gebhart/patrepeval huggingface dataset:
Recognition Elements for 5‘ Exon Substrate Binding to the Candida albicans Group I Intron (2001)

A group I intron precursor and ribozyme were cloned from the large subunit rRNA of the human pathogen Candida albicans. Both the precursor and ribozyme are functional as determined from in vitro assays. Comparisons of dissociation constants for oligonucleotide binding to the ribozyme and to a hexanucleotide mimic of its internal guide sequence lead to a model for recognition of the 5' exon substrate by this intron. In particular, tertiary contacts with the P1 helix that help align the splice site include three 2'-hydroxyl groups, a G.U pair that occurs at the intron's splice junction, and a G.A pair. The free energy contribution that each interaction contributes to tertiary binding is determined. When the G.A pair is replaced with a G-C pair, tertiary interactions to 5' exon mimic 2'-hydroxyl groups are significantly weakened. When the G.A pair is replaced with a G.U pair, tertiary interactions are retained and binding is 10-fold tighter. These results expand our knowledge of substrate recognition by group I introns, and also provide a basis for rational design of oligonucleotide-based therapeutics for targeting group I introns by binding enhancement by tertiary interactions and suicide inhibition strategies.
System design principles (2013)

This chapter first summarizes the system level benefits of using OFDMA as the underlying multiple access technology, and then qualitatively presents the basic system design principles of OFDMA mobile broadband communications in a cellular network. This chapter serves as a preview of many topics to be covered in the remaining chapters of the book. We emphasize the concepts and insights here and leave the quantitative modeling and analysis to the subsequent chapters.
Outbreak of coronavirus disease 2019 (COVID-19) among operating room staff of a tertiary referral center: An epidemiologic and environmental investigation (2021)

Complacency in infection control practices among staff during peak community transmission of SARS-CoV-2 is believed to have driven staff-to-staff transmission. Prompt identification of the outbreak led to rapid interventions, ultimately allowing for uninterrupted surgical service.
Explanted multifocal intraocular lenses (2015)

Mr. van der Mooren, Ms. Langeslag, and Dr. Piers are employees of Abbott Medical Optics, Inc. Drs. Steinert and Tyson are consultants to Abbott Medical Optics Inc.
Modeling the Impact of Depth on Pointing Performance (2016)

An important visual cue for the distance to a target is its binocular depth, the disparity between the left and right eyes. We examined mid-air pointing on a large screen, varying the physical distances (depths) to targets. Welford's two-part formulation provided a better model than the one-part Fitts's Law formulation to predict movement time from movement amplitude and target width. Angular measures suggested by Kopper et al. did not improve the model. Consistent variations of Shoemaker et al.'s k-factor suggest target depth plays a role similar to gain for mid-air pointing. We compared both physical and virtual targets to determine if artificial binocular depth cues induce the same performance as purely physical binocular depth cues. Variation of the k-factor was different when virtual depth and physical depth were not identical. This has implications for calibrating 3-D virtual environments and for the design of interactive 3-D pointing techniques for those environments.
Photo‐Cross‐Linkers Incorporated into G‐Protein‐Coupled Receptors in Mammalian Cells: A Ligand Comparison (2011)

Wer bindet wo? Ein ausbalanciertes System für die Mutagenese nichtnatürlicher Aminosäuren ermöglicht es, für verschiedene Liganden in der natürlichen Umgebung von Säugerzellen die Ligandenbindestellen eines Klasse-II-G-Protein-gekoppelten Rezeptors zu kartieren und unterschiedliche Bindedomänen zu identifizieren.
Electrospun rubber/thermoplastic hybrid nanofibers for localized toughening effects in epoxy resins (2019)

ABSTRACT Synthetic rubber/thermoplastic blends were electrospun from their solutions. The rubber was a solid acrylonitrile/butadiene/acrylic acid copolymer and the thermoplastic was polyacrylonitrile. The aims of this study were to identify suitable systems and processing conditions for obtaining rubber‐based electrospun nanofibers, to investigate the ability of an epoxy resin system to impregnate and swell selected hybrid rubber/thermoplastic mats, and to assess the impact of the nanofibers on the resin morphology and curing behavior. In particular, electrospinning trials were carried out varying the composition of the feed solution and process parameters, such as the applied voltage, the flow rate, and tip‐to‐collector distance. The morphology of the hybrid mats was characterized by scanning electron microscopy and their thermal properties by thermogravimetry. An epoxy resin‐mat monolayer was also prepared and its fracture surface inspected; both rubber nanoparticles and PAN nanofibers were evident. The highly corrugated fracture surfaces suggest activation of local epoxy‐resin toughening mechanisms. Altogether, the results encouraged the application of hybrid mats as interleaves in high‐performance carbon/epoxy composites to contrast delamination. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137 , 48501.
SORBS2transcription is activated by telomere position effect–over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy (2015)

DNA is organized into complex three-dimensional chromatin structures, but how this spatial organization regulates gene expression remains a central question. These DNA/chromatin looping structures can range in size from 10–20 kb (enhancers/repressors) to many megabases during intra- and inter-chromosomal interactions. Recently, the influence of telomere length on chromatin organization prior to senescence has revealed the existence of long-distance chromatin loops that dictate the expression of genes located up to 10 Mb from the telomeres (Telomere Position Effect–Over Long Distances [TPE-OLD]). Here, we demonstrate the existence of a telomere loop at the 4q35 locus involving the sorbin and SH3 domain-containing protein 2 gene, SORBS2 , a skeletal muscle protein using a modification of the chromosome conformation capture method. The loop reveals a cis -acting mechanism modifying SORBS2 transcription. The expression of this gene is altered by TPE-OLD in myoblasts from patients affected with the age-associated genetic disease, facioscapulohumeral muscular dystrophy (FSHD1A, MIM 158900). SORBS2 is expressed in FSHD myoblasts with short telomeres, while not detectable in FSHD myoblasts with long telomeres or in healthy myoblasts regardless of telomere length. This indicates that TPE-OLD may modify the regulation of the 4q35 locus in a pathogenic context. Upon differentiation, both FSHD and healthy myotubes express SORBS2 , suggesting that SORBS2 is normally up-regulated by maturation/differentiation of skeletal muscle and is misregulated by TPE-OLD-dependent variegation in FSHD myoblasts. These findings provide additional insights for the complexity and age-related symptoms of FSHD.
Antibiotic Bactericidal Activity Is Countered by Maintaining pH Homeostasis in Mycobacterium smegmatis (2016)

Antibiotics target specific biosynthetic processes essential for bacterial growth. It is intriguing that several commonalities connect the bactericidal activity of seemingly disparate antibiotics, such as the numerous conditions that confer broad-spectrum antibiotic tolerance. Whether antibiotics kill in a manner unique to their specific targets or by a universal mechanism is a critical and contested subject. Herein, we demonstrate that the bactericidal activity of diverse antibiotics against Mycobacterium smegmatis and four evolutionarily divergent bacterial pathogens was blocked by conditions that worked to maintain intracellular pH homeostasis. Single-cell pH analysis demonstrated that antibiotics increased the cytosolic pH of M. smegmatis, while conditions that promoted proton entry into the cytosol prevented intracellular alkalization and antibiotic killing. These findings led to a hypothesis that posits antibiotic lethality occurs when antibiotics obstruct ATP-consuming biosynthetic processes while metabolically driven proton efflux is sustained despite the loss of proton influx via ATP synthase. Consequently, without a concomitant reduction in respiratory proton efflux, cell death occurs due to intracellular alkalization. Our findings indicate the effects of antibiotics on pH homeostasis should be considered a potential mechanism contributing to antibiotic lethality. IMPORTANCE Since the discovery of antibiotics, mortality due to bacterial infection has decreased dramatically. However, infections from difficult to treat bacteria such as Mycobacterium tuberculosis and multidrug-resistant pathogens have been on the rise. An understanding of the cascade of events that leads to cell death downstream of specific drug-target interactions is not well understood. We have discovered that killing by several classes of antibiotics was stopped by maintaining pH balance within the bacterial cell, consistent with a shared mechanism of antibiotic killing. Our findings suggest a mechanism of antibiotic killing that stems from the antibiotic's ability to increase the pH within bacterial cells by disrupting proton entry without affecting proton pumping out of cells. Knowledge of the core mechanism necessary for antibiotic killing could have a significant impact on the development of new lethal antibiotics and for the treatment of recalcitrant and drug-resistant pathogens.
Challenges and Opportunities for High Performance 32 nm CMOS Technology (2006)

Starting with the 45 nm node, a tradeoff between performance and density exists that become more severe at the 32 nm node. An in-depth analysis of the impact of pitch and increased parasitics on device performance in the 32 nm node is presented. To counteract these effects, reduction of parasitics, gate length scaling, and aggressive stress engineering are necessary. Optimized layout using a "relaxed-pitch" approach is demonstrated to show up to a 15% improvement over conventional layout in ring oscillators. The lower parasitics of SOI provide an additional degree of freedom allowing relaxed pitch designs to enhance performance in critical paths. Simpler device isolation in SOI is also shown to be very beneficial in this generation leading to an improved cost/performance tradeoff compared to previous generations
High Performance High Density Interconnects using Liquid Crystal Polymer-Substrates, Circuits Driven by Mobile Applications (2015)

The goal of the development effort was to prove a new way of creating electrical interconnects that enable much higher density, tuned circuits and connectors driven by the demands of future mobile and computing applications, including wearable and connected devices. The primary results obtained are a method to fabricate package substrates, small form factor rigid and flexible circuits using a material used in the connector industry Liquid Crystal Polymer, and linking circuits and connectors with tuned high density performance not possible with legacy manufacturing. Applications will be detailed in conjunction with the Semiconductor companies that demonstrate substrates and circuits that have high aspect ratio traces with 20–50 micron traces surrounded with fusion bonded LCP that enables impedance matching of 1–2% on high density. The study extends further to connector technology that enables interconnect of the subject substrate or circuit directly into mobile and wearable applications with over 1000 high speed interconnects capable of 28–56 Gb/s performance within a 1/2 inch square area. In addition the study will leverage the formable nature of circuit bearing Liquid Crystal Polymer to create interconnected assemblies with integral antennae, decoupling, RF shielding and die to die interconnect ideal for wearable applications.
Complete processing of a small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from pea requires the amino acid sequence Ile-Thr-Ser. (1988)

Chloroplast import and processing of two precursor proteins with mutations in the carboxyl-terminal region of the transit peptide were examined in vitro. Deletion mutations were introduced into the 57-amino acid transit peptide of a chloroplast protein, the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, from pea. A mutant, PSd48/57, in which nine carboxyl-terminal amino acids of the transit peptide had been deleted, was imported and processed to a series of 13- to 18-kDa polypeptides including the 14-kDa mature small subunit. In contrast, processing of a mutant, PSd45/57, in which an additional three amino acids had been removed, resulted in a series of polypeptides which did not include the mature small subunit. Whereas PSd48/57 was imported as efficiently as the wild-type precursor, import of PSd45/57 was only 25% as efficient as that of the authentic precursor. The mutant precursor proteins PSd48/57 and PSd45/57 are distinguished by a three-amino acid sequence, Ile-Thr-Ser, located in the carboxyl-terminal region of the transit peptide. We show that all or part of this sequence is required for correct processing.
Message-Locked Encryption for Lock-Dependent Messages. (2015)

Abstract. Motivated by the problem of avoiding duplication in storage systems, Bellare, Keelveedhi, and Ristenpart have recently put forward the notion of Message-Locked Encryption (MLE) schemes which subsumes convergent encryption and its variants. Such schemes do not rely on permanent secret keys, but rather encrypt messages using keys derived from the messages themselves. We strengthen the notions of security proposed by Bellare et al. by considering plaintext distributions that may depend on the public parameters of the schemes. We refer to such inputs as lock-dependent messages. We construct two schemes that satisfy our new notions of security for message-locked encryption with lock-dependent messages. Our main construction deviates from the approach of Bellare et al. by avoiding the use of ciphertext components derived deterministically from the messages. We design a fully randomized scheme that supports an equality-testing algorithm defined on the ciphertexts. Our second construction has a deterministic ciphertext component that enables more efficient equality testing. Security for lock-dependent messages still holds under computational assumptions on the message distributions produced by the attacker. In both of our schemes the overhead in the length of the ciphertext is only additive and independent of the message length.
Graphene Oxide: Tunable Nanoscale Interlayer of Graphene with Symmetrical Polyelectrolyte Multilayer Architecture for Lithium Extraction (Adv. Mater. Interfaces 6/2018) (2018)

A symmetrical multilayer architecture of graphene is designed by synthesizing sulfonated 4,4′-diaminodiphenyl sulfone with the ample sulfonate groups and tunable interlayer spacing to exhibit the Li+ extraction from ionic mixtures with Na+, Mg2+ and Ca2+. This is reported by Jiangnan Shen and co-workers in article number 1701449. to exhibit the Li+ extraction from ionic mixtures with Na+, Mg2+ and Ca2+. This is reported by Jiangnan Shen and co-workers in article number 1701449.
Forming interactivity (2002)

The current practice used in the design of physical interactive products (such as handheld devices), often suffers from a divide between exploration of form and exploration of interactivity. This can be attributed, in part, to the fact that working prototypes are typically expensive, take a long time to manufacture, and require specialized skills and tools not commonly available in design studios.We have designed a prototyping tool that, we believe, can significantly reduce this divide. The tool allows designers to rapidly create functioning, interactive, physical prototypes early in the design process using a collection of wireless input components (buttons, sliders, etc.) and a sketch of form. The input components communicate with Macromedia Director to enable interactivity.We believe that this tool can improve the design practice by: a) Improving the designer's ability to explore both the form and interactivity of the product early in the design process, b) Improving the designer's ability to detect problems that emerge from the combination of the form and the interactivity, c) Improving users' ability to communicate their ideas, needs, frustrations and desires, and d) Improving the client's understanding of the proposed design, resulting in greater involvement and support for the design.
Arthroscopic hip preservation surgery (2013)

The technical advances in arthroscopic surgery of the hip, including the improved ability to manage the capsule and gain extensile exposure, have been paralleled by a growth in the number of conditions that can be addressed. This expanding list includes symptomatic labral tears, chondral lesions, injuries of the ligamentum teres, femoroacetabular impingement (FAI), capsular laxity and instability, and various extra-articular disorders, including snapping hip syndromes. With a careful diagnostic evaluation and technical execution of well-indicated procedures, arthroscopic surgery of the hip can achieve successful clinical outcomes, with predictable improvements in function and pre-injury levels of physical activity for many patients.This paper reviews the current position in relation to the use of arthroscopy in the treatment of disorders of the hip.
Uridine triacetate as a life-saving antidote to capecitabine toxicity. (2016)

e21612 Background: Uridine triacetate was approved by FDA in 2015 for adult and pediatric patients who receive an overdose of 5-fluorouracil or capecitabine or who exhibit early-onset, severe or life-threatening toxicities. Early-onset toxicities from capecitabine or 5-FU treatment are due to various metabolic causes, including DPD deficiency, and can be fatal. Uridine triacetate is an oral prodrug of uridine, a direct antagonist of 5-FU, that dilutes and competes with toxic 5-FU metabolites, particularly FUTP incorporation into RNA, reducing morbidity and mortality due to 5-FU and capecitabine. Methods: Uridine triacetate has been studied in 2 trials (173 patients) to date, including 13 who received an overdose of capecitabine or developed early-onset, severe toxicities. The Sponsor (Wellstat Therapeutics) was contacted upon recognition of an overdose or early-onset toxicity and evaluated patient eligibility. Adults (n = 6 overdose and 4 early-onset) were to receive 10 g of uridine triacetate orally every 6 hr for 20 doses. Pediatric patients (n = 3) were to receive 6.2 g/m2 orally every 6 hr for 20 doses. Uridine triacetate was to start within 96 hr following the end of capecitabine. The primary endpoint was survival at 30 days following uridine triacetate. All patients were monitored for safety. Results: All 6 adult capecitabine suicidal overdose cases (up to 28,000 mg at once) and all 3 pediatric patients who accidentally took capecitabine recovered fully within 30 days post-treatment with uridine triacetate. Both patients who presented with multiple severe post-capecitabine toxicities but initiated treatment with uridine triacetate > 96 hr died. In contrast, both patients who presented with similar multiple severe early-onset toxicities but who started uridine triacetate within the recommended 96 hr post capecitabine fully recovered. Only one AE (vomiting) was attributed to uridine triacetate. Conclusions: Uridine triacetate was a safe and effective life-saving treatment for patients following potentially lethal capecitabine overexposure or early-onset toxicities when administered within 96 hr post capecitabine dosing.
Optimal Open-Loop MIMO Precoder Design (2020)

Multiple-input multiple-output (MIMO) is a favorable technique that can improve system capacity and performance through spatial multiplexing. However, the performance gets degraded over the correlated wireless channels. In this letter, we consider a point-to-point MIMO system and jointly optimize both the precoding matrix and the difference between two transmit vectors to resist transmit correlation. The simulation results demonstrate that the proposed method can get average 75% gain comparing with the existing method in terms of the minimum pairwise error probability.
Photochemical Charge Separation in Closely Positioned Donor–Boron Dipyrrin–Fullerene Triads (2011)

A series of molecular triads, composed of closely positioned boron dipyrrin-fullerene units, covalently linked to either an electron donor (donor(1)-acceptor(1)-acceptor(2)-type triads) or an energy donor (antenna-donor(1)-acceptor(1)-type triads) was synthesized and photoinduced energy/electron transfer leading to stabilization of the charge-separated state was demonstrated by using femtosecond and nanosecond transient spectroscopic techniques. The structures of the newly synthesized triads were visualized by DFT calculations, whereas the energies of the excited states were determined from spectral and electrochemical studies. In the case of the antenna-donor(1)-acceptor(1)-type triads, excitation of the antenna moiety results in efficient energy transfer to the boron dipyrrin entity. The singlet-excited boron dipyrrin thus generated, undergoes subsequent energy and electron transfer to fullerene to produce a boron dipyrrin radical cation and a fullerene radical anion as charge-separated species. Stabilization of the charge-separated state in these molecular triads was observed to some extent.
Effect of compliance and hematocrit on wall shear stress in a model of the entire coronary arterial tree (2009)

A hemodynamic analysis is implemented in the entire coronary arterial tree of diastolically arrested, vasodilated pig heart that takes into account vessel compliance and blood viscosity in each vessel of a large-scale simulation involving millions of vessels. The feed hematocrit (Hct) is varied at the inlet of the coronary arterial tree, and the Fahraeus-Lindqvist effect and phase separation are considered throughout the vasculature. The major findings are as follows: 1) vessel compliance is the major determinant of nonlinearity of the pressure-flow relation, and 2) changes in Hct influence wall shear stress (WSS) in epicardial coronary arteries more significantly than in transmural and perfusion arterioles because of the Fahraeus-Lindqvist effect. The present study predicts the flow rate as a second-order polynomial function of inlet pressure due to vessel compliance. WSS in epicardial coronary arteries increases >15% with an increase of feed Hct from 45% to 60% and decreases >15% with a decrease of feed Hct from 45% to 30%, whereas WSS in small arterioles is not affected as feed Hct changes in this range. These findings have important implications for acute Hct changes under vasodilated conditions.
A maximum likelihood approach for identifying human operator remnant in a tracking task (1975)

By applying a maximum likelihood approach to identification with empirical data from a tracking task, the output signal uncorrelated with the input signal (a definition of human operator remnant) can be determined. To obtain this remnant signal, a linear, stationary model describing the human is utilized. The innovations signal, is computed from the difference in the empirical data and the model's output. The remnant can then be identified using the innovations sequence by computing the component of the output signal which is uncorrelated (or orthogonal) to the input signal. Data from a Roll Axis Tracking Simulator is analyzed and remnant is identified to two phases of tracking (with and without motion information).