Miracle-dz/UniFAR-FTUs huggingface dataset:
Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children

The cystic fibrosis (CF) lung microbiome has been studied in children and adults; however, little is known about its relationship to early disease progression. To better understand the relationship between the lung microbiome and early respiratory disease, we characterized the lower airways microbiome using bronchoalveolar lavage (BAL) samples obtained from clinically stable CF infants and preschoolers who underwent bronchoscopy and chest computed tomography (CT). Cross-sectional samples suggested a progression of the lower airways microbiome with age, beginning with relatively sterile airways in infancy. By age two, bacterial sequences typically associated with the oral cavity dominated lower airways samples in many CF subjects. The presence of an oral-like lower airways microbiome correlated with a significant increase in bacterial density and inflammation. These early changes occurred in many patients, despite the use of antibiotic prophylaxis in our cohort during the first two years of life. The majority of CF subjects older than four harbored a pathogen dominated airway microbiome, which was associated with a further increase in inflammation and the onset of structural lung disease, despite a negligible increase in bacterial density compared to younger patients with an oral-like airway microbiome. Our findings suggest that changes within the CF lower airways microbiome occur during the first years of life and that distinct microbial signatures are associated with the progression of early CF lung disease.
The Application of Machine Learning Methods to Intrusion Detection

Network and system security is of paramount importance in the present data communication environment. Hackers and intruders can create many successful attempts to cause the crash of the networks and web services by unauthorized intrusion. New threats and associated solutions to prevent these threats are emerging together with the secured system evolution. Intrusion Detection Systems (IDS) are one of these solutions. The main function of Intrusion Detection System is to protect the resources from threats. It analyzes and predicts the behaviours of users, and then these behaviours will be considered an attack or a normal behaviour. We use Rough Set Theory (RST) and Support Vector Machine (SVM) to detect network intrusions. First, packets are captured from the network, RST is used to pre-process the data and reduce the dimensions. The features selected by RST will be sent to SVM model to learn and test respectively. The method is effective to decrease the space density of data. The experiments compare the results with Principal Component Analysis (PCA) and show RST and SVM schema could reduce the false positive rate and increase the accuracy.
One‐year outcome after prehospital intubation

The aim of physician staffed emergency medical services (EMS) is to supplement other EMS units in the care of prehospital patients. The need for advanced airway management in critical prehospital patients can be considered as one indicator of the severity of the patient's condition. Our primary aim was to study the long‐term outcome of critically ill patients (excluding cardiac arrest) who were intubated by EMS physicians in the prehospital setting.
The Role of Knowledge in Sustainable Agriculture: Evidence from Rice Farms’ Technical Efficiency in Hanoi, Vietnam

This paper examines the production efficiency of 2079 rice farms in Hanoi (Vietnam) in 2018 and the role of formal and informal knowledge on their efficiency. Our empirical results showed that, in general, Hanoi’s rice farms performed quite well in 2018. The differences in the specific performance of each farm could be explained by the farmer’s characteristics (age, education and gender of the head of household) as well as by certain external factors (support programs or distance to city center). We found that self-learning through experience did not obviously improve the farm’s production efficiency whilst education and training were notably important. We further suggest that regional councils and agricultural support programs played an important role in helping farmers improve their efficiency and sustainability.
A Dynamic Region based Limited Feedback Scheme for Efficient Power Allocation in OFDM Systems

This letter proposes a dynamic region based limited feedback scheme for efficient power allocation in orthogonal frequency division multiplexing (OFDM) systems. At the receiver, after obtaining the channel gains of all subcarriers by channel estimation, the maximum and the minimum channel gains can be determined easily. Using the maximum and the minimum channel gains, the proposed scheme divides the range of the channel gains into multiple regions adaptively. Each region is assigned with a unique index. Then each subcarrier will be allocated with the index of the region that its channel gain belongs to. The index information of all subcarriers can be denoted by a code from a predetermined codebook. Along with the maximum and the minimum channel gains, only the codes will be fed back. The feedback information will be used to estimate the channel gains of all subcarriers at the transmitter. The simulation results show that the proposed scheme can improve both the accuracy of feedback channel gain information and the spectral efficiency with less feedback information overhead.
Accuracy of heart rate assessment in atrial fibrillation.

OBJECTIVE To determine the most accurate technique to measure the heart rate during atrial fibrillation by use of three counting intervals, 15, 30, and 60 seconds, and two methods, apical and radial pulse measurement. DESIGN A quasi-experimental, repeated measures factorial design was used to determine absolute error (amount of error ignoring direction of error) between heart rates obtained from six randomly ordered pulse measurements taken of one man in chronic atrial fibrillation by the 94 nurses in the sample and the heart rate recorded by simultaneous electrocardiographic (ECG) and plethysmographic (pleth) recordings. SUBJECTS Nurses in four groups comprised the sample; registered nurses (N = 29), licensed practical nurses (N = 23), nursing students (N = 21), and registered nurses with advanced degrees who are clinical specialists and in faculty positions. RESULTS The heart rate of the man varied from 57 to 111 beats/min (mean 81 beats/min). The mean absolute error rates for the six measurements ranged from 8 beats/min to 20 beats/min, all considered to be important when a 10% error was used as the criteria for clinical significance. The apical method was significantly more accurate than the radial method regardless of whether the ECG or pleth standard was used (ECG--F1.90 = 72.91, p less than 0.0001; pleth--F1.144 = 4.68, p = 0.036). The 60-second counting interval was significantly more accurate regardless of the standard (ECG--F2.180 = 5.19, p = 0.006; pleth--F2.88 = 3.95, p = 0.02). CONCLUSIONS Atrial fibrillation occurs in 2% to 4% of people over 60 years of age and is one of the most difficult dysrhythmias to count. Accurate counts are important when making clinical decisions, yet measurement of heart rate in this study was quite inaccurate. The 60-second count and the apical method were the most accurate statistically, although differences in counting interval error rates were not clinically significant.
Structure of the WipA protein reveals a novel tyrosine protein phosphatase effector from Legionella pneumophila

Legionnaires' disease is a severe form of pneumonia caused by the bacterium Legionella pneumophila. L. pneumophila pathogenicity relies on secretion of more than 300 effector proteins by a type IVb secretion system. Among these Legionella effectors, WipA has been primarily studied because of its dependence on a chaperone complex, IcmSW, for translocation through the secretion system, but its role in pathogenicity has remained unknown. In this study, we present the crystal structure of a large fragment of WipA, WipA435. Surprisingly, this structure revealed a serine/threonine phosphatase fold that unexpectedly targets tyrosine-phosphorylated peptides. The structure also revealed a sequence insertion that folds into an α-helical hairpin, the tip of which adopts a canonical coiled-coil structure. The purified protein was a dimer whose dimer interface involves interactions between the coiled coil of one WipA molecule and the phosphatase domain of another. Given the ubiquity of protein-protein interaction mediated by interactions between coiled-coils, we hypothesize that WipA can thereby transition from a homodimeric state to a heterodimeric state in which the coiled-coil region of WipA is engaged in a protein-protein interaction with a tyrosine-phosphorylated host target. In conclusion, these findings help advance our understanding of the molecular mechanisms of an effector involved in Legionella virulence and may inform approaches to elucidate the function of other effectors.
Purification and partial structural and kinetic characterization of tyrosine aminotransferase from epimastigotes of Trypanosoma cruzi.

Tyrosine aminotransferase was purified to homogeneity from epimastigotes of Trypanosoma cruzi by a method involving chromatography on DEAE-cellulose, gel filtration on Sephacryl S-200 and chromatography on Mono Q in an f.p.l.c. system. The purified enzyme showed a single band in SDS/PAGE, with an apparent molecular mass of 45 kDa. Since the apparent molecular mass of the native enzyme, determined by gel filtration, is 91 kDa, the native enzyme is a dimer of similar subunits. The amino-acid composition was determined, as well as the sequences of three internal peptides obtained by CNBr cleavage at Met residues. Both criteria suggest considerable similarity with the tyrosine aminotransferases from rat and from human liver. The enzyme contains nine 1/2 Cys residues, three free and the others forming three disulphide bridges. The enzyme is not N-glycosylated. The isoelectric point is 4.6-4.8. The optimal pH for the reaction of the enzyme with tyrosine as a substrate is 7.0. The apparent Km values for tyrosine, phenylalanine and tryptophan, with pyruvate as a co-substrate, were 6.8, 17.9 and 21.4 mM, respectively, whereas those for pyruvate, alpha-oxoglutarate and oxaloacetate, with tyrosine as a substrate, were 0.5, 38 and 16 mM respectively. The purified tyrosine aminotransferase acts as an alanine aminotransferase as well and the activity seems to reside in the same enzyme molecule. The results suggest that the enzyme is a general aromatic-amino-acid transaminase, with high sequence similarity to tyrosine aminotransferases from rat and human liver.
Prostaglandin d synthase is a potential novel therapeutic agent for the treatment of gastric carcinomas expressing PPARγ

The antitumor activity of prostaglandin (PG) D2 has been demonstrated against some types of cancer, including gastric cancer. However, exogenous PGD2 is not useful from a clinical point of view because it is rapidly metabolized in vivo. The aim of this study was to clarify the antitumor efficacy of an alternative, PGD synthase (PGDS), on gastric cancer cells. The effects of PGD2 and PGDS on the proliferation of gastric cancer cells were examined in vivo and in vitro. The expression levels of PGD2 receptors and peroxisome proliferator‐activated receptor γ (PPARγ) were evaluated by RT‐PCR. The effects of a PPARγ antagonist or siPPARγ on the proliferation of cancer cells and the c‐myc and cyclin D1 expression were examined in the presence or absence of PGD2 or PGDS. PPARγ was expressed in gastric cancer cell lines, but PGD2 receptors were not. PGD2 and PGDS significantly decreased the proliferation of gastric cancer cells that highly expressed PPARγ. PGDS increased the PGD2 production of gastric cancer cells. A PPARγ antagonist and siPPARγ transfection significantly suppressed the growth‐inhibitory effects of PGD2 and PGDS. Expression of c‐myc and cyclin D1 was significantly decreased by PGD2; this inhibitory effect was suppressed by PPARγ antagonist. Both PGD2 and PGDS significantly decreased subcutaneous tumor growth in vivo. Tumor volume after PGDS treatment was significantly less than PGD2 treatment. These findings suggest that PGDS and PGD2 decrease the proliferation of gastric cancer cells through PPARγ signaling. PGDS is a potentially promising therapeutic agent for gastric cancers that express PPARγ.
Emerging connections between RNA and autophagy

ABSTRACT Macroautophagy/autophagy is a key catabolic process, essential for maintaining cellular homeostasis and survival through the removal and recycling of unwanted cellular material. Emerging evidence has revealed intricate connections between the RNA and autophagy research fields. While a majority of studies have focused on protein, lipid and carbohydrate catabolism via autophagy, accumulating data supports the view that several types of RNA and associated ribonucleoprotein complexes are specifically recruited to phagophores (precursors to autophagosomes) and subsequently degraded in the lysosome/vacuole. Moreover, recent studies have revealed a substantial number of novel autophagy regulators with RNA-related functions, indicating roles for RNA and associated proteins not only as cargo, but also as regulators of this process. In this review, we discuss widespread evidence of RNA catabolism via autophagy in yeast, plants and animals, reviewing the molecular mechanisms and biological importance in normal physiology, stress and disease. In addition, we explore emerging evidence of core autophagy regulation mediated by RNA-binding proteins and noncoding RNAs, and point to gaps in our current knowledge of the connection between RNA and autophagy. Finally, we discuss the pathological implications of RNA-protein aggregation, primarily in the context of neurodegenerative disease.
Bachelor Thesis: The Challenges for Maritime Spatial Planning in Sweden: Results from the compliance process with Directive 2014/89/EU on developing and implementing MSP

This thesis seeks to identify change processes triggered by Directive 2014/89/EU in Swedish law, administration and policies connected to maritime governance within the country. In this regard, it poses the research question of How successful is Sweden in implementing directive 2014/89/EU? The findings indicated that Sweden is facing challenges of institutional and administrative character as well as issues connected to the overall character of spatially planning its maritime areas. This is with regards to the fact that Sweden did not have any MSP established before the Directive came into force and hence, MSP proves to be a completely new planning approach for the country. Nevertheless, the findings of this thesis indicate that Sweden is successfully managing the compliance process until now, although certain aspects of detected compliance challenges are still unsolved.
Calcium sensing receptor regulates cardiomyocyte function through nuclear calcium

Nuclear Ca2+ plays a pivotal role in the regulation of gene expression. IP3 (inositol‐1,4,5‐trisphosphate) is an important regulator of nuclear Ca2+. We hypothesized that the CaR (calcium sensing receptor) stimulates nuclear Ca2+ release through IICR (IP3‐induced calcium release) from perinuclear stores. Spontaneous Ca2+ oscillations and the spark frequency of nuclear Ca2+ were measured simultaneously in NRVMs (neonatal rat ventricular myocytes) using confocal imaging. CaR‐induced nuclear Ca2+ release through IICR was abolished by inhibition of CaR and IP3Rs (IP3 receptors). However, no effect on the inhibition of RyRs (ryanodine receptors) was detected. The results suggest that CaR specifically modulates nuclear Ca2+ signalling through the IP3R pathway. Interestingly, nuclear Ca2+ was released from perinuclear stores by CaR activator‐induced cardiomyocyte hypertrophy through the Ca2+‐dependent phosphatase CaN (calcineurin)/NFAT (nuclear factor of activated T‐cells) pathway. We have also demonstrated that the activation of the CaR increased the NRVM protein content, enlarged cell size and stimulated CaN expression and NFAT nuclear translocation in NRVMs. Thus, CaR enhances the nuclear Ca2+ transient in NRVMs by increasing fractional Ca2+ release from perinuclear stores, which is involved in cardiac hypertrophy through the CaN/NFAT pathway.
We Are What We Eat: Obesity, Income, and Social Comparisons

The empirical evidence of a non-monotone relation between income and obesity is not well explained. We build a theoretical model combining income inequality and social comparisons to explain the link between income and obesity and study tax policy implications for fighting obesity. We assume that differences in food consumption patterns between poor and wealthy households partly reflect positionality, which is the concern for social status. Our key assumption is that positionality for low-calorie food consumption is positively related to a country’s wealth. In this framework, body weight outcomes reflect competing income and positionality effects, yielding the following results. We explain the link between average obesity rates, and standards of living and suggest the existence of a Kuznets curve for obesity. For cross sections of the population, we explain the observed correlation between income and obesity, which is positive in poor countries, and negative rich countries. We find that increasing the relative cost of high-calorie food is less effective at decreasing the relative weight of poor individuals in rich countries than in poor countries.
Development of gemcitabine-adsorbed magnetic gelatin nanoparticles for targeted drug delivery in lung cancer

Magnetic iron oxide nanoparticles (IONPs) were coated with gelatin type B by means of the two-step desolvation method. Drug loading by adsorption was studied under various conditions such as different temperature, contact time, pH, and initial gemcitabine concentration. Further, Langmuir isotherm curves were constracted and constants were calculated. According to the Langmuir isotherm, the Gibbs free energy of the adsorption process at 25°C was − 4.74 kJ/mol. On the other hand, this value at 37°C was − 7.86 kJ/mol. In vitro drug release was performed at pH levels of 5 and 7.4, with gemcitabine-loaded magnetic gelatin nanoparticles and free gemcitabine, and both the results were subsequently compared.
A simplified method for determining the high frequency induction motor equivalent electrical circuit parameters to be used in EMI effect

The aim of this paper is to present a simple method for determining the high frequency parameters of a three-phase induction motor to be used in studies involving variable speed drives with PWM three-phase inverters, in which it is necessary to check the effects caused to the motor by the electromagnetic interference, (EMI) in the differential mode, as well as in the common mode. The motor parameters determination is generally performed in adequate laboratories using accurate instruments, such as very expensive RLC bridges. The method proposed here consists in the identification of the motor equivalent electrical circuit parameters in rated frequency and in high frequency through characteristic tests in the laboratory, together with the use of characteristic equations and curves, shown in the references to be mentioned for determining the motor high frequency parasite capacitances and also through system simulations using dedicated software, like Pspice, determining the characteristic waveforms involved in the differential and common mode phenomena, comparing and validating the procedure through published papers [01].
Novel PEX1 coding mutations and 5′ UTR regulatory polymorphisms

Zellweger syndrome and its milder variants—neonatal adrenoleukodystrophy and infantile Refsum disease—comprise a clinical continuum of diseases referred to as the Zellweger spectrum. Mutations in the PEX1 gene, which consists of 24 exons and encodes a AAA ATPase protein required for peroxisomal protein import, account for approximately two‐thirds of the known Zellweger spectrum patient mutations. In this paper, we report on four novel PEX1 mutations and two polymorphisms in an Australasian cohort. Two of the mutations—c. 1108_1109insA and c. 2391_2392delTC—that lead to the introduction of a premature termination codon in exons 5 and 14, respectively, are associated with the severe Zellweger phenotype. One patient with a milder disease phenotype was a compound heterozygote for two missense mutations (I989T and R998Q), both affecting amino acids in the second, C‐terminal AAA domain of the protein. PTS1 protein import levels in cultured skin fibroblasts from this patient were almost 20% of normal control levels. We have also characterized two co‐segregating polymorphisms in the 5′ UTR of the PEX1 gene. Based on reporter assays, the c. ‐137T>C polymorphism leads to reduced PEX1 expression, whereas the c. ‐53C>G polymorphism leads to increased expression. When present together, these regulatory polymorphisms lead to near‐normal PEX1 expression. Altered PEX1 expression due to the presence of either the c. ‐137T>C or the c. ‐53C>G variant could impact on residual PEX1 function if another co‐allelic mutation was present which did not completely abolish PEX1 function. It also follows that the presence of polymorphisms in the PEX1 promoter region could have implications for patients with mutations in other PEX proteins known to interact with PEX1, such as PEX6. Thus, although not deleterious in control individuals, these polymorphisms could contribute to phenotypic heterogeneity among Zellweger spectrum patients. © 2005 Wiley‐Liss, Inc.
Androgenic responses to resistance exercise: effects of feeding and L-carnitine.

PURPOSE The purpose of this investigation was to determine the effects of 3 wk of L-carnitine L-tartrate (LCLT) supplementation and post-resistance-exercise (RE) feeding on hormonal and androgen receptor (AR) responses. METHODS Ten resistance-trained men (mean+/-SD: age, 22+/-1 yr; mass, 86.3+/-15.3 kg; height, 181+/-11 cm) supplemented with LCLT (equivalent to 2 g of L-carnitine per day) or placebo (PL) for 21 d, provided muscle biopsies for AR determinations, then performed two RE protocols: one followed by water intake, and one followed by feeding (8 kcal.kg body mass, consisting of 56% carbohydrate, 16% protein, and 28% fat). RE protocols were randomized and included serial blood draws and a 1-h post-RE biopsy. After a 7-d washout period, subjects crossed over, and all experimental procedures were repeated. RESULTS LCLT supplementation upregulated (P<0.05) preexercise AR content compared with PL (12.9+/-5.9 vs 11.2+/-4.0 au, respectively). RE increased (P<0.05) AR content compared with pre-RE values in the PL trial only. Post-RE feeding significantly increased AR content compared with baseline and water trials for both LCLT and PL. Serum total testosterone concentrations were suppressed (P<0.05) during feeding trials with respect to corresponding water and pre-RE values. Luteinizing hormone demonstrated subtle, yet significant changes in response to feeding and LCLT. CONCLUSION In summary, these data demonstrated that: 1) feeding after RE increased AR content, which may result in increased testosterone uptake, and thus enhanced luteinizing hormone secretion via feedback mechanisms; and 2) LCLT supplementation upregulated AR content, which may promote recovery from RE.