gebhart/patrepeval huggingface dataset:
Genetic relatedness amongst intestinal spirochaetes isolated from rate and brids. (1996)

Multilocus enzyme electrophoresis was used to determine genetic relationships amongst 32 intestinal spirochaetes (Serpulina spp.) isolated from rats (17), rheas (7), chickens, (4), ducks (2), a swan (1) and a flamingo (1). The strains were divided into 20 electrophoretic types (ETs), with a mean genetic diversity per locus of 0.62. The results were compared with those previously published for porcine intestinal spirochaetes. One strain from a healthy rat, and three rhea strains which were recovered from cases of necrotizing typhlitis, were grouped in the same ETs as certain porcine strains of Serpulina hyodysenteriae. The rhea strains could be differentiated from these by pulsed-field gel electrophoresis. Fifteen of the rat strains were genetically and phenotypically closely related. In contrast the avian strains were genetically more heterogeneous, with pathogenic isolates located in three different genetic groups.
Single-chip computers with microelectromechanical systems-based magnetic memory (invited) (2000)

This article describes an approach for implementing a complete computer system (CPU, RAM, I/O, and nonvolatile mass memory) on a single integrated-circuit substrate (a chip)—hence, the name “single-chip computer.” The approach presented combines advances in the field of microelectromechanical systems (MEMS) and micromagnetics with traditional low-cost very-large-scale integrated circuit style parallel lithographic manufacturing. The primary barrier to the creation of a computer on a chip is the incorporation of a high-capacity [many gigabytes (GB)] re-writable nonvolatile memory (in today’s terminology, a disk drive) into an integrated circuit (IC) manufacturing process. This article presents the following design example: a MEMS-based magnetic memory that can store over 2 GB of data in 2 cm2 of die area and whose fabrication is compatible with a standard IC manufacturing process.
An unsupervised learning approach for facial expression recognition using semi-definite programming and generalized principal component analysis (2009)

In this paper, we consider facial expression recognition using an unsupervised learning framework. Specifically, given a data set composed of a number of facial images of the same subject with different facial expressions, the algorithm segments the data set into groups corresponding to different facial expressions. Each facial image can be regarded as a point in a high-dimensional space, and the collection of images of the same subject resides on a manifold within this space. We show that different facial expressions reside on distinct subspaces if the manifold is unfolded. In particular, semi-definite embedding is used to reduce the dimensionality and unfold the manifold of facial images. Next, generalized principal component analysis is used to fit a series of subspaces to the data points and associate each data point to a subspace. Data points that belong to the same subspace are shown to belong to the same facial expression.
Low-cost Sensor-enabled Freehand 3D Ultrasound (2019)

Volumetric 3D ultrasound provides intuitive visualization and spatial context, but most implementations are expensive, using a sophisticated probe design or a cumbersome position-tracking setup requiring calibration. In this work, we implemented freehand 3D ultrasound using low-cost sensors. A custom probe attachment with a pivoting head was made to accommodate IMUs and optical surface-tracking sensors, plus a microcontroller with USB connection. An external laptop with a custom graphical user interface synchronously acquired sensor data and 2D ultrasound images using a Siemens 9L4 probe (depth = 4 cm) and S2000 scanner with a video capture device. Sensor data was stabilized with a gradient descent orientation filter and used to reconstruct a 3D image volume from 500 2D frames, acquired over an irregular path in an abdominal phantom over 15 seconds. The 3D reconstruction time was 30 seconds, and the quality of the 3D image volume was comparable to that of the raw 2D images. These results demonstrate that freehand 3D ultrasound can be practically achieved using low-cost sensors.
Enhanced UV Laser-Induced Damage Tolerance in CsLiB&gt;inf&lt;6&gt;/inf&lt;O&gt;inf&lt;10&gt;/inf&lt;by Reducing Water Molecule Impurities in the Crystal Volume (2006)

We revealed the harmful effects of water molecules in CsLiB <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</inf> crystal volume on ultraviolet light generation. The reduction of impurities results in lowering nonlinear absorption at 266 nm and significantly enhancing the laser-induced damage tolerance.
Realizable design of field taper via coordinate transformation (2018)

Complex electromagnetic structures can be designed by exploiting the concept of spatial coordinate transformations. In this paper, we define a coordinate transformation scheme that enables one to taper the electric field between two waveguides of different cross-sections. The electromagnetic field launched from the wide input waveguide is compressed in the proposed field tapering device and guided into the narrow output waveguide. In closed rectangular waveguide configurations, the taper can further play the role of a mode selector due to the output waveguide's cut-off frequency. Realizable permittivity and permeability values that can be achieved with common existing metamaterials are determined from the transformation equations and simplified by a proposed parameter reduction method. Both a 2D continuous design model and a potential 3D discretized realization model are presented at microwave frequencies and the performances of the tapering devices are verified by full-wave finite element numerical simulations. Finally, near-field distributions are shown to demonstrate the field tapering functionality.
Asymmetric Synthesis of Silanediol Inhibitors for the Serine Protease Coagulation Cascade Enzyme FXIa (2018)

Silanediol peptidomimetics have been prepared, designed to inhibit the serine protease enzyme Factor XIa (FXIa) for treatment of thrombosis without complete interruption of normal hemostasis. These Arg-[Si]-Ala analogues of the FXIa substrate (FIX) are the first silanediol dipeptide analogues to carry a basic guanidine group. Control of stereochemistry was accomplished using catalytic asymmetric hydrosilylation and addition of a silyllithium intermediate to the Davis-Ellman sulfinimine.
Demonstration of reactive vitreous coatings on reinforcement steel to prevention corrosion and concrete failure : final report on Project F08-AR01 (2016)

The Department of Defense (DoD) Corrosion Prevention and Control Program funded a project to evaluate the corrosion performance of a new vitreous reactive-silicate coating that can be bonded to steel reinforcement bars used in concrete structures.The technology was installed in pavement at Corpus Christi Army Depot (CCAD) where corrosion-induced concrete damage has contributed to costly accidents involving transport of aircraft engines.Test blocks designed and instrumented for accelerated corrosion testing were used to compare the performance of vitreous-coated bars with other types of bars.The vitreous-coated bars installed in CCAD pavement showed no sign of corrosion because atmospheric chlorides could not penetrate to reinforcement depth during the demonstration period.Test block custody was temporarily lost at the installation, during which time they were damaged and experimental controls were disrupted.When the blocks were split open for visual examination, the vitreous-coated samples had various amounts of surface corrosion on the bars and concrete traces.An economic analysis using a conservative service-life assumption for vitreous-coated rebars projected a return on investment of 44.69 over 30 years versus materials and methods currently used at CCAD.The technology requires further refinements and testing before it could be recommended for DoD-wide implementation.
- Chest computed tomography and clinical trials in cystic fibrosis (2015)

Progressive lung disease starts in most children with cystic brosis (CF) in infancy and progresses throughout life.1,2 e most important components of CF lung disease are bronchiectasis, which is an irreversible widening of bronchi, and trapped air which reects small airways disease.3,4 Imaging techniques that can be used to monitor CF lung disease in clinical trials are chest radiography, computed tomography (CT), and magnetic resonance imaging. Of these modalities CT is currently the most sensitive and feasible modality to diagnose and monitor bronchiectasis and trapped air in clinical trials. CT has been recognized as the gold standard for the detection of bronchiectasis since the mid-90s.5,6 Bronchiectasis as detected on inspiratory chest CT scans has been well validated as clinical outcome measure over the last decades.7,10 In more recent years, it has become clear that trapped air is also an early and important feature of CF lung disease. Trapped air can be detected on expiratory CT scans.11 Other structural ndings that can be observed on chest CT in CF and that are of interest in clinical trials are airway wall thickness and mucus impaction.12-14 It is now recognized that inclusion of chest CT-related outcome measures can be of importance in clinical trials as primary or secondary end point to determine the ecacy of an investigational drug treatment on progression of CF lung disease and or to characterize the patient population.15 To use chest CT in clinical trials, safe low-dose well-standardized protocols and reproducible sensitive image analysis of the structural changes of interest are needed. e aim of this chapter is to describe the importance of chest CT-related outcome measures, how CTs can be used in clinical trials, and how images can be analyzed.
Data from Intrathecal Viral Vector Delivery of Trastuzumab Prevents or Inhibits Tumor Growth of Human HER2-Positive Xenografts in Mice (2023)

&lt;div&gt;Abstract&lt;p&gt;Breast cancer brain metastases are a deadly sequela of primary breast tumors that overexpress human epidermal growth factor receptor 2 (HER2); median survival for patients with these tumors is 10 to 13 months from the time of diagnosis. Current treatments for HER2-positive breast cancer brain metastases are invasive, toxic, and largely ineffective. Here, we have developed an adeno-associated virus serotype 9 (AAV9) vector to express the anti-HER2 monoclonal antibody trastuzumab (Herceptin) &lt;i&gt;in vivo&lt;/i&gt;. A single prophylactic intrathecal administration of AAV9.trastuzumab vector in a novel orthotopic &lt;i&gt;Rag1&lt;sup&gt;−/−&lt;/sup&gt;&lt;/i&gt; murine xenograft model of HER2-positive breast cancer brain metastases significantly increased median survival, attenuated brain tumor growth, and preserved both the HER2 antigen specificity and the natural killer cell–associated mechanism of action of trastuzumab. When administered as a tumor treatment, AAV9.trastuzumab increased median survival. Dose-escalation studies revealed that higher doses of AAV9.trastuzumab resulted in smaller tumor volumes. Our results indicate that intrathecal AAV9.trastuzumab may provide significant antitumor activity in patients with HER2-positive breast cancer brain metastases.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Significance:&lt;/b&gt; Intrathecal delivery of trastuzumab via adeno-associated virus has the potential to become a novel, integral part of adjuvant therapy for patients with HER2-positive breast cancer brain metastases. &lt;i&gt;Cancer Res; 78(21); 6171–82. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
High-order optical vortex position detection using a Shack-Hartmann wavefront sensor (2015)

Optical vortex (OV) beams have null-intensity singular points, and the intensities in the region surrounding the singular point are quite low. This low intensity region influences the position detection accuracy of phase singular point, especially for high-order OV beam. In this paper, we propose a new method for solving this problem, called the phase-slope-combining correlation matching method. A Shack-Hartmann wavefront sensor (SH-WFS) is used to measure phase slope vectors at lenslet positions of the SH-WFS. Several phase slope vectors are combined into one to reduce the influence of low-intensity regions around the singular point, and the combined phase slope vectors are used to determine the OV position with the aid of correlation matching with a pre-calculated database. Experimental results showed that the proposed method works with high accuracy, even when detecting an OV beam with a topological charge larger than six. The estimated precision was about 0.15 in units of lenslet size when detecting an OV beam with a topological charge of up to 20.
Chemical Polysialylation and In Vivo Tetramerization Improve Pharmacokinetic Characteristics of Recombinant Human Butyrylcholinesterase-Based Bioscavengers (2015)

Organophosphate toxins (OPs) are the most toxic low-molecular compounds. The extremely potent toxicity of OPs is determined by their specificity toward the nerve system. Human butyrylcholinesterase (hBChE) is a natural bioscavenger against a broad spectrum of OPs, which makes it a promising candidate for the development of DNA-encoded bioscavengers. The high values of the protective index observed for recombinant hBChE (rhBChE) make it appropriate for therapy against OP poisoning, especially in the case of highly toxic warfare nerve agents. Nevertheless, large-scale application of biopharmaceuticals based on hBChE is restricted due to its high cost and extremely rapid elimination from the bloodstream. In the present study, we examine two approaches for long-acting rhBChE production: I) chemical polysialylation and II) in-vivo tetramerization. We demonstrate that both approaches significantly improve the pharmacokinetic characteristics of rhBChE (more than 5 and 10 times, respectively), which makes it possible to use rhBChE conjugated with polysialic acids (rhBChE-CAO) and tetrameric rhBChE (4rhBChE) in the treatment of OP poisonings.
An Effective Epigenetic-PARP Inhibitor Combination Therapy for Breast and Ovarian Cancers Independent of BRCA Mutations (2018)

<b>Purpose:</b> PARP inhibitors (PARPi) are primarily effective against BRCA1/2-mutated breast and ovarian cancers, but resistance due to reversion of mutated BRCA1/2 and other mechanisms is common. Based on previous reports demonstrating a functional role for DNMT1 in DNA repair and our previous studies demonstrating an ability of DNA methyltransferase inhibitor (DNMTi) to resensitize tumors to primary therapies, we hypothesized that combining a DNMTi with PARPi would sensitize PARPi-resistant breast and ovarian cancers to PARPi therapy, independent of BRCA status.<b>Experimental Design:</b> Breast and ovarian cancer cell lines (BRCA-wild-type/mutant) were treated with PARPi talazoparib and DNMTi guadecitabine. Effects on cell survival, ROS accumulation, and cAMP levels were examined. <i>In vivo</i>, mice bearing either BRCA-proficient breast or ovarian cancer cells were treated with talazoparib and guadecitabine, alone or in combination. Tumor progression, gene expression, and overall survival were analyzed.<b>Results:</b> Combination of guadecitabine and talazoparib synergized to enhance PARPi efficacy, irrespective of BRCA mutation status. Coadministration of guadecitabine with talazoparib increased accumulation of ROS, promoted PARP activation, and further sensitized, in a cAMP/PKA-dependent manner, breast and ovarian cancer cells to PARPi. In addition, DNMTi enhanced PARP "trapping" by talazoparib. Guadecitabine plus talazoparib decreased xenograft tumor growth and increased overall survival in BRCA-proficient high-grade serous ovarian and triple-negative breast cancer models.<b>Conclusions:</b> The novel combination of the next-generation DNMTi guadecitabine and the first-in-class PARPi talazoparib inhibited breast and ovarian cancers harboring either wild-type- or mutant-BRCA, supporting further clinical exploration of this drug combination in PARPi-resistant cancers. <i>Clin Cancer Res; 24(13); 3163-75. ©2018 AACR</i>.
Joint audio-visual speech processing for recognition and enhancement. (2003)

Visual speech information present in the speaker’s mouth region has long been viewed as a source for improving the robustness and naturalness of human-computer-interfaces (HCI). Such information can be particularly crucial in realistic HCI environments, where the acoustic channel is corrupted, and as a result, the performance of traditional automatic speech recognition (ASR) systems falls below usability levels. In this paper, we review two general approaches that utilize visual speech to improve ASR in acoustically challenging environments: One directly combines features extracted from the acoustic and visual channels, aiming at superior recognition performance of the resulting audio-visual ASR system. The other seeks to eliminate the noise present in the acoustic features, aiming at their audio-visual based enhancement, and thus resulting in improved speech recognition. We present a number of techniques recently introduced in the literature for bimodal ASR and enhancement, and we study their performance using a suitable audio-visual database. Among the methods considered, our recognition experiments demonstrate that decision based combination of audio and visual features significantly outperforms simpler feature based integration methods for audio-visual ASR. For audio feature enhancement, a non-linear technique is more successful than a regression-based approach. As expected, bimodal ASR and enhancement outperform their audio-only counterparts. 1.
UV-light irradiation effects on oxide superconducting thin films (1991)

Bi/sub 2/Sr/sub 2/CaCu/sub 2/O/sub x/ thin films prepared on
Two- and three-dimensional transoesophageal echocardiography in large swine used as model for transcatheter heart valve therapies: standard planes and values (2016)

2D and 3D TOE can be routinely applied as image guidance in pigs used as a model for the development and training of new techniques to treat heart valve disease.
Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges (2016)

One of the most significant biological discoveries of the last decade is represented by the reality that the vast majority of the transcribed genomic output comprises diverse classes of noncoding RNAs (ncRNAs) that may play key roles and/or be affected by many biochemical cellular processes (i.e., RNA editing), with implications in human health and disease. With 90% of the human genome being transcribed and novel classes of ncRNA emerging (tRNA-derived small RNAs and circular RNAs among others), the great majority of the human transcriptome suggests that many important ncRNA functions/processes are yet to be discovered. An approach to filling such vast void of knowledge has been recently provided by the increasing application of next-generation sequencing (NGS), offering the unprecedented opportunity to obtain a more accurate profiling with higher resolution, increased throughput, sequencing depth, and low experimental complexity, concurrently posing an increasing challenge in terms of efficiency, accuracy, and usability of data analysis software. This review provides an overview of ncRNAs, NGS technology, and the most recent/popular computational approaches and the challenges they attempt to solve, which are essential to a more sensitive and comprehensive ncRNA annotation capable of furthering our understanding of this still vastly uncharted genomic territory.
Pendent polyimides using mellitic acid dianhydride. III. The effect of pendent group functionality on polymer properties (2009)

Abstract Methyl, methoxy, and nitrile (cyano) functional groups were incorporated into the metal–organic pendent group of a co‐polyamic acid, co‐PAA[(3,4′‐ODA/ODPA) 0.9 (3,4′‐ODA/{MADA‐ p ‐Zr(adsp)(Rdsp)}) 0.1 ], in various locations to investigate their effects on polymer chain interactions and film quality. Proton nuclear magnetic resonance and gel permeation chromatography (GPC) performed on solutions of these products were consistent with the expected 10% (mol) functionalized pendent polymeric structures. Thermogravimetric analysis performed on ether‐precipitated samples revealed little functional group effect on imidization temperature (decreases of 5–8°C), but showed a somewhat‐greater effect on decomposition temperature (decreases of 6°C for the 3‐methoxy derivative to 28°C for the methyl derivative). Differential scanning calorimetry performed on imidized powder samples showed that glass transition temperatures increased with the addition of the functional groups from 2°C for the methyl derivative to 19°C for the 3‐methoxy derivative. Imidized films were solvent resistant, transparent, and flexible, with the nitrile derivative least susceptible to crack formation. Light scattering results revealed that the nitrile derivative had the lowest second virial coefficient of the functional groups tested and formed aggregates at room temperature in NMP with n = 2, thus rationalizing its superior film forming properties. Results of contact angle measurements and atomic oxygen exposure of functionalized pendent co‐PI films are included. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Mining Novel Effector Proteins from the Esophageal Gland Cells ofMeloidogyne incognita (2014)

Meloidogyne incognita is one of the most economically damaging plant pathogens in agriculture and horticulture. Identifying and characterizing the effector proteins which M. incognita secretes into its host plants during infection is an important step toward finding new ways to manage this pest. In this study, we have identified the cDNAs for 18 putative effectors (i.e., proteins that have the potential to facilitate M. incognita parasitism of host plants). These putative effectors are secretory proteins that do not contain transmembrane domains and whose genes are specifically expressed in the secretory gland cells of the nematode, indicating that they are likely secreted from the nematode through its stylet. We have determined that, in the plant cells, these putative effectors are likely to localize to the cytoplasm. Furthermore, the transcripts of many of these novel effectors are specifically upregulated during different stages of the nematode's life cycle, indicating that they function at specific stages during M. incognita parasitism. The predicted proteins showed little to no homology to known proteins from free-living nematode species, suggesting that they evolved recently to support the parasitic lifestyle. On the other hand, several of the effectors are part of gene families within the M. incognita genome as well as that of M. hapla, which points to an important role that these putative effectors are playing in both parasites. With the discovery of these putative effectors, we have increased our knowledge of the effector repertoire utilized by root-knot nematodes to infect, feed on, and reproduce on their host plants. Future studies investigating the roles that these proteins play in planta will help mitigate the effects of this damaging pest.