be decreased. Conversely, the levels of several fatty acids such as arachidonic acid (AA, C20:4) and oleic acid (C18:1) were elevated. Mouse embryonic fibroblasts from Drp1‐ and Pex11β‐knockout mice also showed a decrease in the levels of phospholipids containing DHA and AA. Collectively, these results suggest that the dynamics of organelle morphology exert marked effects on the fatty acid composition of phospholipids.
Galaxy clusters with multiple components. I - The dynamics of Abell 98

The nature and evolution of rich galaxy clusters containing multiple condensations is studied. Velocities for 13 members of A98 are presented and the determination of dynamical properties of the individual subclusters is substantially improved. The application of techniques for quantifying gravitational scale lengths are stressed without invocation of the symmetry arguments demanded by the usual parameter fitting procedures. The entire A98 cluster is modeled as a two-body system. The probability that A98 is bound is found to be 98 percent. From this model and the results of previous N-body simulations, it is shown that the most likely description of the system is that it reached maximum expansion about 3.5 billion years ago and is presently in a state of collapse. The subclusters will merge in another three billion years.