Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimicrobial activity of five essential oils against origin strains of the Enterobacteriaceae family

An in vitro assay measuring the antimicrobial activity of essential oils of Coridothymus capitatus (Spanish origanum), Satureja montana, Thymus mastichina (Spanish Origanum majorana), Thymus zygis (Spanish variety of Thymus vulgaris) and Origanum vulgare has been carried out against poultry origin strains of Escherichia coli, Salmonella enteritidis and Salmonella essen, and pig origin strains of enterotoxigenic E. coli (ETEC), Salmonella choleraesuis and Salmonella typhimurium. Using the broth microdilution method, all the essential oils showed an MIC ≥ 2% (v/v) for the two strains of E. coli. The essential oil that showed the highest antimicrobial activity against the four strains of Salmonella was Origanum vulgare (MIC ≤ 1% v/v), followed by Thymus zygis (MIC ≤2% v/v). Thymus mastichina inhibited all the microorganisms at the highest concentration, 4% (v/v), while the rest of the essential oils showed highly variable results. By chemotyping, higher inhibitory capacity was observed in the oils with a higher percentage of phenolic components (carvacrol and thymol) in comparison with oils containing the monoterpenic alcohol linalool. The results of this work confirm the antimicrobial activity of some essential oils, as well as their potential application in the treatment and prevention of poultry and pig diseases caused by salmonella.
Highly Pathogenic Avian Influenza Virus Subtype H5N1 Escaping Neutralization: More than HA Variation

ABSTRACT Influenza A viruses are one of the major threats in modern health care. Novel viruses arise due to antigenic drift and antigenic shift, leading to escape from the immune system and resulting in a serious problem for disease control. In order to investigate the escape process and to enable predictions of escape, we serially passaged influenza A H5N1 virus in vitro 100 times under immune pressure. The generated escape viruses were characterized phenotypically and in detail by full-genome deep sequencing. Mutations already found in natural isolates were detected, evidencing the in vivo relevance of the in vitro-induced amino acid substitutions. Additionally, several novel alterations were triggered. Altogether, the results imply that our in vitro system is suitable to study influenza A virus evolution and that it might even be possible to predict antigenic changes of influenza A viruses circulating in vaccinated populations.
A New Method for Mutual Coupling Correction of Array Output Signal

The method of mutual coupling correction of array output signal is studied in the paper. According to array signal processing's feature, array error model is analyzed and array mutual coupling is studied. The method that smart antennas' channel calibration by BP network in wireless communication is proposed, which improves the accuracy of algorithms, such as the DOA estimation algorithm, Beam Forming algorithm etc.8-unit uniform linear array and 8-unit uniform circular array are simulated by computer, and the results are compared with spatial spectrum lines of before-after correction. The proposed method is effective, for computer simulation experimental results are in line with the theoretical ones.
Studies on the Formation of 6‐Hydroxydopamine in Mouse Brain After Administration of 2,4,5‐Trihydroxyphenylalanine (6‐HydroxyDOPA)

Abstract: 2,4,5‐Trihydroxyphenylalanine (6‐OH‐DOPA) destroys central and peripheral noradrenergic neurons, while sparing dopaminergic neurons. Previous studies indicate that 6‐OH‐DOPA toxicity is mediated by the formation of 6‐hydroxydopamine. However, levels of 6‐hydroxydopamine in brain following peripheral administration of 6‐OH‐DOPA have not been documented. In the current study, 6‐OH‐DOPA and 6‐hydroxydopamine were measured in brain by HPLC with electrochemical detection after intraperitoneal injection of 6‐OH‐DOPA. When mice were injected with 100 mg 6‐OH‐DOPA/kg, 6‐hydroxydopamine levels in the striatum were highest (1.9 μg/g) at 15 min and fell slowly to 24% of the peak value at 4 h. Experiments with reserpine indicated that the relative stability of 6‐hydroxydopamine was largely dependent upon storage in synaptic vesicles. Reserpine (10 mg/kg) lowered striatal 6‐hydroxydopamine levels to 21.6% of control (non‐reserpine‐treated) values at 1 h, and to 8.9% of control values at 4 h. Levels of 6‐hydroxydopamine in the striatum at 1 h were increased 113% by pargyline (100 mg/kg), 145% by α‐methyldopahydrazine (carbidopa; 25 mg/kg), and 261% by pargyline and carbidopa together. Levels of dopamine in the striatum were unchanged at 2.5 h after 200 mg 6‐OH‐DOPA/kg (with pargyline and 50 mg carbidopa/kg), whereas levels of norepinephrine in the frontal cortex fell by 77%. At the same time, 6‐hydroxydopamine levels were 8.8‐fold higher in the striatum (5.54 μ/g) than in the cortex (0.63 μg/g). The latter results show that the striatum is resistant to 6‐OH‐DOPA‐mediated depletion of catechol‐amines even though the concentrations of 6‐hydroxydopamine approach those of endogenous dopamine.
Comparison of different preparation methods of biological samples for FIB milling and SEM investigation

When a new approach in microscopy is introduced, broad interest is attracted only when the sample preparation procedure is elaborated and the results compared with the outcome of the existing methods. In the work presented here we tested different preparation procedures for focused ion beam (FIB) milling and scanning electron microscopy (SEM) of biological samples. The digestive gland epithelium of a terrestrial crustacean was prepared in a parallel for FIB/SEM and transmission electron microscope (TEM). All samples were aldehyde‐fixed but followed by different further preparation steps. The results demonstrate that the FIB/SEM samples prepared for conventional scanning electron microscopy (dried) is suited for characterization of those intracellular morphological features, which have membranous/lamellar appearance and structures with composition of different density as the rest of the cell. The FIB/SEM of dried samples did not allow unambiguous recognition of cellular organelles. However, cellular organelles can be recognized by FIB/SEM when samples are embedded in plastic as for TEM and imaged by backscattered electrons. The best results in terms of topographical contrast on FIB milled dried samples were obtained when samples were aldehyde‐fixed and conductively stained with the OTOTO method (osmium tetroxide/thiocarbohydrazide/osmium tetroxide/thiocarbohydrazide/osmium tetroxide). In the work presented here we provide evidence that FIB/SEM enables both, detailed recognition of cell ultrastructure, when samples are plastic embedded as for TEM or investigation of sample surface morphology and subcellular composition, when samples are dried as for conventional SEM.
Relations of Serum COMP to Cardiovascular Risk Factors and Endothelial Function in Patients with Rheumatoid Arthritis Treated with Methotrexate and TNF-α Inhibitors

Objective. To examine whether serum level of cartilage oligomeric matrix protein (S-COMP) is related to methotrexate (MTX) or to MTX and tumor necrosis factor-α (TNF-α) combination treatment for rheumatoid arthritis (RA); and to investigate whether S-COMP is related to cardiovascular risk factors including endothelial dysfunction and level of anticitrullinated protein antibodies (ACPA) in patients with RA. Methods. Clinical and laboratory measures, including S-COMP and reactive hyperemic index (RHI), were examined in 55 consecutive patients with RA starting with either MTX (n = 34) or MTX and anti-TNF-α treatment (n = 21) at baseline, and after 6 weeks and 6 months. Results. S-COMP was similar in the 2 treatment regimens during followup. We found a positive relationship between S-COMP at baseline and the use of disease-modifying antirheumatic drugs the last year preceding the study (p = 0.001), and a negative relation to current use of systemic glucocorticosteroids (p = 0.044). The nonsignificant change in S-COMP between baseline and the 6-month followup was positively and independently related to change in ACPA level (p = 0.009). There was no significant association between RHI and level of S-COMP at baseline. Conclusion. The cartilage turnover marker S-COMP did not change significantly after 6 months’ treatment with MTX with or without a TNF-α inhibitor in patients with RA. The positive association between S-COMP and ACPA suggests that these factors might interact, and could both be contributors to an unknown link between inflammation and cartilage destruction in patients with RA. S-COMP was not related to endothelial function in patients with RA, or to other cardiovascular risk factors studied. Clinical Trials registration number NCT00902005.
Poly(ADP-Ribosyl) Glycohydrolase Prevents the Accumulation of Unusual Replication Structures during Unperturbed S Phase

ABSTRACT Poly(ADP-ribosyl)ation (PAR) has been implicated in various aspects of the cellular response to DNA damage and genome stability. Although 17 human poly(ADP-ribose) polymerase (PARP) genes have been identified, a single poly(ADP-ribosyl) glycohydrolase (PARG) mediates PAR degradation. Here we investigated the role of PARG in the replication of human chromosomes. We show that PARG depletion affects cell proliferation and DNA synthesis, leading to replication-coupled H2AX phosphorylation. Furthermore, PARG depletion or inhibition per se slows down individual replication forks similarly to mild chemotherapeutic treatment. Electron microscopic analysis of replication intermediates reveals marked accumulation of reversed forks and single-stranded DNA (ssDNA) gaps in unperturbed PARG-defective cells. Intriguingly, while we found no physical evidence for chromosomal breakage, PARG-defective cells displayed both ataxia-telangiectasia-mutated (ATM) and ataxia-Rad3-related (ATR) activation, as well as chromatin recruitment of standard double-strand-break-repair factors, such as 53BP1 and RAD51. Overall, these data prove PAR degradation to be essential to promote resumption of replication at endogenous and exogenous lesions, preventing idle recruitment of repair factors to remodeled replication forks. Furthermore, they suggest that fork remodeling and restarting are surprisingly frequent in unperturbed cells and provide a molecular rationale to explore PARG inhibition in cancer chemotherapy.
Co-reflection in online learning environments

While peer collaboration is the basis for co-learning in many groups, in the classroom the prevailing assumption is that teachers facilitate student learning, through course structure, setting learning tasks and outcomes, presentation, discussion, facilitating small group learning, coaching, and mentoring, among others. Though instructional design models have recognized that learning builds on interactions between learners and their environments (teachers have moved from "sage on the stage" to "guide on the side"), these models tend to focus on individual student learning rather than group learning.
Spike count, spike timing and temporal information in the cortex of awake, freely moving rats

Objective. Sensory processing of peripheral information is not stationary but is, in general, a dynamic process related to the behavioral state of the animal. Yet the link between the state of the behavior and the encoding properties of neurons is unclear. This report investigates the impact of the behavioral state on the encoding mechanisms used by cortical neurons for both detection and discrimination of somatosensory stimuli in awake, freely moving, rats. Approach. Neuronal activity was recorded from the primary somatosensory cortex of five rats under two different behavioral states (quiet versus whisking) while electrical stimulation of increasing stimulus strength was delivered to the mystacial pad. Information theoretical measures were then used to measure the contribution of different encoding mechanisms to the information carried by neurons in response to the whisker stimulation. Main results. We found that the behavioral state of the animal modulated the total amount of information conveyed by neurons and that the timing of individual spikes increased the information compared to the total count of spikes alone. However, the temporal information, i.e. information exclusively related to when the spikes occur, was not modulated by behavioral state. Significance. We conclude that information about somatosensory stimuli is modulated by the behavior of the animal and this modulation is mainly expressed in the spike count while the temporal information is more robust to changes in behavioral state.
A 1200-V, 60-A SiC MOSFET Multichip Phase-Leg Module for High-Temperature, High-Frequency Applications

In this paper, a high-temperature, high-frequency, wire-bond-based multichip phase-leg module was designed, fabricated, and fully tested. Using paralleled Silicon Carbide (SiC) MOSFETs, the module was rated at 1200 V and 60 A, and was designed for a 25-kW three-phase inverter operating at a switching frequency of 70 kHz, and in a harsh environment up to 200 °C, for aircraft applications. To this end, the temperature-dependent characteristics of the SiC MOSFET were first evaluated. The results demonstrated the superiority of the SiC MOSFET in both static and switching performances compared to Si devices, but meanwhile did reveal the design tradeoff in terms of the device's gate oxide stability. Various high-temperature packaging materials were then extensively surveyed and carefully selected for the module to sustain the harsh environment. The electrical layout of the module was also optimized using a modeling and simulation approach, in order to minimize the device parasitic ringing during high-speed switching. Finally, the static and switching performances of the fabricated module were tested, and the 200 °C continuous operation of the SiC MOSFETs was verified.
Erythroblast transformation-specific 2 correlates with vascular smooth muscle cell apoptosis in rat heterotopic heart transplantation model.

BACKGROUND Cardiac allograft vasculopathy (CAV) decreases the long-term survival of heart transplantation recipients. Vascular smooth muscle cell (VSMC) apoptosis is an important pathological feature of CAV. Erythroblast transformation-specific 2 (Ets-2), as a transcription factor, participates in cell apoptosis and plays an important role in organ transplantation. METHODS Hearts from Wistar-Furth (WF:RT1u) rats were heterotopically transplanted into Lewis (Lew:RT1(l)) rats without immunosuppression. Additional syngeneic heterotopic cardiac transplantations were performed in Lewis rats. HE staining was used to identify CAV. Ets-2 expression was examined by western blot. Ets-2 tissue location was examined by immunohistochemical assay and double immunostaining. Cleaved caspase 3 expression was detected by western blot. Co-localization of Ets-2 and cleaved caspase 3 was detected by double immunostaining. Ets-2, p53, cleaved caspase 3 and Bcl-xl expression in rat VSMC line A7R5 was examined after Ets-2 siRNA transfection. TUNEL assay was applied to detect A7R5 apoptosis with or without ETS-2 siRNA transfection. Immunoprecipitation was performed to explore the interaction between Ets-2 and p53. RESULTS Ets-2 expression decreased in the allograft group but had no obvious change in the isograft group. Meanwhile, the phenomenon of CAV was observed in the allograft group and there is neointima formation in the isograft group which is not obvious compared with allograft group. Additionally, Ets-2 expression was opposite to VSMC apoptosis in the allograft group. In vitro, Ets-2 siRNA transfection in A7R5cells resulted in enhanced cell apoptosis. Finally, Ets-2 interacted with p53. CONCLUSIONS Ets-2 might inhibit VSMC apoptosis via p53 pathway. The results further elucidate the molecular mechanism of VSMC apoptosis after heart transplantation during CAV and provide theoretical basis for seeking new specific drug targets for CAV prevention and treatment.
Comparison of DNA sequencing and Roche Linear array in human papillomavirus (HPV) genotyping.

BACKGROUND Human papillomavirus (HPV) is the etiological agent of cervical cancer. HPV genotyping is important to determine the presence of high-risk types. Recently, a new HPV genotyping method, the Roche Linear array genotyping test, was introduced and is compared here with a sequencing-based HPV genotyping system. MATERIALS AND METHODS A series of 102 women (age range 30-55 years) shown to be HPV DNA-positive by PCR were typed by sequencing and the Linear array genotyping assay. RESULTS The sequence analysis revealed the presence of 80 single high-risk types and 22 single low-risk types. With the Linear array, single infections were found in 46 cases, double infections in 37 cases, triple infections in 12 cases, and more than three in 6 cases. One case positive by sequencing gave a negative result by Linear array. Altogether, a concordant single genotype was found in 93 (91.2%) out of the 102 cases and the single-type concordance between the two assays was significant (Spearman rho = 0.849, p = 0.0001; intraclass correlation coefficient (ICC) (ICC = 0.924, 95% CI 0.888-0.949) (p = 0.0001). The majority of the disparate results were due to the detection of multiple types by the Linear array. CONCLUSION The Roche Linear array is a highly accurate assay for HPV genotyping. This is particularly true in the presence of multiple infections which DNA sequencing is unable to resolve.
Pharmacokinetic interaction between itraconazole and metformin in rats: competitive inhibition of metabolism of each drug by each other via hepatic and intestinal CYP3A1/2

BACKGROUND AND PURPOSE Fungal infection is prevalent in patients with diabetes mellitus. Thus, we investigated whether a pharmacokinetic interaction occurs between the anti‐fungal agent itraconazole and the anti‐glycaemic drug metformin, as both drugs are commonly administered together to diabetic patients and are metabolized via hepatic CYP3A subfamily in rats.
Experimental Verification and Optimization Analysis of Warpage for Panel-Level Fan-Out Package

Nowadays, fan-out package is regarded as one of the latest and most potential technologies because it possesses lower cost, thinner profile, and better electrical performance and thermal performance. However, thermally induced warpage in the molding process is a critical issue due to the larger wafer or panel size, the shrinkage of epoxy mold compound (EMC) during the curing stage, and the mismatch of coefficient of thermal expansion (CTE) among the constituent materials during the cooling stage, which needs to be controlled effectively for successful subsequent process of the fan-out package. In this paper, a novel $320 \times 320$ -mm2 panel-level fan-out package based on “Die Last” process is developed. A coreless substrate with redistribution layer is fabricated and bonded onto a low-CTE and high-glass-transition-temperature (Tg) FR4 carrier through thermal release film. The thermally induced warpage issue in the molding process is investigated. A warpage simulation method is presented and verified by Shadow Moiré experiment. The error between the simulation and experimental results is about 4.8%. For the warpage optimization analysis, the effect of geometry structure on the warpage is first investigated by the design of simulation approach. Full factor experiment is conducted, and Minitab statistical software is utilized to analyze the effect of the geometry structure on warpage. It is found that decreasing die thickness and molding thicker EMC can effectively decrease the warpage. Then, the effects of molding temperature and in-plane CTE of FR4 on warpage are studied, respectively. When molding temperature is 120 °C and in-plane CTE of FR4 decreases to 10.5 ppm/°C, the thermally induced warpage in the molding process is only about 0.31 mm, thus subsequent process of fan-out package can be conducted successfully.
Potential Games and Competition in the Supply of Natural Resources

This dissertation discusses the Cournot competition and competitions in the exploitation of common pool resources and its extension to the tragedy of the commons. I address these models by using potential games and inquire how these models reflect the real competitions for provisions of environmental resources. The Cournot models are dependent upon how many firms there are so that the resultant Cournot-Nash equilibrium is dependent upon the number of firms in oligopoly. But many studies do not take into account how the resultant Cournot-Nash equilibrium is sensitive to the change of the number of firms. Potential games can find out the outcome when the number of firms changes in addition to providing the “traditional” Cournot-Nash equilibrium when the number of firms is fixed. Hence, I use potential games to fill the gaps that exist in the studies of competitions in oligopoly and common pool resources and extend our knowledge in these topics. In specific, one of the rational conclusions from the Cournot model is that a firm’s best policy is to split into separate firms. In real life, we usually witness the other way around; i.e., several firms attempt to merge and enjoy the monopoly profit by restricting the amount of output and raising the price. I aim to solve this conundrum by using potential games. I also clarify, within the Cournot competition model, how regulatory intervention in the management of environmental pollution externalities affects the equilibrium number of polluters. In addition, the tragedy of the commons is the term widely used to describe the overexploitation of open-access common-pool resources. Open-access encourages potential resource users to continue to enter the resource up to the point where rents are exhausted. The resulting level of resource use is higher than is socially optimal, and in extreme cases can lead to the collapse of the resource and the communities that may depend on it. In this paper I use the concept of potential games to evaluate the relation between the cost of resource use and the equilibrium number of resource
Accuracy of ICD-9-CM Codes for Identifying Cardiovascular and Stroke Risk Factors

Objectives:We sought to determine which ICD-9-CM codes in Medicare Part A data identify cardiovascular and stroke risk factors. Design and Participants:This was a cross-sectional study comparing ICD-9-CM data to structured medical record review from 23,657 Medicare beneficiaries aged 20 to 105 years who had atrial fibrillation. Measurements:Quality improvement organizations used standardized abstraction instruments to determine the presence of 9 cardiovascular and stroke risk factors. Using the chart abstractions as the gold standard, we assessed the accuracy of ICD-9-CM codes to identify these risk factors. Main Results:ICD-9-CM codes for all risk factors had high specificity (>0.95) and low sensitivity (≤0.76). The positive predictive values were greater than 0.95 for 5 common, chronic risk factors—coronary artery disease, stroke/transient ischemic attack, heart failure, diabetes, and hypertension. The sixth common risk factor, valvular heart disease, had a positive predictive value of 0.93. For all 6 common risk factors, negative predictive values ranged from 0.52 to 0.91. The rare risk factors—arterial peripheral embolus, intracranial hemorrhage, and deep venous thrombosis—had high negative predictive value (≥0.98) but moderate positive predictive values (range, 0.54–0.77) in this population. Conclusions:Using ICD-9-CM codes alone, heart failure, coronary artery disease, diabetes, hypertension, and stroke can be ruled in but not necessarily ruled out. Where feasible, review of additional data (eg, physician notes or imaging studies) should be used to confirm the diagnosis of valvular disease, arterial peripheral embolus, intracranial hemorrhage, and deep venous thrombosis.