Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of DNA extraction methods for PCR‐based detection of Listeria monocytogenes from vegetables

Epidemiological data indicate that raw vegetables are associated with outbreaks of Listeria monocytogenes. Therefore, there is a demand for the availability of rapid and sensitive methods, such as PCR assays, for the detection and accurate discrimination of L. monocytogenes. However, the efficiency of PCR methods can be negatively affected by inhibitory compounds commonly found in vegetable matrices that may cause false‐negative results. Therefore, the sample processing and DNA isolation steps must be carefully evaluated prior to the introduction of such methods into routine practice. In this study, we compared the ability of three column‐based and four magnetic bead‐based commercial DNA isolation kits to extract DNA of the model micro‐organism L. monocytogenes from raw vegetables. The DNA isolation efficiency of all isolation kits was determined using a triplex real‐time qPCR assay designed to specifically detect L. monocytogenes. The kit with best performance, the PowerSoil™ Microbial DNA Isolation Kit, is suitable for the extraction of amplifiable DNA from L. monocytogenes cells in vegetable with efficiencies ranging between 29·6 and 70·3%. Coupled with the triplex real‐time qPCR assay, this DNA isolation kit is applicable to the samples with bacterial loads of 103 bacterial cells per gram of L. monocytogenes.
The effect of price information on test-ordering behavior and patient outcomes in a pediatric emergency department.

OBJECTIVE We sought to determine whether information on hospital charges (prices) would affect test-ordering and quality of patient care in a pediatric emergency department (ED). DESIGN Prospective, nonblind, controlled trial of price information. SETTING Urban, university-affiliated pediatric ED. METHODS We prospectively assessed patients 2 months to 10 years of age with a presenting temperature >/=38.5 degrees C or complaint of vomiting, diarrhea, or decreased oral intake. The assessments were done during three periods: September 1997 through December 1997 (control), January 1998 through March 1998 (intervention), and April 1998 (washout). In the control and washout periods, physicians noted tests ordered on a list attached to each chart. In the intervention period, physicians noted tests ordered on a similar list that included standard hospital charges for each test. Records of each visit were reviewed to determine clinical and demographic information as well as patient disposition. In the control and intervention periods, families of nonadmitted patients were interviewed by telephone 7 days after the visit. RESULTS When controlled for triage level, vital signs, and admission rates, in a multivariate model, charges for tests in the intervention period were 27% less than charges in the control period. The greatest decrease was seen among low-acuity, nonadmitted patients (43%). In telephone follow-up, patients in the intervention period were slightly more likely to have made an unscheduled follow-up visit to a health care provider (24.4% vs 17.8%), but did not differ on improved condition (86.7% vs 83.4%) or family satisfaction (93.8% vs 93.0%). Adjusted charges in the washout period were 15% lower than in the control period and 15% higher than in the intervention period. CONCLUSION Providing price information was associated with a significant reduction in charges for tests ordered on pediatric ED patients with acute illness not requiring admission. This decrease was associated with a slightly higher rate of unscheduled follow-up, but no difference in subjective outcomes or family satisfaction.
Cross-Layer Design of Dynamic Bandwidth Allocation in DVB-RCS

In this paper, a novel cross-layer framework for optimizing the dynamic bandwidth allocation (DBA) of a digital video broadcast (DVB)-return channel satellite (RCS) system using adaptive coding is proposed. The design of the medium access control (MAC) methods taking into account the adaptive physical layer and higher layers' quality of service (QoS) requirements is cast as an optimization problem by using the network utility maximization (NUM) framework applied within the satellite subnetwork. Hierarchical and global solving procedures fully compliant with the DVB-RCS standard are proposed. They do not only provide minimum bandwidth guarantees but also maximize fairness. Further, they allow a joint optimization of the time slot size and overall system efficiency while minimizing signalling overhead. A reduced computational complexity algorithm to solve the DBA problem is presented. In practical terms, it increases the number of connections with absolute and relative QoS requirements the system can manage and facilitates the interoperability of the satellite network within an Internet protocol (IP) environment.
Finger vein recognition using weighted local binary pattern code based on a support vector machine

Finger vein recognition is a biometric technique which identifies individuals using their unique finger vein patterns. It is reported to have a high accuracy and rapid processing speed. In addition, it is impossible to steal a vein pattern located inside the finger. We propose a new identification method of finger vascular patterns using a weighted local binary pattern (LBP) and support vector machine (SVM). This research is novel in the following three ways. First, holistic codes are extracted through the LBP method without using a vein detection procedure. This reduces the processing time and the complexities in detecting finger vein patterns. Second, we classify the local areas from which the LBP codes are extracted into three categories based on the SVM classifier: local areas that include a large amount (LA), a medium amount (MA), and a small amount (SA) of vein patterns. Third, different weights are assigned to the extracted LBP code according to the local area type (LA, MA, and SA) from which the LBP codes were extracted. The optimal weights are determined empirically in terms of the accuracy of the finger vein recognition. Experimental results show that our equal error rate (EER) is significantly lower compared to that without the proposed method or using a conventional method.
Myocardial contractile response to nitric oxide and cGMP.

BACKGROUND Cardiac endothelium releases a number of factors that may modulate performance of underlying cardiac muscle. Nitric oxide (NO), which accounts for the biological activity of the vascular endothelium-derived relaxing factor and relaxes vascular smooth muscle by elevating intracellular cGMP, may be involved in this cardiac modulation. METHODS AND RESULTS We examined the myocardial contractile effects of the NO-releasing nitrovasodilators sodium nitroprusside (SNP), 3-morpholino-sydnonimine (SIN-1), and S-nitroso-N-acetyl-penicillamine (SNAP); of a cGMP analogue, 8-bromo-cGMP; and of the cGMP-phosphodiesterase inhibitor zaprinast in isolated cat papillary muscle. Modulation of these effects by endocardial endothelium (EE) and by cholinergic and adrenergic stimulation was also investigated. Concentration-response curves with addition of NO-releasing nitrovasodilators (SNP, SIN-1, SNAP) and 8-bromo-cGMP resulted in a biphasic inotropic response. Although administration of low concentrations induced a positive inotropic effect, higher concentrations induced a negative inotropic effect. Both NO-induced positive and negative inotropic effects were attenuated by methylene blue, suggesting a role for cGMP. The response to high concentrations of 8-bromo-cGMP was shifted to the right in muscles with damaged EE, whereas cholinergic stimulation shifted the curve leftward. Zaprinast caused a monophasic concentration-dependent positive inotropic effect; damaging the EE shifted the terminal portion of the curve upward. Concomitant cholinergic or adrenergic stimulation modified the response to zaprinast into a negative inotropic response. CONCLUSIONS NO and cGMP induced a concentration-dependent biphasic contractile response. The myocardial contractile effects of NO and cGMP were modulated by the status of EE and by concomitant cholinergic or adrenergic stimulation.
Protein Expression of STRO-1 Cells in Response to Different Topographic Features

Human skeletal stem cells (STRO-1 positive) display distinct responses to different topographical features. On a flat surface, skeletal cells spread, and in vitro, they typically display a polarized, fibroblast-like morphology. However, on microgrooved surfaces, these cells prefer to stretch along the grooves forming a similar morphology to in vivo, bipolarized fibroblasts. In contrast, on nanopits, these cells display a polygonal and osteoblastic phenotype. We have examined mechanotransduction events of STRO-1 positive in response to fibroblastic, microgrooved and osteogenic, controlled disorder nanopit, topographies using proteomics after 3 days in culture. Protein expression profiles were analyzed by difference gel electrophoresis to identify proteins that showed modulation of expression in response to different topographic features to assess early decision events in these cells on these discrete topographies. After only 72 hours in culture, STRO-1 positive displayed differential regulations of families of proteins involved in cell migration and proliferation. The current study indicated that osteogenic decision specific events had already occurred. Runx2 was localized in nuclei of the skeletal stem cells on the osteogenic nanopits; however, few signaling pathway changes were observed. This study demonstrated that micro- and nanotopographies activated skeletal stem cells at different times and with distinct mechanotransduction profiles.
Indoor air studies of fungi contamination at the Department of Pulmonology and Internal Medicine in Kavala Hospital in Greece.

PURPOSE The aim of the study was to assess the presence of airborne fungi and the fungal flora of the walls in the Departments of Pulmonary and Internal Medicine in Kavala Hospital (Greece). MATERIAL AND METHODS The study was carried out at the Department of Pulmonology and Internal medicine in Kavala Hospital. Materials for the tests were: the air samples (in front of the building and the selected rooms) and swabs from the walls. The air pollution was determined using SAS SUPER 100 (Pbi International). The microbial flora from walls was assessed using the Count-Tact applicator and the plate Count-Tact (BioMerieux). Humidity and temperature were evaluated by a thermo-hygrometer. RESULTS The following fungal pathogens isolated from air were Aspergillus, Candida albicans, Candida spp. , and Penicillium species in the Department of Pulmonary. Similar pathogens in the air of Department and Internal Medicine were found. Mean number of fungi colonies isolated from air in the Department of Pulmonology was significantly (p<0.001) higher compared to the Department of Internal Medicine. No significant correlations between CFU of fungi in air and temperature in both Departments were found. CONCLUSIONS The main fungal pathogens isolated from the air samples were Aspergillus and Candida albicans in the Departments of Pulmonary and Internal Medicine in Kavala Hospital. Fungal occurrence in the air of rooms and walls varied between the both departments of the same hospital.
Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were 15N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis—including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)—were all observed to be actively synthesized (15N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of 15N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here demonstrates the active synthesis of a metabolically specific minority of enzymes, revealing the surprising longevity of most proteins over the course of an extended incubation experiment in an established, slow-growing, methane-impacted environmental system.
Comparison of Annoyance from Railway Noise and Railway Vibration

The aim of this study is to compare vibration exposure to noise exposure from railway traffic in terms of equal annoyance, i.e., to determine when a certain noise level is equally annoying as a corresponding vibration velocity. Based on questionnaire data from the Train Vibration and Noise Effects (TVANE) research project from residential areas exposed to railway noise and vibration, the dose response relationship for annoyance was estimated. By comparing the relationships between exposure and annoyance for areas both with and without significant vibration exposure, the noise levels and vibration velocities that had an equal probability of causing annoyance was determined using logistic regression. The comparison gives a continuous mapping between vibration velocity in the ground and a corresponding noise level at the facade that are equally annoying. For equivalent noise level at the facade compared to maximum weighted vibration velocity in the ground the probability of annoyance is approximately 20% for 59 dB or 0.48 mm/s, and about 40% for 63 dB or 0.98 mm/s.
Electromechanical Delay of the Dorsiflexors in Young and Old Women

ii ACKNOWLEDGEMENTS iiiii TABLE OF CONTENTS v LIST OF TABLES viii LIST OF FIGURES viii LIST OF ABBREVIATIONS iviii CHAPTER 1: GENERAL INTRODUCTION 1.0 General Introduction 1 1.1 Electromechanical Delay 1 1.2 Factors that could affect Electromechanical Delay 5 1.2. 1 Fatigue 6 1.2. 2 Potentiation 8 1.2. 3 Lengthening Contractions 9 1.3 Aging 10 1.4 Sex 13 1.5 Voluntary vs. Evoked Measures of EMD 14 CHAPTER 2: INTRODUCTION 18 CHAPTER 3: METHODS 3.1 Subjects 20 3.2 Experimental Arrangement 20 3.3 Experimental Procedure 21 3.4 Fatigue and Recovery Testing Design 22
Molecular Interaction between Cyclophilin D and Adenine Nucleotide Translocase in Cytochrome c Release

Abstract: We propose a model for the mechanism of permeability transition (PT) related cytochrome c release. It is likely that the Ca2+ requirement for the induction of the mitochondrial permeability transition pore (MPTP) opening might be due to the Ca2+‐dependent interaction between cyclophilin D and ANT. We show here that the modification of adenine nucleotide translocase (ANT), which is one of the components of MPTP, can induce two different types of the cytochrome c release. One is dependent on classical PT, resulting in mitochondrial swelling, and is inhibited by cyclosporin A. The other is PT‐independent, without swelling, and is insensitive to cyclosporin A.
Hydrological Modeling in Data-Scarce Catchments: The Kilombero Floodplain in Tanzania

Deterioration of upland soils, demographic growth, and climate change all lead to an increased utilization of wetlands in East Africa. This considerable pressure on wetland resources results in trade-offs between those resources and their related ecosystem services. Furthermore, relationships between catchment attributes and available wetland water resources are one of the key drivers that might lead to wetland degradation. To investigate the impacts of these developments on catchment-wetland water resources, the Soil and Water Assessment Tool (SWAT) was applied to the Kilombero Catchment in Tanzania, which is like many other East African catchments, as it is characterized by overall data scarcity. Due to the lack of recent discharge data, the model was calibrated for the period from 1958–1965 (R2 = 0.86, NSE = 0.85, KGE = 0.93) and validated from 1966–1970 (R2 = 0.80, NSE = 0.80, KGE = 0.89) with the sequential uncertainty fitting algorithm (SUFI-2) on a daily resolution. Results show the dependency of the wetland on baseflow contribution from the enclosing catchment, especially in dry season. Main contributions with regard to overall water yield arise from the northern mountains and the southeastern highlands, which are characterized by steep slopes and a high share of forest and savanna vegetation, respectively. Simulations of land use change effects, generated with Landsat images from the 1970s up to 2014, show severe shifts in the water balance components on the subcatchment scale due to anthropogenic activities. Sustainable management of the investigated catchment should therefore account for the catchment–wetland interaction concerning water resources, with a special emphasis on groundwater fluxes to ensure future food production as well as the preservation of the wetland ecosystem.
Can Current Electronic Systems Meet Drug Safety and Effectiveness Requirements?

BACKGROUND Every health policy jurisdiction is endeavoring to enhance its ability to evaluate drug effectiveness, safety and cost in the real world (pharmacosurveillance). METHODS A nominal group consensus conference of stakeholders finalized data items deemed necessary for pharmacosurveillance. Large administrative datasets (LADs), electronic health records (EHRs) and electronic patient registries (PRs), were investigated as sources of this information and for their vulnerability to methodologic bias. Health data privacy legislation and research guidelines were systematically reviewed for their constraint to linked data resource analyses. RESULTS More than 129 data items were strongly recommended for routine pharmacosurveillance. LADs had very complete information, but restricted to a small number of required data items. EHRs, especially with e-pharmacy links, offer by far the most complete set of health information domains but data entry completeness is highly variable. Adjustment methods for channeling bias are inadequate to mimic randomized trials. Anonymized, linked data held within a secure academic research environment, poses the least privacy concerns. CONCLUSIONS Notwithstanding major technical, methodologic and privacy challenges, individual-level linkage of health data resources poses the best option for pharmacosurveillance today. In future, drug regulators and reimbursement agencies should consider mandatory post-marketing randomized trials.
Biotransformation of anthelmintics and the activity of drug-metabolizing enzymes in the tapeworm Moniezia expansa

SUMMARY The sheep tapeworm Moniezia expansa is very common parasite, which affects ruminants such as sheep, goats as well as other species. The benzimidazole anthelmintics albendazole (ABZ), flubendazole (FLU) and mebendazole (MBZ) are often used to treat the infection. The drug-metabolizing enzymes of helminths may alter the potency of anthelmintic treatment. The aim of our study was to assess the activity of the main drug-metabolizing enzymes and evaluate the metabolism of selected anthelmintics (ABZ, MBZ and FLU) in M. expansa. Activities of biotransformation enzymes were determined in subcellular fractions. Metabolites of the anthelmintics were detected and identified using high performance liquid chromatography/ultra-violet/VIS/fluorescence or ultra-high performance liquid chromatography/mass spectrometry. Reduction of MBZ, FLU and oxidation of ABZ were proved as well as activities of various metabolizing enzymes. Despite the fact that the conjugation enzymes glutathione S-transferase, UDP-glucuronosyl transferase and UDP-glucosyl transferase were active in vitro, no conjugated metabolites of anthelmintics were identified either ex vivo or in vitro. The obtained results indicate that sheep tapeworm is able to deactivate the administered anthelmintics, and thus protects itself against their action.
T-Cell Reactivity against Streptococcal Antigens in the Periphery Mirrors Reactivity of Heart-Infiltrating T Lymphocytes in Rheumatic Heart Disease Patients

ABSTRACT T-cell molecular mimicry between streptococcal and heart proteins has been proposed as the triggering factor leading to autoimmunity in rheumatic heart disease (RHD). We searched for immunodominant T-cell M5 epitopes among RHD patients with defined clinical outcomes and compared the T-cell reactivities of peripheral blood and intralesional T cells from patients with severe RHD. The role of HLA class II molecules in the presentation of M5 peptides was also evaluated. We studied the T-cell reactivity against M5 peptides and heart proteins on peripheral blood mononuclear cells (PBMC) from 74 RHD patients grouped according to the severity of disease, along with intralesional and peripheral T-cell clones from RHD patients. Peptides encompassing residues 1 to 25, 81 to 103, 125 to 139, and 163 to 177 were more frequently recognized by PBMC from RHD patients than by those from controls. The M5 peptide encompassing residues 81 to 96 [M5(81–96) peptide] was most frequently recognized by PBMC from HLA-DR7+DR53+ patients with severe RHD, and 46.9% (15 of 32) and 43% (3 of 7) of heart-infiltrating and PBMC-derived peptide-reactive T-cell clones, respectively, recognized the M5(81–103) region. Heart proteins were recognized more frequently by PBMC from patients with severe RHD than by those from patients with mild RHD. The similar pattern of T-cell reactivity found with both peripheral blood and heart-infiltrating T cells is consistent with the migration of M-protein-sensitized T cells to the heart tissue. Conversely, the presence of heart-reactive T cells in the PBMC of patients with severe RHD also suggests a spillover of sensitized T cells from the heart lesion.