gebhart/patrepeval huggingface dataset:
Characterization of Two Virulent Phages of Lactobacillus plantarum (2012)

We characterized two Lactobacillus plantarum virulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eight L. plantarum strains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least two L. plantarum strains, LMG9211 and WCSF1. The linear double-stranded DNA genome of the pac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that of Pediococcus damnosus phage clP1 and 77% identity with that of L. plantarum phage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of the cos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those of Bacillus and Lactobacillus strains as well as phages. Some phage B2 genes were similar to ORFs from L. plantarum phage LP65 of the Myoviridae family. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.
Inference of non-overlapping camera network topology by measuring statistical dependence (2005)

We present an approach for inferring the topology of a camera network by measuring statistical dependence between observations in different cameras. Two cameras are considered connected if objects seen departing in one camera is seen arriving in the other. This is captured by the degree of statistical dependence between the cameras. The nature of dependence is characterized by the distribution of observation transformations between cameras, such as departure to arrival transition times, and color appearance. We show how to measure statistical dependence when the correspondence between observations in different cameras is unknown. This is accomplished by non-parametric estimates of statistical dependence and Bayesian integration of the unknown correspondence. Our approach generalizes previous work which assumed restricted parametric transition distributions and only implicitly dealt with unknown correspondence. Results are shown on simulated and real data. We also describe a technique for learning the absolute locations of the cameras with Global Positioning System (GPS) side information.
AUTOMATED SHAPE MODIFICATION FOR THE CAD MODEL OF RESIDUAL LIMB (2002)

During the design and fabricating processes of a prosthetic socket, in order to avoid the impair on the pressure-relief areas of the residual limb, such as tibia, the shape of duplicated plaster mold of the residual limb that is used to make the socket should be modified. The study focused on developing an algorithm that employs the techniques of reverse engineering, theories of B-spline and lofted surface, and knot insertion method to modify the shape of a residual limb. Once the regions of PT/PR areas of a residual limb have been specified, the selected scanned points are then transferred to the prototype system developed in this study to implement the required modification. A demonstrated case study has verified the algorithm that can automatically meet the required shape change of that specific residual limb. Based on the shape modification algorithm, an automated prosthetic socket design system that is being developed would then be more feasible.
Low incidence of mutations in EGFR kinase domain in Caucasian patients with head and neck squamous cell carcinoma (2005)

Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are associated with increased sensitivity to tyrosine kinase inhibitors (TKIs) and are present in 10-30% of non-small cell lung carcinoma depending on ethnic origin. EGFR protein is also overexpressed in about 90% of squamous cell carcinoma of head and neck (HNSCC), and treatment with TKIs has shown clinical benefit in a subgroup of these patients. Recently, EGFR mutations were described in three Asian patients with larynx cancer. We screened for EGFR tyrosine kinase mutations in tumour DNA of 100 patients of Caucasian origin with HNSCC by direct sequencing of the hotspot regions. Only one patient with larynx cancer displayed a novel, somatic EGFR missense mutation, K745R, affecting a highly conserved residue within the ATP cleft. Similar to reports in lung cancer, EGFR kinase domain mutations in HNSCC patients seem to show a lower incidence in patients of Caucasian origin.
Magnetic Circuit Design Methodologies for Dual-Coil Transducers * (2002)

Although the electrodynamic drive topology incorporating two axially (not concentrically) placed coils is not a new idea and dates back to the 1950s, recent interest in the design has started a proliferation of the design conception professional and consumer markets. The fundamental design involves two coils that are opposite in phase and reside in oppositely polarized magnetic gaps, thus providing a Lorentz force in the same axial direction. The two gaps are formed from the same magnetic circuit, and both coils are wound on the same form, separated by some distance, connected or wound out of phase, and attached to a single diaphragm. Different design options with magnetic materials, magnetic circuit geometries, and voice-coil topologies are described. The focus is on performance tradeoffs and advantages in weight, power handling, power compression, and distortion relative to a single-gap design.
The prognostic significance of MIB‐1, p53, and DNA flow cytometry in completely resected primary meningiomas (1998)

BACKGROUND Despite the availability of clinical and pathologic parameters of prognosis, the behavior of an individual meningioma may be difficult to predict. In a recent review of gross totally resected (GTR) meningiomas, the authors found strong associations between microscopic brain invasion, increased mitotic rate (≥4/10 high-power fields), the presence of at least 3 of 4 morphologic variables (sheeting, hypercellularity, macronucleoli, and small cells), and decreased recurrence free survival (RFS). In this study, they assessed the prognostic value of three ancillary techniques: DNA flow cytometry, MIB-1 labeling, and p53 protein expression. METHODS The authors evaluated primary GTR meningiomas from 425 patients with DNA flow cytometry, immunostaining for MIB-1, and determination of p53 protein expression. The patients were followed until death or for a median of 8.9 years. RESULTS An MIB-1 labeling index (LI) of ≥4.2%, identified in 8% of cases, was strongly associated with decreased RFS in univariate analysis (P = 0.0001). Fourteen percent contained aneuploid cell populations, and 48% exhibited a p53 LI of >10%. Neither variable was associated with decreased RFS. Further analysis revealed a close association between MIB-1 LI and mitotic index, the latter being the parameter of greatest significance in multivariate analysis. CONCLUSIONS MIB-1 LI is a useful adjunct to routine histologic evaluation of meningiomas and appears to be of greatest value in the evaluation of tumors exhibiting borderline atypia. In contrast, our data suggest that, regarding patients with primary GTR meningiomas, neither flow cytometry nor p53 immunohistochemistry provides useful prognostic information. Cancer 1998;82:2262-2269. © 1998 American Cancer Society.
Associations between respiratory symptoms, lung function and gastro-oesophageal reflux symptoms in a population-based birth cohort (2006)

Several studies have reported an association between asthma and gastro-oesophageal reflux, but it is unclear which condition develops first. The role of obesity in mediating this association is also unclear. We explored the associations between respiratory symptoms, lung function, and gastro-oesophageal reflux symptoms in a birth cohort of approximately 1000 individuals. Information on respiratory symptoms, asthma, atopy, lung function and airway responsiveness was obtained at multiple assessments from childhood to adulthood in an unselected birth cohort of 1037 individuals followed to age 26. Symptoms of gastro-oesophageal reflux and irritable bowel syndrome were recorded at age 26. Heartburn and acid regurgitation symptoms that were at least "moderately bothersome" at age 26 were significantly associated with asthma (odds ratio = 3.2; 95% confidence interval = 1.6–6.4), wheeze (OR = 3.5; 95% CI = 1.7–7.2), and nocturnal cough (OR = 4.3; 95% CI = 2.1–8.7) independently of body mass index. In women reflux symptoms were also associated with airflow obstruction and a bronchodilator response to salbutamol. Persistent wheezing since childhood, persistence of asthma since teenage years, and airway hyperresponsiveness since age 11 were associated with a significantly increased risk of heartburn and acid regurgitation at age 26. There was no association between irritable bowel syndrome and respiratory symptoms. Reflux symptoms are associated with respiratory symptoms in young adults independently of body mass index. The mechanism of these associations remains unclear.
A view on future building system modeling and simulation (2019)

This chapter presents what a future environment for building system modeling and simulation may look like. As buildings continue to require increased performance, more flexible load shifting, better integration of renewable energy and waste heat sources, and better comfort, their energy and control systems are becoming more integrated and complex. The chapter focuses on the modeling, simulation and analysis of building energy and control systems. Such systems can be classified as heterogeneous systems because they involve multiple domains, such as thermodynamics, fluid dynamics, heat and mass transfer, electrical systems, control systems and communication systems. The translation of mathematical models into a simulation program can be fully automated. When translating a model, symbolic processing is important to reduce computing time since many building system simulation problems lead to large, sparse differential algebraic equation systems. Equation-based object-oriented modeling and simulation environments have been applied successfully in numerous demanding industrial applications.
Efficient epidemic-style protocols for reliable and scalable multicast (2003)

Epidemic-style (gossip-based) techniques have recently emerged as a scalable class of protocols for peer-to-peer reliable multicast dissemination in large process groups. These protocols provide probabilistic guarantees on reliability and scalability. However, popular implementations of epidemic-style dissemination are reputed to suffer from two major drawbacks: (a) (Network Overhead) when deployed on a WAN-wide or VPN-wide scale they generate a large number of packets that transit across the boundaries of multiple network domains (e.g., LANs, subnets, ASs), causing an overload on core network elements such as bridges, routers, and associated links; (b) (Lack of Adaptivity) they impose the same load on process group members and the network even under reduced failure rates (viz., packet losses, process failures). lit this paper we report on the (first) comprehensive set of solutions to these problems. The solution is comprised of two protocols: (1) a hierarchical gossiping protocol, and (2) an adaptive multicast dissemination framework that allows use of any gossiping primitive within it. These protocols work within a virtual peer-to-peer hierarchy called the Leaf Box hierarchy. Processes can be allocated in a topologically aware manner to the leaf boxes of this structure, so that (1) and (2) produce low traffic across domain boundaries in the network. In the interests of space, this paper focuses on a detailed discussion and evaluation (through simulations) of only the hierarchical gossiping protocol. We present an overview of the adaptive dissemination protocol and its properties.
High-resolution electron microscopy study of tunnelling junctions with AlN and AlON barriers (2001)

Spin-dependent tunnel junctions with AlON and AlN barriers have been investigated using high-resolution electron microscopy. Plasma gas composition, nitridation time, and deposited Al thickness were studied independently. Plasma-nitrided Al produces thinner tunnel barriers than those obtained with an oxygen or oxygen+nitrogen plasma, for the same plasma exposure time. Experiments to study an increase in plasma nitridation time for a constant Al deposition thickness showed that overexposure to the plasma resulted in a thinner barrier—possibly due to the competing processes of nitride formation and slight etching of the barrier. The AlN barrier thickness increases monotonically with deposited Al thickness for a constant nitridation time. Electron energy loss spectroscopy compositional mapping has confirmed that nitrogen is present in the barrier layer. The roughness between the barrier layer and the two ferromagnetic layers has also been estimated.
Neurosexology (2001)

Background Sexual function can be altered in patients by many neurological disorders affecting the cerebrum, the brain stem, the spinal cord, the spinal roots or the peripheral nerves. It can also be prominently affected in patients with an underlying undiagnosed neurological disease. Traditionally, practising neurologists have not paid much attention to sexual dysfunction in their patients, partly because therapeutic possibilities were scant. Sexual dysfunction, however, is observed in many neurological disorders, and may arise as a primary neurogenic disorder. Although not as obviously limiting as, for instance, paresis and pain, it is most disruptive for patients' lives. With emerging awareness of the primary importance of quality of life as the most important indicator of good patient management, and with the advent of more effective treatment of sexual dysfunction, it is no longer acceptable to ignore this very important dimension of life. In this review we will present the anatomical and physiological basis of the sexual response, the clinical approach to patients with sexual dysfunction, the characteristics of symptoms in neurological disorders, how to take a case history, diagnostic procedures and the treatment possibilities.
Circulating MicroRNAs (2011)

MicroRNAs (miRs) are small, noncoding RNAs that posttranscriptionally control gene expression by inhibiting protein translation or inducing target mRNA destabilization. Besides their intracellular function, recent studies demonstrate that miRs can be exported or released by cells and circulate with the blood in a remarkably stable form. The discovery of circulating miRs opens up intriguing possibilities to use the circulating miR patterns as biomarker for cardiovascular diseases. Cardiac injury as it occurs after acute myocardial infarction increases the circulating levels of several myocardial-derived miRs (eg, miR-1, miR-133, miR-499, miR-208), whereas patients with coronary artery disease or diabetes showed reduced levels of endothelial-enriched miRs, such as miR-126. This review article summarizes the current clinical and experimental studies addressing the role of circulating miRs as a diagnostic or prognostic biomarker in cardiovascular disease. In addition, the mechanisms by which miRs are released and their putative function as long-distance communicators are discussed.
Antibiotics for treating bacterial vaginosis in pregnancy (2005)

Antibiotic treatment can eradicate bacterial vaginosis in pregnancy. However, this review provides little evidence that screening and treating all pregnant women with asymptomatic bacterial vaginosis will prevent preterm birth and its consequences. For women with a previous preterm birth, there is some suggestion that treatment of bacterial vaginosis may reduce the risk of preterm prelabour rupture of membranes and low birthweight.
Reallocating road space to buses and high occupancy vehicles in Leeds (2001)

Securing the most efficient use of existing road space to maximise the efficient and sustainable movement of people and goods has emerged as one of the key issues for urban transport planners. For over ten years Leeds has been implementing an integrated transport strategy, a central part of which is to secure greater efficiency from the existing road network. This paper outlines these policies and focuses on the practical aspects of reallocating road space and traffic capacity by reference to three different projects in Leeds. The measures discussed cover traffic management in the city centre and priority issues on major radial corridors, including the various approaches being adopted within a ‘quality bus initiative’ on a busy radial corridor. The example of the pioneering A647 scheme is used to show how high occupancy vehicle (HOV) lanes can not only assist public transport but also benefit motorists.
An order/disorder/water junction system for highly efficient co-catalyst-free photocatalytic hydrogen generation (2015)

Order/disorder interfacial engineering realizes highly efficient co-catalyst free hydrogen generation.
The aqueous colloidal suspension of ultrathin 2D MCM-22P crystallites (2014)

The action of a tetrapropylammonium hydroxide solution on lamellar zeolite precursor MCM-22P produced a stable aqueous colloidal suspension which was shown by X-ray diffraction, small angle X-ray scattering and atomic force microscopy to contain ultrathin two-dimensional (2D) crystallites, including one-unit cell thick (i.e., 2.5 nm) monolayers.
Ab interno trabeculectomy: Outcomes in exfoliation versus primary open-angle glaucoma (2012)

PURPOSE: To compare outcomes in exfoliation glaucoma versus primary open-angle glaucoma (POAG) after ab interno trabeculectomy alone (Trabectome) or in combination with cataract surgery and intraocular lens (IOL) implantation. SETTING: Trabectome Study Group institutions. DESIGN: Prospective nonrandomized cohort study. METHODS: Outcomes included intraocular pressure (IOP), glaucoma medications, complications, secondary procedures, and success, defined as no secondary surgery and IOP less than 21 mm Hg and a greater than 20% reduction from baseline. RESULTS: In the ab interno trabeculectomy–alone group, the mean preoperative IOP was 29.0 mm Hg ± 7.5 (SD) in exfoliation glaucoma cases and 25.5 ± 7.9 mm Hg in POAG cases (P<.01). At 1 year, the mean decrease in IOP was −12.3 ± 8.0 mm Hg and −7.5 ± 7.4 mm Hg, respectively (P<.01); the secondary procedure rate was 20.9% and 34.9%, respectively (P=.02); and the cumulative probability of success was 79.1% and 62.9%, respectively (P=.004). In the combined ab interno trabeculectomy–IOL group, the mean preoperative IOP was 21.7 ± 8.4 in exfoliation glaucoma cases and 19.9 ± 5.4 mm Hg in POAG cases (P=.06). At 1 year, the mean decrease in IOP was −7.2 ± 7.7 and −4.1 ± 4.6, respectively (P<.01); the secondary procedure rate was 6.7% and 6.1%, respectively (P=.88); and the cumulative probability of success was 86.7% and 91.0% (P=.73), respectively. CONCLUSION: Ab interno trabeculectomy using this new incisional procedure safely lowered IOP to the mid teens, with an overall greater reduction in exfoliation glaucoma and improved success when combined with cataract surgery. Financial Disclosure: No author has a financial or proprietary interest in any material or method mentioned.
Testability of the PAALS auto-align sensor system (2002)

The author addresses the testability design of the precision accelerometer alignment and leveling system (PAALS) auto-align sensor system. The PAALS module is a sensor system for measuring the alignment of avionic packages relative to the system reference axes. PAALS stores the measured alignment parameters in memory as updated by command from the main system computers, and is designed to be co-located on active targeting sub-systems. The PAALS auto-align sensor system is designed to provide accurate alignment data with a high degree of reliability and extremely low maintenance. To achieve these requirements, the PAALS design incorporated testability to verify the accuracy and insure reliability. The testability design consists of four parts: functional partitioning, enhanced reliability design, internal self-test design, and offline testing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High Performance and Reliability Trench Gate Power MOSFET With Partially Thick Gate Oxide Film Structure (PTOx-TMOS) (2006)

We have developed a novel Trench-Gate MOSFET (TMOS) with Partially Thick Gate Oxide Film Structure (PTOx) performing lower dissipation and higher reliability. The PTOx structure consists of thick oxide around trench top (Ttt), thin oxide at trench side (Tts), and thick oxide at trench bottom (Ttb), and is formed by our original simple process characterized by remaining SiN film in trench side oxide. We found out the optimum thickness in Ttb in terms of maximum drain breakdown voltage (Vdss), and the thickness of Ttb is 2 to 3 times larger than that of Tts. For 250V device, optimum thickness of Ttb is 150nm, while Tts is 60nm. We clarified Ron*Qgd reductions of PTOx-TMOS for wide blocking voltage range up to 250V for the first time. Estimated Ron*Qgd reductions compared with conventional devices are 32% at 60V, 28% at 100V, and 25% at 250V. Fabricated PTOx-TMOS of 100V and 250V denote high performance corresponding with estimation, and stress reduction in those gate oxides against high electric field is successfully achieved and promising high reliability.
Imaging in multiple sclerosis: A new spin on lesions (2016)

This article evaluates the most relevant state-of-the-art magnetic resonance (MR) techniques that are clinically available to investigate multiple sclerosis (MS). The presence of hypo- and hyperintense lesions on T1- and T2-weighted magnetic resonance imaging (MRI) sequences in white matter (WM) is a common finding that is occasionally a diagnostic challenge for the radiologist. The technical requirements and how they may help to understand, classify or follow-up these pathologies are briefly summarized. The gold standard for MS diagnosis is pathological correlation. Yet due to limited availability of biopsy and autopsy material, there is a high demand for imaging as a diagnostic as well as prognostic indicator. With the progress in MRI during the last decade, MRI now plays a leading role in the diagnosis and follow-up of MS. A number of correlative pathological and MR studies have helped to define pathological substrates of MS in focal lesions and normal appearing white matter (NAWM). Vascular spaces mimicking MS lesions have been minimized by the enhanced differentiation of WM and grey (GM) matter parenchyma. The aim of this article is to enhance the current understanding of histopathology and radiological characteristics of MS lesions in space and time.