gebhart/patrepeval huggingface dataset:
The Trp Cage Motif as a Scaffold for the Display of a Randomized Peptide Library on Bacteriophage T7 (2007)

Phage libraries displaying linear or disulfide-constrained peptides often yield weak binders, upon screening against a target, and must be optimized to improve affinity. The disadvantages of libraries based on larger complex proteins, such as single chain antibodies, have stimulated interest in the development of smaller nonimmunoglobulin protein scaffolds. A promising candidate is the Trp cage motif, a 20-residue C-terminal sequence of exendin-4. Amino acid substitution within the Trp cage resulted in a 20-mer peptide recognized as an ultrafast cooperative folding miniprotein, with ideal characteristics for the discovery of small structured nonimmunoglobulin motifs having a stable tertiary structure. Although we were unable to display the Trp cage on M13 phage, successful display was achieved using the lytic T7 phage. Interestingly, mutations were observed at a frequency dependent on display valency. A Trp cage library designed with randomized amino acids at seven solvent-exposed positions was developed from 1.6 x 10(9) primary clones in T7Select10-3b. DNA sequencing of 109 library clones revealed 38% mutants and 16% truncations by TAG codons at randomized positions. Amino acid frequencies were largely within expected bounds and DIVAA analysis revealed that the library had an average diversity of 0.67. Utility of the library was demonstrated by identification of HPQ containing Trp cage miniproteins, which bound streptavidin, and AAADPYAQWLQSMGPHSGRPPPR, which bound to human bronchial epithelial cells. A high complexity library based on the Trp cage miniprotein has demonstrated potential for identifying novel cell and protein binding peptides that could be used for the delivery of therapeutic molecules or as target-specific therapeutic agents.
Quantitative assessment of neuropilin-2 as a simple and sensitive diagnostic assay for spitzoid melanocytic lesions (2017)

There is a significant need for the development of diagnostic tools that can precisely distinguish Spitz nevi and spitzoid melanomas. Here, we report the development of a PCR-based quantitative diagnostic assay for spitzoid melanocytic lesions utilizing the expression ratio of neuropilin-2 and melan-A genes in primary tumor specimens. We find that the expression ratio of neuropilin-2/melan-A is significantly increased in spitzoid melanomas compared with Spitz nevi. The diagnostic potential of this quantitative assay was validated in two independent sets of patient samples as demonstrated in a receiver operating characteristic curve analysis showing an area under the curve value of 91.8%. Furthermore, the assay was found to quantitatively distinguish the clinical nature of atypical spitzoid melanocytic lesions that were diagnostically undetermined using histopathologic criteria alone. Our data indicate that this quantitative assay may be used as a tool in determining the diagnostic classification of histologically challenging spitzoid tumors.
Measured Characteristics of Dual Depth Dual Frequency Choke Ring for Multipath Rejection in GPS Receivers (1999)

Dual frequency choke ring design for GPS receivers was
introduced in the paper “The First Dual-Depth Dual-Frequency
Choke Ring”. This design was intended to
provide optimal multipath rejection for both L1 and L2
band, while ordinary choke ring designs have resonant
characteristics and provide optimal multipath rejection
only in L2 band. This work represents a pilot design of
dual-depth dual-frequency choke ring developed by
authors. Measured results are shown in comparison with
characteristics of ordinary single frequency choke ring. It
has been shown that for developed design improvement
of multipath rejection in L1 band is about 10 dB, while
characteristics in L2 band are the same as for ordinary
single frequency choke ring designs.
Adhesion Properties of Catechol-Based Biodegradable Amino Acid-Based Poly(ester urea) Copolymers Inspired from Mussel Proteins (2014)

Amino acid-based poly(ester urea) (PEU) copolymers functionalized with pendant catechol groups that address the need for strongly adhesive yet degradable biomaterials have been developed. Lap-shear tests with aluminum adherends demonstrated that these polymers have lap-shear adhesion strengths near 1 MPa. An increase in lap-shear adhesive strength to 2.4 MPa was achieved upon the addition of an oxidative cross-linker. The adhesive strength on porcine skin adherends was comparable with commercial fibrin glue. Interfacial energies of the polymeric materials were investigated via contact angle measurements and Johnson-Kendall-Roberts (JKR) technique. The JKR work of adhesion was consistent with contact angle measurements. The chemical and physical properties of PEUs can be controlled using different diols and amino acids, making the polymers candidates for the development of biological glues for use in clinical applications.
A cytochrome P450 monooxygenase cDNA (CYP71A10) confers resistance to linuron in transgenic<i>Nicotiana tabacum</i> (2000)

The isolation of a Glycine max cytochrome P450 monooxygenase (P450) cDNA designated CYP71A10 that conferred linuron resistance to laboratory-grown, transgenic Nicotiana tabacum seedlings was previously reported. A nonsegregating transgenic N. tabacum line has been established that possesses two independent copies of the G. max CYP71A10 transgene. Five-week-old progeny plants of this selected line were grown in a controlled environmental chamber and treated with linuron using either pretransplant incorporated (PTI) or postemergence (POST) applications. CYP71A10-transformed N. tabacum was more tolerant to linuron than the wild type for both application methods. The transgenic N. tabacum line tolerated an approximately 16-fold and 12-fold higher rate of linuron than wild-type N. tabacum when the herbicide was applied PTI or POST, respectively. These results provide evidence that plant-derived P450 genes can be employed effectively to confer herbicide resistance to transgenic plants.
Detection of<i>Ehrlichia canis</i>in Canine Carrier Blood and in Individual Experimentally Infected Ticks with a<i>p30</i>-Based PCR Assay (2002)

Detection of vector-borne pathogens is necessary for investigation of their association with vertebrate and invertebrate hosts. The ability to detect Ehrlichia spp. within individual experimentally infected ticks would be valuable for studies to evaluate the relative competence of different vector species and transmission scenarios. The purpose of this study was to develop a sensitive PCR assay based on oligonucleotide sequences from the unique Ehrlichia canis gene, p30, to facilitate studies that require monitoring this pathogen in canine and tick hosts during experimental transmission. Homologous sequences for Ehrlichia chaffeensis p28 were compared to sequences of primers derived from a sequence conserved among E. canis isolates. Criteria for primer selection included annealing scores, identity of the primers to homologous E. chaffeensis sequences, and the availability of similarly optimal primers that were nested within the target template sequence. The p30-based assay was at least 100-fold more sensitive than a previously reported nested 16S ribosomal DNA (rDNA)-based assay and did not amplify the 200-bp target amplicon from E. chaffeensis, the human granulocytic ehrlichiosis agent, or Ehrlichia muris DNA. The assay was used to detect E. canis in canine carrier blood and in experimentally infected Rhipicephalus sanguineus ticks. Optimized procedures for preparing tissues from these hosts for PCR assay are described. Our results indicated that this p30-based PCR assay will be useful for experimental investigations, that it has potential as a routine test, and that this approach to PCR assay design may be applicable to other pathogens that occur at low levels in affected hosts.
The calculation of features for non-stationary signals from moments of the singular value decomposition of Cohen-Posch (positive time-frequency) distributions (2002)

This paper presents a new method for determining the principal features of a non-stationary time series process based on the singular value decomposition (SVD) of the Cohen-Posch (1985) positive time-frequency distribution. This new method uses density functions derived from the SVD singular vectors to generate moments that associate with the principal features of the non-stationary process. Since the SVD singular vectors are orthonormal, the vectors whose elements are composed of the squared-elements of the SVD vectors are discrete density functions. Moments generated from these density functions are the principal features of the non-stationary time series process.
Mechanical Design and Initial Performance Testing of an Apple-Picking End-Effector (2015)

The fresh market apple industry currently relies on manual labor for all harvesting activities. The lack of mechanical harvesting technologies is a serious concern because of rising labor costs and increasingly uncertain labor availability. Researchers have been working for several decades to develop mechanical harvesters for tree fruit. The two fruit removal methods considered include mass mechanical harvesters and selective harvesting with robotics technology. Whereas mass mechanical harvesters have demonstrated unacceptable damage rates, robotic systems have been limited by insufficient speed and robustness. This paper describes the design and analysis of a novel underactuated end-effector fabricated for the robotic harvesting of tree fruit. The device has been optimized around a set of target tasks, the most critical being speed, low complexity, suitability for a highly variable field environment, and the replication of hand picking so as to minimize fruit damage. Development of the end-effector has been facilitated by a thorough study of the dynamic forces involved during the manual harvesting of apples. The end-effector produces a spherical power grasp with a normal force distribution and picking sequence replicating selected human patterns. An underactuated, tendon-driven device with compliant flexure joints has been adopted to improve system performance in the presence of position errors as well as enhance robustness to variable fruit size, shape, and orientation. The prototype end-effector also uses minimal sensors and incorporates open-loop control to reduce complexity and improve picking speed. This paper presents the theoretical analysis of the end-effector kinematics and discusses the selection of key geometric parameters. Experiments have been conducted to determine the normal forces developed during grasping of the apple. Results indicate that open-loop, feedforward control can be used to produce optimal normal force patterns.
Direct observation of stopped light in a whispering-gallery-mode microresonator (2007)

We introduce the definition of group velocity for a system with a discrete spectrum and apply it to a linear resonator. We show that a positive, negative, or zero group velocity can be obtained for light propagating in the whispering-gallery modes of a microspherical resonator. The associated group delay is practically independent of the ring-down time of the resonator. We demonstrate ``stopped light'' in an experiment with a fused silica microsphere.
Simple interferometric method for measuring severally the refractive index and the thickness of transparent plates (2003)

In this paper a new method for measuring simultaneously, thickness and refractive index of transparent plates is proposed. The method is based on a very simple lateral variable shear wavelength scanning interferometer. The transparent plate is made to rotate at controlled and constant angular speed. Radiation from a laser diode propagates though the sample and experiences an even number of reflections at the sample-air interfaces. The emerging wave fronts are laterally sheared with a shear depending from the actual angle of incidence. Varying the emission wavelength of the laser source a variation of the phase of interference signal is obtained. In this way, interferometric signals as function of incidence angle for each laser wavelength λ were obtained. Evaluating phase variations in correspondence of normal incidence, by a simple non-linear fit, it is possible to determine the optical thickness n.d. Then, retrieving the phase of the overall interference signal for all available incidence angles and employing the previously evaluated optical thickness, the refractive index value can be determined. Finally, geometrical thickness d was obtained straightforwardly as end result. The effectiveness and straightforwardness of the method has been demonstrated for a silicon sample and also for a z-cut Lithium Niobate sample.
Mixed Matrix Membrane Materials: An Answer to the Challenges Faced by Membrane Based Gas Separations Today? (2002)

The current status and the limitations faced by available membrane materials used or gas separations are reviewed. One of the biggest challenges that emerges from this survey is the need for materials with enhanced permselectivity with at least equivalent productivity compared to current materials. So called “mixed matrix” materials comprising molecular sieving entities such as zeolites dispersed in conventional polymer materials are possibly attractive solutions to this challenge. These materials ideally offer the excellent transport properties of molecular sieving materials with the processability of polymers, offering a cost effective solution to the need for economical high selectivity membrane materials. The potential impact of mixed matrix materials on the current applications is considered and the status of mixed matrix materials is presented in this paper.
Engineering an Amine Transaminase for the Efficient Production of a Chiral Sacubitril Precursor (2021)

An amine transaminase was engineered for the efficient production of a chiral precursor to sacubitril, (2R,4S)-5-([1,1′-biphenyl]-4-yl)-4-amino-2-methylpentanoic acid, a key component in the blockbuster heart failure drug Entresto. Starting from an enzyme with trace activity and preference for the undesired diastereoisomer, 11 rounds of enzyme evolution were performed. The resultant variant, CDX-043, showed high productivity giving 90% conversion at 75 g/L substrate concentration with 1% enzyme loading with respect to the substrate in 24 h and without the use of an organic cosolvent. The product diastereomeric purity toward the desired (2R,4S)-stereoisomer was >99.9:0.1 d.r. This variant also exhibited high process robustness and could tolerate reaction temperatures up to 65 °C, isopropylamine concentrations of at least 2 M, and reaction times of at least 5 days. A structural analysis of the enzyme variants gave insight into how the mutations affected activity and selectivity. This enzyme variant allows for the efficient and cost-effective production of sacubitril at large scale.
Novel Active Quasi-Circulator With Phase Compensation Technique (2008)

A novel active quasi-circulator using phase compensation technique for wideband isolation is proposed. It is formed by configuring three transistors with a complimenting phase shifter for equalization. It provides wideband frequency operation with sufficient return loss and isolation between ports without the need for passive filters. This compensation technique minimizes the circulator's size compared with conventional ferrite circulators and is compatible with monolithic microwave integrated circuit technology. Experimental results show that the proposed quasi-circulator has insertion losses around 0 dB, return losses better than 10 dB at each ports and minimum isolation around 15 dB from 0.8 to 2.2 GHz. Good agreement is obtained between simulation and experimental results.
Load swing control for an Unmanned Aerial Vehicle with a slung load (2014)

Research in the area of hauling loads using an Unmanned Aerial Vehicle (UAV) has been very restricted. The main obstacle is that the model for the vehicle and the load together is not yet established and available. The next hurdle faced is while designing a controller for an underactuated UAV. Finally, the last obstacle is the control of the load swing during hauling. These challenges make it a very intriguing area of research. The aim of this work is to propose a model for the UAV with a slung load. A feedback linearization controller which helps in trajectory tracking of the UAV and a time-delayed feedback controller to stabilize the load swing angles are also proposed which work together to make the overall system stable.
Multiple description trellis coded quantization (2002)

We present a construction of multiple description trellis coded quantizers. We use the tensor product of trellises to build a trellis which is applicable to multiple description coding. The problems of index assignment and set partitioning for the resulting trellis are considered. The Viterbi algorithm provides the best path for encoding and the design procedure utilizes a generalized Lloyd algorithm. The encoding process simultaneously generates all the transmitted sequences. Furthermore, the complexity of the scheme is almost independent of the rate. The quantizer provides remarkable performance with little encoding complexity.
Mannitol-Enhanced Delivery of Stem Cells and Their Growth Factors across the Blood–Brain Barrier (2014)

Ischemic brain injury in adults and neonates is a significant clinical problem with limited therapeutic interventions. Currently, clinicians have only tPA available for stroke treatment and hypothermia for cerebral palsy. Owing to the lack of treatment options, there is a need for novel treatments such as stem cell therapy. Various stem cells including cells from embryo, fetus, perinatal, and adult tissues have proved effective in preclinical and small clinical trials. However, a limiting factor in the success of these treatments is the delivery of the cells and their by-products (neurotrophic factors) into the injured brain. We have demonstrated that mannitol, a drug with the potential to transiently open the blood-brain barrier and facilitate the entry of stem cells and trophic factors, as a solution to the delivery problem. The combination of stem cell therapy and mannitol may improve therapeutic outcomes in adult stroke and neonatal cerebral palsy.
Starch Liquefaction with a Highly Thermostable Cyclodextrin Glycosyl Transferase from <i>Thermoanaerobacter</i> Species (1991)

A novel process is proposed for enzymatically liquefying starch with a highly thermostable cyclodextrin glycosyl transferase (CGTase). Conditions are described for liquefying 35% dry solids starch at pH 4.5 without added calcium, followed by saccharification to 96% dextrose. The CGTase is produced extracellularly by Thermoanaerobacter sp. ATCC 53,627, a thermophilic obligate anaerobe. This enzyme has a pH optimum activity observed at pH 3.5. The temperature optimum is 95°C. In the absence of starch and calcium, 95% of the activity remains after incubation at 80°C and pH 5.0 for 40 minutes. This CGTase shows the highest stability reported for any CGTase to date. These remarkable properties enable liquefaction of starch at pH 4.5, resulting in a process that can operate at the saccharifying pH of 4.5, thus eliminating the need for pH adjustment.
CryptDB: A Practical Encrypted Relational DBMS (2011)

CryptDB is a DBMS that provides provable and practical privacy in the face of a compromised database server or curious database administrators. CryptDB works by executing SQL queries over encrypted data. At its core are three novel ideas: an SQL-aware en-cryption strategy that maps SQL operations to encryption schemes, adjustable query-based encryption which allows CryptDB to ad-just the encryption level of each data item based on user queries, and onion encryption to efficiently change data encryption levels. CryptDB only empowers the server to execute queries that the users requested, and achieves maximum privacy given the mix of queries issued by the users. The database server fully evaluates queries on encrypted data and sends the result back to the client for final decryption; client machines do not perform any query processing and client-side applications run unchanged. Our evaluation shows that CryptDB has modest overhead: on the TPC-C benchmark on Postgres, CryptDB reduces throughput by 27 % compared to regular Postgres. Importantly, CryptDB does not change the innards of existing DBMSs: we realized the implementation of CryptDB using client-side query rewriting/encrypting, user-defined functions, and server-side tables for public key information. As such, CryptDB is portable; porting CryptDB to MySQL required changing 86 lines of code, mostly at the connectivity layer. 1.
Experiments on Open-Set Speaker Identification with Discriminatively Trained Neural Networks (2019)

This paper presents a study on discriminative artificial neural network classifiers in the context of open-set speaker identification. Both 2-class and multi-class architectures are tested against the conventional Gaussian mixture model based classifier on enrolled speaker sets of different sizes. The performance evaluation shows that the multi-class neural network system has superior performance for large population sizes.
Coded apertures for x-ray scatter imaging (2013)

We examine coding strategies for coded aperture scatter imagers. Scatter imaging enables tomography of compact regions from snapshot measurements. We present coded aperture designs for pencil and fan beam geometries, and compare their singular value spectra with that of the Radon transform and selected volume tomography. We show that under dose constraints scatter imaging improves conditioning over alternative techniques, and that specially designed coded apertures enable snapshot 1D and 2D tomography.
Transversely tapered hybrid electro-optic polymer/sol-gel Mach–Zehnder waveguide modulators (2008)

We show results of a proposed hybrid modulator structure that reduces both the optical loss and half wave voltage (Vπ). A sol-gel waveguide core transversely sandwiched between two Mach–Zehnder arms of electro-optic (EO) polymer cores enables an adiabatic transverse transition between the sol-gel and the EO polymer cores without the need for Y branches. The undercladding thickness is reduced to 3.7μm with negligible further optical loss from the bottom electrode. EO modulation with Vπ of 1.8V at 1550nm is demonstrated using a guest-host EO polymer, with an optical insertion loss of 13.7dB in the transverse magnetic mode.
Single Amino Acid Substitution in α-Conotoxin TxID Reveals a Specific α3β4 Nicotinic Acetylcholine Receptor Antagonist (2018)

The α3β4 nicotinic acetylcholine receptor (nAChR) is an important target implicated in various disease states. α-Conotoxin TxID (1) is the most potent antagonist of α3β4 nAChR, but it also exhibits inhibition of α6/α3β4 nAChR. The results of alanine scanning of 1 suggested a vital role for Ser9 in the selectivity of the peptide. In this study, Ser9 was substituted with a series of 14 amino acids, including some non-natural amino acids, displaying different physicochemical characteristics to further improve the selectivity of 1 toward α3β4 nAChR. The pharmacological activities of the mutants were evaluated using an electrophysiological approach. The best selectivity was obtained with [S9K]TxID, 12, which inhibited α3β4 nAChR with an IC<sub>50</sub> of 6.9 nM and had no effects on other nAChRs. Molecular modeling suggested a possible explanation for the high selectivity of 12 toward α3β4 nAChR, providing deeper insight into the interaction between α-conotoxins and nAChRs as well as potential treatments for nAChR-related diseases.