gebhart/patrepeval huggingface dataset:
Real-world application of next generation sequencing to guide therapeutic options in lymphoma. (2019)

e14645 Background: Despite the increasing availability of targeted and novel therapies, successful treatment of many relapsed/refractory lymphomas remains a challenge. Tumor sequencing is becoming an increasingly available technique to identify potential therapeutic targets; however, there remains considerable uncertainty about the successful application of this data in a “real world” clinical setting. Methods: Herein, we describe 91 lymphoma patients who underwent DNA &amp; RNA sequencing of tumor biopsies via the MIONCOSEQ protocol to identify actionable therapeutic targets. Their charts were reviewed for the clinical use of MIONCOSEQ recommendations. Results: Among the 91 patients were 13 Lymphoma subtypes. Most patients had Stage III/IV disease (68%) at diagnosis, underwent an average of 4 treatments before sequencing (range 0-16) and had approximately 47 distinct molecular alterations (range 2-447). Of the cohort, 60 patients (65%) had actionable targets identified of which 11 ultimately received treatment based on MIONCOSEQ recommendations. The remaining patients did not receive treatment due to multiple reasons: prior CR or on surveillance not requiring treatment (10); death (12); trial ineligibility (4); trial unavailability at the institution (8); patient preference for local treatment (6); and already on alternative treatments (9). Taken as a whole, sequencing late in the disease course and a lack of available clinical trials were identified as barriers for the incorporation of MIONCOSEQ data into clinical practice. Therefore, earlier sequencing and strategies to bolster the availability of targeted therapies may significantly increase the application of genomic data and precision medicine in clinical practice. Conclusions: While next generation sequencing (NGS) is a powerful tool for advancing precision medicine, meaningful clinical application of these results remains a challenge. Our study indicates that early sequencing and improved trial availability could be beneficial in increasing real-world therapeutic options for relapsed/refractory lymphoma. Further research is needed to determine the extent to which a personalized approach, informed by NGS data, improves outcomes.
A new glucose sensor for use in whole blood (1996)

Existing electrochemical glucose sensors are either single use sensors produced in mass fabrication technologies or rather big sensors for multiple use with membranes to be changed frequently. Single use means no sensor maintenance but has the disadvantage that quality control measurements cannot be done with the same sensor used for the sample. Generally also the cost per test is relatively high. Multiple use sensors give the possibility of closer quality control and they are generally cheaper than the single use sensors for higher sample frequency but have the disadvantage of frequent need of remembraning. This often means special training and is a health risk due to sensor contamination by biological fluids. We combined the advantages of both principles meaning that we developed a new glucose sensor for multiple use in an essentially planar technology - thus being able to be produced very cheap. The underlying basic working principle is using glucose oxidase and detecting hydrogen peroxide. Due to the carbon base of the sensor it has a large surface area and therefore a very high sensitivity (microamps range at biological glucose concentrations) although the sensor itself is very small needing only about 10 microL of sample. The sensor shows a linear range of up to 40 mmol/L, a life time in use of far more than 1000 human serum samples and correlation coefficients between plasma and whole blood of r = 0.99. Interferences are well within clinical acceptability. Thus we conclude that this sensor works well in undiluted human body fluids and due to the very cheap production processes the whole sensor can be exchanged when it is old thus eliminating any need for remembraning or special maintenance.
Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data (2008)

Functional analysis and interpretation of large-scale proteomics and gene expression data require effective use of bioinformatics tools and public knowledge resources coupled with expert-guided examination. An integrated bioinformatics approach was used to analyze cellular pathways in response to ionizing radiation. ATM, or ataxia-telangiectasia mutated , a serine-threonine protein kinase, plays critical roles in radiation responses, including cell cycle arrest and DNA repair. We analyzed radiation responsive pathways based on 2D-gel/MS proteomics and microarray gene expression data from fibroblasts expressing wild type or mutant ATM gene. The analysis showed that metabolism was significantly affected by radiation in an ATM dependent manner. In particular, purine metabolic pathways were differentially changed in the two cell lines. The expression of ribonucleoside-diphosphate reductase subunit M2 (RRM2) was increased in ATM-wild type cells at both mRNA and protein levels, but no changes were detected in ATM-mutated cells. Increased expression of p53 was observed 30min after irradiation of the ATM-wild type cells. These results suggest that RRM2 is a downstream target of the ATM-p53 pathway that mediates radiation-induced DNA repair. We demonstrated that the integrated bioinformatics approach facilitated pathway analysis, hypothesis generation and target gene/protein identification.
Bandwidth-tunable filter consisting of SAW resonators and BaSrTiO<inf>3</inf> varactors directly fabricated on a LiTaO<inf>3</inf> wafer (2014)

A prototyped bandwidth-tunable filter consisting of SAW resonators and BaSrTiO3 (BST) varactors is discussed in this paper. In general, the BST varactors require high deposition temperature (>600°C) in order to obtain good varactor performances. Thus special cared wafer integration process of BST varactors onto a 42°YX-LiTaO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> wafer was newly developed to prevent performance deterioration in SAW resonators. The bandwidth-tunable filter composed of ten pieces of both surface acoustic wave (SAW) resonators and BST varactors on the 42°YX-LiTaO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> substrate was successfully fabricated using the integration process. The measured center frequency of the filter is 1GHz, and the 3dB bandwidth is electrically tuned from 4.5 to 9.6MHz by adjusting a DC supply voltage from 0 to 10V.
Hardware-Assisted Point-Based Volume Rendering of Tetrahedral Meshes (2007)

Unstructured volume grids are ubiquitous in scientific computing, and have received substantial interest from the scientific visualization community. In this paper, we take a point-based approach to rendering unstructured grids. In particular, we present a novel method of approximating these irregular elements with point-based primitives amenable to existing hardware acceleration techniques. To improve interactivity to large datasets, we have adapted a level-of-detail strategy. We use a well-known quantitative metric to analyze the image quality achieved by the final rendering.
GaN LED on Quartz Substrate through Wafer Bonding and Layer Transfer Processes (2018)

A method to transfer GaN LED layers (which were grown initially on a Si substrate) to a quartz substrate is proposed and demonstrated. Quartz substrate is chosen due to its optical transparency to enhance the light extraction efficiency. The GaN LED-on-Si substrate was temporarily supported on a Si handle wafer. A quartz substrate was then bonded to the GaN LED layers-containing handle wafer. Finally, the handle wafer was released to realize the GaN LED layers on the quartz substrate. All substrates used were 200 mm in diameter. The transferred film demonstrates excellent optical properties. The GaN LED devices were then fabricated on coupon size samples using standard photolithography techniques and dry etching processes. Through this method, we can improve the light extraction efficiency and hence, benefitial to the integration of Si-CMOS + LED platform for applications such as multi-color microdisplay.
Probing the Activity of Mitragyna Speciosa (Kratom) Alkaloids at Serotonin G Protein‐Coupled Receptors (2022)

The nation’s persistent opioid epidemic requires innovative treatment interventions. Mitragyna speciosa , or kratom, is an alkaloid‐containing tropical plant that has emerged as a potential opioid substitute therapy in recent decades. There are, however, no FDA‐approved uses for kratom, and scientists are actively engaged to elucidate the potential therapeutic benefits and harmful effects of kratom. Studies of kratom alkaloids have mainly focused on their opioid receptor activity, but emerging data show kratom has physiologically‐relevant activity at other biological targets. We recently reported that two kratom alkaloids prevalent in leaves of the kratom plant, speciogynine and paynantheine, bind to serotonin (5‐HT) 5‐HT1ARs and 5‐HT2BRs with affinities (Ki) less ≤100 nM and that their 9‐O‐desmethyl metabolites are efficacious agonists at 5‐HT1ARs (León et al., 2021 PMID: 34467758). We are undertaking studies to evaluate the pharmacology of the most prevalent alkaloids found in kratom leaves at each of the genetically‐encoded 5‐HT G protein‐coupled receptors (GPCRs). To further elucidate 5‐HTR G‐protein transduction pathways modulated by kratom alkaloids, we are utilizing the TRUPATH biosensor platform. By evaluating the potency and efficacy of kratom alkaloids to modulate the activity of unique G alpha subtypes linked to 5‐HTRs, we will provide fundamental 5‐HTR pharmacological characteristics of kratom alkaloids. The 5‐HT2BR is a crucial target for drug safety profiling since activation of this receptor can lead to cardiac valvulopathy. In addition, we are testing kratom alkaloids with an appreciable 5‐HT2BR affinity for their potential mitogenic activity in HEK cells utilizing [3H]thymidine incorporation. This research will provide crucial information about kratom’s pharmacological profile, independent of opioid receptors, that may contribute to its physiological effects.
95%-lower-BER 43%-lower-power intelligent solid-state drive (SSD) with asymmetric coding and stripe pattern elimination algorithm (2011)

This paper presents intelligent solid-state drives (SSDs), which decrease memory errors by 95% and reduce power consumption by 43%. Figure 11.4.1 shows the measured memory cell error in the data retention and program disturb of 4X, 3X and 2Xnm NAND flash memories. As the memory size decreases, both data retention and program disturb errors increase due to the interference, random telegraph noise and reduced electrons. In the scaled NAND, the electric field in the channel increases and the program disturb due to GIDL-induced hot electron injection becomes more significant (Fig. 11.4.1(c)). In conventional SSDs, 20 to 40 b correction per 1 KB codeword error-correcting code (ECC) is used to correct errors. As stronger codes, such as LDPC, are developed, the capability of ECC is close to the Shannon limit of a few percent error correction. Thus, the additional high-reliability scheme is required. As the feature size decreases, the power consumption increases due to the increased bit-line capacitance of NAND. As the space between bitlines decreases, the inter bitline capacitance increases. To overcome reliability and power problems in SSDs, this paper describes two technologies. Asymmetric coding improves memory-cell reliability by 95% without access-time penalty. Stripe pattern elimination algorithm eliminates the worst program data pattern and decreases the power during the program by 43% without circuit area or access time overhead.
Polymethacrylate Sphere-Based Assay for Ultrasensitive miRNA Detection (2020)

Although microRNAs (miRNAs) have emerged as increasingly important target analytes, their biorecognition remains challenging due to their small size, high sequence homology, and low abundance in clinical samples. Nanospheres and microspheres have also gained increasing attention in biosensor applications due to their high specific surface area and the wide variety of compositions available. In this study, chemically designed and synthesized microspheres with active functional groups were used to promote effective miRNA immobilization resulting in better biorecognition. Upon conjugation with fluorescence-labeled complimentary probes, acylate-based spheres have indirectly detected MiR159, offering significantly enhanced analytical sensitivity, specificity, and accuracy while yielding a considerably low limit of detection (LOD) of 40 picomolar. Furthermore, MiR159 presence, which is known to be inversely correlated to breast cancer incidence and progression, was successfully detected in a competitive assay, which is promising for upgrading the current assay to clinical use.
Lola regulates Drosophila olfactory projection neuron identity and targeting specificity (2007)

Our results indicate that lola is required for wiring of axons and dendrites of most PN classes, and suggest a need for its molecular diversity. Expression pattern changes of Gal4 drivers in lola-/- clones imply that lola normally represses the expression of these regulatory elements in a subset of the cells surrounding the AL. We propose that Lola functions as a general transcription factor that regulates the expression of multiple genes ultimately controlling PN identity and wiring specificity.
UVO-Tunable Superhydrophobic to Superhydrophilic Wetting Transition on Biomimetic Nanostructured Surfaces (2007)

A novel strategy for a tunable sigmoidal wetting transition from superhydrophobicity to superhydrophilicity on a continuous nanostructured hybrid film via gradient UV-ozone (UVO) exposure is presented. Along a single wetting gradient surface (40 mm), we could visualize the superhydrophobic (thetaH2O > 165 degrees and low contact angle hysteresis) transition (165 degrees > thetaH2O > 10 degrees ) and superhydrophilic (thetaH2O < 10 degrees within 1 s) regions simply through the optical images of water droplets on the surface. The film is prepared through layer-by-layer assembly of negatively charged silica nanoparticles (11 nm) and positively charged poly(allylamine hydrochloride) with an initial deposition in a fractal manner. The extraordinary wetting transition on chemically modified nanoparticle layered surfaces with submicrometer- to micrometer-scale pores represents a competition between the chemical wettability and hierarchical roughness of surfaces as often occurs in nature (e.g., lotus leaves, insect wings, etc).
Interlaminar epidural steroid injection for degenerative lumbar spinal canal stenosis: does the intervertebral level of performance matter? (2014)

Results suggest that patient symptom improvement is optimized when the ILESI is performed at the intervertebral level of maximal stenosis.
Cryogenic DC and RF characteristics of InP HEMTs with various drain-side recess lengths (2016)

We measured the DC and RF characteristics of InP-based 75-nm-gate In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.52</inf> Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.48</inf> As/In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.63</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.37</inf> As HEMTs with various drain-side recess lengths L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</inf> 's at 300 and 16 K. The kink phenomenon was seen in the current-voltage (I–V) characteristics for all the measured HEMTs at 16 K. The peak cutoff frequency ƒ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> decreases with increasing L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</inf> both at 300 and 16 K. On the other hand, the maximum oscillation frequency ƒ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</inf> shows very complicated behavior both at 300 and 16 K. We found that there exists the most suitable L <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</inf> value to increase ƒ <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</inf> at each temperature and/or drain-source voltage V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ds</inf> .
Anti-LRP5/6 VHHs promote differentiation of Wnt-hypersensitive intestinal stem cells (2019)

Wnt-induced β-catenin-mediated transcription is a driving force for stem cell self-renewal during adult tissue homeostasis. Enhanced Wnt receptor expression due to mutational inactivation of the ubiquitin ligases RNF43/ZNRF3 recently emerged as a leading cause for cancer development. Consequently, targeting canonical Wnt receptors such as LRP5/6 holds great promise for treatment of such cancer subsets. Here, we employ CIS display technology to identify single-domain antibody fragments (VHH) that bind the LRP6 P3E3P4E4 region with nanomolar affinity and strongly inhibit Wnt3/3a-induced β-catenin-mediated transcription in cells, while leaving Wnt1 responses unaffected. Structural analysis reveal that individual VHHs variably employ divergent antigen-binding regions to bind a similar surface in the third β-propeller of LRP5/6, sterically interfering with Wnt3/3a binding. Importantly, anti-LRP5/6 VHHs block the growth of Wnt-hypersensitive Rnf43/Znrf3-mutant intestinal organoids through stem cell exhaustion and collective terminal differentiation. Thus, VHH-mediated targeting of LRP5/6 provides a promising differentiation-inducing strategy for treatment of Wnt-hypersensitive tumors.
Improving Enzyme Activity and Broadening Selectivity for Biological Desulfurization and Upgrading of Petroleum Feedstocks (2003)

The objective of this project was to develop improved biocatalysts for desulfurization and upgrading of petroleum feedstocks. The goal was to improve the activity and broaden the selectivity of desulfurization enzymes using directed evolution as a tool as well as to explore the impact of ring-opening on biological desulfurization
Macromolecular engineering viaring-opening polymerization (1):l-lactide/trimethylene carbonate block copolymers as thermoplastic elastomers (2012)

Poly(L-lactide) (PLLA) is often regarded as tough and brittle while poly(1,3-trimethylene carbonate) (PTMC) is rather considered as a rubbery polymer. In an effort to improve the mechanical properties – especially ductility – of PLLA and thus to widen its field of applications, PLLA–PTMC diblock and triblock copolymers were synthesized through the sequential copolymerization of both L-lactide (L-LA) and trimethylene carbonate (TMC) using several catalytic systems. This process can be effectively catalyzed by inherently different systems ranging from a simple basic organocatalyst such as an amine (i.e., 4-N,N-dimethylaminopyridine, DMAP) or a phosphazene (i.e., 2-tert-butylimino-2-diethylamino-1,3-dimethylperhydro-1,3,2-diazaphosphorine, BEMP), a simple Lewis acidic metallic salt such as aluminum triflate, or a more sophisticated discrete metallo-organic complex derived from a biofriendly metal, namely the β-diiminate zinc complex [(BDIiPr)Zn(N(SiMe3)2)] (BDI = CH(CMeNC6H3-2,6-iPr2)2), [(BDIiPr)Zn(N(SiMe3)2)]. Well-defined diblock PLLA-b-PTMC, triblock PLLA-b-PTMC-b-PLLA and 3-arm star GLY(PTMC-b-PLLA)3 copolymers with controlled molecular features, i.e. controlled functional end-groups and molar masses, rather narrow dispersity values, were thus prepared. The thermo-mechanical properties of the resulting copolymers revealed that a minimal block size of the PTMC and of the PLLA segments within the copolymer of Mn,PTMC = ca. 10 000 g mol−1 and Mn,PLLA = ca. 23 000 g mol−1 enables significant improvement of the elongation at break (εb) of PLLA up to 328%, while maintaining the Young's modulus (E = 2781 MPa) close to that of PLLA (E = 3427 MPa).
Charge Transport in LDPE Nanocomposites Part II—Computational Approach (2016)

A bipolar charge transport model is employed to investigate the remarkable reduction in dc conductivity of low-density polyethylene (LDPE) based material filled with uncoated nanofillers (reported in the first part of this work). The effect of temperature on charge transport is considered and the model outcomes are compared with measured conduction currents. The simulations reveal that the contribution of charge carrier recombination to the total transport process becomes more significant at elevated temperatures. Among the effects caused by the presence of nanoparticles, a reduced charge injection at electrodes has been found as the most essential one. Possible mechanisms for charge injection at different temperatures are therefore discussed.
Strongly correlated quantum walks in optical lattices (2015)

Full control over the dynamics of interacting, indistinguishable quantum particles is an important prerequisite for the experimental study of strongly correlated quantum matter and the implementation of high-fidelity quantum information processing. We demonstrate such control over the quantum walk-the quantum mechanical analog of the classical random walk-in the regime where dynamics are dominated by interparticle interactions. Using interacting bosonic atoms in an optical lattice, we directly observed fundamental effects such as the emergence of correlations in two-particle quantum walks, as well as strongly correlated Bloch oscillations in tilted optical lattices. Our approach can be scaled to larger systems, greatly extending the class of problems accessible via quantum walks.
Dimeric [Mo2S12]2− Cluster: A Molecular Analogue of MoS2 Edges for Superior Hydrogen‐Evolution Electrocatalysis (2015)

Proton reduction is one of the most fundamental and important reactions in nature. MoS2 edges have been identified as the active sites for hydrogen evolution reaction (HER) electrocatalysis. Designing molecular mimics of MoS2 edge sites is an attractive strategy to understand the underlying catalytic mechanism of different edge sites and improve their activities. Herein we report a dimeric molecular analogue [Mo2 S12 ](2-) , as the smallest unit possessing both the terminal and bridging disulfide ligands. Our electrochemical tests show that [Mo2 S12 ](2-) is a superior heterogeneous HER catalyst under acidic conditions. Computations suggest that the bridging disulfide ligand of [Mo2 S12 ](2-) exhibits a hydrogen adsorption free energy near zero (-0.05 eV). This work helps shed light on the rational design of HER catalysts and biomimetics of hydrogen-evolving enzymes.
APPLICATION OF MEMBRANES FROM POLYACRYLONITRITE DOPPED WITH GRAPHEN OXIDE IN PURIFICATION OF INDUSTRIAL WASTEWATER GENERATED DURING PROCESSING OF METALS (2017)

The paper presents results of research on the use of composite membranes of polyacrylonitrile (PAN) doped with graphene oxide (GO) to remove contaminations of galvanic wastewater. Membranes were obtained using phase inversion method from PAN and GO solution in N,N-dimethylformamide (DMF). Wastewater was pre-treated with the flocculant Magnafloc®336. Next, ultrafiltration of the treated wastewater was carried out in the ultrafiltration cell AMICON on the previously prepared PAN/GO composite membranes. Physico-chemical properties and composition of solutions before and after integrated purification process were analyzed by UV-Vis spectrophotometer and atomic absorption spectrometry (AAS). As a result of flocculation from wastewater there have been removed phosphates (97%), chlorides (5,2%), sulfates (5,9%) and iron (82%). In addition, as a result of ultrafiltration was complete removal of phosphate anions (100%) and iron (~91-92%), zinc (68÷84%), lead (65-98%) and cadmium (~67%).