gebhart/patrepeval huggingface dataset:
Uplink zone-based scheduling for LEO satellite based Non-Terrestrial Networks (2022)

To provide coverage to the network devices distributed all over the globe, non-terrestrial networks (NTNs) have been recognized to complement and extend the terrestrial network to remote areas. The Low Earth Orbit (LEO) NTNs face several unprecedented challenges over 5G-NR protocol due to high differential delay and Doppler shifts which drastically impacts the performance of NR-NTN users. In this work, we investigate the impact of large differential delay and Doppler shifts within a NTN cell on the 5G-NR resource allocation and medium access control (MAC) protocol. We then propose an uplink zone-based scheduling technique to address the high differential delay and Doppler shifts for LEO satellites for LEO satellite-based NTNs. Finally, we validate the performance of the proposed strategy by comparing it with the conventional 5G-NR protocol through numerical simulations over the recently developed Samsung&#x2019;s NR-NTN System Level Simulator.
Using Functional Proteome Microarrays to Study Protein Lysine Acetylation (2012)

Emergence of proteome microarray provides a versatile platform to globally explore biological functions of broad significance. In the past decade, researchers have successfully fabricated functional proteome microarrays by printing individually purified proteins at a high-throughput, proteome-wide scale on one single slide. These arrays have been used to profile protein posttranslational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. In this chapter, we summarize our work of using the yeast proteome microarrays to connect protein lysine acetylation substrates to their upstream modifying enzyme, the nucleosome acetyltransferase of H4 (NuA4), which is the only essential acetyltransferase in yeast. We further prove that the reversible acetylation on critical cell metabolism-related enzymes controls life span in yeast. Our studies represent a paradigm shift for the functional dissection of a crucial acetylation enzyme affecting aging and longevity pathways.
A 160 MHz analog equalizer for magnetic disk read channels (2002)

This prototype filter has five taps and operates at 160 MHz clock rate, dissipating 200 mW with 5 V supply. The filter occupies 1.35 mm/sup 2/ in BiCMOS with 0.8 /spl mu/m CMOS. It uses BiCMOS sample-and-hold (S/H) circuits to derive analog discrete-time samples, and CMOS time shared sign-sign LMS (SS-LMS) for coefficient adaptation. It improves on a previous analog signal shuffling structure by: (a) fast master S/H improves the dynamic performance and reduces effect of clock jitter on timing and gain recovery, (b) additional S/H amplifiers alleviate settling time requirements and reduce power, (c) time-interleaved LMS algorithm permits low-cost and low-power coefficient adaptation. DACs for taps and for dc offset cancellation are on-chip.
Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands (2018)

Toll-like receptor 7 (TLR7) is an innate immune receptor for single-stranded RNA (ssRNA) and has important roles in infectious diseases. We previously reported that TLR7 shows synergistic activation in response to two ligands, guanosine and ssRNA. However, the specific ssRNA sequence preference, detailed recognition mode of TLR7 and its ligand, and molecular determinants of TLR7 and TLR8 selectivity remain unknown. Here, we report on TLR7 from a large-scale crystallographic study combined with a multifaceted approach. We reveal that successive uridine-containing ssRNAs fully or moderately bind TLR7, whereas single uridine-containing ssRNAs have reduced affinities. We also reveal the detailed relationships between the chemical structures of ligands and their binding to TLR7. We demonstrate that an engineered TLR8 mutant alters its responsiveness to TLR7-specific ligands. Finally, we identify guanosine 2',3'-cyclic phosphate (2',3'-cGMP) as a possible endogenous ligand for TLR7 with greater affinity than guanosine. The abundant structural information will facilitate future development of treatments targeting TLR7.
Numerical investigation of the nonlinear penetration of pulsed electromagnetic fields into a ferromagnetic shield with a simple exponential permeability model (2004)

Electrically conductive ferromagnetic shielding materials exhibit nonlinear behavior (including magnetic saturation) under intense pulsed electromagnetic field conditions. This paper considers the fundamental problem of a long, thin-walled cylindrical electrically conductive ferromagnetic shield subjected to axially-directed, unipolar, short-duration surface current pulses. A simple idealized relative differential magnetic permeability model is used to portray the nonlinear effects of a field-dependent permeability, including saturation. The transient magnetic field intensity within the shield is investigated using finite difference time domain (FDTD) calculations.
A Full-Length Plasmodium falciparum Recombinant Circumsporozoite Protein Expressed by Pseudomonas fluorescens Platform as a Malaria Vaccine Candidate (2014)

The circumsporozoite protein (CSP) of Plasmodium falciparum is a major surface protein, which forms a dense coat on the sporozoite's surface. Preclinical research on CSP and clinical evaluation of a CSP fragment-based RTS, S/AS01 vaccine have demonstrated a modest degree of protection against P. falciparum, mediated in part by humoral immunity and in part by cell-mediated immunity. Given the partial protective efficacy of the RTS, S/AS01 vaccine in a recent Phase 3 trial, further improvement of CSP-based vaccines is crucial. In this report, we describe the preclinical development of a full-length, recombinant CSP (rCSP)-based vaccine candidate against P. falciparum malaria suitable for current Good Manufacturing Practice (cGMP) production. Utilizing a novel high-throughput Pseudomonas fluorescens expression platform, we demonstrated greater efficacy of full-length rCSP as compared to N-terminally truncated versions, rapidly down-selected a promising lead vaccine candidate, and developed a high-yield purification process to express immunologically active, intact antigen for clinical trial material production. The rCSP, when formulated with various adjuvants, induced antigen-specific antibody responses as measured by enzyme-linked immunosorbent assay (ELISA) and immunofluorescence assay (IFA), as well as CD4+ T-cell responses as determined by ELISpot. The adjuvanted rCSP vaccine conferred protection in mice when challenged with transgenic P. berghei sporozoites containing the P. falciparum repeat region of CSP. Furthermore, heterologous prime/boost regimens with adjuvanted rCSP and an adenovirus type 35-vectored CSP (Ad35CS) showed modest improvements in eliciting CSP-specific T-cell responses and anti-malarial protection, depending on the order of vaccine delivery. Collectively, these data support the importance of further clinical development of adjuvanted rCSP, either as a stand-alone product or as one of the components in a heterologous prime/boost strategy, ultimately acting as an effective vaccine candidate for the mitigation of P. falciparum-induced malaria.
Abstract LB357: CRISPR-Cas9 targeting of somatic mutations selectively kills cancer cells (2023)

Abstract Pancreatic ductal adenocarcinoma (PDAC) accounts for 3% of all cancers but is the 3rd leading cause of cancer death in the United States. This staggering discrepancy is partly because most pancreatic cancers evade early detection and patients most commonly present with metastatic disease. As cancer initiates from a single transformed cell, passenger mutations that accumulate over the course of the patient’s lifetime in that cell are then clonally propagated to the growing tumor and metastases, providing a targetable molecular signature throughout the cancer. Here we propose a CRISPR-Cas9 gene therapy aimed at these tumor-specific somatic mutations. Using whole genome sequencing of rapid autopsy tumor and normal samples from five patient cases, we identified single base substitutions present in tumor tissues and absent in patient-matched normal tissue. A subset (6.6% on average) of these mutations lead to novel protospacer adjacent motif (PAM) sites. These tumor specific PAM sites are necessary for Cas9 binding and DNA scission and are therefore selectively targetable by CRISPR-Cas9 systems. Using a hybrid capture/NGS approach, we demonstrate in patients with multiple metastases that the majority of these novel PAM sites, ~70%, are maintained among the different metastases. Using multitarget sgRNA which cut at a known number of sites in the human genome, we determined a relationship between number of CRISPR-Cas9 cuts and growth inhibition in PDAC cells. We found that 8-10 cut sites in non-coding regions are sufficient to induce &amp;gt;95% cancer cell death. Finally, using cocultures of fluorescently labeled PDAC cells and a multiplexed sgRNA array targeting multiple tumor specific PAMs, we demonstrate selective cell killing of the targeted cell line. Importantly, deep sequencing of patient-matched normal lymphocytes lacking the tumor-specific PAMs treated with the same sgRNA array exhibited no editing at the targeted loci. This work establishes a bioinformatic platform for the discovery of tumor-specific CRISPR targets in the context of metastatic disease and demonstrates selective killing to cancer cells while sparing the patient’s normal cells. These data establish the proof of principle for a gene therapy approach targeting metastatic disease. Citation Format: Kirsten Bowland, Selina Shiqing K. Teh, Alyza Skaist, Ralph H. Hruban, Nicholas J. Roberts, Chrisine Iacobuzio-Donahue, James R. Eshleman. CRISPR-Cas9 targeting of somatic mutations selectively kills cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB357.
Architectural Optimizations for Low-Power $K$-Best MIMO Decoders (2009)

Maximum-likelihood (ML) detection for higher order multiple-input-multiple-output (MIMO) systems faces a major challenge in computational complexity. This limits the practicality of these systems from an implementation point of view, particularly for mobile battery-operated devices. In this paper, we propose a modified approach for MIMO detection, which takes advantage of the quadratic-amplitude modulation (QAM) constellation structure to accelerate the detection procedure. This approach achieves low-power operation by extending the minimum number of paths and reducing the number of required computations for each path extension, which results in an order-of-magnitude reduction in computations in comparison with existing algorithms. This paper also describes the very-large-scale integration (VLSI) design of the low-power path metric computation unit. The approach is applied to a 4times4, 64-QAM MIMO detector system. Results show negligible performance degradation compared with conventional algorithms while reducing the complexity by more than 50%.
Formaldehyde treatment of proteins can constrain presentation to T cells by limiting antigen processing (1994)

Proteins to be used as vaccines are frequently treated with formaldehyde, although little is known about the effects of this treatment on protein antigenicity. To investigate the effect of formaldehyde treatment on antigen recognition by T cells, we compared the in vitro T-cell response to proteins that have been formaldehyde treated with the response to untreated proteins. We found that peripheral blood mononuclear cells from individuals vaccinated with three formaldehyde-treated proteins (pertussis toxin, filamentous hemagglutinin, pertactin) of Bordetella pertussis showed little or no response to the formaldehyde-treated proteins but proliferated very well in response to the corresponding untreated protein. These findings were further confirmed with CD4+ T-cell clones specific for defined epitopes of the bacterial proteins. We found that some epitopes are presented poorly or not at all when formaldehyde-treated proteins are used, whereas other epitopes are equally presented to T-cell clones when either formaldehyde-treated or untreated antigens are used. However, T-cell recognition could be restored by either antigen degradation before formaldehyde treatment or heat denaturation after such treatment. Parallel digestion with trypsin of both formaldehyde-treated and untreated proteins showed that fragments generated from the two forms of the same antigen were different in size. These results demonstrate that formaldehyde treatment can constrain antigen presentation to T cells and that this may be due to an altered proteolytic processing of formaldehyde-treated proteins.
Determination of heavy metals in skin‐whitening cosmetics using microwave digestion and inductively coupled plasma atomic emission spectrometry (2017)

In this study, the determination of noxious heavy metals, cadmium (Cd), bismuth (Bi), mercury (Hg), titanium (Ti), lead (Pb) and metalloid arsenic (As) in skin-whitening cosmetics were examined using microwave digestion and inductively coupled plasma atomic emission spectrometry method. A complete digestion of cosmetics samples was achieved using a mixture of hydrofluoric acid/hydrogen peroxide/nitric acid. The quantification of the target compounds was done by standard addition method. The excellent quality parameters for instance, detection limits, As (4.6 ppb), Bi (7.9 ppb), Cd (0.45 ppb), Hg (3.3 ppb), Pb (3.8 ppb), Ti (4.3 ppb), linearity (<i>r</i><sup>2</sup> > 0.999) and run-to-run and day-to-day precisions with relative standard deviations <3% were obtained. The recovery rates for standard reference materials were found between 90 and 105%. The average concentration of heavy metals in cosmetics samples were in the range of 1.0-12.3 (μg g<sup>-1</sup>, As), 33-7097 (μg g<sup>-1</sup>, Bi), 0.20-0.6 (μg g<sup>-1</sup>, Cd), 0.70-2700 (μg g<sup>-1</sup>, Hg), 1.20-143 (μg g<sup>-1</sup>, Pb) and 2.0-1650 (μg g<sup>-1</sup>, Ti).
Using Remote Sensing Techniques and Hydrological Models in Analyzing Water Drainage Systems Affecting Al-Kharj Governorate (2022)

The research investigates water drainage systems and identifying the flooding area in Al-Kharj, which is the confluence of the valleys of Hanifa, Al-Sulay, Al-Hannaya, Nasah, Al-Haytham, Al-Aqimi, and then Al-Sahba, with a total area 111,491km2, which may cause risks on the natural and human environment in Al-Kharj, whether through water accumulation and stagnation in Low-lying areas and the resulting environmental hazards, or as a result of their inundation on urban areas, causing destructive effects on lives and property.The methodology is based on analyzing the drainage systems affecting the city of Al-Kharj, which is product by many steps and multiple inputs that include the elements of the stage before the surface runoff occurred and then the stage during the runoff, where collecting the largest number of elements affecting each stage and the Methods of evaluation it, then counted and analyzed them to create a topographical and hydrologic model of the drainage systems and analyzed the expected rain condition at different recurring times, especially 100 years. The morphological analysis of the basins, comparing the results of the outputs of the (DEM), tracking the paths of the valleys through topographic maps, satellite visuals, and the field study revealed that there is a mismatch between the outputs due to the interruption of the valleys flow, either for natural or human reasons, as it actually affects only 8 basins with an area 16266.7km2, Hanifa basin consider the most nourished with a water volume 124.6million m3 and a discharge rate of 756.4m3/s.
Structure of putative 4-amino-4-deoxychorismate lyase fromThermus thermophilusHB8 (2009)

The pyridoxal 5'-phosphate-dependent enzyme 4-amino-4-deoxychorismate lyase converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate in one of the crucial steps in the folate-biosynthesis pathway. The primary structure of the hypothetical protein TTHA0621 from Thermus thermophilus HB8 suggests that TTHA0621 is a putative 4-amino-4-deoxychorismate lyase. Here, the crystal structure of TTHA0621 is reported at 1.93 A resolution. The asymmetric unit contained four NCS molecules related by 222 noncrystallographic symmetry, in which the formation of intact dimers may be functionally important. The cofactor pyridoxal 5'-phosphate (PLP) binds to the protein in the large cleft formed by the N-terminal and C-terminal domains of TTHA0621. The high structural similarity and the conservation of the functional residues in the catalytic region compared with 4-amino-4-deoxychorismate lyase (PabC; EC 4.1.3.38) from Escherichia coli suggest that the TTHA0621 protein may also possess 4-amino-4-deoxychorismate lyase activity.
Synthesis of Mesoporous Lithium Titanate Thin Films and Monoliths as an Anode Material for High‐Rate Lithium‐Ion Batteries (2016)

Mesoporous Li<sub>4</sub> Ti<sub>5</sub> O<sub>12</sub> (LTO) thin film is an important anode material for lithium-ion batteries (LIBs). Mesoporous films could be prepared by self-assembly processes. A molten-salt-assisted self-assembly (MASA) process is used to prepare mesoporous thin films of LTOs. Clear solutions of CTAB, P123, LiNO<sub>3</sub> , HNO<sub>3</sub> , and Ti(OC<sub>4</sub> H<sub>9</sub> )<sub>4</sub> in ethanol form gel-like meso-ordered films upon either spin or spray coating. In the assembly process, the CTAB/P123 molar ratio of 14 is required to accommodate enough salt species in the mesophase, in which the Li<sup>I</sup> /P123 ratio can be varied between molar ratios of 28 and 72. Calcination of the meso-ordered films produces transparent mesoporous spinel LTO films that are abbreviated as Cxx-yyy-zzz or CAxx-yyy-zzz (C=calcined, CA=calcined-annealed, xx=Li<sup>I</sup> /P123 molar ratio, and yyy=calcination and zzz=annealing temperatures in Celsius) herein. All samples were characterized by using XRD, TEM, N<sub>2</sub> -sorption, and Raman techniques and it was found that, at all compositions, the LTO spinel phase formed with or without an anatase phase as an impurity. Electrochemical characterization of the films shows excellent performance at different current rates. The CA40-350-450 sample performs best among all samples tested, yielding an average discharge capacity of (176±1) mA h g<sup>-1</sup> at C/2 and (139±4) mA h g<sup>-1</sup> at 50 C and keeping 92 % of its initial discharge capacity upon 50 cycles at C/2.
Novel Genetically Engineered Tetracenomycins (1995)

Genetically engineered hybrid strains , in which the genes of the urdamycin‐producer Streptomyce fradiae are combined with some of the biosynthetic genes of the elloramycin‐producer Streptomyces olivaceus or the genes of the tetracenomycin‐producer Streptomyces glaucescens , assemble novel hybrid antibiotics of the tetracenomycin type. The results prove that this combinatorial biosynthesis method may be a useful alternative for the production of new natural products which can then be screened.
Thermostabilization of inactivated polio vaccine in PLGA-based microspheres for pulsatile release (2016)

Vaccines are a critical clinical tool in preventing illness and death due to infectious diseases and are regularly administered to children and adults across the globe. In order to obtain full protection from many vaccines, an individual needs to receive multiple doses over the course of months. However, vaccine administration in developing countries is limited by the difficulty in consistently delivering a second or third dose, and some vaccines, including the inactivated polio vaccine (IPV), must be injected more than once for efficacy. In addition, IPV does not remain stable over time at elevated temperatures, such as those it would encounter over time in the body if it were to be injected as a single-administration vaccine. In this manuscript, we describe microspheres composed of poly(lactic-co-glycolic acid) (PLGA) that can encapsulate IPV along with stabilizing excipients and release immunogenic IPV over the course of several weeks. Additionally, pH-sensitive, cationic dopants such as Eudragit E polymer caused clinically relevant amounts of stable IPV release upon degradation of the PLGA matrix. Specifically, IPV was released in two separate bursts, mimicking the delivery of two boluses approximately one month apart. In one of our top formulations, 1.4, 1.1, and 1.2 doses of the IPV serotype 1, 2, and 3, respectively, were released within the first few days from 50mg of particles. During the delayed, second burst, 0.5, 0.8, and 0.6 doses of each serotype, respectively, were released; thus, 50mg of these particles released approximately two clinical doses spaced a month apart. Immunization of rats with the leading microsphere formulation showed more robust and long-lasting humoral immune response compared to a single bolus injection and was statistically non-inferior from two bolus injections spaced 1 month apart. By minimizing the number of administrations of a vaccine, such as IPV, this technology can serve as a tool to aid in the eradication of polio and other infectious diseases for the improvement of global health.
Novel synthesis strategies for natural polymer and composite biomaterials as potential scaffolds for tissue engineering (2010)

Recent developments in tissue engineering approaches frequently revolve around the use of three-dimensional scaffolds to function as the template for cellular activities to repair, rebuild and regenerate damaged or lost tissues. While there are several biomaterials to select as three-dimensional scaffolds, it is generally agreed that a biomaterial to be used in tissue engineering needs to possess certain material characteristics such as biocompatibility, suitable surface chemistry, interconnected porosity, desired mechanical properties and biodegradability. The use of naturally derived polymers as three-dimensional scaffolds has been gaining widespread attention owing to their favourable attributes of biocompatibility, low cost and ease of processing. This paper discusses the synthesis of various polysaccharide-based, naturally derived polymers, and the potential of using these biomaterials to serve as tissue engineering three-dimensional scaffolds is also evaluated. In this study, naturally derived polymers, specifically cellulose, chitosan, alginate and agarose, and their composites, are examined. Single-component scaffolds of plain cellulose, plain chitosan and plain alginate as well as composite scaffolds of cellulose-alginate, cellulose-agarose, cellulose-chitosan, chitosan-alginate and chitosan-agarose are synthesized, and their suitability as tissue engineering scaffolds is assessed. It is shown that naturally derived polymers in the form of hydrogels can be synthesized, and the lyophilization technique is used to synthesize various composites comprising these natural polymers. The composite scaffolds appear to be sponge-like after lyophilization. Scanning electron microscopy is used to demonstrate the formation of an interconnected porous network within the polymeric scaffold following lyophilization. It is also established that HeLa cells attach and proliferate well on scaffolds of cellulose, chitosan or alginate. The synthesis protocols reported in this study can therefore be used to manufacture naturally derived polymer-based scaffolds as potential biomaterials for various tissue engineering applications.
Physical Impairment Based Regenerator Placement and Routing in Translucent Optical Networks (2008)

A novel constraint-based routing (CBR) algorithm taking into account the dominant linear and nonlinear fiber optical transmission impairments has been analyzed. It is shown that CBR and intelligent regenerator placement decrease the blocking probability significantly.