gebhart/patrepeval huggingface dataset:
Cloning, synthesis, and characterization of αO-conotoxin GeXIVA, a potent α9α10 nicotinic acetylcholine receptor antagonist (2015)

We identified a previously unidentified conotoxin gene from Conus generalis whose precursor signal sequence has high similarity to the O1-gene conotoxin superfamily. The predicted mature peptide, αO-conotoxin GeXIVA (GeXIVA), has four Cys residues, and its three disulfide isomers were synthesized. Previously pharmacologically characterized O1-superfamily peptides, exemplified by the US Food and Drug Administration-approved pain medication, ziconotide, contain six Cys residues and are calcium, sodium, or potassium channel antagonists. However, GeXIVA did not inhibit calcium channels but antagonized nicotinic AChRs (nAChRs), most potently on the α9α10 nAChR subtype (IC50 = 4.6 nM). Toxin blockade was voltage-dependent, and kinetic analysis of toxin dissociation indicated that the binding site of GeXIVA does not overlap with the binding site of the competitive antagonist α-conotoxin RgIA. Surprisingly, the most active disulfide isomer of GeXIVA is the bead isomer, comprising, according to NMR analysis, two well-resolved but uncoupled disulfide-restrained loops. The ribbon isomer is almost as potent but has a more rigid structure built around a short 310-helix. In contrast to most α-conotoxins, the globular isomer is the least potent and has a flexible, multiconformational nature. GeXIVA reduced mechanical hyperalgesia in the rat chronic constriction injury model of neuropathic pain but had no effect on motor performance, warranting its further investigation as a possible therapeutic agent.
A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria×ananassa Duch.) fruit, a non-climacteric tissue* (2010)

Climacteric and non-climacteric fruits have traditionally been viewed as representing two distinct programmes of ripening associated with differential respiration and ethylene hormone effects. In climacteric fruits, such as tomato and banana, the ripening process is marked by increased respiration and is induced and co-ordinated by ethylene, while in non-climacteric fruits, such as strawberry and grape, it is controlled by an ethylene-independent process with little change in respiration rate. The two contrasting mechanisms, however, both lead to texture, colour, and flavour changes that probably reflect some common programmes of regulatory control. It has been shown that a SEPALLATA(SEP)4-like gene is necessary for normal ripening in tomato. It has been demonstrated here that silencing a fruit-related SEP1/2-like (FaMADS9) gene in strawberry leads to the inhibition of normal development and ripening in the petal, achene, and receptacle tissues. In addition, analysis of transcriptome profiles reveals pleiotropic effects of FaMADS9 on fruit development and ripening-related gene expression. It is concluded that SEP genes play a central role in the developmental regulation of ripening in both climacteric and non-climacteric fruits. These findings provide important information to extend the molecular control of ripening in a non-climacteric fruit beyond the limited genetic and cultural options currently available.
Transmission Electron Microscopy of SrO Containing Multi-Cation Doped α-SiAlON Ceramics (2001)

An advantage of α-SiAlON is that it can accommodate cations of sintering additives and hence reduces the amount of deleterious remnant intergranular amorphous phase. However, it is believed that relatively large cations cannot enter the structure. In this work, TEM-EDX combination is used to find out whether large cations of Sr 2+ can be incorporated into the α-SiAlON structure. The results showed that Sr 2+ can enter the structure if other smaller cations of Ca 2+ or Yb 3+ are also present.
Athermal Compensation of Source Wavelength Drifts for Fiber-Optic Current Sensors (2015)

An athermal fiber-optic retarder introduces controlled wavelength dependent cross-coupling between the two orthogonal polarization states of a fiber-optic current sensor and thus compensates the wavelength dependence of the Faraday effect.
Novel Fucosylated Biomarkers for the Early Detection of Hepatocellular Carcinoma (2009)

Changes in glycosylation, most notably fucosylation, have been associated with the development of hepatocellular carcinoma (HCC). In this report, the levels of fucosylated kininogen (Fc-Kin) and fucosylated alpha-1-antitrypsin were analyzed individually and in combination with the currently used marker, alpha-fetoprotein, and a previously identified biomarker, Golgi protein 73 (GP73), for the ability to distinguish between a diagnosis of cirrhosis and HCC. This analysis was done on serum from 113 patients with cirrhosis and 164 serum samples from patients with cirrhosis plus HCC. The levels of Fc-Kin and fucosylated alpha-1-antitrypsin were significantly higher in patients with HCC compared with those with cirrhosis (P < 0.0001). Greatest performance was achieved through the combination of Fc-Kin, alpha-fetoprotein, and GP73, giving an optimal sensitivity of 95%, a specificity of 70%, and an area under the receiver operating characteristic of 0.94. In conclusion, the altered glycosylation of serum glycoproteins can act as potential biomarkers of primary HCC when used independently or in combination with other markers of HCC.
Static gas conduction cooled slab geometry Nd:glass laser (1985)

We report on the first demonstration of a 10 Hz static gas cooled slab geometry Nd:glass laser. This cooling approach provides thermal control of the slab laser medium while eliminating mounting and optical problems associated with liquid cooling.
Multidimensional Waveform Encoding for Spaceborne Synthetic Aperture Radar Remote Sensing (2011)

This chapter presents a novel fully active digital beamforming technique for radar remote sensing that is based on the concept of multidimensional waveform encoding on transmit. In contrast to the aforementioned techniques, the full area of the antenna aperture is used for both the transmission and the reception of radar pulses. This enables an improved SAR imaging performance while relying on the well established transmit/receive (T/R) module technology. The mandatory expansion of the antenna beam width for wide area illumination is achieved by an innovative spatiotemporal modulation of each transmitted radar pulse. The modulation introduces angular waveform diversity in the transmitted signal and provides, thereby, in the recorded radar echoes additional information about the spatial scatterer distribution. The multidimensional waveform encoding is hence the natural complement to digital beamforming on receive, and the combination of both techniques enables a wealth of new SAR imaging modes that significantly increase the performance, flexibility, and adaptability of future radar systems and missions.
Clinical Validation of a Serum Protein Panel (FLNA, FLNB and KRT19) for Diagnosis of Prostate Cancer (2017)

This study reports on the development of a novel serum protein panel of three prostate cancer biomarkers, Filamin A, Filamin B and Keratin-19 (FLNA, FLNB and KRT19) using multivariate models for disease screening and prognosis. ELISA and IPMRM (LC-MS/MS) based assays were developed and analytically validated by quantitative measurements of the biomarkers in serum. Retrospectively collected and clinically annotated serum samples with PSA values and Gleason scores were analyzed from subjects who underwent prostate biopsy, and showed no evidence of cancer with or without indication of prostatic hyperplasia, or had a definitive pathology diagnosis of prostatic adenocarcinoma. Probit linear regression models were used to combine the analytes into score functions to address the following clinical questions: does the biomarker test augment PSA for population screening? Can aggressive disease be differentiated from lower risk disease, and can the panel discriminate between prostate cancer and benign prostate hyperplasia? Modelling of the data showed that the new prostate biomarkers and PSA in combination were better than PSA alone in identifying prostate cancer, improved the prediction of high and low risk disease, and improved prediction of cancer versus benign prostate hyperplasia.
Fabrication of one-dimensional linear diagnostic and therapeutic high intensity focused ultrasound (HIFU) phased-arrays using lateral-mode coupling method (2010)

Diagnostic and high intensity focused ultrasound (HIFU) phased-arrays provide many advantages over single element transducers, including dynamic focal beam steering capability. These arrays should be fabricated with element-to element pitch smaller than half the wavelength at the resonance frequency to avoid unwanted secondary foci due to grating lobes and side lobes. However, smaller pitch increases the electrical impedance of the array as the resonance frequency increases. The most common way to compensate the impedance increase is to employ electrical matching circuits between an array and RF driving system. However, it is not ideal if the number of array elements increases due to high fabrication cost and effort. In this paper we introduced the lateral mode coupling method to reduce electrical impedance in the fabrication of phased array. Using the lateral mode coupling method, we fabricated and tested one dimensional, linear diagnostic (750 kHz) and HIFU (1.4 MHz) phased-arrays. The averaged electrical impedances of each channel were measured to be 62.3 ± 5.2 Ω for the diagnostic array and 104.5 ± 8.9 Ω at zero phase for the HIFU array, respectively. The averaged maximum surface acoustic intensity of the HIFU array elements was 34 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> prior to failure.
Coherence Diversity in Time and Frequency (2016)

In practice, wireless nodes may have different mobility and/or different scattering environment leading to disparity in coherence time and/or coherence bandwidth. Coherence diversity, as a novel source of gain, exploits fading condition disparity of different nodes to provide gain. Downlink transmission for two wireless nodes is considered in three scenarios of fading conditions disparity: in coherence time, in coherence bandwidth, and in both coherence time and coherence bandwidth. Coherence diversity gain is calculated in the three scenarios using product superposition transmission, and furthermore, numerical simulations are presented to demonstrate the gains.
Gifford–McMahon Cryocoolers (2022)

The Gifford–McMahon (GM) cycle has become the dominant means of producing cryogenic temperatures in small refrigerators primarily because it can utilize mass produced oil-lubricated air-conditioning compressors to build reliable, long life, refrigerators at minimal cost. Separation of the compressor from the relatively small expander using flexible gas lines enables many options for interfacing to different loads. As illustrated in Figure F1.3.1, GM expanders produce refrigeration by (1, 2) passing helium from the compressor at high pressure through a regenerator heat exchanger to a cold expansion space as the displacer moves to the warm end of the cylinder (3, 4) allows the gas to drop to a low pressure, causing it to cool, then returning the gas to the warm end and the compressor as the displacer moves to the cold end. Flow of gas to the displacer is controlled by inlet and outlet valves at the warm end of the expander and their actuation is coordinated with the reciprocation of the displacer. The refrigeration produced per cycle is equal to the area of the P-V diagram. Cooling is available in one or two stage expanders at capacities of up to 2 W at about 4 K and 1,000 W at 80 K.
<title>Tracking of multiple semantic video objects for Internet applications</title> (1998)

This paper introduces a novel tracking system for generic semantic video objects using backward region-based classification. It consists of five elementary steps: region pre-processing, region extraction, region-based motion estimation, region classification and region post-processing. Region pre-processing simplifies the input data. Region extraction finds the basic elements for classification. Region-based motion estimation provides the trajectory information about each basic element. Region classification determines the interior/exterior parts of semantic video objects. Finally, region post-processing cleans the results. We will show solid performance of this generic tracking system with pixel-wise accuracy for Internet applications.
Comparison of the Therapeutic Effects of Native and Anionic Nanofibrillar Cellulose Hydrogels for Full-Thickness Skin Wound Healing (2021)

Nanofibrillar cellulose (NFC)-derived dressings such as films, hydrogels, and aerogels are one of the favorable materials for wound healing due to their proper mechanical properties and water holding ability. However, the therapeutic differences between native and anionic NFC materials are rarely studied. In this report, we compared the differences and addressed the regenerative potential of native and anionic wood-derived NFC hydrogels for wound treatment. In vitro characteristics of the hydrogels were detected using scanning electron microscopy, rheological measurements, and swelling and hemolytic activity assays. Skin regeneration at an early stage after hydrogel treatment was analyzed using an in vivo splinted excisional full-thickness skin wound model in C57BL/6 mice. Both native NFC and anionic NFC (ANFC) hydrogel with differing mechanical and surface properties were shown to be biocompatible. Surprisingly, wounds treated with NFC and ANFC hydrogel did not show any statistical difference compared with control wounds and progressed through normal wound closure, inflammatory response, re-epithelialization, vascularization, and tissue maturation with no signs of fibrosis. The data show here for the first time the therapeutic performance of native and anionic NFC hydrogel in a wound mimicking human wound healing mechanisms. The mechanical properties of native and anionic NFC hydrogels such as the capability to modify material stiffness may also prove to be valuable in the management of wounds in the future.
Influence of bipolar esophageal electrode positioning on measurements of human crural diaphragm electromyogram (1996)

We aimed to describe how the human diaphragm electromyogram (EMGdi) is filtered at different positions within the esophageal hiatus, i.e., in the close proximity of the diaphragm, when obtained with an array of bipolar electrode pairs mounted on an esophageal catheter. We defined the electrically active crural diaphragm musculature that covers the esophagus as the electrically active region of the diaphragm (EARdi) and its center as the EARdi center. EMGdi signals were obtained via a multiple-array esophageal catheter consisting of seven sequential electrode pairs with three different electrode configurations. Subjects (n = 5) performed voluntary contractions of the diaphragm at functional residual capacity. Visual inspection of the signals revealed reversal of signal polarity on either side of the EARdi center. Extreme correlation values (r values close to -1 at 0-ms time offset) were observed for the correlation of signals on either side of the EARdi center. The root mean square (RMS) was reduced at the EARdi center; moving peripherally from the EARdi center (caudally and cephalad), the RMS increased to a peak (range of 2.1-4.1 dB for the different electrode configurations) and then decreased for the most peripheral electrode pairs. From a position where the RMS values peaked, center frequency values increased at the EARdi center (range of 26-29 Hz for the different electrode configurations). Computer simulation yielded similar data to the experimental results. We conclude that electrode positioning within the EARdi severely influences center frequency and RMS values and that the center of the EARdi can be identified via cross-correlation analysis.
An approach for increasing drive-mode bandwidth of MEMS vibratory gyroscopes (2005)

The limitations of the photolithography-based micromachining technologies defines the upper-bound on the performance and robustness of micromachined gyroscopes. Conventional gyroscope designs based on matching (or near-matching) the drive and sense modes are extremely sensitive to variations in oscillatory system parameters that shift the natural frequencies and introduce quadrature errors. Nonconventional design concepts have been reported that increase bandwidth to improve robustness, but with the expense of response gain reduction. This paper presents a new approach that may yield robust vibratory MEMS gyroscopes with better gain characteristics while retaining the wide bandwidth. The approach is based on utilizing multiple drive-mode oscillators with incrementally spaced resonance frequencies to achieve wide-bandwidth response in the drive-mode, leading to improved robustness to structural and thermal parameter fluctuations. Enhanced mode-decoupling is achieved by distributing the linear drive-mode oscillators radially and symmetrically, to form a multidirectional linear drive-mode and a torsional sense-mode; minimizing quadrature error and zero-rate output. The approach has been implemented on bulk-micromachined prototypes fabricated in a silicon-on-insulator (SOI)-based process, and experimentally demonstrated.
Automated aeration management in wastewater treatment: interest of the application to serial basins configuration (1998)

In order to extend the range of application of an existing aeration management logic combining carbon and nitrogen removal, an advanced version was developed. This automated system is devoted to WWTP with a serial configuration of the aeration tanks. The operating strategy gives a priority to the carbon elimination in upstream aeration volumes, whereas downstream elements complete the treatment and optimize the nitrogen removal. The control and command functions of this automated management are based on the analysis of both instant value and time evolution of the oxido-reduction potential. Some setting modifications are specified for the aeration management on upstream cells. Application of this system to full-scale operating plants reveals the total adaptation of the strategy to the serial configuration units. Long-term experiences show that aeration supply is adapted to the required level of treatment, following the load variations. Removal yields are optimized and conformity of the outflows is achieved on the three presented examples. The application of this advanced version of the automated aeration management will help operators in obtaining quality and reliability of the wastewater treatment.
Bipolar nanosecond pulse generation using transmission lines for cell electro-manipulation (2004)

Design and operation of a pulse generator based on fast recovery diodes and shorted transmission lines are presented. The generator produces 3.5 ns wide, plusmn350 V amplitude bipolar pulses into 50-ohm load at the maximum repetition rate of 100 kHz. Short bipolar pulses are used for the studies of biological cell response to high electric fields when the net transfer of charge is undesirable. The bipolar pulse is produced from a unipolar pulse by the parallel connection of a shorted transmission line. This transmission line delays and inverts the initial pulse, so the output is the sum of the initial and the inverted and delayed pulses. Proper terminations both at the entrance and the exit of the transmission line system are essential if one is to avoid spurious pulses. If preserving the exact shape of the pulse is not necessary, a parallel L-C circuit can replace the shorted transmission line. This L-C circuit provides near Gaussian bipolar pulse shapes
Fast OLAP Query Execution in Main Memory on Large Data in a Cluster (2017)

Main memory column-stores have proven to be efficient for processing analytical queries. Still, there has been much less work in the context of clusters. Using only a single machine poses several restrictions: Processing power and data volume are bounded to the number of cores and main memory fitting on one tightly coupled system. To enable the processing of larger data sets, switching to a cluster becomes necessary. In this work, we explore techniques for efficient execution of analytical SQL queries on large amounts of data in a parallel database cluster while making maximal use of the available hardware. This includes precompiled query plans for efficient CPU utilization, full parallelization on single nodes and across the cluster, and efficient inter-node communication. We implement all features in a prototype for running a subset of TPC-H benchmark queries. We evaluate our implementation using a 128 node cluster running TPC-H queries with 30 000 gigabyte of uncompressed data.
Characterization of ABBV-221, a Tumor-Selective EGFR-Targeting Antibody Drug Conjugate (2018)

Depatuxizumab mafodotin (depatux-m, ABT-414) is a tumor-selective antibody drug conjugate (ADC) comprised of the anti-EGFR antibody ABT-806 and the monomethyl auristatin F (MMAF) warhead. Depatux-m has demonstrated promising clinical activity in glioblastoma multiforme (GBM) patients and is currently being evaluated in clinical trials in first-line and recurrent GBM disease settings. Depatux-m responses have been restricted to patients with amplified EGFR, highlighting the need for therapies with activity against tumors with nonamplified EGFR overexpression. In addition, depatux-m dosing has been limited by corneal side effects common to MMAF conjugates. We hypothesized that a monomethyl auristatin E (MMAE) ADC utilizing an EGFR-targeting antibody with increased affinity may have broader utility against tumors with more modest EGFR overexpression while mitigating the risk of corneal side effects. We describe here preclinical characterization of ABBV-221, an EGFR-targeting ADC comprised of an affinity-matured ABT-806 conjugated to MMAE. ABBV-221 binds to a similar EGFR epitope as depatux-m and retains tumor selectivity with increased binding to EGFR-positive tumor cells and greater <i>in vitro</i> potency. ABBV-221 displays increased tumor uptake and antitumor activity against wild-type EGFR-positive xenografts with a greatly reduced incidence of corneal side effects relative to depatux-m. ABBV-221 has similar activity as depatux-m against an EGFR-amplified GBM patient derived xenograft (PDX) model and is highly effective alone and in combination with standard-of-care temozolomide in an EGFRvIII-positive GBM xenograft model. Based on these results, ABBV-221 has advanced to a phase I clinical trial in patients with advanced solid tumors associated with elevated levels of EGFR. <i>Mol Cancer Ther; 17(4); 795-805. ©2018 AACR.</i>
<i>AIS</i> is an oncogene amplified in squamous cell carcinoma (2000)

We and others recently isolated a human p53 homologue (p40/p51/p63/p73L) and localized the gene to the distal long arm of chromosome 3. Here we sought to examine the role of p40/p73L, two variants lacking the N-terminal transactivation domain, in cancer. Fluorescent in situ hybridization (FISH) analysis revealed frequent amplification of this gene locus in primary squamous cell carcinoma of the lung and head and neck cancer cell lines. (We named this locus AIS for amplified in squamous cell carcinoma.) Furthermore, amplification of the AIS locus was accompanied by RNA and protein overexpression of a variant p68(AIS) lacking the terminal transactivation domain. Protein overexpression in primary lung tumors was limited to squamous cell carcinoma and tumors known to harbor a high frequency of p53 mutations. Overexpression of p40(AIS) in Rat 1a cells led to an increase in soft agar growth and tumor size in mice. Our results support the idea that AIS plays an oncogenic role in human cancer.