gebhart/patrepeval huggingface dataset:
A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment (2017)

Ebola virus disease (EVD) is a deadly global public health threat, with no currently approved treatments. Traditional drug discovery and development is too expensive and inefficient to react quickly to the threat. We review published research studies that utilize computational approaches to find or develop drugs that target the Ebola virus and synthesize its results. A variety of hypothesized and/or novel treatments are reported to have potential anti-Ebola activity. Approaches that utilize multi-targeting/polypharmacology have the most promise in treating EVD.
Antibacterial Activity, Penicillinase Stability and Inducing Ability of Different Penicillins (1962)

SUMMARY: There are now at least three main types of antibacterial activity shown by different penicillins-the ordinary penicillin G type, the type shown by methicillin active against penicillinase-producing staphylococci and the ‘broad spectrum’ type of activity shown by α-aminobenzylpenicillin. The inducing capacity of different penicillins can be measured by the concentration required for maximal or half maximal induction, which gives the Michaelis (induction) constant, or by the total amount of enzyme eventually produced. But either of these methods of determining inducing capacity may give misleading results with penicillins which may be easily hydrolysed during the induction process. Of the penicillins used methicillin is by far the best inducer-but it is uncertain how much this is due to a true ‘inducing affinity’ and how much a result of its resistance to hydrolysis.
Scaling model for laser-produced bubbles in soft tissue (1998)

The generation of vapor-driven bubbles is common in many emerging laser-medical therapies involving soft tissues. To successfully apply such bubbles to processes such as tissue break-up and removal, it is critical to understand their physical characteristics. To complement previous experimental and computational studies, an analytic mathematical model for bubble creation and evolution is presented. In this model, the bubble is assumed to be spherically symmetric, and the laser pulse length is taken to be either very short or very long compared to the bubble expansion timescale. The model is based on the Rayleigh cavitation bubble model. In this description, the exterior medium is assumed to be an infinite incompressible fluid, while the bubble interior consists of a mixed liquid-gas medium which is initially heated by the laser. The heated interior provides the driving pressure which expands the bubble. The interior region is assumed to be adiabatic and is described by the standard water equation-of- state, available in either tabular, or analytic forms. Specifically, we use adiabats from the equation-of-state to describe the evolution of the interior pressure with bubble volume. Analytic scaling laws are presented for the maximum size and duration of bubbles as functions of the laser energy and initially heated volume.
Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy (2004)

The 11/25 genotype of the HIV V3 loop is an independent predictor of poor immunological response and more rapid mortality even after starting triple antiretroviral therapy. These results may prove to be useful for the clinical management of HIV-infected individuals.
A pedigree‐based study of mitochondrial d‐loop DNA sequence variation among Arabian horses (2000)

Through DNA sequence comparisons of a mitochondrial D-loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty-two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the Arabian Horse Registry of America, we estimated that this study defined the expected mtDNA haplotypes for at least 89% of Arabian horses registered in the US. The reliability of the studbook recorded maternal lineages of Arabian pedigrees was demonstrated by haplotype concordance among multiple samplings in 14 lines. Single base differences observed within two maternal lines were interpreted as representing alternative fixations of past heteroplasmy. The study also demonstrated the utility of mtDNA sequence studies to resolve historical maternity questions without access to biological material from the horses whose relationship was in question, provided that representatives of the relevant female lines were available for comparison. The data call into question the traditional assumption that Arabian horses of the same strain necessarily share a common maternal ancestry.
Identification of Vibration Properties of Heavy Duty Machine Driveline Parts as a Base for Adequate Condition Monitoring : Axle (2016)

With increasing complexities in the heavy duty construction equipment, early fault detection of certain components in the machine becomes more and more challenging due to too many fault code generated when a failure occurs. The axle is one of such component. The axle transfers driving torque from the transmission to the wheels and axle failure may result in costly downtime of construction equipment. To reduce service cost and to improve uptime, adequate condition monitoring based on sensor data from the axle is considered. Vibration is measured on the axle. Analysis of the data has been carried out using adequate signal processing methods. The results indicate that the vibration properties of the axle are relevant for early fault detection of the axle. In this way; the health of the axle may be continuously monitored on-board using the vibration information and if the axle health starts to degrade a service and/or repair may be scheduled well in advance of a potential axle failure and in that way the downtime of a machine may be reduced.
Microbial findings, sensitivity and outcome in patients with postoperative peritonitis a retrospective cohort study (2019)

We were able to show that the currently used antibiotic regimes with piperacillin/sulbactam and cefotaxime/metronidazole are ineffective in a relevant number of patients with anastomotic leakage. Only meropenem or meropenem/vancomycin cover most of the microbes predominant in postoperative peritonitis.
Flow and Heat Transfer in a Ribbed Channel With Complex Structure Characters (2020)

Abstract The ribbed channels are widely used in the internal cooling structure of turbine blade. Many investigations on this kind of channel were carried on in the channel with rectangle cross section and straight inlet. Nevertheless, in mid-chord region of a real blade, the channel characters are more complex and may affect the heat transfer performance in the channel. The heat transfer investigation in a channel with 3 legs was conducted by numerical simulation. Aim to get the influence of channel structure feature to heat transfer and flow characteristics, the channel was simplified from a real turbine internal cooling channel and main structure features were kept. In order to make the velocity in the first leg close to that in the real structure, the entrance is changed to the contraction entrance. The first leg of channel section is simplified as trapezoid. The legs are connected by 2 U-turns with bend angle for imitating the bend because of the airfoil in real blade. A supplement hole in the inlet of 3rd leg was kept as same as the real channel. Some coolant was supplement to the 3rd leg. Furthermore, 3 rib arrangements (45° ribs, 135° ribs and V-shape ribs) were studied for presenting the interaction between rib arrangement and channel structure character. The results show that: 1) the shape of the inlet cross section has a continuous effect on the irregular velocity in the first leg, the velocity pattern cause by inlet may interact with the secondary flow caused by ribs and lead to different heat transfer distribution compared with the channel with uniform inlet velocity and rectangle cross section. The heat transfer performance in channel with 135° ribs is different from that in the channel with 45° ribs. 2) In the second leg, the secondary flow is generated at the inlet by the bending structure of the leg connection. This secondary flow may suppress or promote the secondary flow produced by ribs. The composed secondary flow leads to the asymmetry flow pattern in the channel and causes the different heat transfer performance in two ribbed walls. 3) In the third leg, the interaction between the flow coming from the supplement hole, the secondary flow caused by ribs and the flow coming from upstream form the complex flow structure. The different rib angle affects the position of high-velocity area. 4) The heat transfer distribution is asymmetry because of the asymmetry channel cross section and bending connecting of legs. The heat transfer performance is different between that in channel with 45° ribs and 135° ribs, whereas is same in the channel with rectangle cross section. Generally speaking, the heat transfer performance is best in the channel with V-shape ribs and is worst in the channel with 45° ribs.
Minimally invasive long saphenous vein harvesting using a laryngoscope. (1998)

Minimally invasive vein harvesting is less traumatic to the extremity with fewer complications and superior patient satisfaction. Although commercial disposable systems are now available to permit minimally invasive harvesting of the saphenous vein, a conventional laryngoscope can be used with much reduced costs.
Clioquinol Mediates Copper Uptake and Counteracts Copper Efflux Activities of the Amyloid Precursor Protein of Alzheimer's Disease (2004)

The key protein in Alzheimer's disease, the amyloid precursor protein (APP), is a ubiquitously expressed copper-binding glycoprotein that gives rise to the Abeta amyloid peptide. Whereas overexpression of APP results in significantly reduced brain copper levels in three different lines of transgenic mice, knock-out animals revealed increased copper levels. A provoked rise in peripheral levels of copper reduced concentrations of soluble amyloid peptides and resulted in fewer pathogenic Abeta plaques. Contradictory evidence has been provided by the efficacy of copper chelation treatment with the drug clioquinol. Using a yeast model system, we show that adding clioquinol to the yeast culture medium drastically increased the intracellular copper concentration but there was no significant effect observed on zinc levels. This finding suggests that clioquinol can act therapeutically by changing the distribution of copper or facilitating copper uptake rather than by decreasing copper levels. The overexpression of the human APP or APLP2 extracellular domains but not the extracellular domain of APLP1 decreased intracellular copper levels. The expression of a mutant APP deficient for copper binding increased intracellular copper levels several-fold. These data uncover a novel biological function for APP and APLP2 in copper efflux and provide a new conceptual framework for the formerly diverging theories of copper supplementation and chelation in the treatment of Alzheimer's disease.
Electron-Ion Luminosity Maximization in the EIC (2021)

The electron-ion luminosity in EIC has a number of limits, including the ion intensity available from the injectors, the total ion beam current, the electron bunch intensity, the total electron current, the synchrotron radiation power, the beam-beam effect, the achievable beta functions at the interaction points (IPs), the maximum angular spreads at the IP, the ion emittances reachable with stochastic or strong cooling, the ratio of horizontal to vertical emittance, and space charge effects. We map the e-A luminosity over the center-of-mass energy range for some ions ranging from deuterons to uranium ions. For e-Au collisions the present design provides for electron-nucleon (e-Au) peak luminosities of 1.7x1033 cm⁻²s⁻¹ with stochastic cooling, and 4.7x1033 cm⁻²s⁻¹ with strong hadron cooling.
Low-power floating-point encoding for signal processing applications (2004)

The IEEE defined a standard for floating-point arithmetic used by processing systems (ANSI/IEEE Std 754-1985). This directive encodes floating point numbers using a maximum of 64 bits: 23 bits of fractional in single precision format and 52 bits of fractional in double precision format. The new multimedia terminals require low-power applications; the most important floating-point units (adders and multipliers) represent a significant part of total power wasted by a modern system-on-chip. They might dissipate less power by using a reduced format representation. To verify this possibility, floating-point operations are simulated by real systems using different formats. We discuss multimedia systems operating in different scenarios, such as wireless communication and image manipulation.
Fast Purcell-enhanced single photon source in 1,550-nm telecom band from a resonant quantum dot-cavity coupling (2012)

High-bit-rate nanocavity-based single photon sources in the 1,550-nm telecom band are challenges facing the development of fibre-based long-haul quantum communication networks. Here we report a very fast single photon source in the 1,550-nm telecom band, which is achieved by a large Purcell enhancement that results from the coupling of a single InAs quantum dot and an InP photonic crystal nanocavity. At a resonance, the spontaneous emission rate was enhanced by a factor of 5 resulting a record fast emission lifetime of 0.2 ns at 1,550 nm. We also demonstrate that this emission exhibits an enhanced anti-bunching dip. This is the first realization of nanocavity-enhanced single photon emitters in the 1,550-nm telecom band. This coupled quantum dot cavity system in the telecom band thus provides a bright high-bit-rate non-classical single photon source that offers appealing novel opportunities for the development of a long-haul quantum telecommunication system via optical fibres.
LYMPHOSCINTIGRAPHY WITH IN-111 LABELED MONOCLONAL ANTIBODIES (1983)

Goodwin, David A.; Meares, Claude F.; McCall, Michael J.; McDevitt, Hugh O.; McTigue, Maureen; Diamanti, Carol I. Author Information
Linearity of Near-Infrared Spectra of Alkanes (2000)

Near-infrared (NIR) spectroscopy is used to monitor a large variety of process flow streams. Hydrocarbons with their strong and resolvable NIR spectral signatures are good candidate analytes. NIR has been exploited to monitor many chemical properties for optimal hydrocarbon utilization particularly for well-characterized flow streams of small variability for end users. The utility of NIR in the context of the production of hydrocarbon resources necessitates application over a much broader range of flow stream conditions. Here we examine the spectral impact of variable temperature, pressure, and composition to determine the robustness of NIR methods in upstream applications.
‘Protective premedication’: an option with gabapentin and related drugs? (2004)

Substantial progress has been made during the last decades in our understanding of acute pain mechanisms, and this knowledge has encouraged the search for novel treatments. Of particular interest has been the observation that tissue injury initiates a number of modulations of both the peripheral and the central pain pathways, which convert the system from a 'physiological' to a 'pathological' mode of processing afferent information. Gabapentin, which binds to the alpha(2)delta subunit of the voltage-dependent calcium channel, is active in animal models of 'pathological' but not in models of 'physiological' pain. Consequently, attention has so far been focused on neuropathic pain as a target for the clinical use of gabapentin and analogues. Recently, several reports have indicated that gabapentin may have a place in the treatment of post-operative pain. This article presents a brief summary of the potential mechanisms of post-operative pain, and a systematic review of the available data of gabapentin and pregabalin for post-operative analgesia. It is concluded that the results with gabapentin and pregabalin in post-operative pain treatment published so far are promising. It is suggested that future studies should explore the effects of 'protective premedication' with combinations of various antihyperanalgesic and analgesic drugs for post-operative analgesia.
New Carbanionic Access to 3-Vinylindoles and 3-Vinylbenzofurans (2002)

[reaction: see text] A simple route to 3-vinylbenzofurans, 3-vinylfuropyridines, and 3-vinylindoles from readily accessible acetylenic precursors is described. A standard halogen-lithium exchange triggers an irreversible addition on the triple bond, according to a 5-exo-dig heterocyclization process, followed by a lithium ethoxide elimination. A final isomerization of the exocyclic allene provides a 1,3-dienic system that can react with acrylates, in thermal or hyperbaric conditions, to provide the expected [4+2] cycloadducts.
Screening and shouting about HCV (2000)

See article on page 277 

In this month's Gut, Ward and colleagues1 report their study of the prevalence of hepatitis C virus (HCV) in women attending an inner London obstetric department (see page 277). The study was well designed and carefully executed. The methodology is valid and the findings are important. The authors make three key observations: that the prevalence of HCV in this population is high (0.8%); that uptake and acceptability of screening for HCV is good; and that many of the cases could not be identified by clinical criteria alone. Each of these findings is important in its own right. Together they reaffirm the importance of hepatitis C as a healthcare problem. They support the case for further investigation of screening strategies for HCV and suggest that antenatal screening should be considered carefully.

Accurate knowledge of the prevalence of a disease is particularly important when it is serious and treatable. In the 1970s the disease later recognised as hepatitis C was thought to be an inconsequential transaminitis that followed blood transfusion. Since the cloning of HCV in 1989, increasing knowledge of the natural history of hepatitis C has revealed a more serious outcome, at least for the minority of individuals who develop progressive fibrosis leading to cirrhosis, liver failure, and liver cancer.2 In the past year, effective treatment has been licensed3and even more effective therapies may follow. Now that more is known of the natural history of hepatitis C and the clinical and cost effectiveness of treatment, accurate knowledge of the true prevalence of HCV infection is very important for those plan- ning, funding, and delivering care to HCV infected individuals.

Early studies found …
Nanoparticles and the Environment (2005)

Nanoparticles are a class of materials with properties distinctively different from their bulk and molecular counterparts. A critical review of the very broad topic of environmental nanoparticles is presented. Because of the vast nature of the topic, the review is focused primarily on gas-borne nanoparticles. The "life history of nanoparticles" is presented, tracking it from its formation to its potential use and eventual fate in the environment. Nanoparticle sources, anthropogenic emissions from industrial and occupational settings, and conversion and formation in the atmosphere are discussed. The ability to characterize and capture these nanoparticles (as would be necessary in a nanoparticle production system), as well as their control (of emissions from an industrial source) is discussed. A description on the use of nanoparticles in environmental technologies and the potential impact on the energy sector is provided. The potential effects on human health and the environment, both adverse and beneficial, are important aspects that need to be considered. As will be evident, the study of "environmental nanoparticles" is a new and fast-growing field. Much work remains to be done before we can fully harness the advantages of nanoparticles and ensure that there are no potential adverse consequences. A set of recommendations for additional work in each area is provided.
Bidirectional control of phospholipase A2 activity by Ca2+/calmodulin-dependent protein kinase II, cAMP-dependent protein kinase, and casein kinase II. (1991)

In preparations of synaptic terminals (synaptosomes) isolated from rat brain, the activity of phospholipase A2 (PLA2), a phospholipid hydrolase that serves a central function in signal transduction, was inhibited in a Ca(2+)-dependent manner by incubation with 60 mM K+ or with the Ca(2+)-selective ionophore ionomycin. Reversal by alkaline phosphatase treatment suggested that this inhibitory effect resulted from phosphorylation of a synaptosomal protein substrate. When lysed synaptosomes were incubated with Ca2+/calmodulin (CaM), purified Ca2+/CAM-dependent protein kinase II (Ca2+/CaM-dependent PK II) and ATP, PLA2 activity in lysates was nearly abolished within 10 min. This effect was accompanied by a marked decrease in the Vmax of the enzyme and little or no change in the Km. Furthermore, Ca2+/CaM with ATP but without exogenous Ca2+/CaM-dependent PK II partially inhibited PLA2 activity, and this effect was prevented by treating the lysates with a selective peptide inhibitor of Ca2+/CaM-dependent PK II. In contrast, incubation of intact synaptosomes with 4 beta-phorbol 12-myristate 13-acetate or of lysed synaptosomes with purified protein kinase C had little or no effect on PLA2 activity. The results strongly suggest that the Ca(2+)-dependent inhibition of PLA2 activity observed in intact nerve endings was produced by activation of the multifunctional Ca2+/CaM-dependent PK II. A membrane-permeable adenylyl cyclase activator, forskolin, enhanced PLA2 activity in intact synaptosomes, and cAMP-dependent protein kinase potentiated PLA2 activity in lysed synaptosomes. Furthermore, another broad-spectrum protein kinase present in synaptic terminals, casein kinase II, also potentiated PLA2 activity in lysed synaptosomes. The effects of both protein kinases were associated with a decrease in Km and no change in Vmax. The results suggest that PLA2 activity in synaptic terminals is subject to bidirectional control by distinct signal transduction pathways. Moreover, mutually antagonistic effects of the Ca2+/CaM-dependent PK II and PLA2 pathways provide a possible molecular mechanism for bidirectional modulation of neurotransmitter release.
Enzymatic Ligation of Large Biomolecules to DNA (2013)

The ability to synthesize, characterize, and manipulate DNA forms the foundation of a range of advanced disciplines including genomics, molecular biology, and biomolecular engineering. In particular for the latter field, DNA has proven useful as a structural or functional component in nanoscale self-assembled structures, antisense therapeutics, microarray diagnostics, and biosensors. Such applications frequently require DNA to be modified and conjugated to other macromolecules, including proteins, polymers, or fatty acids, in order to equip the system with properties required for a particular application. However, conjugation of DNA to large molecular components using classical chemistries often suffers from suboptimal yields. Here, we report the use of terminal deoxynucleotidyl transferase (TdT) for direct enzymatic ligation of native DNA to nucleotide triphosphates coupled to proteins and other large macromolecules. We demonstrate facile synthesis routes for a range of NTP-activated macromolecules and subsequent ligation to the 3' hydroxyl group of oligodeoxynucleotides using TdT. The reaction is highly specific and proceeds rapidly and essentially to completion at micromolar concentrations. As a proof of principle, parallelly labeled oligonucleotides were used to produce nanopatterned DNA origami structures, demonstrating rapid and versatile incorporation of non-DNA components into DNA nanoarchitectures.