gebhart/patrepeval huggingface dataset:
The Lon Protease Is Essential for Full Virulence in Pseudomonas aeruginosa (2012)

Pseudomonas aeruginosa PAO1 lon mutants are supersusceptible to ciprofloxacin, and exhibit a defect in cell division and in virulence-related properties, such as swarming, twitching and biofilm formation, despite the fact that the Lon protease is not a traditional regulator. Here we set out to investigate the influence of a lon mutation in a series of infection models. It was demonstrated that the lon mutant had a defect in cytotoxicity towards epithelial cells, was less virulent in an amoeba model as well as a mouse acute lung infection model, and impacted on in vivo survival in a rat model of chronic infection. Using qRT-PCR it was demonstrated that the lon mutation led to a down-regulation of Type III secretion genes. The Lon protease also influenced motility and biofilm formation in a mucin-rich environment. Thus alterations in several virulence-related processes in vitro in a lon mutant were reflected by defective virulence in vivo.
Latent feature decompositions for integrative analysis of diverse high-throughput genomic data (2012)

A general method for regressing a continuous response upon large groups of diverse genetic covariates via dimension reduction is developed and exemplified. It is shown that allowing latent features derived from different covariate groups to interact aids in prediction when interactions subsist among the original covariates. A means of selecting a subset of relevant covariates from the original set is proposed, and a simulation study is performed to demonstrate the effectiveness of the procedure for prediction and variable selection. The procedure is applied to a high-dimensional lung cancer data set to model the effects of gene expression, copy number variation, and methylation on a drug response.
Enhancement of gmr properties of bottom type spin valve films with ultra-thin free layer covered with specular oxide capping layer (2005)

Summary form only given. The complete presentation was not made available for publication as part of the conference proceedings.
Microoptics Technology (2017)

It has been five years since the publication of the first edition of Microoptics Technology. In that time, optical technology has experienced an unparalleled burst of activity that has produced a body of significant real results that have advanced new materials, devices, and systems. Building on the foundation of the first edition, this comprehensive reference presents an introduction and review of the optics and methods of microoptic elements with particular emphasis on lenses and lens arrays.The author explores advances that emerged from the flurry of activity over the last five years. With two new chapters and another fully expanded, the book covers current and new methods of fabrication of microlenses, as well as refractive, GRIN, and diffractive methods. It also includes chapters on optical devices that utilize the microoptic fabrication methods, including micro-diffraction gratings and optical isolators, together with a discussion of a number of important applications. See what's new in the Second Edition:Coverage of negative refractive index materialsInformation on femto second laser interaction with materialsChapter on photonic crystal has been extensively expandedThe first edition was the first resource to collect all microlens fabrication methods into a single volume. With more than 600 references, tables, equations, drawings, and photographs, Microoptics Technology, Second Edition replaces its predecessor as the gold standard reference in this field.
Roles of biologic breast tissue composition and quantitative image analysis of mammographic images in breast tumor characterization (2014)

Purpose. Investigate whether knowledge of the biologic image composition of mammographic lesions provides imagebased biomarkers above and beyond those obtainable from quantitative image analysis (QIA) of X-ray mammography. Methods. The dataset consisted of 45 in vivo breast lesions imaged with the novel 3-component breast (3CB) imaging technique based on dual-energy mammography (15 malignant, 30 benign diagnoses). The 3CB composition measures of water, lipid, and protein thicknesses were assessed and mathematical descriptors, ‘3CB features’, were obtained for the lesions and their periphery. The raw low-energy mammographic images were analyzed with an established in-house QIA method obtaining ‘QIA features’ describing morphology and texture. We investigated the correlation within the ‘3CB features’, within the ‘QIA features’, and between the two. In addition, the merit of individual features in the distinction between malignant and benign lesions was assessed. Results. Whereas many descriptors within the ‘3CB features’ and ‘QIA features’ were, often by design, highly correlated, correlation between descriptors of the two feature groups was much weaker (maximum absolute correlation coefficient 0.58, p&lt;0.001) indicating that 3CB and QIA-based biomarkers provided potentially complementary information. Single descriptors from 3CB and QIA appeared equally well-suited for the distinction between malignant and benign lesions, with maximum area under the ROC curve 0.71 for a protein feature (3CB) and 0.71 for a texture feature (QIA). Conclusions. In this pilot study analyzing the new 3CB imaging modality, knowledge of breast tissue composition appeared additive in combination with existing mammographic QIA methods for the distinction between benign and malignant lesions.
Devices on the desk area network (1995)

The desk area network was proposed as an architecture suitable for a multimedia workstation. This paper describes how the architecture has evolved and the demonstration workstation that has been constructed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Photorefractive beam splitter for free-space optical interconnections (1998)

A photorefractive beam splitter (PRBS) is introduced as an alternative to a polarizing beam splitter (PBS) for coupling optical power into reflective modulators in a free-space optical interconnection system. The PRBS uses a single diffraction grating recorded in a photorefractive material to redirect the incident laser light into the first diffraction order and onto the modulators. Reflected interconnection light not matching the Bragg angle criteria transmits uncoupled through the beam splitter. Experimental results show that the PRBS provides better, more uniform transmission for off-axis beams than the currently used PBS.
Complex Salvage Procedures for Severe Lower Extremity Nerve Pain (2001)

From 1995 to 1999, the senior author did revision nerve release and vein wrapping (58 limbs in 58 patients) or peripheral nerve stimulation (62 limbs in 62 patients) to relieve intractable lower extremity nerve pain. Vein wrapping was done if the patient had temporary relief after a previous nerve release, if there was evidence of scarring around the nerve, and if nerve pain was triggered by mechanical stimulation. Peripheral nerve stimulation was done when previous nerve operations provided no relief or if the nerve pain was more constant and spontaneous without mechanical provocation. The duration of symptoms preoperatively averaged 52 months, and the number of previous peripheral neurosurgical interventions averaged 2.5. Postoperatively, the average pain improvement was rated as 60% for the patients who had vein wrapping and 41% for the patients who had peripheral nerve stimulation. Of the patients who had vein wrapping, 53% were satisfied, 14% were somewhat satisfied, and 33% were dissatisfied. Of the patients who had peripheral nerve stimulation, 61% were satisfied, 21% were somewhat satisfied, and 18% were dissatisfied. Most patients (78%) stated they would undergo the procedures again.
rodletless mutants of Aspergillus fumigatus (1994)

Conidia of Aspergillus fumigatus adhere in vitro to host proteins and cells via the outer cell wall layer. The rodA gene of A. fumigatus was cloned by homology with the rodA gene of Aspergillus nidulans, which is involved in the structure of the rodlets characteristic of the surface layer. The A. fumigatus RODA protein sequence has 85% similarity to that of A. nidulans RODA; the sequence codes for a hydrophobin, a low-molecular-weight protein moderately hydrophobic and rich in cysteines. The gene was disrupted with the hygromycin B resistance gene. By transformation of protoplasts with the disrupted gene, RodA- mutants were generated. These mutants are deficient in the ability to disperse their conidia; their conidia lack the rodlet layer and are hydrophilic. The adhesion of the rodletless conidia to collagen and bovine serum albumin was lower than that of the wild type; in contrast, there was no difference between RodA- and RodA+ conidia in adhesion to pneumocytes, fibrinogen, and laminin, suggesting that RODA is not the receptor for these cells and proteins. RodA- conidia were pathogenic for mice.
Supplementary Figure 3 from Sangivamycin-like Molecule 6 Exhibits Potent Anti-Multiple Myeloma Activity through Inhibition of Cyclin-Dependent Kinase-9 (2023)

&lt;p&gt;PDF file, 90K, GSK-3β and CDK1 inhibitors fail to reduce MM cell viability.&lt;/p&gt;
ChemInform Abstract: Elemental Fluorine. Part 10. Selective Fluorination of Pyridine, Quinoline, and Quinoxaline Derivatives with Fluorine—Iodine Mixtures. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
P3: Toward Privacy-Preserving Photo Sharing (2013)

With increasing use of mobile devices, photo shar-ing services are experiencing greater popularity. Aside from providing storage, photo sharing services enable bandwidth-efficient downloads to mobile devices by performing server-side image transformations (resizing, cropping). On the flip side, photo sharing services have raised privacy concerns such as leakage of photos to unauthorized viewers and the use of algorithmic recog-nition technologies by providers. To address these con-cerns, we propose a privacy-preserving photo encoding algorithm that extracts and encrypts a small, but signif-icant, component of the photo, while preserving the re-mainder in a public, standards-compatible, part. These two components can be separately stored. This technique significantly reduces the accuracy of automated detec-tion and recognition on the public part, while preserving the ability of the provider to perform server-side trans-formations to conserve download bandwidth usage. Our prototype privacy-preserving photo sharing system, P3, works with Facebook, and can be extended to other ser-vices as well. P3 requires no changes to existing services or mobile application software, and adds minimal photo storage overhead. 1
Usage of Smartphone Data to Derive an Indicator for Collaborative Mobility between Individuals (2017)

The potential of geospatial big data has been drawing attention for a few years. Despite the larger and larger market penetration of portable technologies (nomadic and wearable devices like smartphones and smartwatches), their opportunities for travel behavior analysis are still relatively unexplored. The main objective of our study is to extract the human mobility patterns from GPS traces in order to derive an indicator for enhancing Collaborative Mobility (CM) between individuals. The first step, extracting activity duration and location, is done using state-of-the-art automated recognition tools. Sensors data are used to reconstruct individual’s activity location and duration across time. For constructing the indicator, in a second step, we defined different variables and methods for specific case studies. Smartphone sensor data are being collected from a limited number of individuals and for one week. These data are used to evaluate the proposed indicator. Based on the value of the indicator, we analyzed the potential for identifying CM among groups of users, such as sharing traveling resources (e.g., carpooling, ridesharing, parking sharing) and time (rescheduling and reordering activities).
Reconfigurable Antennas for Wireless and Space Applications (2012)

Reconfigurable antennas, with the ability to radiate more than one pattern at different frequencies and polarizations, are necessary in modern telecommunication systems. The requirements for increased functionality (e.g., direction finding, beam steering, radar, control, and command) within a confined volume place a greater burden on today's transmitting and receiving systems. Reconfigurable antennas are a solution to this problem. This paper discusses the different reconfigurable components that can be used in an antenna to modify its structure and function. These reconfiguration techniques are either based on the integration of radio-frequency microelectromechanical systems (RF-MEMS), PIN diodes, varactors, photoconductive elements, or on the physical alteration of the antenna radiating structure, or on the use of smart materials such as ferrites and liquid crystals. Various activation mechanisms that can be used in each different reconfigurable implementation to achieve optimum performance are presented and discussed. Several examples of reconfigurable antennas for both terrestrial and space applications are highlighted, such as cognitive radio, multiple-input–multiple-output (MIMO) systems, and satellite communication.
A Novel Feeder-Free Culture System for Human Pluripotent Stem Cell Culture and Induced Pluripotent Stem Cell Derivation (2013)

Correct interactions with extracellular matrix are essential to human pluripotent stem cells (hPSC) to maintain their pluripotent self-renewal capacity during in vitro culture. hPSCs secrete laminin 511/521, one of the most important functional basement membrane components, and they can be maintained on human laminin 511 and 521 in defined culture conditions. However, large-scale production of purified or recombinant laminin 511 and 521 is difficult and expensive. Here we have tested whether a commonly available human choriocarcinoma cell line, JAR, which produces high quantities of laminins, supports the growth of undifferentiated hPSCs. We were able to maintain several human pluripotent stem cell lines on decellularized matrix produced by JAR cells using a defined culture medium. The JAR matrix also supported targeted differentiation of the cells into neuronal and hepatic directions. Importantly, we were able to derive new human induced pluripotent stem cell (hiPSC) lines on JAR matrix and show that adhesion of the early hiPSC colonies to JAR matrix is more efficient than to matrigel. In summary, JAR matrix provides a cost-effective and easy-to-prepare alternative for human pluripotent stem cell culture and differentiation. In addition, this matrix is ideal for the efficient generation of new hiPSC lines.
Zyklusabhängige Beschwerdesymptomatik nach vaginaler Hysterektomie mit Morcellement infolge der inkompletten Entfernung eines Uterus mit fokaler intramuraler Endometriose (2004)

Die Symptomatik zyklusabhängiger Unterbauchbeschwerden bei Frauen im gebärfähigen Alter lässt immer an eine Endometriose als mögliche Ursache denken.
Development of an interstitial cystitis risk score for bladder permeability (2017)

The BP-RS Score quantifies UIC risk, indicative of a bladder permeability defect etiology in a subset of IC patients. The Bladder Permeability Defect Risk Score is the first validated urine biomarker assay for interstitial cystitis/bladder pain syndrome.
Synthesis of 2,4-Diaminopteridines with Bulky Lipophilic Groups at the 6-Position as Inhibitors of Pneumocystis carinii, Toxoplasma gondii, and Mammalian Dihydrofolate Reductase (1997)

Summary Ten previously undescribed 2,4-diamino-6-(2-naphthylamino )methylpteridines with lipophilic chlorine or long-chain alkyl groups on the naphthyl moiety and either hydrogen or a methyl group on N 10 were synthesized from the appropriate 2-naphthylamine or N-methyl-2-naphthylamine by reaction with 2-amino-5-chloromethylpyrazine-3-carbonitrile and ring closure with guanidine . One analogue with a methyl group at the 7 -position was also prepared. The N 10 -unsubstituted analogues were consistently less active than the N1o-methyl analogues as inhibitors of Pneumocystis carin ii, Toxoplasma gondii, and rat liver dihydrofolate reductase. However the potency of the series as a whole was relatively low against all three enzymes, with the best inhibitors giving ICoo values only in the 0.1-1.0 ~M range and several giving IC50 values in the 10-100 ~M range. Moreover, while several compounds with ICso values of &lt;10 ~M showed some selectivity for the Pnellmocystis carinii and/or Toxoplasma gondii enzyme relative to the rat liver enzme, the magnitude of this effect was marginal «4-fold). Assays were also performed against purified human dihydrofolate reductase and against wild-type and methotrexateresistant human leukemic lymphoblasts in culture. Activity against the enzyme was very low, the best inhibitors giving only 50-70% inhibition at 10 ~M. Although none of the compounds inhibited the growth of wild-type CEM cells by more than 20% at 1 ~M, several were more active (60-75% inhibition at 1 ~M) against the methotrexate-resistant subline CEM/MTX, which is defective in methotrexate and reduced folate transport, than they were against the methotrexate-sensitive parental CEM cells. Overall the results suggest that 2,4-diamino-6-substituted pteridines with chlorine or long-chain alkyl substituents in the 2-naphthyl moiety and hydrogen or a methyl group on NIO are not likely to be therapeutically useful agents.
An Assessment of Effects of Vaccination on Genetic Resistance to Marek’s Disease (1974)

Relationship between resistance to Marek’s disease (MD) and production traits in vaccinated and non-vaccinated birds was studied over two generations in two Leghorn strains under selection for high egg production and related characters. In two experiments female progeny of a total of 116 sires and 758 dams were injected with MD virus at 3 weeks and survivors examined for lesions of MD at 12 weeks of age. Full sisters of the challenged birds were placed on 497 day egg production tests in which they were adventitiously exposed to MD. In the second generation all birds on the egg production test were vaccinated for MD. Average heritability of resistance to MD among birds injected with MD virus was .61. Heritability of laying house livability which included mortality from MD and from other causes was .11. Correlations between resistance to MD and production traits indicate that birds genetically more resistant to MD tend to have lower body weight, to mature earlier and to lay smaller eggs. Positive genetic correlations observed between resistance to MD and the egg production rate in vaccinated birds would tend to maintain or increase the genetic resistance to MD in populations under selection for high egg production, even though vaccination would reduce the effects of natural selection for resistance.
Coherent ST Codes for Flat Fading Channels (2006)

This chapter contains sections titled: Delay Diversity ST Codes ST Trellis Codes Orthogonal ST Block Codes Quasi-Orthogonal ST Block Codes ST Linear Complex Field Codes Linking OSTBC, QO-STBC, and STLCFC Designs Closing Comments
Optimum transmission conditions of solitons by pre-emphasis technique (1990)

By using the ‘pre-emphasis technique’, under certain loss-limit and dispersion-limit constraints, there always exists an optimum combination of input pulse-width and preemphasis factor for a specific carrier wavelength to maximise the bitrate-length product.
Somatic allelic deletion of nm23 in human cancer. (1991)

Tumor progression to the metastatic phenotype is accompanied in certain cell types by reduced expression of the nm23 gene. We have localized human nm23-H1 to chromosome 17 by somatic cell hybrid analysis. Regional localization in the CEPH database and in situ hybridization is reported. Somatic allelic deletion of nm23-H1 was observed in human breast, renal, colorectal, and lung carcinoma DNA samples, as compared to DNA from matched normal tissues. A homozygous deletion of nm23-H1 was observed in a lymph node metastasis of a colorectal carcinoma, indicating that nm23-H1 can be recessively inactivated. The data identify nm23-H1 as a novel, independent locus for allelic deletion in human cancer, a characteristic shared with previously described suppressor genes.
Feasibility Study of a New Method for Low-Complexity Fetal Movement Detection From Abdominal ECG Recordings (2015)

Fetal movement counting can provide valuable information on the fetal health, as a strong decrease in the number of movements can be seen as a precursor to fetal death. Typically, assessment of fetal health by fetal movement counting relies on the maternal perception of fetal activity. The percentage of detected movements is strongly subject dependent and with undivided attention of the mother varies between 37% and 88%. Various methods to assist in fetal movement detection exist based on a wide spectrum of measurement techniques. However, these are unsuitable for ambulatory or long-term observation. In this paper, a novel low-complexity method for fetal movement detection is presented based on amplitude and shape changes in the abdominally recorded fetal ECG. This method was compared to a state-of-the-art method from the literature. Using ultrasound-based movement annotations as ground truth, the presented method outperforms the state-of-the-art abdominal-ECG based method, with a sensitivity, specificity, and accuracy of 56%, 68%, and 63%, respectively. Additionally, a significant reduction in algorithm complexity is achieved, possibly enabling continuous ambulatory fetal movement detection and early detection of reduced fetal motility.
Buoy geometry and its influence on survivability for a point absorbing wave energy converter: Scale experiment and CFD simulations (2017)

For wave energy to be an economically viable energy\nsource, the technology has to withstand power levels\nduring storms that can be close to 50 times higher than\nduring normal operating conditions [1], and withstand\nmany years of wear. The impact of high wave loads is\nstudied not only within the field of wave energy, but\nhas long been a subject of study for ships, platforms\nand other offshore structures.\nTo model the force on the device under extreme and/or\novertopping waves is a difficult task. Experiments are\nexpensive and difficult to implement, and numerical methods are either very computationally demanding CFDmethods, or less accurate approximative methods. In\naddition, the performance and experienced forces during extreme waves are model dependent, and different\noffshore structures must be studied independently.\nHere, a 1:20 scale model of the Uppsala University\npoint-absorber type wave energy converter (WEC) [2]\nhas been tested in extreme wave conditions at the COAST\nLaboratory Ocean Basin at Plymouth University. The\nWEC consists of a linear generator connected to a buoy\nat the sea surface, and performance of two different\nbuoys is studied: a cylinder and cylinder with moonpool. Two types of wave sets have been used: focused\nwaves embedded into regular waves, and irregular waves.\nIn [3], the line forces measured in the experiment\nwere studied, since this is a parameter of high relevance for device survivability. The focus of this paper\nis on comparing the performance of the two buoys, and\non analysing the experimental data using a numerical\nmodel. A fully non-linear computational fluid dynamics\n(CFD) model based on OpenFOAM is presented and\nvalidated.