Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermal Structure and Aerosols in Mars’ Atmosphere From TIRVIM/ACS Onboard the ExoMars Trace Gas Orbiter: Validation of the Retrieval Algorithm

The Atmospheric Chemistry Suite (ACS) onboard the ExoMars Trace Gas Orbiter monitors the Martian atmosphere through different spectral intervals in the infrared light. We present a retrieval algorithm tailored to the analysis of spectra acquired in nadir geometry by Thermal InfraRed channel in honor of professor Vassilii Ivanovich Moroz (TIRVIM), the thermal infrared channel of ACS. Our algorithm simultaneously retrieves vertical profile of atmospheric temperature up to 50 km, surface temperature, and integrated optical depth of dust and water ice clouds. The specificity of the TIRVIM data set lies in its capacity to resolve the diurnal cycle over a 54 sol period. However, it is uncertain to what extent can the desired atmospheric quantities be accurately estimated at different times of day. Here we first present an Observing System Simulation Experiment (OSSE). We produce synthetic observations at various latitudes, seasons and local times and run our retrieval algorithm on these synthetic data, to evaluate its robustness. Different sources of biases are documented, in particular regarding aerosol retrievals. Atmospheric temperature retrievals are found robust even when dust and/or water ice cloud opacities are not well estimated in our OSSE. We then apply our algorithm to TIRVIM observations in April–May 2018 and perform a cross‐validation of retrieved atmospheric temperature and dust integrated opacity by comparisons with thousands of colocated Mars Climate Sounder (MCS) retrievals. Most differences between TIRVIM and MCS atmospheric temperatures can be attributed to differences in vertical sensitivity. Daytime dust opacities agree well with each other, while biases are found in nighttime dust opacity retrieved from TIRVIM at this season.
Current status and Prospects on Adequacy Evaluation of Bulk Power Systems with Wind Power Integration

The adequacy assessment of bulk power system with high levels of intermittent generation capacity presents many problems;especially networks with high levels of wind energy penetration require careful consideration because wind is a highly variable energy resource.Thus,the adequacy of the system needs urgent re-evaluation after the wind power integration.This paper introduces the worldwide results and progress of the studies on bulk power system adequacy assessment with wind power integration,including the adequacy indexes and evaluation methods,the reliability model of wind farms and the impacts on bulk power system adequacy caused by wind power integration.Based on this,the paper proposes the possible development tendency on bulk power system adequacy evaluation with wind power integration.
Mean-field equations for neural populations with q-Gaussian heterogeneities.

Describing the collective dynamics of large neural populations using low-dimensional models for averaged variables has long been an attractive task in theoretical neuroscience. Recently developed reduction methods make it possible to derive such models directly from the microscopic dynamics of individual neurons. To simplify the reduction, the Cauchy distribution is usually assumed for heterogeneous network parameters. Here we extend the reduction method for a wider class of heterogeneities defined by the q-Gaussian distribution. The shape of this distribution depends on the Tsallis index q and gradually changes from the Cauchy distribution to the normal Gaussian distribution as this index changes. We derive the mean-field equations for an inhibitory network of quadratic integrate-and-fire neurons with a q-Gaussian-distributed excitability parameter. It is shown that the dynamic modes of the network significantly depend on the form of the distribution determined by the Tsallis index. The results obtained from the mean-field equations are confirmed by numerical simulation of the microscopic model.
Hypertrophic Scar Following Excisional Surgery and Full-Thickness Skin Grafting Due to Rhinophyma Treated with 1064 nm Q-Switched Neodymium:Yttrium Aluminum Garnet Laser

Abstract Rhinophyma is characterized by progressive enlargement of the nasal skin, which is considered to be an advanced stage of phymatous rosacea. Esthetic disfigurement makes surgical treatment necessary for this condition. Hypertrophic scars are the consequence of alterations in the skin’s healing process following surgical interventions. Laser may be the treatment of choice in hypertrophic scars. We reported a case of hypertrophic scars following excisional surgery and full-thickness skin grafting due to rhinophyma in an 18-year-old male who was consulted from the Department of Plastic Surgery and Reconstruction. The 1064 nanometer (nm) Q-switched Neodymium: Yttrium Aluminum Garnet (QS Nd:YAG) with 4 mm spot size, 1.5 J/cm2 and 1 Hz was applied to the hypertrophic scars for three sessions within one month interval. Clinical improvement was observed as indicated by the patient’s Vancouver scar scale score and spectrophotometry result, and no side effects were found. Nd:YAG laser is a non-ablative device that targets hemoglobin, water, and melanin. Any thermal effects on dermal tissue containing blood vessels could result in reduced blood flow through the capillaries in the dermal papillae. QS Nd:YAG-induced selective photothermolysis was responsible for collagen breakdown and reduced collagen production in hypertrophic scars. The 1064 nm QS Nd:YAG laser gave good results in this case although more treatment sessions may be recommended and a longer follow-up is necessary in order to assess the stability of the result.
An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element

Abstract Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore, QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.
ROS-Induced Oxidative Damage and Mitochondrial Dysfunction Mediated by Inhibition of SIRT3 in Cultured Cochlear Cells

Sensorineural hearing loss (SNHL) is one of the most common causes of disability worldwide. Previous evidence suggests that reactive oxygen species (ROS) may play an important role in the occurrence and development of SNHL, while its mechanism remains unclear. We cultured dissected organs of Corti in medium containing different concentrations (0, 0.25, 0.5, 0.75, 1, and 1.25 mM) of hydrogen peroxide (H2O2) and established a four-concentration model of 0, 0.5, 0.75, and 1 mM to study different degrees of damage. We examined ROS-induced mitochondrial damage and the role of sirtuin 3 (SIRT3). Our results revealed that the number of ribbon synapses and hair cells appeared significantly concentration-dependent decrease with exposure to H2O2. Outer hair cells (OHCs) and inner hair cells (IHCs) began to be lost, and activation of apoptosis of hair cells (HCs) was observed at 0.75 mM and 1 mM H2O2, respectively. In contrast with the control group, the accumulation of ROS was significantly higher, and the mitochondrial membrane potential (MMP) was lower in the H2O2-treated groups. Furthermore, the expression of SIRT3, FOXO3A, and SOD2 proteins declined, except for an initial elevation of SIRT3 between 0 and 0.75 mM H2O2. Administration of the selective SIRT3 inhibitor 3-(1H-1,2,3-triazol-4-yl) pyridine resulted in increased damage to the cochlea, including loss of ribbon synapses and hair cells, apoptosis of hair cells, more production of ROS, and reduced mitochondrial membrane potential. Thoroughly, our results highlight that ROS-induced mitochondrial oxidative damage drives hair cell degeneration and apoptosis. Furthermore, SIRT3 is crucial for preserving mitochondrial function and protecting the cochlea from oxidative damage and may represent a possible therapeutic target for SNHL.
Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent, Treponema pallidum

Abstract The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
Quantifying the effect of sagittal plane joint angle variability on bipedal fall risk

Falls are a major issue for bipeds. For elderly adults, falls can have a negative impact on their quality of life and lead to increased medical costs. Fortunately, interventional methods are effective at reducing falls assuming they are prescribed. For biped robots, falls prevent them from completing required tasks. Thus, it is important to understand what aspects of gait increase fall risk. Gait variability may be associated with increased fall risk; however, previous studies have not investigated the variation in the movement of the legs. The purpose of this study was to determine the effect of joint angle variability on falling to determine which component(s) of variability were statistically significant. In order to investigate joint angle variability, a physics-based simulation model that captured joint angle variability as a function of time through Fourier series was used. This allowed the magnitude, the frequency mean, and the frequency standard deviation of the variability to be altered. For the values tested, results indicated that the magnitude of the variability had the most significant impact on falling, and specifically that the stance knee flexion variability magnitude was the most significant factor. This suggests that increasing the joint variability magnitude may increase fall risk, particularly if the controller is not able to actively compensate. Altering the variability frequency had little to no effect on falling.
Glucocorticoid minimizes local anesthetic infusion requirement through adductor canal block and improves perioperative prosthetic joint range of motion in total knee arthroplasty

Introduction The use of glucocorticoid as local anesthetic adjuvant in single-injection adductor canal block (ACB) is well-documented but its effects in the presence of an indwelling catheter is unclear. The purpose of this study was to determine the impacts of one-time perineural glucocorticoid injection on continuous adductor canal block in patients undergoing total knee arthroplasty. Methods A single center retrospective study of 95 patients undergoing unilateral total knee arthroplasty (TKA) was performed. Patients were divided into three groups based on adjuvant received through ACB before continuous catheter placement: a control group with no adjuvant (N = 41), a treatment group with dexamethasone (DEX) as adjuvant (N = 33) and another treatment group with DEX/ Methylprednisolone acetate (MPA) as adjuvant (N = 21). The primary outcome was the amount of ropivacaine administered via patient controlled ACB catheter. Secondary outcomes included numeric pain score, perioperative opioid usage, immediately postoperative prosthetic knee joint active range of motion (AROM), opioid usage at 6 weeks and 3 months, length of stay and discharge disposition. Results Patients in both treatment groups demonstrated a statistically significant decrease in the requirement of self-administered ropivacaine than the control group on postoperative day (POD) 1 (p<0.001) and POD 2 (p<0.001). There was no significant difference in opioid consumption and pain scores between either treatment group vs. control. Compared to control (66%), more home disposition was observed in the DEX (88%, p = 0.028) and DEX/MPA group (95%, p = 0.011). Conclusion This study suggested that single dose perineural glucocorticoid injection with DEX or DEX/MPA significantly decreased the dose of local anesthetic ropivacaine infusion required through continuous ACB for TKA while maintaining comparable level of pain score and opioid consumption, and significantly more patients were discharged home.
Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex

The Reithrodontomys tenuirostris species group is considered “the most specialized” within the genus Reithrodontomys from morphological and ecological perspectives. Previous studies based on molecular data recommended changes in the taxonomy of the group. In particular, R. microdon has been the most taxonomically questioned, with the suggestion that it constitutes a complex of cryptic species. We analyzed the phylogenetic relationships of the R. tenuirostris species group using DNA sequences from the mitochondrial Cytochrome b gene and Intron 7 of the nuclear beta fibrinogen gene. In addition, divergence times were estimated, and possible new taxa delimited with three widely used species delimitation methods. Finally, possible connectivity routes based on shared haplotypes were tested among the R. microdon populations. All species were recovered as monophyletic with the exception of R. microdon, whose individuals were grouped into four different haplogroups, one of which included specimens of R. bakeri. Diversification within the R. tenuirostris species group began about 3 Ma, in the Pleistocene. The bGMYC and STACEY delimitation methods were congruent with each other, delimiting at the species-level each haplogroup within R. microdon, while the mPTP suggested a greater number of species. Moreover, none of the haplogroups showed potential connectivity routes between them, evidencing lack of gene flow. Our results suggest the existence of a higher number of species in the R. tenuirostris group, because we show that there are four species within what is currently recognized as R. microdon.
Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon

Abstract Eukaryotic genomes harbor hundreds of rRNA genes, many of which are transcriptionally silent. However, little is known about selective regulation of individual rDNA units. In Drosophila melanogaster, some rDNA repeats contain insertions of the R2 retrotransposon, which is capable to be transcribed only as part of pre-rRNA molecules. rDNA units with R2 insertions are usually inactivated, although R2 expression may be beneficial in cells with decreased rDNA copy number. Here we found that R2-inserted rDNA units are enriched with HP1a and H3K9me3 repressive mark, whereas disruption of the heterochromatin components slightly affects their silencing in ovarian germ cells. Surprisingly, we observed a dramatic upregulation of R2-inserted rRNA genes in ovaries lacking Udd (Under-developed) or other subunits (TAF1b and TAF1c-like) of the SL1-like complex, which is homologues to mammalian Selective factor 1 (SL1) involved in rDNA transcription initiation. Derepression of rRNA genes with R2 insertions was accompanied by a reduction of H3K9me3 and HP1a enrichment. We suggest that the impairment of the SL1-like complex affects a mechanism of selective activation of intact rDNA units which competes with heterochromatin formation. We also propose that R2 derepression may serve as an adaptive response to compromised rRNA synthesis.
Opioids Regulate the Immune System: Focusing on Macrophages and Their Organelles

Opioids are the most widely used analgesics and therefore have often been the focus of pharmacological research. Macrophages are the most plastic cells in the hematopoietic system. They show great functional diversity in various organism tissues and are an important consideration for the study of phagocytosis, cellular immunity, and molecular immunology. The expression of opioid receptors in macrophages indicates that opioid drugs act on macrophages and regulate their functions. This article reviewed the collection of research on effects of opioids on macrophage function. Studies show that opioids, both endogenous and exogenous, can affect the function of macrophages, effecting their proliferation, chemotaxis, transport, phagocytosis, expression of cytokines and chemokine receptors, synthesis and secretion of cytokines, polarization, and apoptosis. Many of these effects are closely associated with mitochondrial function and functions of other organelles in macrophages. Therefore, in depth research into effects of opioids on macrophage organelles may lead to some interesting new discoveries. In view of the important role of macrophages in HIV infection and tumor progression, this review also discusses effects of opioids on macrophages in these two pathological conditions.
A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph

Abstract Detecting signals of selection from genomic data is a central problem in population genetics. Coupling the rich information in the ancestral recombination graph (ARG) with a powerful and scalable deep-learning framework, we developed a novel method to detect and quantify positive selection: Selection Inference using the Ancestral recombination graph (SIA). Built on a Long Short-Term Memory (LSTM) architecture, a particular type of a Recurrent Neural Network (RNN), SIA can be trained to explicitly infer a full range of selection coefficients, as well as the allele frequency trajectory and time of selection onset. We benchmarked SIA extensively on simulations under a European human demographic model, and found that it performs as well or better as some of the best available methods, including state-of-the-art machine-learning and ARG-based methods. In addition, we used SIA to estimate selection coefficients at several loci associated with human phenotypes of interest. SIA detected novel signals of selection particular to the European (CEU) population at the MC1R and ABCC11 loci. In addition, it recapitulated signals of selection at the LCT locus and several pigmentation-related genes. Finally, we reanalyzed polymorphism data of a collection of recently radiated southern capuchino seedeater taxa in the genus Sporophila to quantify the strength of selection and improved the power of our previous methods to detect partial soft sweeps. Overall, SIA uses deep learning to leverage the ARG and thereby provides new insight into how selective sweeps shape genomic diversity.
Early rRNA processing is a stress-dependent regulatory event whose inhibition maintains nucleolar integrity

Abstract The production of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here, we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but is independently regulated. Failure to coordinately control ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils how the rapid translational shut-off in response to stress coordinates with rRNA synthesis production to maintain nucleolar integrity.
Detection of breast cancer by ATR-FTIR spectroscopy using artificial neural networks

In this study, three (3) neural networks (NN) were designed to discriminate between malignant (n = 78) and benign (n = 88) breast tumors using their respective attenuated total reflection Fourier transform infrared (ATR-FTIR) spectral data. A proposed NN-based sensitivity analysis was performed to determine the most significant IR regions that distinguished benign from malignant samples. The result of the NN-based sensitivity analysis was compared to the obtained results from FTIR visual peak identification. In training each NN models, a 10-fold cross validation was performed and the performance metrics–area under the curve (AUC), accuracy, positive predictive value (PPV), specificity rate (SR), negative predictive value (NPV), and recall rate (RR)–were averaged for comparison. The NN models were compared to six (6) machine learning models–logistic regression (LR), Naïve Bayes (NB), decision trees (DT), random forest (RF), support vector machine (SVM) and linear discriminant analysis (LDA)–for benchmarking. The NN models were able to outperform the LR, NB, DT, RF, and LDA for all metrics; while only surpassing the SVM in accuracy, NPV and SR. The best performance metric among the NN models was 90.48% ± 10.30% for AUC, 96.06% ± 7.07% for ACC, 92.18 ± 11.88% for PPV, 94.19 ± 10.57% for NPV, 89.04% ± 16.75% for SR, and 94.34% ± 10.54% for RR. Results from the proposed sensitivity analysis were consistent with the visual peak identification. However, unlike the FTIR visual peak identification method, the NN-based method identified the IR region associated with C–OH C–OH group carbohydrates as significant. IR regions associated with amino acids and amide proteins were also determined as possible sources of variability. In conclusion, results show that ATR-FTIR via NN is a potential diagnostic tool. This study also suggests a possible more specific method in determining relevant regions within a sample’s spectrum using NN.