gebhart/patrepeval huggingface dataset:
Conditional gene vectors regulated in cis (2008)

Non-integrating gene vectors, which are stably and extrachromosomally maintained in transduced cells would be perfect tools to support long-term expression of therapeutic genes but preserve the genomic integrity of the cellular host. Small extrachromosomal plasmids share some of these ideal characteristics but are primarily based on virus blueprints. These plasmids are dependent on viral trans-acting factors but they can replicate their DNA molecules in synchrony with the chromosome of the cellular host and segregate to daughter cells in an autonomous fashion. On the basis of the concept of the latent origin of DNA replication of Epstein-Barr virus, oriP, we devised novel derivatives, which exclusively rely on an artificial replication factor for both nuclear retention and replication of plasmid DNA. In addition, an allosteric switch regulates the fate of the plasmid molecules, which are rapidly lost upon addition of doxycycline. Conditional maintenance of these novel plasmid vectors allows the reversible transfer of genetic information into target cells for the first time.
Synthetic peptides derived from the β2−β3 loop of<i>Raphanus sativus</i>antifungal protein 2 that mimic the active site (2001)

Rs-AFPs are antifungal proteins, isolated from radish (Raphanus sativus) seed or leaves, which consist of 50 or 51 amino acids and belong to the plant defensin family of proteins. Four highly homologous Rs-AFPs have been isolated (Rs-AFP1-4). The structure of Rs-AFP1 consists of three beta-strands and an alpha-helix, and is stabilized by four cystine bridges. Small peptides deduced from the native sequence, still having biological activity, are not only important tools to study structure-function relationships, but may also constitute a commercially interesting target. In an earlier study, we showed that the antifungal activity of Rs-AFP2 is concentrated mainly in the beta2-beta3 loop. In this study, we synthesized linear 19-mer peptides, spanning the entire beta2-beta3 loop, that were found to be almost as potent as Rs-AFP2. Cysteines, highly conserved in the native protein, are essential for maintaining the secondary structure of the protein. Surprisingly, in the 19-mer loop peptides, cysteines can be replaced by alpha-aminobutyric acid, which even improves the antifungal potency of the peptides. Analogous cyclic 19-mer peptides, forced to adopt a hairpin structure by the introduction of one or two non-native disulfide bridges, were also found to possess high antifungal activity. The synthetic 19-mer peptides, like Rs-AFP2 itself, cause increased Ca2+ influx in pregerminated fungal hyphae.
Leveraging Smart-Phone Cameras and Image Processing Techniques to Classify Mosquito Species (2018)

Mosquito borne diseases continue to pose grave dangers to global health. An important step in combating their spread in any area is to identify the type of species prevalent there. To do so, trained personnel lay local mosquito traps, and after collecting trapped specimens, they visually inspect each specimen to identify the species type and log their counts. This process takes hours and is cognitively very demanding. In this paper, we design a smart-phone based system that allows anyone to take images of a still mosquito that is either alive or dead (but still retaining its physical form) and automatically classifies the species type. Our system integrates image processing, feature selection, unsupervised clustering, and an SVM based machine learning algorithm for classification. Results with a total of 101 mosquito specimens spread across nine different vector carrying species (that were captured from a real outdoor trap in Tampa, Florida) demonstrate high accuracy in species identification. When implemented as a smart-phone application, the latency and energy consumption were minimal. With our system, the currently manual process of species identification and recording can be sped up, while also minimizing the ensuing cognitive workload of personnel. Secondly, ordinary citizens can use our system in their own homes for self-awareness and information sharing with public health agencies.
Gradient scaling phenomenon in microsize flexoelectric piezoelectric composites (2007)

The flexoelectric-type piezoelectric composites offer an alternative avenue for the development of piezoelectric ceramics, and since the flexoelectric response is diminished rather than enhanced in lead containing compositions, one of the merits of such composites is that those of highest sensitivity will be lead-free. The composites are fabricated by using certain nonpiezoelectric components with a texture symmetry which breaks up applied uniform fields, leading to the field gradients in the active flexoelectric components of the composites. Since these induced field gradients increase as the composite dimensions decrease, it is logical to expect that the piezoelectric performance of such composites would be enhanced with their reduced sizes. In this letter, we report the experimental studies that confirm such a gradient scaling phenomenon in two flexoelectric piezoelectric composites. The fabrication and measurement of the composites are discussed.
Fully Automatic Sliding Motion Compensated and Simultaneous 4D-CBCT via Bilateral Filtering (2021)

We developed a bilateral filtering based fully automatic sliding motion compensated 4D-CBCT scheme. Both digital phantom and initial patient pilot studies confirmed the improved motion estimation and image reconstruction ability. It can be used as a 4D-CBCT image guidance tool for lung SBRT treatment.
<i>trans–cis</i>and<i>trans–cis–trans</i>Microstructure Evolution of Azobenzene Liquid‐Crystal Polymer Networks (2011)

Abstract The photomechanics of azobenzene LCNs is modeled using a nonlinear continuum mechanics approach that couples photoisomerization of liquid crystal domain structures with light absorption and deformation of a glassy polymer network. The effects during UV‐stimulated trans–cis photomechanical deformation versus blue‐green light ( trans–cis–trans ) photomechanical deformation are simulated. Different bending deformation is predicted by assuming liquid‐crystal order/disorder behavior during trans–cis photoisomerization in comparison to light‐polarization‐driven reorientation of the trans phase during potential trans‐cis‐trans photoisomerization. Light‐controlled deformation mechanisms offer support for improved control of photo‐responsive morphing structures with a single blue‐green polarized light source. magnified image
pH (low) insertion peptide (pHLIP) inserts across a lipid bilayer as a helix and exits by a different path (2010)

What are the molecular events that occur when a peptide inserts across a membrane or exits from it? Using the pH-triggered insertion of the pH low insertion peptide to enable kinetic analysis, we show that insertion occurs in several steps, with rapid (0.1 sec) interfacial helix formation, followed by a much slower (100 sec) insertion pathway to give a transmembrane helix. The reverse process of unfolding and peptide exit from the bilayer core, which can be induced by a rapid rise of the pH from acidic to basic, proceeds approximately 400 times faster than folding/insertion and through different intermediate states. In the exit pathway, the helix-coil transition is initiated while the polypeptide is still inside the membrane. The peptide starts to exit when about 30% of the helix is unfolded, and continues a rapid exit as it unfolds inside the membrane. These insights may guide understanding of membrane protein folding/unfolding and the design of medically useful peptides for imaging and drug delivery.
Overcoming the fundamental limitation of frequency-domain fluorescence lifetime imaging microscopy spatial resolution (2021)

We propose and demonstrate the first analytical model of the spatial resolution of frequency-domain (FD) fluorescence lifetime imaging microscopy (FLIM) that explains how it is fundamentally different with the common resolution limit of the conventional fluorescence microscopy. Frequency modulation (FM) capture effect is also observed by the model, which results in distorted FLIM measurements. A super-resolution FLIM approach based on a localization-based technique, super-resolution radial fluctuations (SRRF), is presented. In this approach, we separately process the intensity and lifetime to generate a super-resolution FLIM composite image. The capability of the approach is validated both numerically and experimentally in fixed cells sample.
A novel method for generating and screening peptides and libraries displayed on adenovirus fiber (2007)

Capsid-displayed adenoviral peptide libraries have been a significant, yet unfeasible goal in biotechnology. Three barriers have made this difficult: the large size of the viral genome, the low efficiency of converting plasmid-based genomes into packaged adenovirus and the fact that library amplification is hampered by the ability of two (or more) virus to co-infect one cell. Here, we present a novel vector system, pFex, which is capable of overcoming all three barriers. With pFex, modified fiber genes are recombined into the natural genetic locus of adenovirus through unidirectional Cre-lox recombination. Modified-fiber genes can be directly shuttled into replicating viral genomes in mammalian cells. The 'acceptor' vector does not contain the fiber gene, and therefore does not propagate until it has received a 'donor' fiber gene. Therefore, This methodology overcomes the low efficiency of transfecting large viral genomes and bypasses the need for transition to functional virus. Thus, with a fiber-shuttle library, one can generate and evaluate large numbers of fiber-modified adenovirus simultaneously. Finally, successful fiber genes can be rescued from virus and recombined back into shuttle plasmids, avoiding the need to propagate mixed viral pools. For proof of principal, we use this new system to screen a capsid-displayed peptide library for retargeted viral infection.
A large scale memory (LAMSTAR) neural network for medical diagnosis (2002)

Discusses applications of the LAMSTAR network to a medical diagnostic case; specifically, to a urologic medical diagnosis. The LAMSTAR network is a self trained network based on SOM (Self-Organizing-Map) modules. It employs arrays of link-weight vectors to channel information vertically and horizontally through the network to facilitate fast memory retrieval. For diagnosis, the LAMSTAR network displays the diagnosis with suggestions to perform specific further tests. Also, the network interpolate/extrapolate those subwords (states of car systems), that were not present in the input word. As a medical diagnostic tool, the LAMSTAR network evaluates patients' conditions and long term forecasting after removal of kidney stones. The LAMSTAR network attempts to predict the treatment's results (failure/success) by analyzing the correlations among 100 patients (input words), each described by 17 subwords. The paper thus illustrates the scope of applications of the LAMSTAR network.
Extended scalability and functionalities of MRAM based on thermally assisted writing (2011)

MRAM are already used in low density applications such as microcontrollers or for spatial/avionics applications where they benefit from their radiation hardness. Thermally assisted writing allows extending the downsize scalability of both FIMS and STT-MRAM below the 20nm node. Within a few years, MRAM can play an important role in the memory hierarchy of electronic circuits. They may be first used as DRAM replacement below the 20nm node and in a second step even closer the logic units (Fig.10).
Demonstration of programmable optical multicasting in a regional/metro area network (2001)

We propose and demonstrate a novel optical multicast network using a wavelength-selective optical cross-connect and a multiwavelength optical source. The system allows wavelength-division-multiplexing optical sources to be separately maintained by a service provider and remotely modulated by an independent content provider. In our demonstration, a multiwavelength optical source and a common modulator are shared among the users receiving the multicast signal.
Lithium niobate waveguide polarisation convertor (1988)

A wavelength-insensitive, integrated-optic lithium niobate device capable of arbitrary polarisation transformations is described. Detailed investigation of the experimental performance shows excellent agreement with the theoretically predicted behaviour.
Design of robust differential microphone arrays with orthogonal polynomials (2015)

Differential microphone arrays have the potential to be widely deployed in hands-free communication systems thanks to their frequency-invariant beampatterns, high directivity factors, and small apertures. Traditionally, they are designed and implemented in a multistage way with uniform linear geometries. This paper presents an approach to the design of differential microphone arrays with orthogonal polynomials, more specifically with Jacobi polynomials. It first shows how to express the beampatterns as a function of orthogonal polynomials. Then several differential beamformers are derived and their performance depends on the parameters of the Jacobi polynomials. Simulations show the great flexibility of the proposed method in terms of designing any order differential microphone arrays with different beampatterns and controlling white noise gain.
Design of an orthotic device for full or partial gravity-balancing of a human upper arm during motion (2004)

Gravity balancing is often used in industrial machines to decrease the required actuator efforts during motion. In the literature, a number of methods have been proposed for gravity balancing that include counterweights, springs, and auxiliary parallelograms that determine the center of mass. However, these concepts have not yet been seriously applied to rehabilitation machines. This paper presents the underlying theory and design of an orthosis for the human upper arm that can fully or partially balance the human arm over the range of its motion. This design combines the use of auxiliary parallelograms to determine the center of mass along with springs to achieve a full or partial gravity balanced orthosis design. A first prototype is being constructed to demonstrate the effectiveness of the idea. Future prototypes will have parameters that will be tuned to the geometry and inertia of a human subject and tailor it to an individual's needs.
Salivary Gland Thrombostasin Isoforms Differentially Regulate Blood Uptake of Horn Flies Fed on Control- and Thrombostasin-Vaccinated Cattle (2010)

Thrombostasin (TS) is an anticlotting protein found in saliva of Haematobia irritans (horn flies). The polymorphic nature of the ts gene was first associated with success of horn flies blood feeding on a laboratory host, New Zealand White rabbits. In this study, we report results of similar studies testing blood uptake of horn flies feeding on a natural host, cattle. These studies confirmed the association of ts genotype with blood uptake of horn flies and showed that it was host species specific. In contrast to rabbits, blood uptake volumes of homozygous ts10 horn flies were lower than those of other ts genotypes when fed on control (ovalbumin-vaccinated) cattle. Cattle vaccinated with recombinant protein isoforms, rTS9 or rTB8, resisted horn fly feeding by yielding lower blood volumes compared with flies feeding on control cattle. The specific impact of vaccination, however, varied by ts genotype of flies. Cattle vaccinated with isoform rTS9 resisted flies of ts2, ts9, and tb8 genotype. Vaccination with isoform rTB8 produced resistance to ts8, ts9, and tb8 genotype flies. Horn flies of genotype ts10 were not affected by vaccination with either TS isoform and fed as well on rTS9- and rTB8-vaccinated as on control-vaccinated cattle. These experimental results confirm the efficacy of vaccines targeting horn fly salivary proteins and provide new insight into the dynamics of horn fly-cattle interactions in nature.
SSDM (2013)

Software Managed Multicore (SMM) architectures have been proposed as a solution for scaling the memory architecture. In an SMM architecture, there are no caches, and each core has only a local scratchpad memory. If all the code and data of the task to be executed on an SMM core cannot fit on the local memory, then data must be managed explicitly in the program through DMA instructions. While all code and data need to be managed, an efficient technique to manage stack data is of utmost importance since an average of 64% of all accesses may be to stack variables [16]. In this paper, we formulate the problem of stack data management optimization on an SMM core. We then develop both an ILP and a heuristic - SSDM (Smart Stack Data Management) to find out where to insert stack data management calls in the program. Experimental results demonstrate SSDM can reduce the overhead by 13X over the state-of-the-art stack data management technique [10].
Iterative computation of current and field distributions in multilayer frequency selective surfaces (1992)

A coupled integral equation formulation of analysing a generalised multilayer frequency selective surface is described. An iterative spectral technique has been adopted for the calculation of the induced currents, aperture fields and the plane wave transmission coefficient. In this scheme, the error is minimised using variational expressions for the element current in each of the unit cell areas of the multilayer structure. The effect of the distance separating the arrays and state of incidence to the rate of convergence and the transmission coefficient is discussed. The analysis described in the paper is not restricted to identical element geometries.
Treatment planning guided RF hyperthermia (2012)

Recent developments in simulation technology have expanded clinical use of hyperthermia treatment planning (HTP). HTP involves simulation of 1) the induced power absorption and 2) the induced temperature elevation distribution. Specifically the electromagnetic (EM) simulators have evolved into reliable tools providing accurate predictions of the absorbed power distributions applied during radiofrequency (RF) hyperthermia (HT). Such simulation tools are imperative for optimizing the energy delivery by phased array applicators with over four independent antennas. Consequently, HTP is currently being utilized in the clinic before, and during, deep-regional HT. For deep-local HT this strategy has even stronger potential but, due to steep thermal gradients, also more stringent quality requirements. In this paper, we exemplify the clinical implementation process for planning guided HT using phased-array HT applicators by reporting the steps taken for the HYPERcollar, a head and neck HT applicator. Besides treatment guidance, HTP allows applicator development, investigations into improved heating strategies and detailed assessment of confounding influences. In this way, treatment quality can been assessed and improved offline making HTP an inevitible tool in the improvement of deep-local HT when aiming at target conformal heat delivery.
Growth and scintillation properties of Nd doped LiCaAlF<inf>6</inf> scintilltor (2009)

Nd <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> 0.5% doped single crystal LiCaAlF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> scintillator was grown by the micro-pulling down (¿-PD) method. It was cut and polished to the physical dimension of 1 × 2 × 7 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . In transmittance spectrum, Nd <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> 5d-4f absorption observed at 175 nm and the transmittance became 80% at wavelength longer than 180 nm. Excited by 160 nm, Nd <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> 5d-4f emission appeared at 180 nm. X-ray induced radio-luminescence spectrum showed the similar feature with the photoluminescence one. When coupled with PMT and irradiated by <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">241</sup> Am ¿-ray, the absolute light yield resulted 50 ph/5.5 MeV ¿.
clSPARSE (2016)

Sparse linear algebra is a cornerstone of modern computational science. These algorithms ignore the zero-valued entries found in many domains in order to work on much larger problems at much faster rates than dense algorithms. Nonetheless, optimizing these algorithms is not straightforward. Highly optimized algorithms for multiplying a sparse matrix by a dense vector, for instance, are the subject of a vast corpus of research and can be hundreds of times longer than naïve implementations. Optimized sparse linear algebra libraries are thus needed so that users can build applications without enormous effort.
Smooth Vertical Surface Climbing With Directional Adhesion (2008)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Designed Ligands as Probes for the Catalytic Binding Mode in Mo-Catalyzed Asymmetric Allylic Alkylation We thank the National Science Foundation and the National Institutes of Health for their generous support of the work carried out at Stanford. I.H. thanks the Japan Society for the Promotion of Science for a postdoctoral fellowship. Mass spectra were provided by the Mass Spectrometry Facility at the University of California, San Francisco, which is supported by the NIH Division of Research Resources. (2002)

Unusual coordination in the asymmetric allylic alkylation catalyzed by molybdenum (see scheme) was revealed by a study on several ligands, for example, 1. Unexpectedly, only the nitrogen atom of one picolinamide group coordinates to Mo, while the other amide group rigidifies the system. Based on the effectiveness of the bisdeprotonated ligand, the observed reaction can be rationalized and new ligands can be designed for asymmetric induction in allylic alkylations.