Miracle-dz/UniFAR-FTUs huggingface dataset:
Virulence and Stress Responses of Shigella flexneri Regulated by PhoP/PhoQ

The two-component signal transduction system PhoP/PhoQ is an important regulator for stress responses and virulence in most Gram-negative bacteria, but characterization of PhoP/PhoQ in Shigella has not been thoroughly investigated. In the present study, we found that deletion of phoPQ (ΔphoPQ) from Shigella flexneri 2a 301 (Sf301) resulted in a significant decline (reduced by more than 15-fold) in invasion of HeLa cells and Caco-2 cells, and less inflammation (− or +) compared to Sf301 (+++) in the guinea pig Sereny test. In low Mg2+ (10 μM) medium or pH 5 medium, the ΔphoPQ strain exhibited a growth deficiency compared to Sf301. The ΔphoPQ strain was more sensitive than Sf301 to polymyxin B, an important antimicrobial agent for treating multi-resistant Gram-negative infections. By comparing the transcriptional profiles of ΔphoPQ and Sf301 using DNA microarrays, 117 differentially expressed genes (DEGs) were identified, which were involved in Mg2+ transport, lipopolysaccharide modification, acid resistance, bacterial virulence, respiratory, and energy metabolism. Based on the reported PhoP box motif [(T/G) GTTTA-5nt-(T/G) GTTTA], we screened 38 suspected PhoP target operons in S. flexneri, and 11 of them (phoPQ, mgtA, slyB, yoaE, yrbL, icsA, yhiWX, rstA, hdeAB, pagP, and shf–rfbU-virK-msbB2) were demonstrated to be PhoP-regulated genes based on electrophoretic mobility shift assays and β-galactosidase assays. One of these PhoP-regulated genes, icsA, is a well-known virulence factor in S. flexneri. In conclusion, our data suggest that the PhoP/PhoQ system modulates S. flexneri virulence (in an icsA-dependent manner) and stress responses of Mg2+, pH and antibacterial peptides.
Parallel solution Methods and preconditioners for Evolution equations

The recent development of the high performance computer platforms shows a clear trend towards heterogeneity and hierarchy. In order to utilize the computational power, particular attention must be paid to ﬁnding new algorithms or adjust existing ones so that they better match the HPC computer architecture. In this work we consider an alternative to classical time-stepping methods based on use of time-harmonic properties and discuss solution approaches that allow eﬃcient utilization of modern HPC resources. The method in focus is based on a truncated Fourier expansion of the solution of an evolutionary problem. The analysis is done for linear equations and it is remarked on the possibility to use two- or multilevel mesh methods for nonlinear problems, which can enable further, even higher degree of parallelization. The arising block matrix system to be solved admits a two-by-two block form with square blocks, for which a very eﬃcient preconditioner exists. It leads to tight eigenvalue bounds for the preconditioned matrix and, hence, to a very fast convergence of a preconditioned Krylov subspace or iterative reﬁnement method. The analytical background is shown as well as some illustrating numerical examples.
Low Back Pain Hospitalization: Recent United States Trends and Regional Variations

Study Design. This study describes recent United States trends and regional variations in the management of low back pain. Objectives. The authors investigated recent temporal trends and compared practices in different geographic regions. Summary of Background Data. Controversy exists concerning the appropriate medical and surgical management of patients with low back pain. Methods. National Hospital Discharge Survey data from 1979 through 1990 were analyzed. Case selection was based on previously developed algorithms intended to exclude nonmechanical causes of back pain. Results. Over the period of study, nonsurgical hospitalizations for low back pain decreased dramatically. In contrast, low back operation rates, particularly for fusion surgery, increased substantially. In recent years, surgery and hospitalization rates were highest in the South and lowest in the West. Conclusions. Rapidly increasing surgical rates and wide geographic variations suggest the need for a more consistent approach to back problems. [Key words: low back pain management, trends, regional variations, practice patterns] Spine 1994;19:1207–1213
Data Channel Design and Performance for LTE Narrowband IoT

In 3GPP Rel-13, a narrowband system based on Long Term Evolution (LTE) is being introduced to provide wide-area cellular connectivity for the Internet of Things. This system, named Narrowband Internet of Things (NB-IoT), can be deployed in three different operation modes - (1) stand-alone as a dedicated carrier, (2) in-band within the occupied bandwidth of a wideband LTE carrier, and (3) within the guard-band of an existing LTE carrier. The design targets of NB-IoT include low-cost devices, high coverage (20-dB improvement over GPRS), long device battery life (more than 10 years), and massive capacity. Latency is relaxed although a delay budget of 10 seconds is the target for exception reports. This paper discusses the design and performance of the downlink and uplink data channels. Although the design of these channels is based on LTE, there are some differences, particularly in the uplink, with the introduction of subcarrier-level transmission. The similarities have enabled rapid specification, while the enhancements in the design enable the achievement of the stated targets for NB-IoT.
Some relations between mutual information and estimation error in Wiener space

The model considered is that of ``signal plus white noise. '' Known connections between the noncausal filtering error and mutual information are combined with new ones involving the causal estimation error, in a general abstract setup. The results are shown to be invariant under a wide class of causality patterns; they are applied to the derivation of the causal estimation error of a Gaussian nonstationary filtering problem and to a multidimensional extension of the Yovits--Jackson formula.
N2,N2-dimethylguanosine-specific tRNA methyltransferase contains both nuclear and mitochondrial targeting signals in Saccharomyces cerevisiae

The TRM1 gene of Saccharomyces cerevisiae encodes a tRNA modification enzyme, N2,N2-dimethylguanosine-specific tRNA methyltransferase, which modifies both mitochondrial and cytoplasmic tRNAs. The enzyme is targeted to mitochondria for the modification of mitochondrial tRNAs. Cellular fractionation and indirect immunofluorescence studies reported here demonstrate that this enzyme is also localized to the nucleus. Further, immunofluorescence experiments using strains that overproduce the enzyme show a staining at the periphery of the nucleus suggesting that the enzyme is found in a subnuclear destination near or at the nuclear membrane. There is no obvious cytoplasmic staining in these overproducing strains. Fusion protein technology was used to begin to localize sequences involved in the nuclear targeting of this enzyme. Indirect immunofluorescence studies indicate that sequences between the first 70 and 213 NH2-terminal amino acids of the methyltransferase are sufficient to target Escherichia coli beta-galactosidase to nuclei.
Validation and downscaling of Advanced Scatterometer (ASCAT) soil moisture using ground measurements in the Western Cape, South Africa

Satellite-based remote sensing of soil water content (SWC) is a promising technology for hydrological applications to overcome large spatiotemporal variabilities of SWC. This study investigated the performance of the Advanced Scatterometer (ASCAT) soil moisture product on METOP satellite (∼12.5 km and downscaled to ∼1 km resolution), against ground measurements of SWC taken with a Hydrosense II probe along transects of 360–820 m on agricultural and natural land at locations in the Western Cape. The ASCAT products estimated fairly accurately seasonal trends of SWC; performance was better on lower slopes (R2 = 0.66) and uniform vegetation. ASCAT 12.5 km performed better in estimating SWC than the downscaled product (average concordance coefficient = 0.60 and 0.39, and R2 = 0.84 and 0.74, respectively). ASCAT 12.5 km was more responsive to rainfall events, whilst the downscaled product was more sensitive to vegetation characteristics (normalised difference vegetation index and land surface temperature). In situations with ground measurement networks and data availability constraints, remote sensing could be a feasible alternative to monitor SWC for hydrological applications at the meso-scale (regional scale).
Learning Adversary Behavior in Security Games: A PAC Model Perspective

Recent applications of Stackelberg Security Games (SSG), from wildlife crime to urban crime, have employed machine learning tools to learn and predict adversary behavior using available data about defender-adversary interactions. Given these recent developments, this paper commits to an approach of directly learning the response function of the adversary. Using the PAC model, this paper lays a firm theoretical foundation for learning in SSGs (e.g., theoretically answer questions about the numbers of samples required to learn adversary behavior) and provides utility guarantees when the learned adversary model is used to plan the defender's strategy. The paper also aims to answer practical questions such as how much more data is needed to improve an adversary model's accuracy. Additionally, we explain a recently observed phenomenon that prediction accuracy of learned adversary behavior is not enough to discover the utility maximizing defender strategy. We provide four main contributions: (1) a PAC model of learning adversary response functions in SSGs; (2) PAC-model analysis of the learning of key, existing bounded rationality models in SSGs; (3) an entirely new approach to adversary modeling based on a non-parametric class of response functions with PAC-model analysis and (4) identification of conditions under which computing the best defender strategy against the learned adversary behavior is indeed the optimal strategy. Finally, we conduct experiments with real-world data from a national park in Uganda, showing the benefit of our new adversary modeling approach and verification of our PAC model predictions.
An AeroCom Assessment of Black Carbon in Arctic Snow and Sea Ice

Abstract. Though many global aerosols models prognose surface deposition, only a few models have been used to directly simulate the radiative effect from black carbon (BC) deposition to snow and sea ice. Here, we apply aerosol deposition fields from 25 models contributing to two phases of the Aerosol Comparisons between Observations and Models (AeroCom) project to simulate and evaluate within-snow BC concentrations and radiative effect in the Arctic. We accomplish this by driving the offline land and sea ice components of the Community Earth System Model with different deposition fields and meteorological conditions from 2004 to 2009, during which an extensive field campaign of BC measurements in Arctic snow occurred. We find that models generally underestimate BC concentrations in snow in northern Russia and Norway, while overestimating BC amounts elsewhere in the Arctic. Although simulated BC distributions in snow are poorly correlated with measurements, mean values are reasonable. The multi-model mean (range) bias in BC concentrations, sampled over the same grid cells, snow depths, and months of measurements, are −4.4 (−13.2 to +10.7) ng g−1 for an earlier phase of AeroCom models (phase I), and +4.1 (−13.0 to +21.4) ng g−1 for a more recent phase of AeroCom models (phase II), compared to the observational mean of 19.2 ng g−1. Factors determining model BC concentrations in Arctic snow include Arctic BC emissions, transport of extra-Arctic aerosols, precipitation, deposition efficiency of aerosols within the Arctic, and meltwater removal of particles in snow. Sensitivity studies show that the model–measurement evaluation is only weakly affected by meltwater scavenging efficiency because most measurements were conducted in non-melting snow. The Arctic (60–90° N) atmospheric residence time for BC in phase II models ranges from 3.7 to 23.2 days, implying large inter-model variation in local BC deposition efficiency. Combined with the fact that most Arctic BC deposition originates from extra-Arctic emissions, these results suggest that aerosol removal processes are a leading source of variation in model performance. The multi-model mean (full range) of Arctic radiative effect from BC in snow is 0.15 (0.07–0.25) W m−2 and 0.18 (0.06–0.28) W m−2 in phase I and phase II models, respectively. After correcting for model biases relative to observed BC concentrations in different regions of the Arctic, we obtain a multi-model mean Arctic radiative effect of 0.17 W m−2 for the combined AeroCom ensembles. Finally, there is a high correlation between modeled BC concentrations sampled over the observational sites and the Arctic as a whole, indicating that the field campaign provided a reasonable sample of the Arctic.
Psychoeducation for psychotic patients.

BACKGROUND Psychoeducation programs have been shown in the last two decades to significantly improve the post-hospital discharge care of individuals with schizophrenia by demonstrated effects on rehospitalization rates, compliance with medication and knowledge. The benefits of psychoeducation can be sustained for up to seven years although most studies have not shown such enduring benefit. Psychoeducation is a type of psychotherapeutic support that aims to provide broad and adequate information on psychotic disorders for both patients and their families. METHOD The purpose of the group psychoeducational program at the Psychiatric clinic in Olomouc is to familiarize patients with the core of the disorder, explain the part played by pharmacotherapy, teach recognition of the warning signs of relapse, to advise on communication problems within families, and finally the training of social skills. RESULTS Patients perceive the program as meaningful and helpful in better understanding their lives.
Seasonal Acclimatization in Summer versus Winter to Changes in the Sweating Response during Passive Heating in Korean Young Adult Men

We investigated the sweating response during passive heating (partial submersion up to the umbilical line in 42±0.5℃ water, 30 min) after summer and winter seasonal acclimatization (SA). Testing was performed in July during the summer, 2011 [summer-SA; temp, 25.6±1.8℃; relative humidity (RH), 82.1±8.2%] and in January during the winter, 2012 (winter-SA; temp, -2.7±2.9℃; RH, 65.0±13.1%) in Cheonan (126°52'N, 33.38'E), Republic of Korea. All experiments were carried out in an automated climatic chamber (temp, 25.0±0.5℃: RH, 60.0±3.0%). Fifteen healthy men (age, 23.4±2.5 years; height, 175.0±5.9 cm; weight, 65.3±6.1 kg) participated in the study. Local sweat onset time was delayed during winter-SA compared to that after summer-SA (p< 0.001). Local sweat volume, whole body sweat volume, and evaporative loss volume decreased significantly after winter-SA compared to those after summer-SA (p<0.001). Changes in basal metabolic rate increased significantly after winter-SA (p< 0.001), and tympanic temperature and mean body temperature were significantly lower after summer-SA (p<0.05). In conclusion, central sudomotor acitivity becomes sensitive to summer-SA and blunt to winter-SA in Rebubic of Korea. These results suggest that the body adjusts its temperature by economically controlling the sweating rate but does not lower the thermal dissipation rate through a more effective evaporation scheme after summer-SA than that after winter-SA.
Robust consensus tracking for a class of high-order multi-agent systems

In this paper, we study the robust consensus tracking problem for a class of high-order multi-agent systems with unmodelled dynamics and unknown disturbances. A continuous robust control algorithm is designed for each agent of the high-order multi-agent system to enable robust asymptotic consensus tracking of a desired trajectory signal. By utilizing Lyapunov analysis methods and an invariance-like theorem, sufficient conditions for globally asymptotic tracking are established. Finally, a numerical simulation is provided to show the effectiveness of the proposed algorithm.
Associations of age-dependent IGF-I SDS with cardiovascular diseases and risk conditions: cross-sectional study in 6773 primary care patients.

OBJECTIVE We aimed at investigating the association of age-dependent IGF-I SDS with diabetes, dyslipidemia, hypertension, and heart diseases, in a large patient sample. BACKGROUND IGF-I has been suggested to be associated with several diseases and a prognostic marker for the development of cardiovascular diseases and risk factors. The findings, though, have been inconsistent possibly due to the methodological factors. METHODS We studied 6773 consecutive primary care patients, aged 18+ years, in a cross-sectional, epidemiological study in primary care, Diabetes Cardiovascular Risk-Evaluation: Targets and Essential Data for Commitment of Treatment study. All patients underwent a standardized clinical diagnostic and laboratory assessment. IGF-I levels were measured with an automated chemiluminescence assay system. We calculated the odds ratios (OR) for diseases in quintiles of IGF-I, and additionally analyzed the association of age-dependent IGF-I SDS with these conditions. RESULTS After multiple adjustments for confounders, we found increased ORs for coronary artery disease in patients with high IGF-I. Women, but not men, with low IGF-I also showed increased ORs for coronary artery disease. Dyslipidemia was positively associated with IGF-I. Type 2 diabetes showed a curvilinear association with IGF-I SDS. CONCLUSIONS The findings suggest the existence of multiple and complex interactions between IGF-I and several health conditions. The complex nature of disease- and subgroup-specific associations along with the methodological factors can be held responsible for divergent findings in previous studies.
Hyperbaric oxygen preconditioning: a reliable option for neuroprotection

Brain injury is the leading cause of death and disability worldwide and clinically there is no effective therapy for neuroprotection. Hyperbaric oxygen preconditioning (HBO-PC) has been experimentally demonstrated to be neuroprotective in several models and has shown efficiency in patients undergoing on-pump coronary artery bypass graft (CABG) surgery. Compared with other preconditioning stimuli, HBO is benign and has clinically translational potential. In this review, we will summarize the results in experimental brain injury and clinical studies, elaborate the mechanisms of HBO-PC, and discuss regimes and opinions for future interventions in acute brain injury.
Neural oscillations as a translational tool in schizophrenia research: Rationale, paradigms and challenges

Neural oscillations have received recently a great deal of interest in schizophrenia research because of the possibility to integrate findings from non-invasive electro/magnetoencephalographical recordings with pre-clinical research, which could potentially lead to the identification of pathophysiological mechanisms and novel treatment targets. In the current paper, we review the potential as well as the challenges of this approach by summarizing findings on alterations in rhythmic activity from both animal models and human data which have implicated dysfunctional neural oscillations in the explanation of cognitive deficits and certain clinical symptoms of schizophrenia. Specifically, we will focus on findings that have examined neural oscillations during 1) perceptual processing, 2) working memory and executive processes and 3) spontaneous activity. The importance of the development of paradigms suitable for human and animal models is discussed as well as the search for mechanistic explanation for oscillatory dysfunctions.
A Toxoplasma MORN1 Null Mutant Undergoes Repeated Divisions but Is Defective in Basal Assembly, Apicoplast Division and Cytokinesis

The membrane occupation and recognition nexus protein 1 (MORN1) is highly conserved among apicomplexan parasites and is associated with several structures that have a role in cell division. Here we dissected the role of MORN1 using the relatively simple budding process of Toxoplasma gondii as a model. Ablation of MORN1 in a conditional null mutant resulted in pronounced defects suggesting a central role for MORN1 in apicoplast segregation and in daughter cell budding. Lack of MORN1 resulted in double-headed parasites. These Janus-headed parasites form two complete apical complexes but fail to assemble a basal complex. Moreover, these parasites were capable of undergoing several more budding rounds resulting in the formation of up to 16-headed parasites conjoined at the basal end. Despite this segregation defect, the mother's cytoskeleton was completely disassembled in every budding round. Overall this argues that successful completion of the budding is not required for cell cycle progression. None of the known basal complex components, including a set of recently identified inner membrane complex (IMC) proteins, localized correctly in these multi-headed parasites. These data suggest that MORN1 is essential for assembly of the basal complex, and that lack of the basal complex abolishes the contractile capacity assigned to the basal complex late in daughter formation. Consistent with this hypothesis we observe that MORN1 mutants fail to efficiently constrict and divide the apicoplast. We used the null background provided by the mutant to dissect the function of subdomains of the MORN1 protein. This demonstrated that deletion of a single MORN domain already prevented the function of MORN1 whereas a critical role for the short linker between MORN domains 6 and 7 was identified. In conclusion, MORN1 is required for basal complex assembly and loss of MORN1 results in defects in apicoplast division and daughter segregation.
Nucleolin links to arsenic-induced stabilization of GADD45α mRNA

The present study shows that arsenic induces GADD45α (growth arrest and DNA damage inducible gene 45α) mainly through post-transcriptional mechanism. Treatment of the human bronchial epithelial cell line, BEAS-2B, with arsenic(III) chloride (As3+) resulted in a significant increase in GADD45α protein and mRNA. However, As3+ only exhibited a marginal effect on the transcription of the GADD45α gene. The accumulation of GADD45α mRNA is largely achieved by the stabilization of GADD45α mRNA in the cellular response to As3+. As3+ is able to induce binding of mRNA stabilizing proteins, nucleolin and less potently, HuR, to the GADD45α mRNA. Although As3+ was unable to affect the expression of nucleolin, treatment of the cells with As3+ resulted in re-distribution of nucleolin from nucleoli to nucleoplasm. Silencing of the nucleolin mRNA by RNA interference reversed As3+-induced stabilization of the GADD45α mRNA and accumulation of the GADD45α protein. Stabilization of GADD45α mRNA, thus, represents a novel mechanism contributing to the production of GADD45α and cell cycle arrest in response to As3+.