Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Dynamics of Pseudomonas aeruginosa during Transition from Overlapping To Non-Overlapping Cell Cycles

The coordination of gene expression with the cell cycle has so far been studied only in a few bacteria, the bottleneck being the need for synchronized cultures. Here, we determined replication-associated effects on transcription by comparing Pseudomonas aeruginosa cultures that differ in their growth mode and number of replicating chromosomes. ABSTRACT Bacteria either duplicate their chromosome once per cell division or a new round of replication is initiated before the cells divide, thus cell cycles overlap. Here, we show that the opportunistic pathogen Pseudomonas aeruginosa switches from fast growth with overlapping cell cycles to sustained slow growth with only one replication round per cell division when cultivated under standard laboratory conditions. The transition was characterized by fast-paced, sequential changes in transcriptional activity along the ori-ter axis of the chromosome reflecting adaptation to the metabolic needs during both growth phases. Quorum sensing (QS) activity was highest at the onset of the slow growth phase with non-overlapping cell cycles. RNA sequencing of subpopulations of these cultures sorted based on their DNA content, revealed a strong gene dosage effect as well as specific expression patterns for replicating and nonreplicating cells. Expression of flagella and mexE, involved in multidrug efflux was restricted to cells that did not replicate, while those that did showed a high activity of the cell division locus and recombination genes. A possible role of QS in the formation of these subpopulations upon switching to non-overlapping cell cycles could be a subject of further research. IMPORTANCE The coordination of gene expression with the cell cycle has so far been studied only in a few bacteria, the bottleneck being the need for synchronized cultures. Here, we determined replication-associated effects on transcription by comparing Pseudomonas aeruginosa cultures that differ in their growth mode and number of replicating chromosomes. We further show that cell cycle-specific gene regulation can be principally identified by RNA sequencing of subpopulations from cultures that replicate only once per cell division and that are sorted according to their DNA content. Our approach opens the possibility to study asynchronously growing bacteria from a wide phylogenetic range and thereby enhance our understanding of the evolution of cell cycle control on the transcriptional level.
Temporal hierarchy of cortical responses reflects core-belt-parabelt organization of auditory cortex in musicians.

Human auditory cortex (AC) organization resembles the core-belt-parabelt organization in nonhuman primates. Previous studies assessed mostly spatial characteristics; however, temporal aspects were little considered so far. We employed co-registration of functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) in musicians with and without absolute pitch (AP) to achieve spatial and temporal segregation of human auditory responses. First, individual fMRI activations induced by complex harmonic tones were consistently identified in four distinct regions-of-interest within AC, namely in medial Heschl's gyrus (HG), lateral HG, anterior superior temporal gyrus (STG), and planum temporale (PT). Second, we analyzed the temporal dynamics of individual MEG responses at the location of corresponding fMRI activations. In the AP group, the auditory evoked P2 onset occurred ~25 ms earlier in the right as compared with the left PT and ~15 ms earlier in the right as compared with the left anterior STG. This effect was consistent at the individual level and correlated with AP proficiency. Based on the combined application of MEG and fMRI measurements, we were able for the first time to demonstrate a characteristic temporal hierarchy ("chronotopy") of human auditory regions in relation to specific auditory abilities, reflecting the prediction for serial processing from nonhuman studies.
Michelson interferometer studies of temperature patterns in DC point-to-plane electrical discharges in air

A Michelson interferometer was used to study steady-state DC discharges in a point-to-plane gap of about 4 mm in ambient air. This interferometer made it possible to observe rectilinear fringes in the spark gap system. Isothermal curves for such discharges have been derived from the measurement of the displacement of the fringes due to heating of the system by the discharge. Various types of discharge were studied, mainly in the steady-state regimes with currents up to 1 mA, for both positive and negative points. Temperature rises exceeding 100 degrees C were found for the largest values of current and for currents exceeding 40 mu A the cathode was always hotter than the anode. The electric wind participates in the heat exchange process. These results are of interest because they supply information on energy balances and on glow to arc transitions for which a 'heating time' plays an important part.
Effects of long‐term fertilizer practices on rhizosphere soil nitrogen mineralization in the double‐cropping rice field

Nitrogen (N) was an important indictor in change of soil fertility, which was closely related with N mineralization process. However, there is still need to further study on how rhizosphere soil N mineralization in paddy field response to different fertilizer management. Therefore, the influence of long‐term (37‐years) fertilizer regime on rhizosphere soil N mineralization, ammonification and nitrification rates, and its relationship under the double‐cropping paddy field in southern of China were investigated in this study. The field experiment included following fertilizer regimes: inorganic fertilizer alone (MF), rice straw and inorganic fertilizer (RF), 30% organic manure and 70% inorganic fertilizer (OM), and no application of any fertilizer as a control (CK). The result indicated that rhizosphere soil organic carbon (SOC), total N, NO3‐N, and NH4‐N contents in paddy field with OM and RF treatments were increased. The result showed that rhizosphere soil NO2−‐N and mineral N contents with OM and RF treatments were increased, and the order of soil NO2−‐N and mineral N contents with all fertilizer treatments was showed as OM > RF > MF > CK. This result proved that soil aerobic and anaerobic N mineralization rates in paddy field with OM and RF treatments were higher than that of CK and MF treatments. Compared with MF treatment, soil ammonification rate with RF and OM treatments increased by 45.16% and 67.74%, soil nitrification rate with RF and OM treatments increased by 45.71% and 77.14%, respectively. There had significantly positively correlation between soil net mineralization, nitrification rate and SOC, total N contents. As a result, applied with rice straw and organic manure was a good measure to improve soil N mineralization in the double‐cropping rice field.
Bases d'ondelettes sur les courbes corde-arc, Noyau de Cauchy et Espaces de Hardy Associés.

Se construyen dos bases incondicionales de L2(R) adaptadas al estudio de la integral de Cauchy sobre una curva cuerda-arco, y se extiende la construccion a L2(Rd). Esto permite obtener una prueba simple del "Teorema T(b)" de G. David, J.L. Journe u S. Semmes. Se define un espacio de Hardy ponderado Hb1(Rd) caracterizado por las bases anteriores. Finalmente se aplican estos metodos al estudio del potencial de doble capa sobre una superficie lipschitziana.
High-resolution spectroscopic survey of 671 GK giants. I. Stellar atmosphere parameters and abundances

A high-resolution spectroscopic survey of 671 G and K field giants is described. Broad-band Johnson colors have been calibrated against recent, accurate effective temperature, T(eff), measurements for stars in the range 3900-6000 K. A table of polynomial coefficients for 10 color-T(eff) relations is presented. Stellar atmosphere parameters, including T(eff), log g, Fe/H, and microturbulent velocity, are computed for each star, using the high-resolution spectra and various published photometric catalogs. For each star, elemental abundances for a variety of species have been computed using a LTE spectrum synthesis program and the adopted atmosphere parameters. 62 refs.
Mitochondrial control of microglial phagocytosis by the translocator protein and hexokinase 2 in Alzheimer’s disease

Significance Microglia are responsible for protecting the brain. Defense demands the rapid production of large amounts of energy. But how microglial metabolism is controlled to fuel defense responses such as phagocytosis remains poorly understood. We demonstrate that mitochondrial translocator protein (TSPO) and hexokinase-2 play key roles in the control of microglial metabolism and phagocytosis by coordinating the balance of energy production via two major metabolic pathways. Microglia lacking TSPO resembled dysfunctional microglia observed in aging and Alzheimer's disease, and this could be partially reversed by blocking hexokinase-2 binding to the mitochondria. We find that targeting mitochondrial hexokinase-2 binding may offer an immunotherapeutic approach to inhibit glycolytic metabolic reprogramming and promote microglial phagocytosis in Alzheimer’s disease.
Improved Monte Carlo Sampling for Conict Probability Estimation

Probabilistic alerting systems for airborne collision avoidance often depend upon accurate estimates of the probability of con ict. Analytical, numerical approximation, and Monte Carlo methods have been applied to con ict probability estimation. The advantage of a Monte Carlo approach is the greater exibility a orded in modeling the stochastic behavior of aircraft encounters, but typically many samples are required to provide an adequate con ict probability estimate. One approach to improve accuracy with fewer samples is to use importance sampling, where trajectories are sampled according to a proposal distribution that is di erent from the one speci ed by the model. This paper suggests several di erent sample proposal distributions and demonstrates how they result in signi cantly improved estimates.
The role of gender in cognitive outcomes from stroke

Abstract Objective: Stroke can cause cognitive impairment, which can lead to challenges returning to day-to-day activities. Knowing what factors are associated with cognitive impairment post-stroke can be useful for predicting outcomes and guiding rehabilitation. One such factor is gender: previous studies are inconclusive as to whether gender influences cognitive outcomes post-stroke. Accounting for key variables, we examined whether there are gender differences in cognitive outcomes after stroke. Method: We analyzed data from neuropsychological assessments of 237 individuals tested in the chronic epoch (≥ 3 months) following ischemic stroke. Using ANCOVA and linear mixed modeling, we examined gender as a predictor of cognition as measured by general cognitive ability (g), Full-Scale IQ, and 18 cognitive tests, controlling for age at stroke onset, education, premorbid intelligence, and lesion volume. Results: There were no significant gender differences in overall cognitive outcomes as measured by g (p = .887) or Full-Scale IQ (p = .801). There were some significant gender differences on specific cognitive tests, with women outperforming men on scores from the Rey Auditory Verbal Learning Test (ps < .01) and men outperforming women on the Wechsler Adult Intelligence Scale Arithmetic and Information subtests (ps < .01). Conclusions: Our findings indicate that men and women have similar overall cognitive outcomes after stroke, when demographic and lesion factors are accounted for. Although men and women differed in their performance on some individual cognitive tests, neither gender performed systematically better or worse. However, for learning, working memory, and verbal knowledge/comprehension, gender may be an important predictor of outcome post-stroke.
Regional variation in knowledge and practice regarding common zoonoses among livestock farmers of selective districts in Nepal

Background The majority of Nepalese people are involved in farming. However, due to limited knowledge of zoonoses and poor preventive practices on the part of livestock farmers, vulnerabilities to zoonotic diseases are very high. The main objective of this study was to assess the regional variation in zoonoses-related knowledge and preventive practices of livestock farmers in different ecological regions of Nepal. Material and methods Descriptive cross-sectional quantitative research design was followed in the study. The total sample size was 380 livestock farmers from randomly selected three ecological regions of Nepal. Systematic sampling techniques were applied for data collection. Data were entered into an excel sheet and then imported into Statistical Package for Social Sciences (SPSS) software. The data were calculated using descriptive statistics. Univariate, and bivariate analyses were performed, and the result of the study was presented in the form of text and tables based on their nature. Results Of the studied six zoonotic diseases, most of the respondents (95.8%) knew about zoonotic bird flu; 90.7% of them, were about rabies; and 54.2% knew about swine flu. However, a few respondents knew about bovine tuberculosis, neurocysticercosis, and brucellosis. Ecologically, the highest number of respondents in Nawalpur had knowledge of rabies (95.3%), and swine flu (61.6%), whereas 98.3% of them had knowledge of avian influenza in Tanahun; and 12.5% of neurocysticercosis in Manang. Regarding zoonoses preventive practices such as regular hand washing with soap water, mask-wearing, gloves, boots, the respondents’ representation of 60.8%, 6.6%, 1.8%, and 1.3% respectively in such practices show that although these are easy and cost-effective, personal protective equipment (PPE), such preventive practices were extremely underperformed. Not only that, only 12% of respondents maintain a standard distance (>15m.) between their house and shed. Similarly, 17% still consumed meat from sick animals, and vaccination of livestock was also found poor coverage (36%) in the study. Conclusions Livestock farmers need to be more knowledgeable about many common zoonotic diseases, and their preventive practices still need improvement, with significant regional variation in the study. This has invited various zoonosis threats for them. Therefore, it is recommended that the interventional programs related to common zoonoses be conducted for livestock farmers to solve the problem.
On a Problem of Friedman and its Solution by Rybakov: Decidability of the Admissible Rules in Intuitionistic Propositional Logic

Rybakov (1984) proved that the admissible rules of IPC are decidable. We give a proof of the same theorem, using the same core idea, but couched in the many notions that have been developed in the mean time. In particular, we illustrate how the argument can be interpreted as using refinements of the notions of exactness and extendibility.
Host Factors Associated with Gut Mycobiome Structure

The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. However, research on human gut mycobiome is still rare. ABSTRACT Recent studies revealed a significant role of the gut fungal community in human health. Here, we investigated the content and variation of gut mycobiota among subjects from the European population. We explored the interplay between gut fungi and various host-related sociodemographic, lifestyle, health, and dietary factors. The study included 923 participants. Fecal DNA samples were analyzed by whole-metagenome high-throughput sequencing. Subsequently, fungi taxonomic profiles were determined and accompanied by computational and statistical analyses of the association with 53 host-related factors. Fungal communities were characterized by a high prevalence of Saccharomyces, Candida, and Sporisorium. Ten factors were found to correlate significantly with the overall mycobiota variation. Most were diet related, including the consumption of chips, meat, sodas, sweetening, processed food, and alcohol, followed by age and marital status. Differences in α- and/or β-diversity were also reported for other factors such as body mass index (BMI), job type, autoimmunological diseases, and probiotics. Differential abundance analysis revealed fungal species that exhibited different patterns of changes under specific conditions. The human gut mycobiota is dominated by yeast, including Saccharomyces, Malassezia, and Candida. Although intervolunteer variability was high, several fungal species persisted across most samples, which may be evidence that a core gut mycobiota exists. Moreover, we showed that host-related factors such as diet, age, and marital status influence the variability of gut mycobiota. To our knowledge, this is the first large and comprehensive study of the European cohort in terms of gut mycobiota associations with such an extensive and differentiated host-related set of factors. IMPORTANCE The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. However, research on human gut mycobiome is still rare. Moreover, the large European-based cohort study is missing. Here, we analyzed the first large European cohort in terms of gut mycobiota associations with a differentiated host-related set of factors. Our results showed that chips, meat, sodas, sweetening, processed food, beer, alcohol consumption, age, and marital status were associated with the variability of gut mycobiota. Moreover, our analysis revealed changes in abundances at the fungal species level for many investigated factors. Our results can suggest potentially valuable paths for further, narrowly focused research on gut mycobiome and its impact on human health. In the coming era of gut microbiome-based precision medicine, further research into the relationship between different mycobial structures and host-related factors may result in new preventive approaches or therapeutic procedures.
An APOS Analysis of Students' Understanding of the Concept of a Limit of a Function

This article reports on a study which used the APOS (Action‐Process‐Object‐Schema) theory framework to investigate university students’ understanding of limits of functions. The relevant limit concepts were taught to undergraduate science students at a university in Kwazulu‐Natal in South Africa. This paper reports on the analysis of students’ responses to four types of questions on limits of functions. The findings of this study confirmed that the limit concept is one that students find difficult to understand, and suggests that this is possibly the result of many students not having appropriate mental structures at the process, object and schema levels.
Deep Learning-based Approach to Predict Pulmonary Function at Chest CT.

Background Low-dose chest CT screening is recommended for smokers with the potential for lung function abnormality, but its role in predicting lung function remains unclear. Purpose To develop a deep learning algorithm to predict pulmonary function with low-dose CT images in participants using health screening services. Materials and Methods In this retrospective study, participants underwent health screening with same-day low-dose CT and pulmonary function testing with spirometry at a university affiliated tertiary referral general hospital between January 2015 and December 2018. The data set was split into a development set (model training, validation, and internal test sets) and temporally independent test set according to first visit year. A convolutional neural network was trained to predict the forced expiratory volume in the first second of expiration (FEV1) and forced vital capacity (FVC) from low-dose CT. The mean absolute error and concordance correlation coefficient (CCC) were used to evaluate agreement between spirometry as the reference standard and deep-learning prediction as the index test. FVC and FEV1 percent predicted (hereafter, FVC% and FEV1%) values less than 80% and percent of FVC exhaled in first second (hereafter, FEV1/FVC) less than 70% were used to classify participants at high risk. Results A total of 16 148 participants were included (mean age, 55 years ± 10 [SD]; 10 981 men) and divided into a development set (n = 13 428) and temporally independent test set (n = 2720). In the temporally independent test set, the mean absolute error and CCC were 0.22 L and 0.94, respectively, for FVC and 0.22 L and 0.91 for FEV1. For the prediction of the respiratory high-risk group, FVC%, FEV1%, and FEV1/FVC had respective accuracies of 89.6% (2436 of 2720 participants; 95% CI: 88.4, 90.7), 85.9% (2337 of 2720 participants; 95% CI: 84.6, 87.2), and 90.2% (2453 of 2720 participants; 95% CI: 89.1, 91.3) in the same testing data set. The sensitivities were 61.6% (242 of 393 participants; 95% CI: 59.7, 63.4), 46.9% (226 of 482 participants; 95% CI: 45.0, 48.8), and 36.1% (91 of 252 participants; 95% CI: 34.3, 37.9), respectively. Conclusion A deep learning model applied to volumetric chest CT predicted pulmonary function with relatively good performance. © RSNA, 2023 Supplemental material is available for this article.
Immune-cell infiltration in high-grade soft tissue sarcomas; prognostic implications of tumor-associated macrophages and B-cells

Abstract Background Soft tissue sarcomas are rare, morphologically, and genetically heterogenous. Though the tumors display abundant tumor stroma with infiltrating immune cells, the prognostic impact of various immunologic markers in sarcoma remains poorly defined. We aimed to characterize the immune landscape of a treatment-naïve cohort of soft tissue sarcoma of the extremities and the trunk wall with correlations to metastasis-free survival. Materials and Methods We surveyed immunohistochemical expression patterns for CD163, CD20, CD3, CD8, and FOXP3 in 134 adult high-grade leiomyosarcomas, liposarcomas, and synovial sarcomas. Results Macrophages outnumbered tumor-infiltrating lymphocytes. High CD163 infiltration was identified in 49% of the tumors and was overrepresented (66%) in leiomyosarcoma compared to liposarcoma (46%) and synovial sarcoma (9%). Tumor-grade also correlated with CD163 positivity with high expression in 53% of the high-grade lesions and 28% in low-grade tumors. Infiltrating CD3, CD8 and FOXP3-positive T-cells were significantly more prevalent in leiomyosarcomas than in liposarcomas/synovial sarcomas. CD20+ B-cells were identified only in 14% of the STS. Correlation to established prognostic factors revealed a correlation between CD163+ macrophages and necrosis and predicted an increased risk of metastases. No correlation between CD20+ B-cells and known prognostic factors could be established, though CD20+ B-cells infiltration predicted improved overall survival. Conclusion We confirm that tumor-infiltrating macrophages outnumber tumor-infiltrating lymphocytes in soft tissue sarcoma and signify an increased risk of metastasis. CD20+ B-cells are scarce in STS and correlate to improved survival. To date, immunotherapeutic strategies directed against T-cells have shown limited effect in soft tissue sarcoma. Our observations suggest that immunomodulatory agents focusing on macrophages may be worthwhile for further investigations in this tumor type. Further studies exploring the prognostic and predictive significance of CD20+ B cells are warranted.