gebhart/patrepeval huggingface dataset:
Exploring the development of endotoxin tolerance and anti-endotoxin activity of LL-37 in mammalian cells (134.55) (2009)

Abstract The innate immune response is the first line of defense against microorganisms. However, its over-stimulation can result in excessive inflammation that can lead to deadly syndromes like sepsis. Initially, septic patients exhibit a high immune response, which later shifts towards an immunosuppressive state. This state may be related with a phenomenon called endotoxin tolerance, which is a reduced capacity to respond to antigens. Recent studies have demonstrated that cationic host defense peptides, such as LL-37, have broad immunomodulatory activities like diminishing inflammatory responses. Therefore, the purpose of these two phenomena may be to reduce the immune response and control excessive inflammation. Although much studied, mechanisms that lead to their development are not clear. In this work, time course analysis by RT-qPCR, western blot, and microarrays on human peripheral blood mononuclear cells and monocytic cell line, have shown similar patterns in the up- and down-regulation of important immune players like pro/anti-inflammatory mediators, and negative regulators during the development of endotoxin tolerance and anti-endotoxin activity of LL-37. Results from this work may not only help clarify how each of these phenomena occur, but also may find a link between them. This work has been supported by Genome British Columbia and Genome Prairie for the Pathogenomics of Innate Immunity Research Program, and by the Foundation for the National Institutes of Health and Canadian Institutes for Health Research through the Grand Challenges in Global Health Initiative.
Controlled Microfabrication of High‐Aspect‐Ratio Structures in Silicon at the Highest Etching Rates: The Role of H2O2 in the Anodic Dissolution of Silicon in Acidic Electrolytes (2016)

In this work the authors report on the controlled electrochemical etching of high‐aspect‐ratio (from 5 to 100) structures in silicon at the highest etching rates (from 3 to 10 µm min −1 ) at room temperature. This allows silicon microfabrication entering a previously unattainable region where etching of high‐aspect‐ratio structures (beyond 10) at high etching rate (over 3 µm min −1 ) was prohibited for both commercial and research technologies. Addition of an oxidant, namely H 2 O 2 , to a standard aqueous hydrofluoric (HF) acid electrolyte is used to dramatically change the stoichiometry of the silicon dissolution process under anodic biasing without loss of etching control accuracy at the higher depths (up to 200 µm). The authors show that the presence of H 2 O 2 reduces the valence of the dissolution process to 1, thus rendering the electrochemical etching more effective, and catalyzes the etching rate by opening a more efficient path for silicon dissolution with respect to the well‐known Gerischer mechanism, thus increasing the etching speed at both shorter and higher depths.
Dynamic visceral ischemia in type A dissection (2021)

A 59-year-old man was referred with Stanford type-A (DeBakey type-I) aortic dissection, abdominal pain, and reduced perfusion of the left leg. Lactate levels were elevated (7.5 mmol/L) and, on computed tomography (CT), the true aortic lumen at the visceral segment appeared compromised (Figure 1). A sternotomy was performed and extended as a laparotomy to a point mid-way between the xyphoid process and the umbilicus. The bowel appeared viable, with poor peristalsis; the hepatic artery and the superior mesenteric artery (SMA) demonstrated weak/intermittent pulsation. Both were interrogated with Doppler (MiraQ™, Medistim): flow velocity appeared variable, with a distinctive periodic cycle lasting five pulsations (Figure 2). The patient underwent hemiarch repair. On completion, the bowel was still viable with good peristalsis and strong pulsation in the visceral arteries. Postoperatively, femoral pulses were palpable; lactate levels normalized. The patient tested positive for COVID-19 but recovered uneventfully, aside for a peri-pancreatic collection detected on CT, which required no intervention. This case sheds light on the physiopathology of ischemia due to functional occlusion of aortic branches in acute dissection. It is widely known that pressure in the false lumen can obliterate aortic branches either by flattening the septum against their origins or by extending the dissection along their course. Intuitively, one may assume that dynamic occlusion occurs periodically during a single cardiac cycle. Our findings, however, demonstrated a more complex pattern, with a period of five cycles, during which peak velocity varied fourfold. The case also highlights the pitfalls of investigating (dynamic) acute dissection with static imaging modalities. Due to its high resolution and image acquisition speed, CT is considered the gold-standard,1 although it can only visualize contrast in the aortic lumen(s) at a specific point in time. Magnetic resonance imaging/angiography does not have this limitation and is emerging as an alternative technique for dynamic aortic imaging in acute aortic syndromes.2 In our case, extemporaneous use of Doppler equipment normally used to interrogate coronary grafts provided dynamic information. Finally, the case confirms that obliteration of the false lumen at the entry tear usually results in resolution of dynamic ischemia. In this patient, the high lactate and his symptoms/signs led us to inspect the bowel due to a high suspicion of impending intestinal gangrene. We were prepared to directly perfuse the SMA and/or the celiac axis on-pump during the hemiarch repair. Fortunately, the findings at laparotomy were reassuring and the patient was able to undergo a proximal repair without major complications. Informed consent and ethical approval were waived for this report, which contains no patient identifiable data. The authors declare that there are no conflict of interests.
A New Regime of Nanoscale Thermal Transport: Collective Diffusion Counteracts Dissipation Inefficiency (2014)

We uncover a new regime of nanoscale thermal transport that dominates when the separation between heat sources is small compared with the substrate’s dominant phonon mean free paths. Surprisingly, the interplay between neighboring heat sources can facilitate efficient, diffusive-like heat dissipation.
Biomonitoring of Arsenic in Urine and Saliva of Children Playing on Playgrounds Constructed from Chromated Copper Arsenate-Treated Wood (2010)

Children may be exposed to arsenic during contact with structures treated with chromated copper arsenate (CCA). A high frequency of hand-to-mouth activity may increase their risk of ingesting arsenic. Previous work showed that arsenic concentrations in the hand-wash samples of children playing on CCA playgrounds were four times higher than those playing on non-CCA playgrounds. It is not clear whether playing on CCA playgrounds results in elevated overall exposure to arsenic. The objective of this study was to perform arsenic biomonitoring in children to determine whether playing on CCA-treated playgrounds substantially contributes to their overall exposure to arsenic. One hundred and twenty five saliva samples from 61 children and 101 urine samples from 45 children were collected after children played on 8 CCA and 8 non-CCA playgrounds. Arsenic speciation analysis was conducted using high performance liquid chromatography combined with inductively coupled plasma mass spectrometry. The arsenic species detected in the urine and saliva samples from children playing on CCA and non-CCA playgrounds were similar. Dimethylarsinic acid and arsenobetaine were the main arsenic species found in urine samples. The sum of inorganic trivalent and pentavalent arsenic, monomethylarsonic acid, and dimethylarsinic acid in urine was 15 +/- 28 microg/L in the CCA group and 12 +/- 23 microg/L in the non-CCA group (p = 0.60). The sum of these species in saliva was 1.1 +/- 2.1 microg/L in the CCA group and 1.4 +/- 1.1 microg/L in the non-CCA group (p = 0.32). These results show that there is no significant difference in the concentration or speciation of arsenic between the samples from children playing on CCA and non-CCA playgrounds. Contact with CCA playgrounds is not likely to significantly contribute to the overall arsenic exposure in children; other sources such as dietary arsenic may be a main contributor to their overall exposure.
Growth-inhibitory Effect of Diphenylhydantoin on Murine Astrocytomas (1979)

In previous work reported from this laboratory we found that diphenylhydantoin (DPH) inhibited the growth of 7 of 10 tissue-cultured human astrocytoma cell lines in a microtiter system. In this report we describe significant growth inhibition by DPH of two murine astrocytoma tissue cultures and correlate these in vitro findings with the in vivo activity of DPH in rat subcutaneous and intracranial tumor models. In the in vivo studies, rats were inoculated either subcutaneously or intracranially with RT9 or C6 rat gliomas. DPH or placebo was injected intraperitoneally in doses ranging from 50 to 150 mg/kg daily for 15 days. The DPH-treated rats showed significantly slower rates of tumor growth than untreated rats (p less than 0.01) in both the subcutaneous and intracranial models. At sacrifice, the tumor volume of the rats with subcutaneous tumors treated with DPH (100 mg/kg daily) was 62% less than the tumor volume of the control rats. Also, the number of "clonogenic" cells and thus, indirectly, the number of actively dividing tumor cells was 54% less in the intracranial tumors of the DPH-treated rats. These findings indicate that DPH may be a potentially useful adjunctive agent in the clinical chemotherapy of astrocytic tumors. Furthermore, the data presented indicate that in vitro test results are predictive for in vivo effects, supporting the idea that tissue culture can be used to screen for the effectiveness of clinically used chemotherapeutic agents.
Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka, Russia (2012)

Desulfurococcus fermentans is the first known cellulolytic archaeon. This hyperthermophilic and strictly anaerobic crenarchaeon produces hydrogen from fermentation of various carbohydrates and peptides without inhibition by accumulating hydrogen. The complete genome sequence reported here suggested that D. fermentans employs membrane-bound hydrogenases and novel glycohydrolases for hydrogen production from cellulose.
Clonal Origin of Bladder Cancer (1992)

A number of bladder tumors can arise from the uncontrolled spread of a single transformed cell. These tumors can then grow independently with variable subsequent genetic alterations.
Shallow Training is cheap but is it good enough? Experiments with Medical Fact Coding (2015)

A typical NLP system for medical fact coding uses multiple layers of supervision involving factattributes, relations and coding. Training such a system involves expensive and laborious annotation process involving all layers of the pipeline.
Direct-Drive Wind Generator Concept with Non-Rare-Earth PM Flux Intensifying Stator and Reluctance Outer Rotor (2022)

This paper proposes a novel concept for an electric generator in which both ac windings and permanent magnets (PMs) are placed in the stator. Concentrated windings with a special pattern and phase coils placed in separate slots are employed. The PMs are positioned in a spoke-type field concentrating arrangement, which provides high flux intensification and enables the use of lower remanence and energy non-rare earth magnets. The rotor is exterior to the stator and has a simple and robust reluctance-type configuration without any active electromagnetic excitation components. The principle of operation is introduced based on the concept of virtual work with closed-form analytical airgap flux density distributions. Initial and parametric design studies were performed using electromagnetic FEA for a 3MW direct-drive wind turbine generator employing PMs of different magnetic remanence and specific energy. Results include indices for the goodness of excitation and the goodness of the electric machine designs; loss; and efficiency estimations, indicating that performance comparable to PM synchronous designs employing expensive and critical supply rare-earth PMs may be achieved with non-rare earth PMs using the proposed configuration.
Tantalum Pentoxide waveguide chip developed directly on thin transparent substrate for fluorescence microscopy of biological cells (2019)

Super-resolution optical microscopy (commonly referred to optical nanoscopy) offers unprecedented opportunities, the rapid adoption of it is presently hindered mainly due to low throughput, complex set-up, high cost, and the need for specialized operators. Recently, photonic chip-based optical nanoscopy was realized that circumvents reduce the cost and complexity of present day nanoscopy. In this research work, we have unleash the true impact chip-based nanoscopy by realizing photonic chip made of high refractive index material (Ta&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;5&lt;/sub&gt;) on top of thin and transparent substrate for highresolution, large f-o-v, aberration-free bioimaging of thick cells. Waveguide chips on 180μm thin transparent Silica substrate enable the imaging of biological sample using an inverted optical microscope which was not possible on opaque silicon (Si) substrate.
Humeral resurfacing arthroplasty: rationale, indications, technique, and results. (2007)

Humeral head resurfacing arthroplasty has evolved into a reliable method of shoulder arthroplasty designed to restore the natural anatomy of an arthritic or damaged articular humeral surface. Recent implant changes have improved the ability of the surface replacement implants to recreate the humeral head surface and the initial implant fixation. Instrument changes have improved the ability to place the implant in the anatomical position that recreates an individual's humeral articular surface posterior offset, neck-shaft angle, and version. These implant and instrument changes have led to a more refined surgical technique that avoids the complications associated with use of stemmed implants. Minimal bone resection occurs in shoulder resurfacing arthroplasty--the result being bone stock preservation, which is important in active or young patients with shoulder arthritis. Cementless surface replacements have been shown to provide results comparable to those of stemmed implants similar in diagnosis and follow-up. In this article, I outline the current rationale for resurfacing arthroplasty implants and the indications for their use. I also present the surgical technique and review the results of proximal humeral resurfacing arthroplasty.
Studies on the active site of succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase. Characterization using analogs of tetrahydrodipicolinate. (1986)

Cyclic and acyclic analogs of tetrahydrodipicolinate (THDPA) are evaluated in a study of the active site of succinyl-CoA:tetrahydrodipicolinate N-succinyltransferase. In addition to the natural substrate, THDPA, one cyclic and several acyclic compounds are also succinylated. 2-Hydroxytetrahydropyran-2,6-dicarboxylic acid is a potent competitive inhibitor having a Kis of 58 nM. Based on the results of this study, a stereochemical model for the succinylation of THDPA is proposed. The major features of this model are as follows. 1) The succinylase binds THDPA (L-configuration). 2) Hydration of the imine group follows to give 2-hydroxypiperidine-2,6-dicarboxylic acid in which the two carboxyl groups are trans. 3) Succinylation then occurs and the ring opens to give the acyclic product. It is suggested that 2-hydroxytetrahydropyran-2,6-dicarboxylic acid is a transition state analog by virtue of the fact that it structurally resembles the hydrated intermediate.
Electron vortices in semiconductors devices (2005)

The hydrodynamic model of electron transport in semiconductors is analyzed and, in analogy with vortices in fluid mechanics, the curl of electron velocity is defined as electron vorticity, and the transport equation for the electron vorticity is derived. Aside from the classical hydrodynamic sources of vorticity, collision terms in the continuity and momentum equations are identified as sources and sinks of electron vorticity. Similar to three-dimensional fluid flows there is a vortex stretching term in the vorticity equation. This term could be responsible for the possible cascade of electron kinetic energy to small scales and formation of chaotic turbulent electron transport regimes. A scale analysis of the electron vorticity equation is performed and the relative order of magnitude of each sources of vorticity is found. This analysis and the calculation of electron mean-free-path due to electron–electron and electron–phonon scatterings characterize a transport regime with significant electron vorticity effects. Furthermore, conditions for observation of electron vortices in semiconductor devices are predicted.
Successive Convex Approximation for Phase Retrieval with Dictionary Learning (2021)

Phase retrieval aims at reconstructing unknown signals from magnitude measurements of linear mixtures. In this paper, we consider the phase retrieval with dictionary learning problem, which includes an additional prior information that the measured signal admits a sparse representation over an unknown dictionary. The task is to jointly estimate the dictionary and the sparse representation from magnitude-only measurements. To this end, we study two complementary formulations and propose efficient parallel algorithms based on the successive convex approximation framework. The first algorithm is termed compact-SCAphase and is preferable in the case of less diverse mixture models. It employs a compact formulation that avoids the use of auxiliary variables. The proposed algorithm is highly scalable and has reduced parameter tuning cost. The second algorithm, referred to as SCAphase, uses auxiliary variables and is favorable in the case of highly diverse mixture models. It also renders simple incorporation of additional side constraints. The performance of both methods is evaluated when applied to blind sparse channel estimation from subband magnitude measurements in a multi-antenna random access network. Simulation results demonstrate the efficiency of the proposed techniques compared to state-of-the-art methods.
Analysis of Epidemic Model for Performance Evaluation of Rechargeable Wireless Sensor Network (2021)

Wireless sensor network (WSN) is a decentralized network system which consists of sensor nodes, and these nodes are connected through wireless link. Due to decentralized network system and resource constraint WSN faces security threat. Malware (malicious signals, worm, Trajan horse, virus etc.) attacks on the sensor node of WSN and make them paralyze and steal information from the network. Malware attack also increases the energy consumption of Sensor nodes of WSN. It just begins to spread from an infected node, and spread across the entire WSN with the help of neighboring nodes. Therefore, security of WSN against attack of malware is an inescapable need. On the basis of earlier works and consideration of charging mechanism of sensor nodes, and considering the effect of coverage and connectivity, proposed a SILRD (Susceptible - Infectious – Low Energy – Recovered –Dead) model with vital dynamics. The propose model investigates the dynamics of malware propagation in WSN and also explain sensor node’s energy consumption. The system’s stability has analyzed in terms of local and global of malware-free and endemic equilibrium. For the investigation of system dynamics, the expression of basic reproduction number has computed, which is also utilized to analyze state of malware in WSN. The effect of charging, coverage and connectivity is explained in this paper.
Role of Cations in RNA Folding and Function (2018)

Inorganic cations and their hydrates are essential for life on Earth. Water molecules are oriented and polarized by cations, forming acidic metal hydrates with increased potential for participation in hydrogen bonding function in enzymatic activity and proton donation. Cations associate with RNA through a continuum of interactions, from neutralization of net charge to first-shell coordination of backbone phosphates. Cation coordination by RNA alters geometry of the hydrated cation and the structure of the RNA. The earliest available data suggests that the ribosome large subunit of the Last Universal Common Ancestor originated and has continued to evolve, with dependence on Mg2+ for folding of long, complex ribosomal RNA (rRNA), giving indirect support to catalysis of peptide bond formation. The phosphodiester backbone of rRNA is a frequent, though not exclusive, site of Mg2+ interaction. Two specific geometries of Mg2+-phosphodiester complexes support local and long-range interactions, including an intricate intra- and inter-domain network of interactions. Other natural ribozymes, in contrast, tolerate folding and function with a broader range of cations, perhaps from evolutionary necessity.
Apolipoprotein &#x0395; ε4 Frequency Is Increased among Chinese Patients with Frontotemporal Dementia and Alzheimer's Disease (2013)

The relationship between the apolipoprotein E (ApoE) ε4 genotype and an increased risk of developing Alzheimer's disease (AD) has been well established in Caucasians but is less established among other ethnicities. ApoE ε4 has also been associated with several other neurological disorders. Whether ApoΕ4 ε4 is a risk factor for frontotemporal dementia (FTD) remains controversial. This study examined 432 patients with AD, 62 with FTD, and 381 sex- and age-matched controls. The ApoE ε4 allele frequency was significantly increased among patients in the AD and FTD groups compared with controls. The frequency of the ApoΕ ε4 allele was 24.86% in late-onset AD (p < 0.01), 18.02% in early-onset AD (p < 0.01), 16.13% in FTD (p < 0.01), and 7.34% in controls. ApoΕ ε4 prevalence was similar in the FTD and AD groups. The present study suggests that the ApoE ε4 allele is a risk factor for both disorders.
Comparison of different PMD compensator configurations based on outage probability (2002)

As the bit rate of fiberoptic transmission systems increases to 10 Gbit/s, 40 Gbit/s, and beyond, polarization mode dispersion (PMD) inherent in the optical fiber and present in the optical components of the system becomes a limiting factor to error-free transmission. Numerous optical and electronic techniques have been proposed to mitigate the effects of PMD, and several of these solutions are now becoming commercially available. There is, of course, a trade-off between the complexity (and therefore the cost) of a PMD compensator and the performance of the device. In this study, we compare the performance of three relatively simple PMD compensator configurations.
Extremely high-brightness kW-class fiber coupled diode lasers with wavelength stabilization (2011)

TeraDiode has produced ultra-high brightness fiber-coupled direct diode lasers. A fiber-coupled direct diode laser with a power level of 1,040 W from a 200 &mu;m core diameter, 0.18 numerical aperture (NA) output fiber at a single center wavelength was demonstrated. This was achieved with a novel beam combining and shaping technique using COTS diode lasers. The fiber-coupled output corresponds to a Beam Parameter Product (BPP) of 18 mm-mrad and is the lowest BPP kW-class direct diode laser yet reported. The laser has been used to demonstrate laser cutting and welding of steel sheet metal up to 6.65 mm thick. Higher brightness fiber-coupled diode lasers, including a module with 418 W of power coupled to a 100 &mu;m, 0.15 NA fiber, have also been demonstrated.