gebhart/patrepeval huggingface dataset:
Search for Shorter Portions of the Proline‐Rich Antimicrobial Peptide Fragment Bac5(1–25) That Retain Antimicrobial Activity by Blocking Protein Synthesis (2019)

The spread of antibiotic-resistant pathogens has boosted the search for new antimicrobial drugs. Proline-rich antimicrobial peptides are promising lead compounds for the development of next-generation antibiotics, given their very low cytotoxicity and their good antimicrobial activity targeting the bacterial ribosome. Bac5(1-25) is an N-terminal fragment of the bovine proline-rich antimicrobial peptide Bac5, whose mode of action has been recently described. In this work we tested a number of Bac5(1-25) fragments, and we characterized their antimicrobial activity against Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Staphylococcus aureus, Salmonella enterica, and Pseudomonas aeruginosa. We evaluated their cytotoxicity toward human cells and their efficacy in inhibiting bacterial protein synthesis. This allowed us to identify some shorter fragments of Bac5(1-25) with a good balance between antibacterial efficacy, protein synthesis inhibition, and ease/cost-effectiveness of synthesis, suitable as lead compounds to develop new antibacterials.
Efficiency of generation of the sum and difference frequencies in the field of multimode and multifrequency laser radiation (1989)

A theoretical analysis is made of the process of generation of the sum or difference frequency in the field of multimode and multifrequency pump radiation. An allowance is made for the aperture effect under rapid energy exchange conditions. It is shown analytically that on increase in the length of a nonlinear crystal in which the generation process takes place the efficiency of conversion reaches saturation monotonically after a weak maximum. The saturation value of the conversion efficiency increases monotonically on increase in the power of multimode low-frequency pump radiation and attains a limit of 50% in respect of the number of photons. At low pump powers the saturation conversion efficiency is proportional to the square root of the pump power.
MAC layer design for statistical multiplexing of voice and data over EGPRS (2002)

The General Packet Radio Service (GPRS) was introduced by ETSI to meet the ever-increasing demand for wireless data over the GSM radio interface. Enhanced GPRS (EGPRS Phase 1) was later introduced in order to increase the spectrum efficiency and data throughput by using 8-PSK modulation and link adaptation techniques. While (E)GPRS uses packet-switched technology to efficiently transmit best-effort data, real-time services (e.g. voice) are currently supported only via circuit-switched systems. This service separation reduces the potential spectrum efficiency gain resulting from multiplexing different services on the same radio channel. This paper describes the key new concepts needed to support statistical multiplexing of different radio access bearer classes over the GSM/EDGE radio access network (GERAN) air interface. The focus is on the definition of new traffic and control channels to support statistical multiplexing of speech, real-time data, and non-real-time data, and the corresponding new MAC procedures that are needed to guarantee quality of service (QoS).
Metasurfaces for biomedical applications: imaging and sensing from a nanophotonics perspective (2021)

Metasurface is a recently developed nanophotonics concept to manipulate the properties of light by replacing conventional bulky optical components with ultrathin (more than 104 times thinner) flat optical components. Since the first demonstration of metasurfaces in 2011, they have attracted tremendous interest in the consumer optics and electronics industries. Recently, metasurface-empowered novel bioimaging and biosensing tools have emerged and been reported. Given the recent advances in metasurfaces in biomedical engineering, this review article covers the state of the art for this technology and provides a comprehensive interdisciplinary perspective on this field. The topics that we have covered include metasurfaces for chiral imaging, endoscopic optical coherence tomography, fluorescent imaging, superresolution imaging, magnetic resonance imaging, quantitative phase imaging, sensing of antibodies, proteins, DNAs, cells, and cancer biomarkers. Future directions are discussed in twofold: application-specific biomedical metasurfaces and bioinspired metasurface devices. Perspectives on challenges and opportunities of metasurfaces, biophotonics, and translational biomedical devices are also provided. The objective of this review article is to inform and stimulate interdisciplinary research: firstly, by introducing the metasurface concept to the biomedical community; and secondly by assisting the metasurface community to understand the needs and realize the opportunities in the medical fields. In addition, this article provides two knowledge boxes describing the design process of a metasurface lens and the performance matrix of a biosensor, which serve as a "crash-course" introduction to those new to both fields.
Near-Equilibrium Measurements of Nonequilibrium Free Energy (2012)

A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a nonequilibrium ensemble is that it is larger than that of the same system at equilibrium. Herein, we derive a formally exact expression for the probability distribution of a driven system, which involves path ensemble averages of the work over trajectories of the time-reversed system. From this we find a simple near-equilibrium approximation for the free energy in terms of an excess mean time-reversed work, which can be experimentally measured on real systems. With analysis and computer simulation, we demonstrate the accuracy of our approximations for several simple models.
Withaferin A: a proteasomal inhibitor promotes healing after injury and exerts anabolic effect on osteoporotic bone (2013)

Withania somnifera or Ashwagandha is a medicinal herb of Ayurveda. Though the extract and purified molecules, withanolides, from this plant have been shown to have different pharmacological activities, their effect on bone formation has not been studied. Here, we show that one of the withanolide, withaferin A (WFA) acts as a proteasomal inhibitor (PI) and binds to specific catalytic β subunit of the 20S proteasome. It exerts positive effect on osteoblast by increasing osteoblast proliferation and differentiation. WFA increased expression of osteoblast-specific transcription factor and mineralizing genes, promoted osteoblast survival and suppressed inflammatory cytokines. In osteoclast, WFA treatment decreased osteoclast number directly by decreasing expression of tartarate-resistant acid phosphatase and receptor activator of nuclear factor kappa-B (RANK) and indirectly by decreasing osteoprotegrin/RANK ligand ratio. Our data show that in vitro treatment of WFA to calvarial osteoblast cells decreased expression of E3 ubiquitin ligase, Smad ubiquitin regulatory factor 2 (Smurf2), preventing degradation of Runt-related transcription factor 2 (RunX2) and relevant Smad proteins, which are phosphorylated by bone morphogenetic protein 2. Increased Smurf2 expression due to exogenous treatment of tumor necrosis factor α (TNFα) to primary osteoblast cells was decreased by WFA treatment. This was corroborated by using small interfering RNA against Smurf2. Further, WFA also blocked nuclear factor kappa-B (NF-kB) signaling as assessed by tumor necrosis factor stimulated nuclear translocation of p65-subunit of NF-kB. Overall data show that in vitro proteasome inhibition by WFA simultaneously promoted osteoblastogenesis by stabilizing RunX2 and suppressed osteoclast differentiation, by inhibiting osteoclastogenesis. Oral administration of WFA to osteopenic ovariectomized mice increased osteoprogenitor cells in the bone marrow and increased expression of osteogenic genes. WFA supplementation improved trabecular micro-architecture of the long bones, increased biomechanical strength parameters of the vertebra and femur, decreased bone turnover markers (osteocalcin and TNFα) and expression of skeletal osteoclastogenic genes. It also increased new bone formation and expression of osteogenic genes in the femur bone as compared with vehicle groups (Sham) and ovariectomy (OVx), Bortezomib (known PI), injectible parathyroid hormone and alendronate (FDA approved drugs). WFA promoted the process of cortical bone regeneration at drill-holes site in the femur mid-diaphysis region and cortical gap was bridged with woven bone within 11 days of both estrogen sufficient and deficient (ovariectomized, Ovx) mice. Together our data suggest that WFA stimulates bone formation by abrogating proteasomal machinery and provides knowledge base for its clinical evaluation as a bone anabolic agent.
Correction for Tohya et al., “Whole-Genome Sequencing-Based Re-Identification of Pseudomonas putida/ fluorescens Clinical Isolates Identified by Biochemical Bacterial Identification Systems” (2023)

Volume 10, no. 2, e02491-21, 2022, https://doi.org/10.1128/spectrum.02491-21. The following taxonomy section should appear in the main article and not in the supplemental material. (A revised supplemental material file is included with this Author Correction.)
Variable-speed-drive range utilising brushless synchronous motors (1988)

AC drive systems are taking an increasing proportion of the UK electric variable-speed-drives market. Recent studies indicate that the proportion taken by AC drives has risen from approximately 20% of the market in 1984, to 25% in 1986
A migration-enhanced edge computing support for mobile devices in hostile environments (2017)

First research activities are starting to recognize the suitability of edge computing approaches in several Internet-of-Things (IoT) and Cyber-Physical Systems (CPS) application domains, for instance, to better address scalability issues and to improve reactivity via local control decisions and actuation. The paper originally proposes the design and implementation of an extended edge computing platform, specifically designed for the support of mobile services when provisioned in so-called hostile environments. In particular, our original platform is capable of proactive migration of virtualized functions in response to provision-time device mobility. The paper provides a practical contribution in terms of design and implementation of proactive migration as an extension of the Elijah platform, available for the community of researchers/practitioners in the field. In addition, the paper contributes with lessons learnt from deployment and experimentation, including experimental results about the performance achievable when adopting simple but effective strategies for proactive migration.
ChemInform Abstract: Asymmetric Synthesis of Diethyl α‐Amino‐α‐alkyl‐ phosphonates by Alkylation of Chiral Phosphonoglycine Equivalents: Role of Chelating Effects. (1993)

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.
Analyzing the performance of hierarchical collective algorithms on ARM-based multicore clusters (2022)

MPI is the de facto communication standard library for parallel applications in distributed memory architectures. Collective operations performance is critical in HPC applications as they can become the bottleneck of their executions. The advent of larger node sizes on multicore clusters has motivated the exploration of hierarchical collective algorithms aware of the process placement in the cluster and the memory hierarchy. This work analyses and compares several hierarchical collective algorithms from the literature that do not form part of the current MPI standard. We implement the algorithms on top of OpenMPI using the shared-memory facility provided by MPI-3 at the intra-node level and evaluate them on ARM-based multicore clusters. From our results, we evidence aspects of the algorithms that impact the performance and applicability of the different algorithms. Finally, we propose a model that helps us to analyze the scalability of the algorithms.
Bergamottin is a competitive inhibitor of CYP1A1 and is antimutagenic in the Ames test (2012)

Grapefruit juice (GJ) is a well known Cytochrome P450 (CYP) inhibitor; CYP3A is one of the most affected subfamily leading to anticarcinogenic and antimutagenic effects when GJ is administered to experimental animals in combination with mutagenic/carcinogenic agents metabolized by CYP3A. Bergamottin, naringin and dihydroxybergamottin are three main constituents contained within GJ and their inhibitory effect against CYP3A4 has been well documented. Reports suggest that CYP3A is not the only one affected but CYP1A and 2B are also affected by GJ. To explore this last possibility in depth we tested the in vitro capacity of bergamottin, naringin and dihydroxybergamottin to inhibit the activity of CYP1A and 2B subfamilies and found that bergamottin showed the strongest inhibitory effect and naringin showed no inhibition at all. Therefore, we decided to biochemically characterize the inhibitory properties of bergamottin. CYP1A1 Supersome® used in this study showed a Km(app)=0.0723 μM and a Vm(app)=6.141 μU/pmol with substrate ethoxyresorufin, and the biochemical characterization of bergamottin CYP1A1 inhibitory effect revealed that it is a competitive inhibitor with a Ki=10.703 nM. We also confirmed the antimutagenicity of this compound against the mutagenic effect of 3-methylcholanthrene and benzo[a]pyrene in the Ames test.
The Deterministic Mine Burial Prediction System (2009)

Abstract : This report documents the NRL Deterministic Mine Burial Prediction System; the software, which runs in MATLAB, is an attachment to this report. The purpose of the system is to provide a user-friendly software for operating newer, deterministic, mine burial prediction models for impact and scour burial that are products of a combined six-year program between ONR and NRL. This report presents an overview of the software, documents input data and computer platform requirements, and provides a user's guide with walkthroughs of example cases. A presentation of results and analysis from exercising the system to simulate impact and scour burial experiments using operational or operational-like inputs follow. Based on nonparametric hypothesis testing of simulation results with empirical data, the statistics generated from simulations of impact burial appear to provide useful predictions and uncertainty estimates when the simulations account for geotechnical variations. For scour burial, the use of the Simulating Waves Nearshore or WaveWatch-III model to drive the scour module qualitatively followed empirical burial trends, with variations in wave height prediction appearing to be a more significant factor in determining the accuracy of the scour burial prediction than uncertainty in grain size. Overall, the tests provide encouragement for the use of new mine burial prediction models to provide reasonable predictions of burial from operational input data.
A Generalized Bulk-Degradation Model for Hydrogel Networks Formed from Multivinyl Cross-linking Molecules (2001)

A theoretical model has been developed to describe the degradation behavior of hydrogels formed from multivinyl cross-linking molecules. Kinetic information was incorporated into the model to predict the cleavage of the cross-links and structural information was included to describe the mass loss from the network. Mass loss from the networks was shown to depend on many parameters, such as the number of vinyl groups on the cross-linking molecule and the average number of cross-linking molecules reacted into each kinetic chain. Other parameters that influenced the mass loss profile are the weight fraction of the network that is contained in the cross-linking molecule, the propensity to form primary cycles, and the hydrolysis kinetic constant. Two other macroscopic properties, volumetric swelling ratio and compressive modulus, were examined as a function of the average number of cross-links per kinetic chain. Through this modeling approach, the degradation of many realistic systems can be understood and predicted, providing insight into the design of degradable hydrogel networks with the desired properties.
Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) induces tolerogenic dendritic cells that delay onset of type 1 diabetes by enhancing CD4+CD25+Foxp3+ regulatory T cells (50.33) (2009)

Abstract Impairment in dendritic cell (DC) functions is implicated in defective immune regulation that leads to type-1 diabetes (T1D) in both humans and the established non-obese diabetic (NOD) mouse model. In this study, we examined the roles of DC modulators such as GM-CSF and Flt3-L to affect DC function and prevent T1D development in NOD mice. Both GM-CSF and FLT3-L could suppress the development of T1D if treatment was initiated earlier in life prior to the development of clinical diabetes. However, unlike Flt3-L, GM-CSF was far more effective in suppressing T1D even when administered at later stages of insulitis. Ongoing periodic treatment of NOD mice with GM-CSF prevented the development of T1D and the animals remained healthy until 3 months after cessation of the treatment. Adoptive transfer of CD4+CD25+ T cells from GM-CSF-treated mice could suppress effector T cell response and T1D in NOD-SCID mice, and this suppression was associated with enhanced IL-10 and TGF-β1 production. Moreover, adoptive transfer of GM-CSF-exposed DCs to naive NOD mice resulted in an expansion of Foxp3+ T cells and a significant delay in T1D onset. These results indicate that primarily the GM-CSF renders DCs tolerogenic resulting in subsequent Treg induction and delayed onset of T1D in NOD mice. NIH 1RO1AI058190
MEASUREMENT OF URINARY FLOW RATE USING ULTRASOUND IN YOUNG BOYS AND INFANTS (2001)

Urinary flow rates can be measured accurately using ultrasound in boys who produce small volumes and/or who are not toilet trained and also in infants. In future studies ultrasound will be applied to subsets of male infants with bladder dysfunction.
Mechanical Behavior of a Supported Lipid Bilayer under External Shear Forces (2009)

Shear forces from a pressure-driven bulk flow in a microfluidic channel can be used to induce and control the motion of a supported lipid bilayer (SLB) formed on the walls of the channel. We here present a theoretical model that relates the experimentally observed drift velocities of an egg yolk phosphatidylcholine (egg PC) SLB to the hydrodynamic drag force from the bulk flow, the intermonolayer friction coefficient, b, of the bilayer, and the friction coefficient, bls, between the lower leaflet of the bilayer and the supporting substrate. The drift velocity and diffusivity of the lipids in the SLB were obtained by photobleaching a delimited area of fluorescently labeled lipids and subsequently monitoring the recovery and convective motion of the bleached spot. A striking observation was that the drift velocity of the lipids was observed to be nearly 6 orders of magnitude smaller than the bulk velocity at the center of the channel. This predicts a value for bls that is at least 25 times as high as predicted by the traditional model with the SLB and the support spaced by a homogeneous 1 nm thick film of water. In addition, the intermonolayer friction coefficient was estimated to 2x10(7) Pa s/m, a value that increased after addition of glycerol to the bulk solution. This increase was accompanied by an equal decrease in the lipid diffusivity, with both observations indicating an increased viscous drag within the bilayer when glycerol was added to the bulk solution.
Nerve Entrapment (2015)

Nerve entrapment syndromes are common in the general population, and are managed by a wide variety of medical and surgical specialists. A thorough understanding of the pathophysiology of nerve compression and appropriate clinical workup are critical in the overall management of these conditions. There remain several topics of controversy regarding the surgical management of nerve entrapment syndromes, including multiple points of nerve compression, carpal tunnel release under local anesthesia, open versus endoscopic decompression surgery, the "best" operation for primary cubital tunnel surgery, and revision decompression surgery. This article attempts to provide a concise summary of the advances in the basic and clinical science of peripheral nerve entrapment.
Improved Document Modelling with a Neural Discourse Parser (2019)

Despite the success of attention-based neural models for natural language generation and classification tasks, they are unable to capture the discourse structure of larger documents. We hypothesize that explicit discourse representations have utility for NLP tasks over longer documents or document sequences, which sequence-to-sequence models are unable to capture. For abstractive summarization, for instance, conventional neural models simply match source documents and the summary in a latent space without explicit representation of text structure or relations. In this paper, we propose to use neural discourse representations obtained from a rhetorical structure theory (RST) parser to enhance document representations. Specifically, document representations are generated for discourse spans, known as the elementary discourse units (EDUs). We empirically investigate the benefit of the proposed approach on two different tasks: abstractive summarization and popularity prediction of online petitions. We find that the proposed approach leads to improvements in all cases.
Rhodium-Catalyzed Hydrogenation–Desymmetrization of Cyclohexadienones (2018)

Key words rhodium catalysis - desymmetrization - cyclohexadienones - hydrogenation
Holmes: A Comprehensive Anomaly Detection System for Daily In-home Activities (2015)

Advances in wireless sensor networks have enabled the monitoring of daily activities of elderly people. The goal of these monitoring applications is to learn normal behavior in terms of daily activities and look for any deviation, i.e., Anomalies, so that alerts can be sent to relatives or caregivers. However, human behavior is very complex, and many existing anomaly detection systems are too simplistic which cause many false alarms, resulting in unreliable systems. We present Holmes, a comprehensive anomaly detection system for daily in-home activities. Holmes accurately learns a resident's normal behavior by considering variability in daily activities based not only on a per day basis, but also considering specific days of the week, different time periods such as per week and per month, and collective, temporal, and correlation based features. This approach of learning complicated normal behaviors reduces false alarms. Also, based on resident and expert feedback, Holmes learns semantic rules that explain specific variations of activities in specific scenarios to further reduce false alarms. We evaluate Holmes using data collected from our own deployed system, public data sets, and data collected by a senior safety system provider company from an elderly resident's home. Our evaluation shows that compared to state of the art systems, Holmes reduces false positives and false negatives by at least 46% and 27%, respectively.
A Head Mounted Digital Image Warping Prosthesis for Age-Related Macular Degeneration (2014)

University of Minnesota M.S. thesis. May 2014. Major: Mechanical Engineering. Advisor:Arthur Erdman, PhD. 1 computer file (PDF); viii, 158 pages, appendices A-D.