gebhart/patrepeval huggingface dataset:
A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots (2016)

The development of rapid, robust and high performance point-of-care diagnostics relies on the advancement and combination of various areas of research. We have developed an assay for the detection of multiple mRNA molecules that combines DNA nanotechnology with fluorescent nanomaterials. The core switching mechanism is toehold-mediated strand displacement. We have used fluorescent quantum dots (QDs) as signal transducers in this assay, as they bring many benefits including bright fluorescence and multiplexing abilities. The resulting assay is capable of multiplexed detection of long RNA targets against a high concentration of background non-target RNA, with high sensitivity and specificity and limits of detection in the nanomolar range using only a standard laboratory plate reader. We demonstrate the utility of our QD-based system for the detection of two genes selected from a microarray-derived tuberculosis-specific gene expression signature. Levels of up- and downregulated gene transcripts comprising this signature can be combined to give a disease risk score, making the signature more amenable for use as a diagnostic marker. Our QD-based approach to detect these transcripts could pave the way for novel diagnostic assays for tuberculosis.
Degradation of p-cresol, resorcinol, and phenol in anaerobic membrane bioreactors under saline conditions (2021)

Treating petrochemical wastewater is a challenge for conventional anaerobic reactors. One example is coal gasification wastewater that, besides its salinity, is rich in toxic and inhibitory aromatics, such as phenol, cresols, and resorcinol. Studies have shown that phenol and p-cresol share the same degradation intermediates, whereas resorcinol is degraded via another route. This study investigated the simultaneous degradation of p-cresol or resorcinol with phenol under anaerobic saline conditions. Batch experiments with anaerobic phenol-degrading biomass were conducted to assess the feasibility of the degradation of p-cresol and resorcinol. Volumetric uptake rates of 11.4 ± 2.4 mgp-cresol·L–1d–1 and 4.2 ± 1.9 mgresorcinol·L–1d–1 were determined. The effect of p-cresol and resorcinol on the specific methanogenic activity and the cell viability in phenol-degrading and non-adapted biomass was assessed. Half maximal inhibitory concentration (IC50) values of 0.73 gp-cresol·L-1 and 3.00 gresorcinol·L-1 were estimated for phenol-degrading biomass, whereas IC50 values of 0.60 gp-cresol·L-1 and 0.25 gresorcinol·L-1 were estimated for the non-adapted biomass. p-Cresol caused a higher decrease in the non-damaged cell counts in comparison to resorcinol. Two anaerobic membrane bioreactors under saline conditions [8 g Na+·L–1] were fed with mixtures of either phenol-p-cresol or phenol-resorcinol. At an influent phenol concentration of 2 g·L-1, maximum conversion rates of 22 mgp-cresol·gVSS-1d–1 and 16 mgresorcinol·gVSS–1d–1 were found. In both AnMBRs, Syntrophorhabdus sp. and Methanosaeta sp. were the most abundant bacteria and methanogen, respectively. The feasibility of simultaneous conversion of phenolic compounds under saline conditions in AnMBRs opens novel perspectives for the high-rate anaerobic treatment of chemical wastewater.
Loop-gap cavities for pulsed x-ray ESR spectrometers (1995)

(1) Background: Deficiencies of mitochondrial fatty acid oxidation (FAO) define a subgroup of inborn errors of metabolism, with medium-chain acyl-CoA dehydrogenase deficiency (MCAD) and very long-chain acyl-CoA dehydrogenase deficiency (VLCAD) being two of the most common. Hypoketotic hypoglycemia is a feared clinical complication and the treatment focuses on avoiding hypoglycemia. In contrast, carnitine uptake deficiency (CUD) is treated as a mild disease without significant effects on FAO. Impaired FAO has experimentally been shown to impair glucagon secretion. Glucagon is an important glucose-mobilizing hormone. If and how glucagon is affected in patients with VLCAD or MCAD remains unknown. (2) Methods: A cross-sectional study was performed with plasma hormone concentrations quantified after four hours of fasting. Patients with VLCAD (<i>n</i> = 10), MCAD (<i>n</i> = 7) and CUD (<i>n</i> = 6) were included. (3) Results: The groups were similar in age, sex, weight, and height. The glucagon and insulin levels were significantly lower in the VLCAD group compared to the CUD group (<i>p</i> < 0.05, respectively). The patients with CUD had glucagon concentrations similar to the normative data. No significant differences were seen in GLP-1, glicentin, glucose, amino acids, or NEFAs. (4) Conclusions: Low fasting concentrations of glucagon are present in patients with VLCAD and cannot be explained by altered stimuli in plasma.
Ultra-High Refractive Index Sensing Structure Based on a Metal-Insulator-Metal Waveguide-Coupled T-Shape Cavity with Metal Nanorod Defects (2019)

An ultra-high plasmonic refractive index sensing structure composed of a metal-insulator-metal (MIM) waveguide coupled to a T-shape cavity and several metal nanorod defects is proposed and investigated by using finite element method. The designed plasmonic MIM waveguide can constitute a cavity resonance zone and the metal nanorod defects can effectively trap the light in the T-shape cavity. The results reveal that both the size of defects in wider rectangular cavity and the length of narrower rectangular cavity are primary factors increasing the sensitivity performance. The sensitivity can achieve as high as 8280 nm/RIU (RIU denotes the refractive index unit), which is the highest sensitivity reported in plasmonic MIM waveguide-based sensors to our knowledge. In addition, the proposed structure can also serve as a temperature sensor with temperature sensitivity as high as 3.30 nm/°C. The designed structure with simplicity and ease of fabrication can be applied in sensitivity nanometer scale refractive index sensor and may potentially be used in optical on-chip nanosensor.
Intensity leveling and false coloring of fluorescence-based 3D histology with FalseColor-Python (2021)

Fluorescence-based slide-free digital pathology techniques, including 3D microscopy, are gaining interest as alternatives to traditional slide-based histology. Since pathologists are accustomed to the appearance of standard histology stains, the ability to render grayscale fluorescent images with color palettes that mimic traditional histology is valuable. We present FalseColor-Python, an open-source rapid digital-staining package that renders two-channel fluorescence images to mimic standard histology. Our package offers consistent color-space representations that are robust to both intra-specimen and inter-specimen variations in staining and imaging conditions, along with GPU-accelerated methods to process large datasets efficiently.
Stygiolobus azoricus gen. nov., sp. nov. Represents a Novel Genus of Anaerobic, Extremely Thermoacidophilic Archaebacteria of the Order Sulfolobales (1991)

On the basis of three isolates (strains FC6T [T = type strain], FC4, and RG1) of extremely thermophilic chemolithoautotrophic archaebacteria obtained from solfataric fields on ão Miguel Island, Azores, the new genus Stygiolobus is described. These isolates grow obligately chemolithotrophically by reduction of S0 with H2 (H2-S0 lithotrophy) and are the first strictly anaerobic members of the order Sulfolobales. With a DNA G+C content of 38 mol%, the Stygiolobus isolates resemble Sulfolobus spp., which, however, are faculatively organotrophic and aerobic S0 oxidizers. The new isolates are also distinct from Acidianus spp., which resemble Stygiolobus by growing by H2-S0 lithotrophy. However, Acidianus spp. can also grow aerobically by S0 oxidation and have G+C contents of 31 mol%. At this time, only one species of the genus Stygiolobus is known, Stygiolobus azoricus sp. nov.; the type strain of S. azoricus is strain FC6 (= DSM 6296).
Noninvasive Measurement of Brachial Wall Mechanics During Flow-Mediated Vasodilation Using 2D Ultrasound Strain Tensor Imaging (2008)

Atherosclerosis has become one of the contributing factors of cardiovascular diseases. Endothelial dysfunction is considered a key factor in the development of atherosclerosis [1]. Flow-mediated vasodilatation (FMD) measurement in brachial and other conduit arteries has become a common method to asses the endothelial function in vivo [2]. Fluid shear-stress increases due to blood flow increases, thus stimulating endothelial cell production and release of nitric oxide, a potent endogenous vasodilator. The mechanical behavior of the arterial wall during vasodilatation is considered an indication for endothelial health. In FMD measurement, the endothelium-dependent variation in arterial diameter in response to reactive ischemia-induced hyperemia is measured by comparing the luminal diameter of the brachial artery before and after the ischemia of the forearm induced by pressurizing a cuff [3]. Ultrasound imaging modalities has been widely used in the FMD analysis as a noninvasive low-cost tool, which can be used to track the arterial diameter change with time. Most of the FMD measurements in the literature are based on tracing the vessel wall boundary manually. Since this process is time consuming and may introduce human errors, automatic measurement techniques have been implemented [3,4]. These techniques utilize image processing algorithms to identify the edges of arterial walls, and then calculate the relative displacement change with time.
Supplementary Figure 1 from Neutrophil Extracellular Traps Promote the Development and Progression of Liver Metastases after Surgical Stress (2023)

&lt;p&gt;Supplementary Figure 1. Flow cytometric analysis of purity of neutrophil isolation technique from bone marrow of mice.&lt;/p&gt;
Rapid characterization of Bacillus spores targeting species‐unique peptides produced with an atmospheric pressure matrix‐assisted laser desorption/ionization source (2005)

New and improved strategies are eagerly sought for the rapid identification of microorganisms, particularly in mixtures. Mass spectrometry remains a powerful tool for this purpose. Small acid-soluble proteins (SASPs), which are relatively abundant in Bacillus spores, represent potential biomarkers for species characterization. Despite sharing extensive sequence homology, these proteins differ sufficiently in sequence for discrimination between species. This work focuses on the differences in sequence between SASPs from various Bacillus species. Compilation of SASP sequences from protein database searches, followed by in silico trypsin digestion and analysis of the resulting fragments, identified several species-specific peptides that could be targeted for analysis using mass spectrometry. This strategy was tested and found to be successful in the characterization of Bacillus spores both from individual species and in mixtures. Analysis was performed using an ion trap mass spectrometer with an atmospheric pressure MALDI source. This instrumentation offers the advantage of increased speed of analysis and accurate precursor ion selection for tandem mass spectrometric analysis compared with vacuum matrix-assisted laser desorption/ionization and time-of-flight instruments. The identification and targeting of species-specific peptides using this type of instrumentation offers a rapid, efficient strategy for the identification of Bacillus spores and can potentially be applied to different microorganisms.
Expression of human MutS homolog 2 (hMSH2) protein in resting and proliferating cells. (1996)

The hMSH2 protein plays an important role in the DNA mismatch repair system. Since this system is involved in the correction of errors that occur during DNA replication, we studied the expression of hMSH2 protein in resting and DNA-replicating cells, as well as through the cell cycle in cell types with different growth characteristics. Using Western blot analysis, we showed that hMSH2 protein was detectable in resting peripheral blood lymphocytes and thymocytes. However, when these cells were induced to proliferate, the protein level increased at least 12-fold. In cell-cycle dependent expression studies we chose two DNA mismatch repair proficient cell lines (HEL and HeLa-S3), and flow cytometry was used to monitor cell-cycle progression. At every phase in the cell cycle, the steady-state level of hMSH2 was higher than in resting lymphocytes or thymocytes, and only minor variations of expression level were observed through the cell cycle. In particular, a two to fourfold decrease in hMSH2 expression occurred at G1 in HEL and at early S phase in HeLa-S3, but higher expression levels resumed during the replicative and postreplicative phases of the cell cycle. Interestingly, hMSH2 protein expression decreased fourfold when HEL cells were induced to differentiate along the megakaryocyte lineage, when continuous DNA replication occurs without mitosis. These results suggest that a basal level of hMSH2 protein expression is necessary for resting and differentiated cells, and that increased hMSH2 protein expression is required when DNA replication is activated and followed by mitosis.
A Comparison of Two Cause-of-Death Classification Systems for Deaths among Women of Reproductive Age in Menoufia, Egypt (1988)

Mortality data ascertained from sources other than a death registration system can validate the accuracy of the system, but this information is rarely obtained. Data on 1979 deaths among reproductive age women were collected in the 1981-1983 Reproductive Age Mortality Survey (RAMOS) in the governorate of Menoufia, Egypt, and compared with data on these deaths as recorded by the Egyptian death registration system. Although the distribution of the causes of death were similar, there were substantial differences between classification systems for deaths due to particular causes. Over half of the deaths classified differently by the systems were those assigned to circulatory disease on the death certificate. In contrast, there was a high rate of agreement between systems in the classification of trauma deaths. About half (52.4%) of cancer deaths had the same site-specific cancer diagnosis assigned by RAMOS. The percentage of deaths assigned to maternal causes was three times higher in RAMOS (19.2%) than on death certificates (6.1%). Reported mortality rates for this often-preventable cause of death have been substantially underestimated in national death registration systems. Such underreporting masks the need for additional prenatal care and maternal health programmes.
Cost-of-illness of lung disease in the TriVeneto Region, Italy: the GOLD Study. (2002)

Lung diseases imply a high consumption of healthcare resources representing a burden for patients and their families as well as for the society. The aim of the Global Outcomes in Lung Diseases (GOLD) study was to perform a cost-of-illness analysis of three pathologies affecting the lower respiratory tract: community-acquired pneumonia (CAP), chronic obstructive pulmonary disease (COPD) and bronchial asthma (BA). This observational study was conducted in a large region of northeast Italy, Triveneto, between 1999 and 2000. Patients of both sexes and aged > or = 14 years, were randomly selected from 28 identified centres of pneumology; patients were considered eligible if they had been visited at least twice at the centre during the observational period. Study periods were different for the three pathologies: for BA and COPD the recruitment period lasted 8 weeks and the follow-up period 12 months; for CAP, given the acute nature of the disease, two recruitment periods (May and November) were identified with a follow-up lasting 6 months. After collecting information for each patient (age, sex, risk factors, severity of the disease, occupation), data were recorded by each centre in a dedicated software program and then sent to a central database where final results were analysed. Cost-of-illness analysis was conducted within the framework of the National Healthcare System (NHS). Consumption of medical resources used during the follow-up period was valued according to market prices and published official tariffs. A total number of 1068 patients (596 men and 458 women) were selected: 42.5% were affected by BA, 46.3% by COPD, and 11.2% by CAP. Mean cost per patient/year for patients affected by BA and COPD ranged from Euro 608 to 2457 and from Euro 1500 to 3912, respectively, depending on illness severity. Mean cost per episode of CAP was Euro 1586. This study confirms the findings of other studies published in the international literature, demonstrating that asthma and COPD are often misdiagnosed and mistreated and so their management, especially for the most severe patients, becomes complex and highly expensive. The use of preventive, specialised care could help in achieving early diagnosis and treatment of these patients.
Using the natural‐frequency concept in remote probing of the earth (1976)

A technique is given for determining the thicknesses and the electrical constitutive parameters of a planar‐layered medium such as a coal seam in a mine environment. Time‐domain experimental data are analyzed with Prony's method to determine the natural frequencies of the layered medium. Explicit relations are given (for dielectric layers) for determining the thicknesses and dielectric constants from the experimentally determined natural frequency results. Explicit expressions are also given (for conductive layers) for calculating the electrical thickness from natural frequency results. The method is illustrated with sample numerical results.
Anti-SAG1 peptide antibodies inhibit the penetration ofToxoplasma gondiitachyzoites into enterocyte cell lines (2001)

The initial attachment of Toxoplasma tachyzoites to the target host cell is an important event in the life-cycle of the parasite and a critical stage in infection. Previous studies have shown that polyclonal antibodies directed against the major surface antigen of Toxoplasma gondii (SAG1) inhibit the infection of enterocyte cell lines. Here, we demonstrate that antibodies raised against a central peptide (V41T) of SAG1 and the SAG1 protein itself are able to inhibit the infection of various cell lines by the tachyzoites. Antibodies directed against SAG1 peptides were used to define a site on the SAG1 antigen that interacts with the host cell. The epitope carried by V41T was identified on the tachyzoite surface by immunofluorescence. The peptide sequence seems to be conserved in all the members of the SAG1 Related Sequence family (SRS). Using undifferentiated and differentiated Caco-2 cells, we found that tachyzoites enter preferentially via the basolateral side of the cell. These findings highlight the role of the SRS family members in the mediation of host cell invasion.
Using the NINDS Consensus Diagnostic Criteria for Traumatic Encephalopathy Syndrome on 4 Cohorts of Retired Contact Sport Athletes (2022)

Physicians are often asked by retired contact sports athletes and their families to determine if their clinical picture is related to TES and/or CTE. Physicians may turn to the NINDS consensus criteria for guidance in making such determinations. The data presented here may assist physicians in evaluating the reliability and validity of using the consensus criteria in living subjects.
A Decision Method of Critical Rejection Level Taking Defect Detectability of NDT into Account (1981)

In the present paper, consideration has been carried out of the relationship between the defect detectability of NDT and the repair rate of welds and the reliability of inspected welds.In order to get a certain high quality level of welds, critical level for repair Acr should be set smaller than the critical allowable defect size acr. That is, acr/Acr is the factor of safety to defect detectability of NDT.The more setting smaller of critical level for repair or deteriorating the accuracy of defect measuring by NDT, the more repair rate of welds γ increases. Increasing of γ does not always realize increasing of the reliability of welds R. In the case of deteriorating of accuracy of measuring the defect, k decreases even if γ increases.The reliability of welds increasess according to increasing repair rate in the case of increasing sampling ratio or in the case of inspecting with emphasis on higher defective joints even if sampling-ratio is equal to the case of random sampling.Based on the above consideration, the decision method is discussed of the rational inspection method for assuring a certain reliability of welds and also minimizing the total cost of inspection.
Simplified modelling the mode instability threshold of high power fiber amplifiers in the presence of photodarkening (2015)

In this paper we present a simple model to predict the behavior of the transversal mode instability threshold when different parameters of a fiber amplifier system are changed. The simulation model includes an estimation of the photodarkening losses which shows the strong influence that this effect has on the mode instability threshold and on its behavior. Comparison of the simulation results with experimental measurements reveal that the mode instability threshold in a fiber amplifier system is reached for a constant average heat load value in good approximation. Based on this model, the expected behavior of the mode instability threshold when changing the seed wavelength, the seed power and/or the fiber length will be presented and discussed. Additionally, guidelines for increasing the average power of fiber amplifier systems will be provided.
The Aging of Elastic and Muscular Arteries (2003)

There are significant differences in the rate of age-related decline in vascular stiffness in elastic arteries of nondiabetic compared with diabetic arteries. Diabetic arteries appear to age at an accelerated rate at an earlier age and then reach a functional plateau.
Non‐CLL‐like monoclonal B‐cell lymphocytosis in the general population: Prevalence and phenotypic/genetic characteristics (2010)

Non-CLL-like MBL cases frequently show biclonality, in association with MZL-, LPL-, MCL-like, or unclassifiable phenotypic profiles. As with CLL-like MBL, the frequency of non-CLL-like MBL increases with age, with a clear predominance of males.
Applying a market mechanism to optimizing the utilization of computing resources (2012)

Large enterprises possess massive quantities of computing systems. The costs of running and managing these systems, and capital investments for new hardware, are significant. Optimizing the utilization of those computing systems can produce significant savings for the enterprise. However, the optimization in a multinational, multi-divisional, multi-geographic enterprise is complicated by the large scale of business usage purposes and the heterogeneity of the systems. This paper proposes a solution by introducing a market-like environment for directing workload migration from less efficient systems to more efficient systems. Migration sources and targets are treated as sellers and buyers in a transaction in this environment, and a Computing Environment Entitlement Contract (CEEC) is used as the unit of trade. A Market Maker is also introduced to ensure that matched buyers and sellers complete the transaction.