julilili42/papers huggingface dataset:
Stimulation of Eryptosis by Afatinib
2018-01-01

Background/Aims: The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor afatinib is primarily utilized for the treatment of non-small cell lung carcinoma. The drug is at least partially effective by triggering suicidal tumor cell death. Side effects of afatinib treatment include anemia. At least in theory, afatinib induced anemia could be secondary to stimulation of suicidal erythrocyte death or eryptosis, characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Signaling potentially stimulating eryptosis include increase of cytosolic Ca2+ activity ([Ca2+]i), induction of oxidative stress, and increase of ceramide abundance. The present study explored, whether afatinib induces eryptosis and, if so, whether its effect involves Ca2+ entry, oxidative stress, and/or ceramide. Methods: Flow cytometry was employed to quantify phosphatidylserine exposure at the cell surface from annexin-V-binding, cell volume from forward scatter, [Ca2+]i from Fluo3-fluorescence, reactive oxygen species (ROS) abundance from DCFDA dependent fluorescence, and ceramide abundance utilizing specific antibodies. Results: A 48 hours exposure of human erythrocytes to afatinib (≥ 4 μg/ml) significantly increased the percentage of annexin-V-binding cells and significantly decreased forward scatter. Afatinib significantly increased Fluo3-fluorescence, DCFDA fluorescence and ceramide abundance. The effect of afatinib on annexin-V-binding and forward scatter was significantly blunted by removal of extracellular Ca2+. Conclusions: Afatinib triggers phospholipid scrambling of the erythrocyte cell membrane, an effect at least in part due to Ca2+ entry, oxidative stress, and ceramide.
Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
2018-01-01

The first transmission and scanning electron microscopical studies in combination with freeze-fracture technology have disclosed some important morphological and ultrastructural features in the freshwater oligotrichid <i>Limnostrombidium viride</i>. (I) The dikinetids (paired basal bodies) of the girdle kinety have a club-shaped cilium associated only with each left basal body. The electron-dense (paraflagellar) body on one side of its "9×2+2"-axoneme and the regular array of intramembranous particles indicate a sensory, perhaps photoreceptor function of these club-shaped cilia. (II) The stichomonad endoral membrane is proximally covered by a cytoplasmic fold and distally by multiple membranous layers. Thus entirely covered, the endoral is probably no longer involved in food capture; nonetheless, its associated microtubules might stabilise the cytopharynx. (III) Instead of a contractile vacuole, a horizontal ring-canal with supposed osmoregulatory function occurs. (IV) The extrusive nature of the trichites is not only observed in electron micrographs, but the attachment sites of these organelles also display a rosette of "8+1"-particles in the P-face of freeze-fracture replicas typical for ciliate extrusomes. (V) The neoformation organelle, the subsurface tube in which stomatogenesis takes place, shows short basal bodies and normal axonemes about 1 μm long. It is accompanied by numerous membrane vesicles, which might provide membrane material for the outgrowing cilia.
Taurolidine Sensitivity of Eryptosis, the Suicidal Erythrocyte Death
2018-01-01

Background/Aims: The taurine derivative Taurolidine is effective against diverse bacteria and tumor growth. In the treatment of cancer, the substance is effective in part by triggering suicidal death or apoptosis of tumor cells. The Taurolidine-induced apoptosis involves mitochondria. Erythrocytes lack mitochondria but are nevertheless able to enter suicidal erythrocyte death or eryptosis, which is characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Signaling of eryptosis includes increase of cytosolic Ca2+ activity ([Ca2+]i), oxidative stress and ceramide. The present study explores, whether Taurolidine induces eryptosis and, if so, which cellular mechanisms are involved. Methods: Phosphatidylserine exposure at the cell surface was estimated using annexin-V-binding, cell volume using forward scatter, [Ca2+]i using Fluo3-fuorescence, reactive oxygen species (ROS) formation using 2’,7’-dichlorodihydrofuorescein (DCF)-dependent fluorescence, and ceramide abundance using specific antibodies. Results: A 48 hours exposure of human erythrocytes to Taurolidine (60 μg/ml) significantly enhanced the percentage of annexin-V-binding cells, significantly decreased forward scatter and significantly increased Fluo3-fluorescence and ceramide abundance, but not DCF-fluorescence. The effect of Taurolidine on annexin-V-binding was virtually abrogated by removal of extracellular Ca2+. Conclusion: Taurolidine triggers cell shrinkage and phospholipid scrambling of the erythrocyte cell membrane, an effect at least in part due to Ca2+ entry and paralleled by increase of ceramide abundance.
Reaction Time Predicts Brain–Computer Interface Aptitude
2018-01-01

There is evidence that 15-30% of the general population cannot effectively operate brain-computer interfaces (BCIs). Thus the BCI performance predictors are critically required to pre-screen participants. Current neurophysiological and psychological tests either require complicated equipment or suffer from subjectivity. Thus, a simple and objective BCI performance predictor is desirable. Neurofeedback (NFB) training involves performing a cognitive task (motor imagery) instructed via sensory stimuli and re-adjusted through ongoing real-time feedback. A simple reaction time (SRT) test reflects the time required for a subject to respond to a defined stimulus. Thus, we postulated that individuals with shorter reaction times operate a BCI with rapidly updated feedback better than individuals with longer reaction times. Furthermore, we investigated how changing the feedback update interval (FUI), i.e., modification of the feedback provision frequency, affects the correlation between the SRT and BCI performance. Ten participants attended four NFB sessions with FUIs of 16, 24, 48, and 96 ms in a randomized order. We found that: 1) SRT is correlated with the BCI performance with FUIs of 16 and 96 ms; 2) good and poor performers elicit stronger ERDs and control BCIs more effectively (i.e., produced larger information transfer rates) with 16 and 96 ms FUIs, respectively. Our findings suggest that SRT may be used as a simple and objective surrogate for BCI aptitude with FUIs of 16 and 96 ms. It also implies that the FUI customization according to participants SRT measure may enhance the BCI performance.
Inhibition of Erythrocyte Cell Membrane Scrambling Following Energy Depletion and Hyperosmotic Shock by Alectinib
2018-01-01

Background/Aims: The anaplastic lymphoma kinase (ALK) inhibitor alectinib is clinically used for the treatment of ALK positive non-small-cell lung cancer. At least in part the substance is effective by triggering suicidal death or apoptosis of tumor cells. Erythrocytes are lacking mitochondria and nuclei, key organelles of apoptosis but are, similar to apoptosis of nucleated cells, able to enter suicidal erythrocyte death or eryptosis. Stimulators of eryptosis include energy depletion, hyperosmotic shock, oxidative stress, and increase of cytosolic Ca2+ activity ([Ca2+]i). The present study explored, whether alectinib influences eryptosis. Methods: Flow cytometry was employed to quantify phosphatidylserine exposure at the cell surface from annexin-V-binding and cell volume from forward scatter. Measurements were made without or with energy depletion (glucose deprivation for 48 hours), hyperosmotic shock (+550mM sucrose for 6 hours), oxidative stress (50 min exposure to 0.3 mM tert-butylhydroperoxide), and Ca2+ loading (60 minutes treatment with 1 μM Ca2+ ionophore ionomycin). Results: A 48 hours exposure of human erythrocytes to alectinib (150-600 ng/ml) did not significantly modify the percentage of annexin-V-binding cells and forward scatter. Energy depletion, hyperosmotic shock, oxidative stress and Ca2+ loading were each followed by profound and significant increase of the percentage annexin-V-binding erythrocytes and a significant decrease of forward scatter. The effects of energy depletion and hyperosmotic shock, but not of oxidative stress or Ca2+ loading on annexin-V-binding were significantly blunted in the presence of alectinib (150-600 ng/ml). In none of the conditions was forward scatter significantly modified by alectinib. Conclusion: Alectinib inhibits cell membrane scrambling following energy depletion and hyperosmotic shock.
Recurrent 8-Year Ongoing Unilateral Breast Seroma Formation after PIP Implant Removal—A Case Report and Review of the Literature
2018-01-01

Abstract Late seroma formation is a rare complication after implant-based breast enlargement surgery and even less frequent after implant removal. This case report presents a case of painful recurrent seroma formation after the removal of a ruptured Poly Implants Prothèse implant. A 52-year-old patient presented herself in our clinic with a clinical history of recurrent unilateral seroma of the right breast over a period of 8 years after the initial unilateral implant removal. Removal of the remaining implant and complete bilateral capsulectomy was performed. Intraoperative findings revealed a macroscopically thickened capsule with signs of chronic inflammation on the affected side. The clinical history and the macroscopic appearance of the capsule demanded histopathological exclusion of a possible anaplastic large cell lymphoma. Histopathological and microbiological analysis of the capsule and encapsulated material revealed no signs of malignancy or infection. Immediate soft tissue reconstruction of the breast was successfully performed using autologous fat transfer. An aesthetically satisfying result regarding symmetry and volume was achieved, and no further seroma formation was observed within a 6-month follow-up period. Level of evidence: V, Case Report.
Fair Resource Sharing for Stateless-Core Packet-Switched Networks With Prioritization
2018-01-01

We propose an activity-based congestion management (ABC) to enforce fair bandwidth sharing among users in packet-based communication networks without requiring per-user information in forwarding nodes. Activity relates to the sent data rate of a user and its contracted reference rate. Activity meters monitor user traffic at edge nodes and add activity information to packets. Forwarding nodes utilize this information to preferentially drop packets with high activity values in case of congestion. In this paper, we significantly simplify the behavior of ABC's control devices: the activity meter in edge nodes and the activity AQM in forwarding nodes. Moreover, we introduce scheduling priorities for ABC, provide means to avoid starvation of non-prioritized traffic through prioritized traffic, and means to disincentivize prioritized transmission of non-realtime traffic. We study the fairness achieved with and without ABC using packet-based simulation, mostly under challenging conditions where a heavy user wants to monopolize a bottleneck's bandwidth. We investigate bandwidth sharing for non-responsive traffic, for responsive traffic, and a mixture of both. The effect of traffic prioritization is studied. We explore the impact of configuration parameters and recommend meaningful system parameters. We illustrate their impact on system dynamics and show that ABC expedites sporadic uploads, which improves the quality of experience for interactive applications. Finally, we compare the performance of ABC with the one of CSFQ whose objective is the same as the one of ABC, but significantly differs with regard to signaled information and algorithmic approach. Summarizing, ABC creates an ecosystem, where users can maximize their throughput if they do not exceed their fair share on the bottleneck link. This incentivizes the usage of congestion-controlled transport protocols. Moreover, ABC protects traffic from users applying congestion control against traffic overload from users not leveraging congestion control, even if the latter send prioritized traffic.
Donor-stabilised molecular Mg/Al-bimetallic hydrides
2018-01-01

Low-molecular organometallic hydride complexes of the type [(do)<sub>x</sub>Mg{(μ<sub>2</sub>-H)(AlMe<sub>3</sub>)}<sub>2</sub>] form in ethereal solvents and display inherent reactivity of existing magnesium hydrido bonding.
The isitethical? Exchange responsible research and innovation for disaster risk management
2018-01-01

This paper describes the IsITethical? Exchange, a European knowledge and service hub we are developing with and for diverse parties involved in crisis and disaster risk management. Their commitment to European values and fundamental rights underpins the rationale of the initiative, which is to support European societies' need for high quality innovation to balance the benefits of IT with fundamental human rights and values, especially privacy and data protection. The initiative is led by researchers at Lancaster University and builds on many years of collaborative design research with a wide range of international practitioners, academics, and commercial IT designers.
Automatic Focus Annotation: Bringing Formal Pragmatics Alive in Analyzing the Information Structure of Authentic Data
2018-01-01

Ramon Ziai, Detmar Meurers. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.
Interaction techniques for a neural-guided hand exoskeleton
2018-01-01

People with motor disabilities – e.g. in the hand – due to brain and spinal cord injuries often suffer an extensive loss of autonomy, performance and quality of life. Although the limitations of a brain-controlled hand exoskeleton can be reduced to a certain extent, the usability for everyday use is still insufficient. In this short paper we describe a research project in progress for a new human-machine interaction concept, based on a brain-computer interface and augmented reality glasses, which aims to improve the usability of brain-controlled hand exoskeletons.
Reactant or reagent? Oxidation of H2 at electronically distinct nickel-thiolate sites [Ni2(μ-SR)2]+ and [Ni–SR]+
2018-01-01

The chemical bond between a Lewis-acidic metal and a Brønsted/Lewis-basic sulphur donor provides M–S structures with functional properties that are relevant for a variety of processes such as the heterolytic cleavage of H<sub>2</sub>.
Drug-Use Identification from Tweets with Word and Character N-Grams
2018-01-01

This paper describes our systems in social media mining for health applications (SMM4H) shared task. We participated in all four tracks of the shared task using linear models with a combination of character and word n-gram features. We did not use any external data or domain specific information. The resulting systems achieved above-average scores among other participating systems, with F1-scores of 91.22, 46.8, 42.4, and 85.53 on tasks 1, 2, 3, and 4 respectively.
Identification of Natural Product Biosynthetic Gene Clusters from Bacterial Genomic Data
2018-01-01

The frequent re-isolation of known compounds is one of the main challenges of traditional screening methods for natural products drug discovery. The ability to connect natural products to the genes that encode them and vice versa has the potential to revolutionize discovery efforts. Increasingly sophisticated bioinformatic tools are being developed that are able to not only identify biosynthetic genes in sequenced genomes but can also predict the product class or structure in silico. This information can then guide targeted discovery of new compounds. In this chapter, we will describe how to prioritize bacterial strains for genome sequencing and how biosynthetic gene clusters can be identified in bacterial genomes. We will also give a short introduction on how comparative genomics can help to identify different congeners of a specific class of natural products of interest and what the limitations of structure prediction are. We will not attempt to be exhaustive but will rather provide examples that the reader can actively follow.
Contrast instead of comparison: Evidence from West Tibetan differentiating property ascriptions
2018-01-01

Non-equative comparisons are typically interpreted in terms of degree semantics. That is, the comparee is thought to have the same property as the standard, but to a different degree. In this paper I should like to introduce a different way of conceptualising differences, namely categorical contrasting, where one focuses more on the contrast than on the gradualness of the difference. Two items are described as being essentially different with respect to a certain property, and this can imply that the standard against which an item is contrasted lacks the property in question. In order to show that this approach is more suitable for the Tibetic languages, especially the West Tibetan varieties spoken in Ladakh, I will not only discuss the standard ways of expressing differences, but also some more marginal constructions at the limit of acceptability.
Effects of temporal primary-tone arrangement on DPOAE properties in humans
2018-01-01

Distortion-product otoacoustic emissions (DPOAEs) emerge as a by-product of the nonlinear amplification of sound waves in the cochlea when presenting two tones of frequencies f1 and f2. According to a widely accepted model, DPOAEs comprise two main components, which can be separated in the time domain using short stimulus pulses. The present study utilized two acquisition paradigms with different primary-tone arrangements, denoted as SP-f1 and SP-f2, to investigate the nonlinear-distortion component arising near the f2-tonotopic site on the basilar membrane. In SP-f2, a conventional paradigm, the f1 tone was presented for 25 ms, whereas the f2 tone was switched on 5 ms after f1 onset for frequency-dependent durations between 3 and 11 ms to elicit the DPOAE. SP-f1 interchanged the temporal arrangement and durations of the primary tones. DPOAEs were recorded at eight frequencies (f2 = 1 – 8 kHz; f2/f1 = 1.2) and five primary-tone levels L2 = 30 – 70 dB SPL in 56 normal-hearing ears from 33 subjects. Comparison between the corresponding DPOAE responses revealed significantly larger amplitudes and shorter latencies of the nonlinear-distortion component for SP-f1, i.e. when the f1 short pulse triggers DPOAE generation.
Distinguishing coercion and underspecification in Type Composition Logic
2018-01-01

This paper investigates the meaning adaptability of change of state (CoS) verbs. Itargues that both coercion and underspecification are necessary mechanisms in order to properlyaccount for the semantic adaptability observable for CoS verbs in combination with theircomplements. This type of meaning adaptability has received little formal attention to date,although some recent work has already led the way on this topic (Spalek, 2014; Lukassek andSpalek, 2016; Asher et al., 2017). Our paper is part of a cross-linguistic case study of Germaneinfrieren and Spanish congelar (‘freeze’). We model the meaning adaptability of this test casewithin Type Composition Logic (TCL) (Asher, 2011). We build on Asher’s coercion mechanismand introduce an additional mechanism for underspecification that exploits the fine-grained typesystem in TCL.Keywords: lexical semantics, change of state verbs, coercion, underspecification, Type CompositionLogic.
Stimulus domain transfer in recurrent models for large scale cortical population prediction on video
2018-01-01

To better understand the representations in visual cortex, we need to generate better predictions of neural activity in awake animals presented with their ecological input: natural video. Despite recent advances in models for static images, models for predicting responses to natural video are scarce and standard linear-nonlinear models perform poorly. We developed a new deep recurrent network architecture that predicts inferred spiking activity of thousands of mouse V1 neurons simultaneously recorded with two-photon microscopy, while accounting for confounding factors such as the animal's gaze position and brain state changes related to running state and pupil dilation. Powerful system identification models provide an opportunity to gain insight into cortical functions through in silico experiments that can subsequently be tested in the brain. However, in many cases this approach requires that the model is able to generalize to stimulus statistics that it was not trained on, such as band-limited noise and other parameterized stimuli. We investigated these domain transfer properties in our model and find that our model trained on natural images is able to correctly predict the orientation tuning of neurons in responses to artificial noise stimuli. Finally, we show that we can fully generalize from movies to noise and maintain high predictive performance on both stimulus domains by fine-tuning only the final layer's weights on a network otherwise trained on natural movies. The converse, however, is not true.
Use of Gene Expression Analysis for Discrimination of Primary and Secondary Adenocarcinoma of the Liver
2018-01-01

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Due to late diagnosis and resistance to chemotherapy, most patients with cholangiocarcinoma have an unfavorable prognosis. Despite the use of immunohistochemistry (IHC) in clinical routine, differentiation between intrahepatic cholangiocarcinoma (ICC) and secondary adenocarcinomas of the liver is frequently not clear, leading to false diagnosis and treatment decisions. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Oligonucleotide microarrays (Affymetrix Hu133A&lt;sup&gt;©&lt;/sup&gt;) were used for gene expression analysis of ICC (&lt;i&gt;n&lt;/i&gt; = 11) and secondary adenocarcinomas (colorectal metastases; &lt;i&gt;n&lt;/i&gt; = 6). By two-dimensional cluster analysis a specific gene expression profile of these tumors was established and confirmed by real-time polymerase chain reaction and IHC. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; A total of 338 genes were significantly dysregulated (gene expression/fc ≥2; dysregulation in ≥60%) in both tumor groups. Using two-dimensional cluster analysis a fast, clear, and reproducible differentiation between ICC and colorectal metastases was possible in all cases. As potential biomarkers for differentiation, twelve genes (ICC: &lt;i&gt;KRT7&lt;/i&gt;, &lt;i&gt;DBN1&lt;/i&gt;, &lt;i&gt;LCTB&lt;/i&gt;, &lt;i&gt;LIF&lt;/i&gt;, &lt;i&gt;STK17A&lt;/i&gt;, &lt;i&gt;PIGF&lt;/i&gt;; metastases: &lt;i&gt;TDGF1&lt;/i&gt;, &lt;i&gt;HOXA9&lt;/i&gt;, &lt;i&gt;TFF3&lt;/i&gt;, &lt;i&gt;MYB&lt;/i&gt;, &lt;i&gt;ABP1&lt;/i&gt;, &lt;i&gt;BCL11A&lt;/i&gt;) were detected and will be used for further investigations. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; A specific gene expression profile for discrimination of primary and secondary adenocarcinoma of the liver could be established. In addition, marker genes for both cancers and their potential use as discrimination markers in clinical routine were also described partially for the first time.