gebhart/patrepeval huggingface dataset:
Structural Determinants for Ligand-Receptor Conformational Selection in a Peptide G Protein-coupled Receptor (2007)

G protein coupled receptors (GPCRs) modulate the majority of physiological processes through specific intermolecular interactions with structurally diverse ligands and activation of differential intracellular signaling. A key issue yet to be resolved is how GPCRs developed selectivity and diversity of ligand binding and intracellular signaling during evolution. We have explored the structural basis of selectivity of naturally occurring gonadotropin-releasing hormones (GnRHs) from different species in the single functional human GnRH receptor. We found that the highly variable amino acids in position 8 of the naturally occurring isoforms of GnRH play a discriminating role in selecting receptor conformational states. The human GnRH receptor has a higher affinity for the cognate GnRH I but a lower affinity for GnRH II and GnRHs from other species possessing substitutions for Arg(8). The latter were partial agonists in the human GnRH receptor. Mutation of Asn(7.45) in transmembrane domain (TM) 7 had no effect on GnRH I affinity but specifically increased affinity for other GnRHs and converted them to full agonists. Using molecular modeling and site-directed mutagenesis, we demonstrated that the highly conserved Asn(7.45) makes intramolecular interactions with a highly conserved Cys(6.47) in TM 6, suggesting that disruption of this intramolecular interaction induces a receptor conformational change which allosterically alters ligand specific binding sites and changes ligand selectivity and signaling efficacy. These results reveal GnRH ligand and receptor structural elements for conformational selection, and support co-evolution of GnRH ligand and receptor conformations.
Terahertz integrated device using a transferred thin-film GaAs layer on silicon substrates (2007)

We developed thin-film GaAs transfer technique for integrated terahertz (THz) generating and detecting devices. Photoconductive switch elements on Si substrate are important for avoiding GaAs absorption to measure in wide frequency range. THz emission amplitude and Fourier transform spectrum band range become larger by replacing GaAs substrate with Si substrate. Transmission line device with the transferred GaAs layer on Si substrate is also fabricated for high sensitive sensors. It was found that peak shift of THz pulse was proportional to apply volume of samples and the sensitivity strongly depended upon the width of the transmission line.
Design of TCR Structural Variants That Retain or Invert the Normal Activation Signal (2021)

We designed variant human TCRs composed of the full-length TCRα/β or extracellular and transmembrane domains of the associated CD3 subunits fused to polypeptides derived from proteins thought to either enhance or inhibit normal T cell function. First, we showed that the C termini of both the TCR α- and β-chains can accommodate specific additional sequences, without abrogating complex formation or acute sensitivity of the receptor. Replacement of ITAMs with ITIM-containing intracellular domains inverted the TCR signal (i.e., created a ligand-dependent inhibitory receptor). The normal signaling function of the CD3 complex was transferable to the TCR by eliminating all CD3 ITAMs and grafting three to six ITAMs onto the C termini of the α/β-chains, with no effect on acute sensitivity. The observation that TCR variants of such diverse C-terminal composition can fold and function as signaling receptors demonstrates substantial structural and functional malleability of TCRs. These results add to knowledge about TCR structure-function with regard to acute signaling and may provide a route to use TCRs in different ways for T cell therapy.
Sequential differential ray tracing formulation for homogeneous and gradient-index lenses using automatic differentiation (2023)

A differential ray tracing (DRT) formulation for the analysis and design of arbitrary optical systems is presented. An approach based on sequential rays is proposed to define a functional representation of the ray path, where the gradient information associated with the ray path is obtained using an automatic differentiation technique. The proposed DRT algorithm is neither constrained to a specific optical system geometry nor restricted to a set of surface types or material definition.
Non-invasive tests of neurovascular function. (1987)

This paper describes the value of non-invasive neurovascular function tests in the clinical setting. Painful transcutaneous electrical nerve stimulation (TENS) of the dorsum of the foot evoked axon reflex vasodilatation, measured by laser Doppler flowmetry. In addition, acetylcholine and sodium nitrite (NaNO2) were iontophoresed to cause vasodilatation by endothelium-dependent and -independent mechanisms, respectively. Compared with healthy volunteers, diabetic patients with clinically diagnosed neuropathy showed reduced electrical axon reflex flare responses. These responses in one additional subject were absent in a region of denervated skin. Acetylcholine responses, but not NaNO2 responses, were also depressed in patients with diabetic neuropathy. Such reduced cutaneous nocifensor functions may contribute to some symptoms and complications of diabetes mellitus.
Determination of Hydroxybenzenes in Exhaled Cigarette Smoke (2008)

Abstract This study describes the results regarding the evaluation of retention efficiency by humans of hydroxybenzenes (phenols) from mainstream cigarette smoke. Over twenty phenols were evaluated in the exhaled smoke of a commercial cigarette with 10.6 mg ‘tar’ [U.S. Federal Trade Commission (FTC) ‘tar’ is defined as the weight of total particulate matter minus nicotine and water]. The test was performed on ten human subjects. The exhaled smoke was collected using a vacuum assisted technique that avoids strain in exhaling the smoke. The study showed that the phenols were retained with high efficiency from cigarette smoke, typically above 80%. Only 4-ethylresorcinol, and C 3 -dihydroxybenzenes (C 3 indicating any alkyl with three carbon atoms) were retained less efficiently with retention values around 70%. The high retention of this class of compounds was expected since phenols are polar compounds with relatively low molecular weights between 94 (for phenol) and 152 (for a propyl-dihydroxybenzene).
Acucise Endopyelotomy/Endoureterotomy (2010)

SAGE-Journals-Accessible-Video-Player 10.1089/vid.2009.0035.M1 sj-vid-1-vid-10.1089_vid.2009.0035
Electrical modeling of high-speed source synchronous communication (2003)

The basic electrical package modeling issues for source synchronous communication are discussed, and modeling techniques are reviewed. A new fine-grained approach that include all essential package features are discussed, with emphasis on coupled and delta-I noises and the interactions between the clock and the signal bus waveforms.
Network vector quantization (2002)

A network source code is an optimal source code for a network. To design network source codes, we require each node to have a single encoder, which jointly encodes all messages transmitted by that node, and a single decoder, which jointly decodes all messages arriving at that node. Given a distribution over the sources, the design of the network source code jointly optimizes all encoders and decoders to obtain the best performance with respect to a user-defined priority schedule over the rates and distortions of the system. In this paper we focus on fixed-rate codes and address the implementation of an existing design algorithm for optimal network vector quantizers. Implementing the design algorithm is not straightforward since each encoder must choose its reproduction based on the expected behavior of sources that are unknown to it. We describe a new implementation approach and demonstrate its performance on a three-node network. In addition, we extend the design algorithm to allow the decoder at each node to use side information (specifically, the messages that are to be encoded by the encoder at the same node).
EUS-Guided Pancreatic Cyst Sampling With a Novel Trans-Needle Biopsy Forceps: Initial Experience in a Pilot Study (2018)

Introduction: Endoscopic ultrasound (EUS) guided sampling [fine needle aspiration (FNA) or fine needle biopsy (FNB)] of pancreatic cystic lesions is a key step in determining underlying pathology and its appropriate management. Recently a novel trans-needle forceps (Moray forceps(MBF), US endoscopy) has been introduced for tissue diagnosis of pancreatic cystic lesion. This study was designed to evaluate if Moray forceps in addition to conventional needle cytology/biopsy and fluid analysis helps improve the diagnostic yield of EUS guided pancreatic cyst sampling Methods: All consecutive patients with pancreatic cysts, who underwent EUS FNA/FNB with or without use of MBF between 6/30/2016 and 5/30/2018 were included. All procedures were done using either FNA 25G, 19G [Expect, Boston Scientific] or FNB-22G [SharkCore; Medtronics]. Patient’s demographics, procedural details and diagnostic yield were obtained from the electronic record. Pancreatic cyst CEA > 192 mg/dl was considered diagnostic of mucinous cystic lesions. Results: Within the study period a total of 44 patients [21 with MBF (group A) and 23 without MBF (group B)] underwent EUS-guided sampling of pancreatic cysts. Nine patients underwent EUS twice (either failed diagnosis, or enlarging cyst) during the study period, once without and once with the use of Moray forceps. For data analysis these 9 patients were included only in group A. Median age between the two groups was comparable [Group A 66±13 vs. Group B 68± 8. Median cyst size in group A was 3±2.1 and in group B was 1.9± 1. Using all 3 diagnostic tools (fluid CEA, needle cytology/biopsy and MBF), cyst diagnosis was made in 13/21 (62%) in group A vs. 7/14 (50%) in group B. This was not statistically significant (p=0.49). Cytological or histological diagnosis was achieved in 12/21 (57 %) group A versus 4/14 (%) group B patients. This also was not significant (p=0.097). In the 9 patients who had a repeat EUS with MBF, tissue diagnostic yield increased from 11 % (1/9) to 56 % (5/9). This was statistically significant (p-value = 0.0073). Seven of 21 patients were diagnosed as serous cyst adenomas (SCA), based on MBF findings. Conclusion: In patients undergoing EUS-guided pancreatic cyst sampling, there is a trend towards increasing diagnostic yield with use of Moray biopsy forceps, but this reached statistical significance only In patients who undergone repeat sampling. Larger randomized studies are needed to confirm results of our pilot study.
Selective, Electrochemically Activated Biofunctionalization of In2O3 Nanowires Using an Air-Stable Surface Modifier (2011)

Selective electrochemically activated biofunctionalization of In(2)O(3) nanowires (NWs) has been achieved, using monolayer coatings of p-dimethoxybenzene derivatives. Monolayer coatings of 4-(2,5-dimethoxyphenyl)butyl-phosphonic acid (DMP-PA) were deposited on planar indium-tin oxide (ITO) electrodes and In(2)O(3) NWs. The electrochemical behavior of the monolayer coating was first studied using ITO electrodes, as a model system for In(2)O(3) nanowires. When a potential of 950 mV vs a Ag/AgCl reference electrode is applied to an ITO electrode coated with DMP-PA in PBS buffer, the p-dimethoxyphenyl groups are converted to p-benzoquinone (BQ). The electrochemically formed benzoquinone groups react readily with alkyl thiol groups via a Michael addition. The reaction strategy optimized on ITO was applied to an In(2)O(3) NW mat sample coated with DMP-PA. Applying a potential of 950 mV to metal electrodes deposited on NWs converts the DMP-PA NW coating to BQ-PA, which reacts with a thiol-terminated 20-base oligonucleotide. These NWs showed strong fluorescence response after paring with the dye labeled compliment, demonstrating that the probe was bound to the NW surface and that it remained active toward hybridization with its compliment. The unactivated DMP-PA coated NWs showed no response, demonstrating the selective electrochemical functionalization of NWs and the potential of using them in multiplex sensing. We also compared the p-dimethoxybenzene derivative to the conventional hydroquinone analog. The results show that the former can largely enhance the selectivity during the functionalization of both ITO and In(2)O(3) NWs.
Reevaluating Cathepsin D as a biomarker for breast cancer: Serum activity levels versus histopathology (2010)

Cathepsin D is a lysosomal hydrolase involved in intra- and extracellular proteolysis. This enzyme is aberrantly produced and processed in malignancy, and most notably is over-secreted into the tumor cell microenvironment. This hyper-secretion may lead to excessive degradation of the extracellular matrix, and contribute to tumor progression and metastases. These phenomena have been established in vitro, and there is evidence that Cathepsin D is similarly dysregulated in human breast cancer patients. Because breast cancer lacks an effective screening or surveillance biomarker, here we address the hypothesis that serum Cathepsin D activity may be useful to assess the presence or progression of breast cancer in females. While representative histologic sections from various disease-specific cohorts confirm previous findings that increased Cathepsin D production and secretion correlate with tumor progression, we report no difference in serum Cathepsin D activity between patients who are disease free, patients with pre-invasive or limited invasive disease, and patients with metastatic disease. Furthermore, in patients with known metastatic disease, there were no clinical variables associated with significantly different serum Cathepsin D activity. However, the immunohistochemical localization of Cathepsin D expression in histopathologic sections from breast cancer patients correlates with disease progression. Based on the serum results, and in contradistinction to Cathepsin D localization in breast cancer tissues, our findings support using Cathepsin D as a reliable histopathology biomarker for disease progression, but not for serum screening.
Assessment of radio frequency ablation treatment of hepatic tumors (2006)

It is fundamentally important that all cancerous cells be adequately destroyed during Radio Frequency Ablation (RFA) procedures. To help achieve this goal, probe manufacturers advise physicians to increase the treatment region by one centimeter (1cm) in all directions around the diseased tissue. This enlarged treatment region provides a buffer to insure that cancer cells that migrated into surrounding tissue are adequately treated and necrose. Even though RFA is a minimally invasive, image-guided procedure, it is difficult for physicians to confidently follow the specified treatment protocol. In this paper we visually assess an RFA treatment by comparing a registered image set containing the untreated tumor, including the 1 cm safety boundary, to that of an image set containing the treated region acquired one month after surgery. For this study, we used Computerized Tomography images as both the tumor and treated regions are visible. To align the image sets of the abdomen, we investigate three different registration techniques; an affine transform that minimizes the correlation ratio, a point (or landmark) based 3D thin-plate spline approach, and a nonlinear B-spline elastic registration methodology. We found the affine registration technique simple and easy to use because it is fully automatic. Unfortunately, this method resulted in the largest visible discrepancy between the liver in the fused images. The thin-plate spline technique required the physician to identify corresponding landmarks in both image sets, but resulted in better visual accuracy in the fused images. Finally, the non-linear, B-spline, elastic registration technique used the registration results of the thin-plate spline method as a starting point and then required a significant amount of computation to determine its transformation, but also provided the most visually accurate fused image set.
The seed oil from Pistacia terebinthus from Chios Island (Greece) as a promising source of functional crude material (2021)

Pistacia terebinthus (terebinth or turpentine tree), (Anacardiaceae) is a small tree growing widely in the Mediterranean area. This wild Pistacia species has been used in folk medicine and human nutrition [1], while its seeds and oil have shown several bioactive properties.
Efficacy of Photobiomodulation for Attention Deficit Hyperactivity Disorder (ADHD): Case Studies (2022)

Extensive research has now been conducted and published for the treatment of dementia or Alzheimer’s disease, traumatic brain injury (TBI) and other brain disorders using photobiomodulation (PBM), also known as low-level laser therapy (LLLT). However, minimal information is available regarding the use of LLLT for the treatment of Attention Deficit Hyperactivity Disorder (ADHD). We have been using LLLT in our practice for over 15 years addressing chronic pain and injury issues. However, our work with brain injuries is more recent, and we have published three case studies, one describing a serious traumatic brain injury and two describing our success with dementia/Alzheimer’s disease and PTSD. Currently, there is very little published evidence regarding efficacious therapy for ADHD. The case studies presented here, suggest that LLLT can provide alleviation of these symptoms, with some improvement reported after just a single treatment, without any need for pharmaceutical intervention.
Validation of High Dynamic Range Imaging to Luminance Measurement (2005)

High dynamic range imaging is a set of techniques that allows for a far greater dynamic range of exposure than normal digital imaging techniques. The intention is to accurately represent the dynamic range of lighting levels found in real scenes, ranging from direct sunlight to deep shadows. Various software packages have emerged that translate these HDR images into high resolution luminance maps. This paper tests the accuracy of one such package, taking into consideration different Munsell hues, values and chroma. It investigates the impact of different light spectra, spatial frequency, vignetting, and thermal noise on the accuracy of luminance measurements and determines the potential errors.
ChemInform Abstract: Neotame: Synthesis, Stereochemistry, and Sweetness. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Globular-shaped variable lymphocyte receptors B antibody multimerized by a hydrophobic clustering in hagfish (2018)

In hagfish and lampreys, two representative jawless vertebrates, the humoral immunity is directly mediated by variable lymphocyte receptors B (VLRBs). Both monomeric VLRBs are structurally and functionally similar, but their C-terminal tails differ: lamprey VLRB has a Cys-rich tail that forms disulfide-linked pentamers of dimers, contributing to its multivalency, whereas hagfish VLRB has a superhydrophobic tail of unknown structure. Here, we reveal that VLRBs obtained from hagfish plasma have a globular-shaped multimerized form (approximately 0.6 to 1.7 MDa) that is generated by hydrophobic clustering instead of covalent linkage. Electron microscopy (EM) and single-particle analysis showed that the multimerized VLRBs form globular-shaped clusters with an average diameter of 28.7 ± 2.2 nm. The presence of VLRBs in the complex was confirmed by immune-EM analysis using an anti-VLRB antibody. Furthermore, the hydrophobic hagfish C-terminus (HC) was capable of triggering multimerization and directing the cellular surface localization via a glycophosphatidylinositol linkage. Our results strongly suggest that the hagfish VLRB forms a previously unknown globular-shaped antibody. This novel identification of a structurally unusual VLRB complex may suggest that the adaptive immune system of hagfish differs from that of lamprey.
Single molecule detection of direct, homologous, DNA/DNA pairing (2009)

Using a parallel single molecule magnetic tweezers assay we demonstrate homologous pairing of two double-stranded (ds) DNA molecules in the absence of proteins, divalent metal ions, crowding agents, or free DNA ends. Pairing is accurate and rapid under physiological conditions of temperature and monovalent salt, even at DNA molecule concentrations orders of magnitude below those found in vivo, and in the presence of a large excess of nonspecific competitor DNA. Crowding agents further increase the reaction rate. Pairing is readily detected between regions of homology of 5 kb or more. Detected pairs are stable against thermal forces and shear forces up to 10 pN. These results strongly suggest that direct recognition of homology between chemically intact B-DNA molecules should be possible in vivo. The robustness of the observed signal raises the possibility that pairing might even be the "default" option, limited to desired situations by specific features. Protein-independent homologous pairing of intact dsDNA has been predicted theoretically, but further studies are needed to determine whether existing theories fit sequence length, temperature, and salt dependencies described here.
Quality Factor of Micropillar Cavity (2006)

We study micropillar cavity and we show that their Q-factor can exhibit an oscillatory behavior. We provide an analysis of the physical mechanisms at the origin of these oscillations and a comparison with experimental measurements.
Reducibility and Completeness in Private Computations (2000)

We define the notions of reducibility and completeness in (two-party and multiparty) private computations. Let g be an n-argument function. We say that a function f is reducible to a function g if n honest-but-curious players can compute the function fn -privately, given a black box for g (for which they secretly give inputs and get the result of operating g on these inputs). We say that g is complete (for private computations) if every function f is reducible to g. In this paper, we characterize the complete boolean functions: we show that a boolean function g is complete if and only if g itself cannot be computed n-privately (when there is no black box available). Namely, for n-argument boolean functions, the notions of completeness and n-privacy are complementary. This characterization provides a huge collection of complete functions any nonprivate boolean function!) compared to very few examples that were given (implicitly) in previous work. On the other hand, for nonboolean functions, we show that these two notions are not complementary.
Supplementary Table 4 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;XLSX file - 35K, Sensitivities to TYK2 knockdown and JAK Inhibitor I treatment, and phosphorylation status of downstream signaling molecules in T-ALL cell lines and Ba/F3 clones.&lt;/p&gt;
Speed and area tradeoffs in cluster-based FPGA architectures (2000)

One way to reduce the delay and area of field-programmable gate arrays (FPGAs) is to employ logic-cluster-based architectures, where a logic cluster is a group of logic elements connected with high-speed local interconnections. In this paper, we empirically evaluate FPGA architectures with logic clusters ranging in size from 1 to 20, and show that compared to architectures with size 1 clusters, architectures with size 8 clusters have 23% less delay (30% faster clock speed) and require 14% less area. We also show that FPGA architectures with large cluster sizes can significantly reduce design compile time-an increasingly important concern as the logic capacity of FPGA's rises. For example, an architecture that uses size 20 clusters requires seven times less compile time than an architecture with size 1 clusters.