gebhart/patrepeval huggingface dataset:
Apoptosis induced by exposure to a low steady-state concentration of H2O2 is a consequence of lysosomal rupture (2001)

We have re-examined the lysosomal hypothesis of oxidative-stress-induced apoptosis using a new technique for exposing cells in culture to a low steady-state concentration of H2O2. This steady-state technique mimics the situation in vivo better than the bolus-administration method. A key aspect of H2O2-induced apoptosis is that the apoptosis is evident only after several hours, although cells may become committed within a few minutes of exposure to this particular reactive oxygen species. In the present work, we were able to show, for the first time, several correlative links between the triggering effect of H2O2 and the later onset of apoptosis: (i) a short (15min) exposure to H2O2 caused almost immediate, albeit limited, lysosomal rupture; (ii) early lysosomal damage, and later apoptosis, showed a similar dose-related response to H2O2; (iii) both events were inhibited by pre-treatment with iron chelators, including desferrioxamine. This compound is known to be taken up by endocytosis only and thus to become localized in the lysosomal compartment. After exposure to oxidative stress, when cells were again in standard culture conditions, a time-dependent continuous increase in lysosomal rupture was observed, resulting in a considerably lowered number of intact lysosomes in apoptotic cells, whereas non-apoptotic cells from the same batch of oxidative-stress-exposed cells showed mainly intact lysosomes. Taken together, our results reinforce earlier findings and strongly suggest that lysosomal rupture is an early upstream initiating event, and a consequence of intralysosomal iron-catalysed oxidative processes, when apoptosis is induced by oxidative stress.
Cost (2015)

Abstract The meaning, measurement, and management of cost have long been primary concerns of operations management ( OM ) practitioners and academics.
Residual C-peptide in type 1 diabetes: what do we really know? (2014)

Connecting peptide, or C-peptide, is a protein that joins insulin's α and B chains in the proinsulin molecule. During insulin synthesis, C-peptide is cleaved from proinsulin and secreted in an equimolar concentration to insulin from the β cells. Because C-peptide experiences little first-pass clearance by the liver, and because levels are not affected by exogenous insulin administration, it may be used as a marker of endogenous insulin production and a reflection of β-cell function. Residual β-cell function, as measured by C-peptide in those with type 1 diabetes (T1D), has repeatedly been demonstrated to be clinically important. The Eisenbarth model of type 1 diabetes postulated immune-mediated linear loss of β cells, with clinical diagnosis occurring when there was insufficient insulin secretion to meet glycemic demand. Moreover, the model also implied that all individuals with T1D rapidly and inevitably progressed to absolute insulin deficiency. Correspondingly, it was assumed that most people with longstanding T1D would show little to no residual C-peptide secretion. While more than a quarter century of data confirms that this model remains largely true and appropriately serves as the basis for prevention studies, accumulating evidence suggests that the natural history of β-cell function before, during and after diagnosis is more complex. In this review, we discuss the clinical benefits of residual insulin secretion and present recent data about the natural history of insulin secretion in those with, or at risk for T1D.
Product reservoir computing: Time-series computation with multiplicative neurons (2015)

Echo state networks (ESN), a type of reservoir computing (RC) architecture, are efficient and accurate artificial neural systems for time series processing and learning. An ESN consists of a core of recurrent neural networks, called a reservoir, with a small number of tunable parameters to generate a high-dimensional representation of an input, and a readout layer which is easily trained using regression to produce a desired output from the reservoir states. Certain computational tasks involve real-time calculation of high-order time correlations, which requires nonlinear transformation either in the reservoir or the readout layer. Traditional ESN employs a reservoir with sigmoid or tanh function neurons. In contrast, some types of biological neurons obey response curves that can be described as a product unit rather than a sum and threshold. Inspired by this class of neurons, we introduce a RC architecture with a reservoir of product nodes for time series computation. We find that the product RC shows many properties of standard ESN such as short-term memory and nonlinear capacity. On standard benchmarks for chaotic prediction tasks, the product RC maintains the performance of a standard nonlinear ESN while being more amenable to mathematical analysis. Our study provides evidence that such networks are powerful in highly nonlinear tasks owing to high-order statistics generated by the recurrent product node reservoir.
Handover based on AP load in software defined Wi-Fi systems (2017)

Existing wireless systems do not work efficiently under changing environment. Due to its inflexible and proprietary hardware based architectural limitations it's not easy for an operator to change the network strategy under heavy loads, which enables vendors to try and implement new networking protocols. The software defined network (SDN) is proposed to bring flexibility and programmability, which allows the control plane of switch to be controlled and managed remotely using open-flow channels. Taking the advantage of SDN in wireless networks, a new SDN based Wi-Fi architecture is introduced and an access point (AP) load balance based handover algorithm is proposed. Mininet Wi-Fi emulator is used to construct the desired topology for experiments and performance analysis. Simulation results show a successful handover from an overloaded AP to a lightly loaded AP. A significant improvement observed in the throughput with low latency.
Slowing Na+ Channel Inactivation Prolongs QT Interval and Aggravates Adrenaline-Induced Arrhythmias (2001)

We investigated the effects of prolonged repolarization induced by slowed inactivation of Na+ channel on adrenaline-induced arrhythmias in halothane anesthetized, closed-chest dogs. We used sea anemone toxins (ATX-II and Anthopleurin-A) to prolong ventricular repolarization and examined their effects on adrenaline arrhythmias. Sea anemone toxins prolonged the QTc- and JTc-intervals (P<0.01), but did not affect the PQ interval, QRS duration, heart rate and mean blood pressure. Although sea anemone toxins did not induce any arrhythmias by themselves, under the treatment with these toxins, arrhythmias were induced by non-arrhythmia-inducing doses of adrenaline in four dogs out of seven and the control arrhythmias induced by adrenaline were aggravated. These results indicate that, similar to the inhibition of K+ channels by class III drugs, which we have already reported, slowing Na+ channel inactivation with QTc prolongation also aggravates adrenaline-induced arrhythmias.
Preparation and Characterization of Liposomes Incorporating Hydrophobic Poly(amino acid)s with Different Secondary Structure. (1994)

Incorporation of hydrophobic poly(amino acid) into liposomal membranes was achieved by the polymerization of N-carboxy anhydrides of amino acids in the egg yolk phosphatidylcholine (EyPC) bilayer under reduced pressure at 30 degrees C. The trapped volumes for the liposomes with and without polypeptides were 8.1-10.3 l mol-1 and 11.4 l mol-1, respectively. The permeability barrier abilities of liposomal membranes were lowered by the incorporation of polypeptides into the membrane bilayers. Water permeation across the membrane bilayer was more effective for the liposome with the alpha-helical polypeptide than for that with the beta-sheeted one.
Abstract 4368: High-throughput phenotyping of lung cancer somatic mutations (2016)

Abstract Recent cancer genome sequencing and analysis has identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood, limiting the use of this genetic knowledge for clinical decision-making. Here we describe a new high-throughput approach, expression-based variant impact phenotyping (eVIP), which uses gene expression changes to infer somatic mutation impact. We generated a lentiviral expression library representing 53 genes and 194 somatic mutations identified in primary lung adenocarcinomas. Next, we introduced this library into A549 lung adenocarcinoma cells and 96 hours later performed gene expression profiling using Luminex-based L1000 profiling. We built a computational pipeline, eVIP, to compare mutant and wild-type expression signatures to infer whether variants were gain-of-function, change-of-function, loss-of-function, or neutral. Overall, eVIP identified 69% of mutations as impactful whereas 31% appeared functionally neutral. A very high rate, 92%, of missense mutations in the KEAP1 and STK11 tumor suppressor genes were found to inactivate or diminish protein function. As a complementary approach, we assessed which mutations are epistatic to EGFR or capable of initiating xenograft tumor formation in vivo. A subset of the impactful mutations identified by eVIP could induce xenograft tumor formation in mice and/or confer resistance to cellular EGFR inhibition. Among these mutations were 20 rare or non-canonical somatic variants in clinically-actionable or -relevant oncogenes including EGFR S645C, ARAF S214C and S214F, ERBB2 S418T, and PIK3CA E600K. eVIP can, in principle, characterize any genetic variant, independent of prior knowledge of gene function. Further application of eVIP should significantly advance the pace of functional characterization of mutations identified from genome sequencing. Citation Format: Alice H. Berger, Angela N. Brooks, Xiaoyun Wu, Yashaswi Shrestha, Candace Chouinard, Federica Piccioni, Mukta Bagul, Atanas Kamburov, Marcin Imielinski, Larson Hogstrom, Cong Zhu, Xiaoping Yang, Sasha Pantel, Ryo Sakai, Nathan Kaplan, David Root, Rajiv Narayan, Ted Natoli, David Lahr, Itay Tirosh, Pablo Tamayo, Gad Getz, Bang Wong, John Doench, Aravind Subramanian, Todd R. Golub, Matthew Meyerson, Jesse S. Boehm. High-throughput phenotyping of lung cancer somatic mutations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4368.
Use of the bispectrum to analyse properties of the human electrocardiograph. (1998)

The bispectrum and bicoherence spectrum have been shown to be powerful techniques for identifying different types of nonlinear system responses. This paper presents an introduction to bispectral techniques applied to biomedical signals and examines the bispectral properties of the human electrocardiograph (ECG). The bispectrum proves to be an effective tool for representing and distinguishing different ECG response types. Bispectral ECG analysis is non-invasive and may prove to be a useful discriminant diagnostic.
Immunology of Giardia and Cryptosporidium Infections Martin (1992)

Giardiasis and cryptosporidiosis occur in immunocompetent persons, and as opportunistic infections in immunocompromised individuals. The causative organisms of giardiasis (Giardia lamblia) and cryptosporidiosis (Cryptosporidium parvum) have markedly different life cycles, but currently available evidence suggests that intestinal antibody plays a major part in host protection against both parasites. In the case of G. lamblia, the evidence points to a role for intestinal antitrophozoite antibody in blocking adherence of trophozoites to intestinal epithelium, with consequent removal of trophozoites from the intestine by peristalsis. Similarly, recent work supports the view that C. parvum infection can be prevented or interrupted by antibody that binds to Cryptosporidium life cycle stages present in the intestinal lumen (sporozoites and merozoites). Molecular characterization of G. lamblia and C. parvum immunodominant antigens would facilitate future studies aimed at determining whether vaccination against giardiasis or cryptosporidiosis is feasible.
Numerical simulation of hot-carrier transport in silicon bipolar transistors (1983)

Conventional numerical simulations of bipolar transistors assume that the carrier transport processes in the device can be described by the semiconductor equations with electric-field dependent mobility and the Einstein relation between the mobility and diffusion coefficient. These assumptions are not generally valid for the large electric fields, current densities, and concentration gradients present in advanced bipolar transistors. In this work, we present a new numerical bipolar device simulation which provides a better description of the carrier transport processes in these devices. Specifically, the carrier mobilities and diffusion coefficients are treated as functions of the average carrier energy and the thermoelectric current resulting from spatial variations in the carrier energies is included. The required carrier energies are calculated using energy balance equations. The results of this simulation are compared with those calculated using a conventional bipolar-device simulation, and the differences are discussed.
Identifying compromised systems through correlation of suspicious traffic from malware behavioral analysis (2016)

Malware detection may be accomplished through the analysis of their infection behavior. To do so, dynamic analysis systems run malware samples and extract their operating system activities and network traffic. This traffic may represent malware accessing external systems, either to steal sensitive data from victims or to fetch other malicious artifacts (configuration files, additional modules, commands). In this work, we propose the use of visualization as a tool to identify compromised systems based on correlating malware communications in the form of graphs and finding isomorphisms between them. We produced graphs from over 6 thousand distinct network traffic files captured during malware execution and analyzed the existing relationships among malware samples and IP addresses.
Molecular Imprinting Utilizing an Amide Functional Group for Hydrogen Bonding Leading to Highly Efficient Polymers (1997)

In this paper we report the synthesis of molecularly imprinted polymers (MIPs) using an amide as the hydrogen-bonding functional group. All the amide MIPs made in this investigation exhibited good enantiomeric recognition of the imprinted species when evaluated by high-performance liquid chromatography (HPLC). Most of the amide MIPs were synthesized in a polar organic solvent (acetonitrile). By contrast, when a carboxyl group was used as the hydrogen-bonding functional group, MIPs made in acetonitrile exhibited only very weak recognition and in some cases no recognition at all with the print molecules tested. The amide MIPs also showed much improved load capacity. This suggests that for a number of cases the protocol described could be employed to reduce background, nonspecific binding compared to polymers using carboxyl groups, by avoiding an excess of negatively charged functionalities. It was shown that the tailing and peak asymmetry problems often associated with the use of MIPs in HPLC could be overcome by using linear gradient elution. The specificities of amide MIPs in terms of size, shape, and hydrogen-bonding selectivity were also investigated in detail. Finally, amide MIPs also showed good enantiomeric recognition in aqueous media.
Englerin A Selectively Induces Necrosis in Human Renal Cancer Cells (2012)

The number of renal cancers has increased over the last ten years and patient survival in advanced stages remains very poor. Therefore, new therapeutic approaches for renal cancer are essential. Englerin A is a natural product with a very potent and selective cytotoxicity against renal cancer cells. This makes it a promising drug candidate that may improve current treatment standards for patients with renal cancers in all stages. However, little is known about englerin A's mode of action in targeting specifically renal cancer cells. Our study is the first to investigate the biological mechanism of englerin A action in detail. We report that englerin A is specific for renal tumor cells and does not affect normal kidney cells. We find that englerin A treatment induces necrotic cell death in renal cancer cells but not in normal kidney cells. We further show that autophagic and pyroptotic proteins are unaffected by the compound and that necrotic signaling in these cells coincided with production of reactive oxygen species and calcium influx into the cytoplasm. As the first study to analyze the biological effects of englerin A, our work provides an important basis for the evaluation and validation of the compound's use as an anti-tumor drug. It also provides a context in which to identify the specific target or targets of englerin A in renal cancer cells.
A Content Analysis of Living Organ Donation Materials from Certified Transplant Centers (2020)

Despite the fact that living organ donation has the great potential to reduce the shortage of transplantable organs, it is still surrounded by many misconceptions, ethical concerns, and myths. Research conducted to understand factors contributing to public misconceptions related to living organ donation is rare. This research takes a content analytic approach to uncover how living organ donation is portrayed in materials developed and delivered by transplant centers across 11 regions. A total of 332 unique materials were analyzed. The results revealed that living kidney donation dominated the corpus of data whereas other living organ donations were largely overlooked. Benefits and risks associated with living organ donation were relatively evenly presented; however, social support necessary to donors and recipients and available resources to obtain social support were not sufficiently addressed. Embedded in these materials were 46 personal narrative stories. Analysis of these stories showed a focus on undirected living organ donation and revealed a wide range of emotional experiences. Significant regional differences were found in several themes, such as benefits and risks, and social support. Inconsistent information regarding living organ donation was present. Practical implications are discussed.
Ferroelectric switch for spin injection (2005)

A method for the switching of the spin polarization of the electric current injected into a semiconductor is proposed, based on injecting spins from a diluted magnetic semiconductor through a ferroelectric tunnel barrier. We show that the reversal of the electric polarization of the ferroelectric results in a sizable change in the spin polarization of the injected current, thereby providing a two-state electrical control of this spintronic device. We also predict a possibility of switching of tunneling magnetoresistance in magnetic tunnel junctions with a ferroelectric barrier and coexistence of tunneling magnetoresistance and giant electroresistance effects in these multiferroic tunnel junctions.
Genetics of Chemotaxis and Thermotaxis in the Nematode <i>Caenorhabditis Elegans</i> (1999)

Molecular genetic analysis of chemotaxis and theramotaxis in Caenorhabditis elegans has revealed the molecular bases of olfaction, taste, and thermosensation, which, in turn, has demonstrated that sensory signaling in C. elegans is very similar to that in vertebrates. A cyclic nucleotide-gated channel (TAX-2/TAX-4) that is highly homologous to the olfactory and photoreceptor channels in vertebrates is required for taste and thermosensation, in addition to olfaction. A cation channel (OSM-9) that is closely related to a capsaicin receptor channel is required for olfactory adaptation in one olfactory neuron and olfactory sensation in the other olfactory neuron. A novel G alpha protein (ODR-3) is essential for olfactory responses in all olfactory neurons and aversive responses in a polymodal sensory neuron. A G protein-coupled seven-transmembrane receptor (ODR-10) is the first olfactory receptor whose ligand was elucidated. Using chemotaxis and thermotaxis as behavioral paradigms, neural plasticity including learning and memory can be studied genetically in C. elegans.
Gut Feelings (2023)

Abstract This article reads Sheena Patel's 2022 I'm a Fan as a major intervention into literary representations of women online, particularly within the context of Patel's materialist rendering of the operations of race, gender, and class in platform economies. Patel writes against a tendency toward what this article terms an emergent “flatness” in representations of women online, manifested aesthetically, ideologically, and affectively. Patel's debut offers an alternatively “de-flattened” account of life on the internet, partly through a focus on the hungry body of its narrator: an insistence that the internet is for women in particular “not a still, flat, surface thing” is explored via its effects on the feeling body. This article considers how I'm a Fan employs questions of algorithmic desire, taste and aesthetics, and the concept of autofiction as a “masticated life,” rematerializing, and therefore repoliticizing, gendered encounters with the platform.
In situ annealing enhancement of the optical properties and laser device performance of InAs quantum dots grown on Si substrates (2016)

The addition of elevated temperature steps (annealing) during the growth of InAs/GaAs quantum dot (QD) structures on Si substrates results in significant improvements in their structural and optical properties and laser device performance. This is shown to result from an increased efficacy of the dislocation filter layers (DFLs); reducing the density of dislocations that arise at the Si/III-V interface which reach the active region. The addition of two annealing steps gives a greater than three reduction in the room temperature threshold current of a 1.3 μm emitting QD laser on Si. The active region of structures grown on Si have a room temperature residual tensile strain of 0.17%, consistent with cool down from the growth temperature and the different Si and GaAs thermal expansion coefficients. This strain limits the amount of III-V material that can be grown before relaxation occurs.
Network architecture and SONET services in the NASA-ARPA Gigabit Satellite Network using NASA's Advanced Communications Technology Satellite (ACTS) (1994)

Abstract : The Gigabit Satellite Network, a project jointly sponsored by ARPA and NASA, will provide long-haul STS-3 (155.54 Mb/s) and STS-12 (622.08 Mb/s) point-to-point and point-to-multipoint full-duplex services over NASA's Advanced Communications Technology Satellite (ACTS). Data multiplexing over the satellite will be accomplished using TDMA techniques coordinated with the switching and beam hopping facilities provided on-board the ACTS. Transmissions to the satellite will be protected using Reed-Solomon encoding, providing almost error-free clear-sky transmissions and, in the case of rain-fade, bit error rates better than 10(exp -11) 99.0% of the time. Unique to the system architecture are a TDMA frame structure an satellite synchronization mechanisms that, together, will allow (1) very efficient utilization of the satellite capacity, (2) over-the-satellite closed-loop synchronization of network configurations with up to 64 earth stations, and (3) earth station initial acquisition without collisions with existing signaling or data traffic. The end-user interfaces will use fiber-optics and will be compatible with SONET standards for fiber-based terrestrial networks. The terrestrial interfaces at the earth stations will perform the function of conventional SONET multiplexers and, as such, can be readily integrated with standard SONET fiber or radio-based terrestrial networks. As SONET multiplexers in the SONET hierarchy, the earth stations will synchronize the geographically-separated end-user interfaces.