gebhart/patrepeval huggingface dataset:
Evaluation of the Feasibility of Screening Patients for Early Signs of Lung Carcinoma in Web Search Logs (2016)

A statistical model that predicts the appearance of strong evidence of a lung carcinoma diagnosis via analysis of large-scale anonymized logs of web search queries from millions of people across the United States.To evaluate the feasibility of screening patients at risk of lung carcinoma via analysis of signals from online search activity.We identified people who issue special queries that provide strong evidence of a recent diagnosis of lung carcinoma. We then considered patterns of symptoms expressed as searches about concerning symptoms over several months prior to the appearance of the landmark web queries. We built statistical classifiers that predict the future appearance of landmark queries based on the search log signals. This was a retrospective log analysis of the online activity of millions of web searchers seeking health-related information online. Of web searchers who queried for symptoms related to lung carcinoma, some (n = 5443 of 4 813 985) later issued queries that provide strong evidence of recent clinical diagnosis of lung carcinoma and are regarded as positive cases in our analysis. Additional evidence on the reliability of these queries as representing clinical diagnoses is based on the significant increase in follow-on searches for treatments and medications for these searchers and on the correlation between lung carcinoma incidence rates and our log-based statistics. The remaining symptom searchers (n = 4 808 542) are regarded as negative cases.Performance of the statistical model for early detection from online search behavior, for different lead times, different sets of signals, and different cohorts of searchers stratified by potential risk.The statistical classifier predicting the future appearance of landmark web queries based on search log signals identified searchers who later input queries consistent with a lung carcinoma diagnosis, with a true-positive rate ranging from 3% to 57% for false-positive rates ranging from 0.00001 to 0.001, respectively. The methods can be used to identify people at highest risk up to a year in advance of the inferred diagnosis time. The 5 factors associated with the highest relative risk (RR) were evidence of family history (RR = 7.548; 95% CI, 3.937-14.470), age (RR = 3.558; 95% CI, 3.357-3.772), radon (RR = 2.529; 95% CI, 1.137-5.624), primary location (RR = 2.463; 95% CI, 1.364-4.446), and occupation (RR = 1.969; 95% CI, 1.143-3.391). Evidence of smoking (RR = 1.646; 95% CI, 1.032-2.260) was important but not top-ranked, which was due to the difficulty of identifying smoking history from search terms.Pattern recognition based on data drawn from large-scale web search queries holds opportunity for identifying risk factors and frames new directions with early detection of lung carcinoma.
On battery State of Charge estimation: A new mixed algorithm (2008)

A new SoC estimation algorithm is presented. The estimation is performed mixing the Coulomb-Counting and the Model-Based estimation approaches. The algorithm was tested on a brand new lithium-ion cell which use a nanoscale technology able to grant a more powerful and safer lithium-ion battery than the batteries currently on the market. The cell, called A123-M1, was first characterized and then identified. The cell was identified with a equivalent electrical circuits model which is usually called 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> Randle model: the used test-bench and the identification process are described. Then the SoC estimation problem is described. A briefly review of the state of art of SoC estimation is given and the drawbacks of the methods which are usually used are presented. Finally the new mixed estimation algorithm is described: the algorithm scheme and the results are shown.
Deciphering Antigenic Determinants of Streptococcus pneumoniae Serotype 4 Capsular Polysaccharide using Synthetic Oligosaccharides (2015)

Streptococcus pneumoniae is a major cause of mortality and morbidity worldwide. More than 90 S. pneumoniae serotypes are distinguished based on the structure of their primary targets to the human immune system, the capsular polysaccharides (CPSs). The CPS of the prevalent serotype 4 (ST4) is composed of tetrasaccharide repeating units and is included in existing pneumococcal vaccines. Still, the structural antigenic determinants that are essential for protective immunity, including the role of the rare and labile cyclic trans-(2,3) pyruvate ketal modification, remain largely unknown. Molecular insights will support the design of synthetic subunit oligosaccharide vaccines. Here, we identified the key antigenic determinants of ST4 CPS with the help of pyruvated and nonpyruvated synthetic repeating unit glycans. Glycan arrays revealed oligosaccharide antigens recognized by antibodies in the human reference serum. Selected depyruvated ST4 oligosaccharides were used to formulate neoglycoconjugates and immunologically evaluated in mice. These oligosaccharides were highly immunogenic, but the resulting antiglycan antibodies showed only limited binding to the natural CPS present on the bacterial surface. Glycan array and surface plasmon resonance analysis of murine polyclonal serum antibodies as well as monoclonal antibodies revealed that terminal sugars are important in directing the immune responses. The pyruvate modification on the oligosaccharide is needed for cross-reactivity with the native CPS. These findings are an important step toward the design of oligosaccharide-based vaccines against S. pneumoniae ST4.
The molecular etiology of deafness and auditory performance in the postlingually deafened cochlear implantees (2020)

Abstract Recent advances in molecular genetic testing (MGT) have improved identification of genetic aetiology of candidates for cochlear implantation (CI). However, whether genetic information increases CI outcome predictability in post-lingual deafness remains unclear. Therefore, we evaluated the outcomes of CI with respect to genetic aetiology and clinical predictors by comparing the data of study subjects; those with an identified genetic aetiology (GD group), and those without identifiable variants (GUD group). First, we identified the genetic aetiology in 21 of 40 subjects and also observed genetic etiologic heterogeneity. The GD group demonstrated significantly greater improvement in speech perception scores over a 1-year period than did the GUD group. Further, inverse correlation between deafness duration and the 1-year improvement in speech perception scores was tighter in the GD group than in the GUD group. The weak correlation between deafness duration and CI outcomes in the GUD group might suggest the pathophysiology underlying GUD already significantly involves the cortex, leading to lesser sensitivity to further cortex issues such as deafness duration. Under our MGT protocol, the correlation between deafness duration and CI outcomes were found to rely on the presence of identifiable genetic aetiology, strongly advocating early CI in individual with proven genetic aetiologies.
Clay particles - potential of positron annihilation lifetime spectroscopy (PALS) for studying interlayer spacing (2011)

Characterisation of clays is generally achieved by traditional methods, such as X-ray diffraction (XRD) and transmission electron microscopy (TEM). However, clays are often difficult to characterise due to lack of long-range order, thus these tools are not always reliable. Because interlayer spacing in clays can be adjusted to house molecules, there is growing interest to use these materials for drug delivery. Positron annihilation lifetime spectroscopy (PALS) was examined as an alternative tool to characterise a series of well-known clays. XRD of two layered double hydroxides; MgAl-LDH and MgGd-LDH, natural hectorite, fluoromica and laponite, and their PALS spectra were compared. XRD data was used to calculate the interlayer d- spacing in these materials and results show a decrease in interlayer spacing as the heavy metal ions are substituted for those of large ionic radii. Similar results were obtained for PALS data. This preliminary study suggests PALS has potential as a routine tool for characterising clay particles. Further work will examine the sensitivity and reliability of PALS to percent of metal doping and hydration in clay microstructure.
The SETDB1 histone methyltransferase is recurrently amplified in and accelerates melanoma (2011)

The most common mutation in human melanoma, BRAF(V600E), activates the serine/threonine kinase BRAF and causes excessive activity in the mitogen-activated protein kinase pathway[subscript 1, 2]. BRAF(V600E) mutations are also present in benign melanocytic naevi3, highlighting the importance of additional genetic alterations in the genesis of malignant tumours. Such changes include recurrent copy number variations that result in the amplification of oncogenes[subscript 4, 5]. For certain amplifications, the large number of genes in the interval has precluded an understanding of the cooperating oncogenic events. Here we have used a zebrafish melanoma model to test genes in a recurrently amplified region of chromosome 1 for the ability to cooperate with BRAF(V600E) and accelerate melanoma. SETDB1, an enzyme that methylates histone H3 on lysine 9 (H3K9), was found to accelerate melanoma formation significantly in zebrafish. Chromatin immunoprecipitation coupled with massively parallel DNA sequencing and gene expression analyses uncovered genes, including HOX genes, that are transcriptionally dysregulated in response to increased levels of SETDB1. Our studies establish SETDB1 as an oncogene in melanoma and underscore the role of chromatin factors in regulating tumorigenesis.
Industrial Trent Combustor — Combustion Noise Characteristics (1999)

Thermoacoustic resonance is a difficult technical problem that is experienced by almost all lean-premixed combustors. The Industrial Trent combustor is a novel dry-low-emissions (DLE) combustor design, which incorporates three stages of lean premixed fuel injection in series. The three stages in series allow independent control of two stages — the third stage receives the balance of fuel to maintain the desired power level — at all power conditions. Thus, primary zone and secondary zone temperatures can be independently controlled. This paper examines how the flexibility offered by a 3-stage lean premixed combustion system permits the implementation of a successful combustion noise avoidance strategy at all power conditions and at all ambient conditions. This is because at a given engine condition (power level and day temperature) a characteristic “noise map” can be generated on the engine, independently of the engine running condition. The variable distribution of heat release along the length of the combustor provides an effective mechanism to control the amplitude of longitudinal resonance modes of the combustor. This approach has allowed the Industrial Trent combustion engineers to thoroughly “map out” all longitudinal combustor acoustic modes and design a fuel schedule that can navigate around regions of combustor thermoacoustic resonance. Noise mapping results are presented in detail, together with the development of noise prediction methods (frequency and amplitude) that have allowed the noise characteristics of the engine to be established over the entire operating envelope of the engine.
Characteristics of civil aviation atmospheric hazards (1994)

Clear air turbulence, wake vortices, dry hail, and volcanic ash are hazards to civil aviation that have not been brought to the forefront of public attention by a catastrophic accident. However, these four hazards are responsible for major and minor injuries, emotional trauma, significant aircraft damage, and in route and terminal area inefficiency. Most injuries occur during clear air turbulence. There is significant aircraft damage for any volcanic ash encounter. Rolls induced by wake vortices occur near the ground. Dry hail often appears as an area of weak echo on the weather radar. This paper will present the meteorological, electromagnetic, and spatiotemporal characteristics of each hazard. A description of a typical aircraft encounter with each hazard will be given. Analyzed microwave and millimeter wave sensor systems to detect each hazard will be presented.
Prospective evaluation of malignant cell seeding after percutaneous endoscopic gastrostomy in patients with oropharyngeal/esophageal cancers (2013)

This study showed that malignant cells were present in 22.5 % of patients immediately after pull-through PEG placement; local metastases were verified at follow-up in 9.4 %, all of which were from esophageal squamous cell carcinoma. This risk is particularly high in the older age group and in patients with higher tumor stages. Therefore, pull-through PEG placement should be avoided in these patients and direct access PEG favored instead.
Effects of anti‐hypertensive interventions on the inflammatory response in the spontaneously hypertensive rat (2013)

Clinical and pre‐clinical studies have found inflammation to be a contributing factor in the genesis of various forms hypertension. Current clinical interventions, such as renal denervation, target the autonomic nervous system to treat hypertension, however the effects of these blood pressure lowering strategies on the immune system are unknown. The current study examined immune cell activation and tissue infiltration following autonomic denervation procedures in an animal model of neurogenic hypertension. As determined by flow cytometry, the spontaneously hypertensive rat (SHR) exhibited a significant increase in the percentage of T lymphocytes (CD3+) in both the brainstem (3.3 ± 0.4 vs 1.6 ± 0.2; p=0.003) and aortic tissue (17.2 ± 1.6 vs 9.9 ± 2.1; p=0.01) compared to the normotensive control. These animals then underwent either renal denervation (RD) or carotid sinus denervation (CSD). Blood pressure in the SHR was significantly lowered following both RD and CSD. Compared to non‐denervated SHR, the total circulating leukocytes (CD45+) and CD3+ cells were attenuated following blood pressure lowering in the RD and CSD groups (p&lt;0.001). These data suggest that reducing blood pressure with procedures targeting the autonomic nervous system is paralleled by reductions in tissue inflammation associated with hypertension. Supported by NIH‐HL107675–01, Marie Curie‐IIF – 276147 and British Heart Foundation.
Rapid and Detailed Characterization of Transgene Insertion Sites in Genetically Modified Plants via Nanopore Sequencing (2021)

Molecular characterization of genetically modified plants can provide crucial information for the development of detection and identification methods, to comply with traceability, and labeling requirements prior to commercialization. Detailed description of the genetic modification was previously a challenging step in the safety assessment, since it required the use of laborious and time-consuming techniques. In this study an accurate, simple, and fast method was developed for molecular characterization of genetically modified (GM) plants, following a user-friendly workflow for researchers with limited bioinformatic capabilities. Three GM events from a diverse array of crop species-perennial ryegrass, white clover, and canola-were used to test the approach that exploits long-read sequencing by the MinION device, from Oxford Nanopore Technologies. The method delivered a higher degree of resolution of the transgenic events within the host genome than has previously been possible with the standard Illumina short-range sequencing strategies. The flanking sequences, copy number, and presence of backbone sequences, and overall transgene insertion structure were determined for each of the plant genomes, with the additional identification of moderate-sized secondary insertions that would have previously been missed. The proposed workflow takes only about 1 week from DNA extraction to analyzed result, and the method will complement the existing approaches for molecular characterization of GM plants, since it makes the process faster, simpler, and more cost-effective.
An Efficient Reference Image Sharing Method for the Image-Division Parallel Video Encoding Architecture (2022)

This paper proposes an efficient reference image sharing method for the image-division parallel video encoding architecture. This method efficiently reduces the amount of data transfer by using pre-transfer with area prediction and on-demand transfer with a transfer management table. Experimental results show that the data transfer can be reduced to 19.8-35.3% of the conventional method on average without major degradation of coding performance. This makes it possible to reduce the required bandwidth of the inter-chip transfer interface by saving the amount of data transfer.
Terahertz applications of frequency selective surfaces: analysis, design, fabrication and testing (2006)

In this paper, metallodielectric IR FSS filters were synthesized using fractal and GA techniques with fabrication constraints. Measured results show excellent agreement with PMM simulation. The synthesis of DFSS for near-IR filter applications was performed using a GA. The advantages of DFSS include low loss at visible wavelengths and polarization independent filter responses. Designs for low loss IR NIMs based on FSS were also discussed. Future work includes fabricating FSS and DFSS filters that operate at near-IR and visible wavelengths
13-valent pneumococcal conjugate vaccine immune sera protects against pneumococcal serotype 1, 3, and 5 bacteremia in a neonatal rat challenge model (2011)

PCV7 was first licensed in the United States in 2000 based on clinical efficacy studies. Since the introduction, PCV7 has demonstrated protective effectiveness for each of the vaccine serotypes. More recently, PCV13 has been licensed in more than 60 countries based on serological noninferiority to PCV7 for the shared serotypes and noninferiority to the least immunogenic serotypes of PCV7 for the additional 6 serotypes in PCV13. To evaluate whether the functional antibody responses to serotypes 1, 3, and 5 were sufficient to protect animals challenged with virulent strains of these serotypes, rhesus macaques were immunized with three clinical doses of PCV13. The macaques mounted robust anti-capsular polysaccharide IgG and opsonophagocytic killing (OPA) responses to each serotype contained in the vaccine. Pooled pre-immunization sera and post-immunization serum pools were tested in a neonatal rat bacteremia model. Passive transfer of pooled post-immunization sera, but not pre-immunization sera, protected neonatal rats from lethal IP challenge with serotype 1, 3, or 5 strains. The functional activity of PCV13 immune sera against a virulent type 3 strain was further evaluated using sera from human children immunized with 4 doses of PCV7 or PCV13. Pooled sera from children immunized with PCV13, but not pooled sera from children immunized with PCV7, which does not contain the serotype 3 polysaccharide conjugate, protected neonatal rats from lethal IP challenge with a highly encapsulated and virulent serotype 3 strain. These data suggest that PCV13 will provide protection against pneumococcal serotype 1, 3, and 5 disease in human populations, even at relatively low OPA titers.
A Sub-nL Differential Scanning Calorimetry Chip for Liquid Crystal Phase Transition Characterization (2022)

This paper presents a sub-nL differential scanning calorimetry (DSC) chip for liquid crystal phase transition characterization. This is the first DSC chip capable of measuring a liquid sample at a sub-nL volume capacity. The chip achieves a heat-flow resolution of 6.29 nW, the highest among state-of-the-art demonstrations [1]. The chip features suspended twin membranes that house self-enclosed silicon nitride microchannels. The design realizes a low system heat capacitance of 2.3 μJ/K and thus minimizes the deformation in the DSC thermogram and the shift of transition temperature at an increased temperature scanning rate. Those distortions of the DSC measurement result have typically been observed at increased scanning rates for commercial DSC and other DSC chips. The compact chip comprises solid materials to facilitate measurement under low vacuum and offer superior sensitivity and low noise.
Risk Effect Minimization Using Flexible Product and Process Design (1999)

Abstract This paper addresses robust product development practices by evaluating the flexibility of the development process and the resulting product and process designs. A flexible design has the ability to change performance while requiring only minor time and costs to change the design parameters. A design change might be necessary if the actual design performance is not matched by the predicted design performance. The described methodology utilizes response surfaces for multiple performance attributes to assess the utility across the design space. This utility is optimized with respect to the robustness against noise and prediction inaccuracies. Based on this design, non-dominant pareto optimal sets of all feasible design changes are then developed to asses potential performance gains against the time and cost needed to incur the change assuming correct performance predictions. While robust design practices seek to reduce the risk of design change, the proposed method rather accepts the risk of design change and minimizes the potential negative effects.
The Laser Doppler: A Non-invasive Measure of Cochlear Blood Flow (1984)

The present investigation demonstrates the utility of the laser Doppler flowmeter to provide a measure of cochlear blood flow dynamics. Cochlear and cutaneous blood flow were compared with arterial blood pressure during and following exposure to Angiotensin II, 5% carbon monoxide, 100% oxygen, mannitol, and saline. The observations indicate that: 1) cochlear blood flow generally parallels cutaneous blood flow; however, 2) when cutaneous beds vasoconstrict (e.g., AII, alpha-agonists), cochlear blood flow parallels blood pressure; and, 3) under the influence of agents that affect peripheral and central circulation (5% CO, 100% O2), cochlear blood flow may dissociate from cutaneous blood flow and blood pressure. The implications of these findings are discussed in terms of local control mechanisms that may be involved in the inner ear vasculature.
Precoding Based Peak-to-Average Power Ratio Reduction for Optical OFDM demonstrated on Compatible Single-Sideband Modulation with Direct Detection (2008)

Clipping-aided precoding is suggested for effective PAPR reduction to improve performance of OFDM. Up to 3.7 dB PAPR reduction is shown. Performance improvements in required OSNR and dispersion tolerance are demonstrated on compatible SSB.