Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Medicinal Chemistry and Pharmaceutics
Title: Application of camelid heavy-chain variable domains (VHHs) in prevention and treatment of bacterial and viral infections
Abstract: ABSTRACT Camelid heavy-chain variable domains (VHHs) are the smallest, intact, antigen-binding units to occur in nature. VHHs possess high degrees of solubility and robustness enabling generation of multivalent constructs with increased avidity – characteristics that mark their superiority to other antibody fragments and monoclonal antibodies. Capable of effectively binding to molecular targets inaccessible to classical immunotherapeutic agents and easily produced in microbial culture, VHHs are considered promising tools for pharmaceutical biotechnology. With the aim to demonstrate the perspective and potential of VHHs for the development of prophylactic and therapeutic drugs to target diseases caused by bacterial and viral infections, this review article will initially describe the structural features that underlie the unique properties of VHHs and explain the methods currently used for the selection and recombinant production of pathogen-specific VHHs, and then thoroughly summarize the experimental findings of five distinct studies that employed VHHs as inhibitors of host–pathogen interactions or neutralizers of infectious agents. Past and recent studies suggest the potential of camelid heavy-chain variable domains as a novel modality of immunotherapeutic drugs and a promising alternative to monoclonal antibodies. VHHs demonstrate the ability to interfere with bacterial pathogenesis by preventing adhesion to host tissue and sequestering disease-causing bacterial toxins. To protect from viral infections, VHHs may be employed as inhibitors of viral entry by binding to viral coat proteins or blocking interactions with cell-surface receptors. The implementation of VHHs as immunotherapeutic agents for infectious diseases is of considerable potential and set to contribute to public health in the near future.
Extracted statement — Type of nanoparticles: VHHs
Research field: Medicinal Chemistry and Pharmaceutics
Title: Novel coronavirus-like particles targeting cells lining the respiratory tract
Abstract: Virus like particles (VLPs) produced by the expression of viral structural proteins can serve as versatile nanovectors or potential vaccine candidates. In this study we describe for the first time the generation of HCoV-NL63 VLPs using baculovirus system. Major structural proteins of HCoV-NL63 have been expressed in tagged or native form, and their assembly to form VLPs was evaluated. Additionally, a novel procedure for chromatography purification of HCoV-NL63 VLPs was developed. Interestingly, we show that these nanoparticles may deliver cargo and selectively transduce cells expressing the ACE2 protein such as ciliated cells of the respiratory tract. Production of a specific delivery vector is a major challenge for research concerning targeting molecules. The obtained results show that HCoV-NL63 VLPs may be efficiently produced, purified, modified and serve as a delivery platform. This study constitutes an important basis for further development of a promising viral vector displaying narrow tissue tropism.
Extracted statement — Type of nanoparticles: VLPs
Research field: Medicine and Health
Title: Staﬀ Shortage in German Intensive Care Units During the COVID-19 Pandemic - Not only a Sensed Dilemma: Results from a Nationwide Survey
Abstract: Background: The surge in patients during the COVID-19 pandemic has exacerbated the looming problem of staﬀ shortage in German ICUs possibly leading to worse outcomes for patients. Methods: Within the German Evidence Ecosystem CEOsys network, we conducted an online national mixed-methods survey assessing the standard of care in German ICUs treating patients with COVID-19. Results: A total of 171 German ICUs reported a median ideal number of patients per intensivist of 8 (interquartile range, IQR = 3rd quartile - 1st quartile = 4.0) and per nurse of 2.0 (IQR = 1.0). For COVID-19 patients, the median target was a maximum of 6.0 (IQR = 2.0) patients per intensivist or 2.0 (IQR = 0.0) patients per nurse. Targets for intensivists were rarely met by 15.2% and never met by 3.5% of responding institutions. Targets for nursing staﬃng could rarely be met in 32.2% and never in 5.3% of responding institutions.Conclusions: Shortages of staﬃng in the critical care setting are eminent during the COVID-19 pandemic and might not only negatively aﬀect patient outcomes, but also staﬀ wellbeing and healthcare costs. A joint eﬀort that scrutinizes the demands and structures of our health care system seems fundamental to be prepared for the future.
Extracted statement — has research problem: COVID-19
Research field: Molecular and Cellular Neuroscience
Title: Aldehyde dehydrogenase 2 activity and aldehydic load contribute to neuroinflammation and Alzheimer’s disease related pathology
Abstract: Abstract Aldehyde dehydrogenase 2 deficiency (ALDH2*2) causes facial flushing in response to alcohol consumption in approximately 560 million East Asians. Recent meta-analysis demonstrated the potential link between ALDH2*2 mutation and Alzheimer’s Disease (AD). Other studies have linked chronic alcohol consumption as a risk factor for AD. In the present study, we show that fibroblasts of an AD patient that also has an ALDH2*2 mutation or overexpression of ALDH2*2 in fibroblasts derived from AD patients harboring ApoE ε4 allele exhibited increased aldehydic load, oxidative stress, and increased mitochondrial dysfunction relative to healthy subjects and exposure to ethanol exacerbated these dysfunctions. In an in vivo model, daily exposure of WT mice to ethanol for 11 weeks resulted in mitochondrial dysfunction, oxidative stress and increased aldehyde levels in their brains and these pathologies were greater in ALDH2*2/*2 (homozygous) mice. Following chronic ethanol exposure, the levels of the AD-associated protein, amyloid-β, and neuroinflammation were higher in the brains of the ALDH2*2/*2 mice relative to WT. Cultured primary cortical neurons of ALDH2*2/*2 mice showed increased sensitivity to ethanol and there was a greater activation of their primary astrocytes relative to the responses of neurons or astrocytes from the WT mice. Importantly, an activator of ALDH2 and ALDH2*2, Alda-1, blunted the ethanol-induced increases in Aβ, and the neuroinflammation in vitro and in vivo. These data indicate that impairment in the metabolism of aldehydes, and specifically ethanol-derived acetaldehyde, is a contributor to AD associated pathology and highlights the likely risk of alcohol consumption in the general population and especially in East Asians that carry ALDH2*2 mutation.
Extracted statement — keywords: Alda-1
Research field: Molecular and Cellular Neuroscience
Title: Aldehyde dehydrogenase 2 activity and aldehydic load contribute to neuroinflammation and Alzheimer’s disease related pathology
Abstract: Abstract Aldehyde dehydrogenase 2 deficiency (ALDH2*2) causes facial flushing in response to alcohol consumption in approximately 560 million East Asians. Recent meta-analysis demonstrated the potential link between ALDH2*2 mutation and Alzheimer’s Disease (AD). Other studies have linked chronic alcohol consumption as a risk factor for AD. In the present study, we show that fibroblasts of an AD patient that also has an ALDH2*2 mutation or overexpression of ALDH2*2 in fibroblasts derived from AD patients harboring ApoE ε4 allele exhibited increased aldehydic load, oxidative stress, and increased mitochondrial dysfunction relative to healthy subjects and exposure to ethanol exacerbated these dysfunctions. In an in vivo model, daily exposure of WT mice to ethanol for 11 weeks resulted in mitochondrial dysfunction, oxidative stress and increased aldehyde levels in their brains and these pathologies were greater in ALDH2*2/*2 (homozygous) mice. Following chronic ethanol exposure, the levels of the AD-associated protein, amyloid-β, and neuroinflammation were higher in the brains of the ALDH2*2/*2 mice relative to WT. Cultured primary cortical neurons of ALDH2*2/*2 mice showed increased sensitivity to ethanol and there was a greater activation of their primary astrocytes relative to the responses of neurons or astrocytes from the WT mice. Importantly, an activator of ALDH2 and ALDH2*2, Alda-1, blunted the ethanol-induced increases in Aβ, and the neuroinflammation in vitro and in vivo. These data indicate that impairment in the metabolism of aldehydes, and specifically ethanol-derived acetaldehyde, is a contributor to AD associated pathology and highlights the likely risk of alcohol consumption in the general population and especially in East Asians that carry ALDH2*2 mutation.
Extracted statement — proteins detected by western blot : ALDH2
Research field: Nanoscience and Nanotechnology
Title: ZnO Nanotube Arrays as Biosensors for Glucose
Abstract: Highly oriented single-crystal ZnO nanotube (ZNT) arrays were prepared by a two-step electrochemical/chemical process on indium-doped tin oxide (ITO) coated glass in an aqueous solution. The prepared ZNT arrays were further used as a working electrode to fabricate an enzyme-based glucose biosensor through immobilizing glucose oxidase in conjunction with a Nafion coating. The present ZNT arrays-based biosensor exhibits high sensitivity of 30.85 μA cm−2 mM−1 at an applied potential of +0.8 V vs. SCE, wide linear calibration ranges from 10 μM to 4.2 mM, and a low limit of detection (LOD) at 10 μM (measured) for sensing of glucose. The apparent Michaelis−Menten constant KMapp was calculated to be 2.59 mM, indicating a higher bioactivity for the biosensor.
Extracted statement — Reference Electrode: ITO
Research field: Nanoscience and Nanotechnology
Title: Highly Sensitive Electromechanical Piezoresistive Pressure Sensors Based on Large-Area Layered PtSe2 Films
Abstract: Two-dimensional (2D) layered materials are ideal for micro- and nanoelectromechanical systems (MEMS/NEMS) due to their ultimate thinness. Platinum diselenide (PtSe2), an exciting and unexplored 2D transition metal dichalcogenide material, is particularly interesting because its low temperature growth process is scalable and compatible with silicon technology. Here, we report the potential of thin PtSe2 films as electromechanical piezoresistive sensors. All experiments have been conducted with semimetallic PtSe2 films grown by thermally assisted conversion of platinum at a complementary metal–oxide–semiconductor (CMOS)-compatible temperature of 400 °C. We report high negative gauge factors of up to −85 obtained experimentally from PtSe2 strain gauges in a bending cantilever beam setup. Integrated NEMS piezoresistive pressure sensors with freestanding PMMA/PtSe2 membranes confirm the negative gauge factor and exhibit very high sensitivity, outperforming previously reported values by orders of magnitude. We employ density functional theory calculations to understand the origin of the measured negative gauge factor. Our results suggest PtSe2 as a very promising candidate for future NEMS applications, including integration into CMOS production lines.
Extracted statement — Material: PtSe2
Research field: Nanoscience and Nanotechnology
Title: Bioinspired Cocatalysts Decorated WO3 Nanotube Toward Unparalleled Hydrogen Sulfide Chemiresistor
Abstract: Herein, we incorporated dual biotemplates, i.e., cellulose nanocrystals (CNC) and apoferritin, into electrospinning solution to achieve three distinct benefits, i.e., (i) facile synthesis of a WO3 nanotube by utilizing the self-agglomerating nature of CNC in the core of as-spun nanofibers, (ii) effective sensitization by partial phase transition from WO3 to Na2W4O13 induced by interaction between sodium-doped CNC and WO3 during calcination, and (iii) uniform functionalization with monodispersive apoferritin-derived Pt catalytic nanoparticles (2.22 ± 0.42 nm). Interestingly, the sensitization effect of Na2W4O13 on WO3 resulted in highly selective H2S sensing characteristics against seven different interfering molecules. Furthermore, synergistic effects with a bioinspired Pt catalyst induced a remarkably enhanced H2S response ( Rair/ Rgas = 203.5), unparalleled selectivity ( Rair/ Rgas < 1.3 for the interfering molecules), and rapid response (<10 s)/recovery (<30 s) time at 1 ppm of H2S under 95% relative humidity level. This work paves the way for a new class of cosensitization routes to overcome critical shortcomings of SMO-based chemical sensors, thus providing a potential platform for diagnosis of halitosis.
Extracted statement — Target gas: H2S
Research field: Nanoscience and Nanotechnology
Title: Sensitive Electronic-Skin Strain Sensor Array Based on the Patterned Two-Dimensional α-In2Se3
Abstract: Two-dimensional (2D) layered semiconductors have emerged as a highly attractive class of materials for flexible and wearable strain sensor-centric devices such as electronic-skin (e-skin). This is primarily due to their dimensionality, excellent mechanical flexibility, and unique electronic properties. However, the lack of effective and low-cost methods for wafer-scale fabrication of these materials for strain sensor arrays limits their potential for such applications. Here, we report growth of large-scale 2D In2Se3 nanosheets by templated chemical vapor deposition (CVD) method, using In2O3 and Se powders as precursors. The strain sensors fabricated from the as-grown 2D In2Se3 films show 2 orders of magnitude higher sensitivity (gauge factor ∼237 in −0.39% to 0.39% uniaxial strain range along the device channel length) than what has been demonstrated from conventional metal-based (gauge factor: ∼1–5) and graphene-based strain sensors (gauge factor: ∼2–4) in a similar uniaxial strain range. The integrated ...
Extracted statement — Material: In2Se3
Research field: Nanoscience and Nanotechnology
Title: MoS2
-Based Tactile Sensor for Electronic Skin Applications
Abstract: A conformal tactile sensor based on MoS2 and graphene is demonstrated. The MoS2 tactile sensor exhibits excellent sensitivity, high uniformity, and good repeatability in terms of various strains. In addition, the outstanding flexibility enables the MoS2 strain tactile sensor to be realized conformally on a finger tip. The MoS2 -based tactile sensor can be utilized for wearable electronics, such as electronic skin.
Extracted statement — Material: MoS2
Research field: Nanoscience and Nanotechnology
Title: Kirigami-Inspired Highly Stretchable Nanoscale Devices Using Multidimensional Deformation of Monolayer MoS2
Abstract: Two-dimensional (2D) layered materials, such as MoS2, are greatly attractive for flexible devices due to their unique layered structures, novel physical and electronic properties, and high mechanical strength. However, their limited mechanical strains (<2%) can hardly meet the demands of loading conditions for most flexible and stretchable device applications. In this Article, inspired from Kirigami, the ancient Japanese art of paper cutting, we design and fabricate nanoscale Kirigami architectures of 2D layered MoS2 on a soft substrate of polydimethylsiloxane (PDMS) using a top-down fabrication process. Results show that the Kirigami structures significantly improve the reversible stretchability of flexible 2D MoS2 electronic devices, which is increased from 0.75% to ∼15%. This increase in flexibility is originated from a combination of multidimensional deformation capabilities from the nanoscale Kirigami architectures consisting of in-plane stretching and out-of-plane deformation. We further discover a ...
Extracted statement — Material: MoS2
Research field: Nanoscience and Nanotechnology
Title: Piezoresistive strain sensor based on monolayer molybdenum disulfide continuous film deposited by chemical vapor deposition
Abstract: In this paper, a centimeter-scale monolayer molybdenum disulfide (MoS2) film deposition method has been developed through a simple low-pressure chemical vapor deposition (LPCVD) growth system. The growth pressure dependence on film quality is investigated in this LPCVD system. The layer nature, electrical characteristic of the as-grown MoS2 films indicate that high quality films have been achieved. In addition, a hydrofluoric acid treated SiO2/Si substrate is used to improve the quality of the MoS2 films. Piezoresistive strain sensor based on the monolayer MoS2 film elements is fabricated by directly patterning metal contact pads on MoS2 films through a silicon stencil mask. A gauge factor of 104 ± 26 under compressive strain is obtained by using a four-point bending method, which may inspire new possibilities for two-dimensional (2D) material-based microsystems and electronics.
Extracted statement — Material: MoS2
Research field: Nanoscience and Nanotechnology
Title: Stretchable, Transparent, Ultrasensitive, and Patchable Strain Sensor for Human–Machine Interfaces Comprising a Nanohybrid of Carbon Nanotubes and Conductive Elastomers
Abstract: UNLABELLED Interactivity between humans and smart systems, including wearable, body-attachable, or implantable platforms, can be enhanced by realization of multifunctional human-machine interfaces, where a variety of sensors collect information about the surrounding environment, intentions, or physiological conditions of the human to which they are attached. Here, we describe a stretchable, transparent, ultrasensitive, and patchable strain sensor that is made of a novel sandwich-like stacked piezoresisitive nanohybrid film of single-wall carbon nanotubes (SWCNTs) and a conductive elastomeric composite of polyurethane (PU)-poly(3,4-ethylenedioxythiophene) polystyrenesulfonate ( PEDOT PSS). This sensor, which can detect small strains on human skin, was created using environmentally benign water-based solution processing. We attributed the tunability of strain sensitivity (i.e., gauge factor), stability, and optical transparency to enhanced formation of percolating networks between conductive SWCNTs and PEDOT phases at interfaces in the stacked PU-PEDOT:PSS/SWCNT/PU-PEDOT:PSS structure. The mechanical stability, high stretchability of up to 100%, optical transparency of 62%, and gauge factor of 62 suggested that when attached to the skin of the face, this sensor would be able to detect small strains induced by emotional expressions such as laughing and crying, as well as eye movement, and we confirmed this experimentally.
Extracted statement — Sensing material: SWCNT/PU-PEDOT:PSS
Research field: Natural Language Processing
Title: End-to-end Sequence Labeling via Bi-directional LSTM-CNNs-CRF
Abstract: State-of-the-art sequence labeling systems traditionally require large amounts of task-specific knowledge in the form of hand-crafted features and data pre-processing. In this paper, we introduce a novel neutral network architecture that benefits from both word- and character-level representations automatically, by using combination of bidirectional LSTM, CNN and CRF. Our system is truly end-to-end, requiring no feature engineering or data pre-processing, thus making it applicable to a wide range of sequence labeling tasks. We evaluate our system on two data sets for two sequence labeling tasks --- Penn Treebank WSJ corpus for part-of-speech (POS) tagging and CoNLL 2003 corpus for named entity recognition (NER). We obtain state-of-the-art performance on both the two data --- 97.55\% accuracy for POS tagging and 91.21\% F1 for NER.
Extracted statement — model: CRF
Research field: Natural Language Processing
Title: GATE: an architecture for development of robust HLT applications
Abstract: In this paper we present GATE, a framework and graphical development environment which enables users to develop and deploy language engineering components and resources in a robust fashion. The GATE architecture has enabled us not only to develop a number of successful applications for various language processing tasks (such as Information Extraction), but also to build and annotate corpora and carry out evaluations on the applications generated. The framework can be used to develop applications and resources in multiple languages, based on its thorough Unicode support.
Extracted statement — Tool name: GATE
Research field: Natural Language Processing
Title: Overview of the BioCreative VI text-mining services for Kinome Curation Track
Abstract: Abstract The text-mining services for kinome curation track, part of BioCreative VI, proposed a competition to assess the effectiveness of text mining to perform literature triage. The track has exploited an unpublished curated data set from the neXtProt database. This data set contained comprehensive annotations for 300 human protein kinases. For a given protein and a given curation axis [diseases or gene ontology (GO) biological processes], participants’ systems had to identify and rank relevant articles in a collection of 5.2 M MEDLINE citations (task 1) or 530 000 full-text articles (task 2). Explored strategies comprised named-entity recognition and machine-learning frameworks. For that latter approach, participants developed methods to derive a set of negative instances, as the databases typically do not store articles that were judged as irrelevant by curators. The supervised approaches proposed by the participating groups achieved significant improvements compared to the baseline established in a previous study and compared to a basic PubMed search.
Extracted statement — data source: MEDLINE
Research field: Natural Language Processing
Title: Coreference Resolution in Biomedical Texts: a Machine Learning Approach
Abstract: Motivation: Coreference resolution, the process of identifying different mentions of an entity, is a very important component in a text-mining system. Compared with the work in news articles, the existing study of coreference resolution in biomedical texts is quite preliminary by only focusing on specific types of anaphors like pronouns or definite noun phrases, using heuristic methods, and running on small data sets. Therefore, there is a need for an in-depth exploration of this task in the biomedical domain. Results: In this article, we presented a learning-based approach to coreference resolution in the biomedical domain. We made three contributions in our study. Firstly, we annotated a large scale coreference corpus, MedCo, which consists of 1,999 medline abstracts in the GENIA data set. Secondly, we proposed a detailed framework for the coreference resolution task, in which we augmented the traditional learning model by incorporating non-anaphors into training. Lastly, we explored various sources of knowledge for coreference resolution, particularly, those that can deal with the complexity of biomedical texts. The evaluation on the MedCo corpus showed promising results. Our coreference resolution system achieved a high precision of 85.2% with a reasonable recall of 65.3%, obtaining an F-measure of 73.9%. The results also suggested that our augmented learning model significantly boosted precision (up to 24.0%) without much loss in recall (less than 5%), and brought a gain of over 8% in F-measure.
Extracted statement — data source: MEDLINE
Research field: Natural Language Processing
Title: End-to-end Sequence Labeling via Bi-directional LSTM-CNNs-CRF
Abstract: State-of-the-art sequence labeling systems traditionally require large amounts of task-specific knowledge in the form of hand-crafted features and data pre-processing. In this paper, we introduce a novel neutral network architecture that benefits from both word- and character-level representations automatically, by using combination of bidirectional LSTM, CNN and CRF. Our system is truly end-to-end, requiring no feature engineering or data pre-processing, thus making it applicable to a wide range of sequence labeling tasks. We evaluate our system on two data sets for two sequence labeling tasks --- Penn Treebank WSJ corpus for part-of-speech (POS) tagging and CoNLL 2003 corpus for named entity recognition (NER). We obtain state-of-the-art performance on both the two data --- 97.55\% accuracy for POS tagging and 91.21\% F1 for NER.
Extracted statement — Result: NER