gebhart/patrepeval huggingface dataset:
Cloning and characterization of two related serotonergic receptors from the brain and the reproductive system of Aplysia that activate phospholipase C (1995)

Serotonin (5-HT) plays important roles in various behavioral and physiological processes in Aplysia californica. These include feeding, locomotion, circadian rhythm, learning and memory, synaptic plasticity, and synaptic growth. Serotonin modulates these various functions by interacting with different 5-HT receptor subtypes that are coupled to various second-messenger systems. We report here the isolation and characterization of the first two serotonergic receptors from Aplysia californica, Ap5-HTB1 and Ap5-HTB2, using a strategy based on the amino acid sequence homology among G-protein-coupled biogenic amine receptors. Ap5-HTB1 and Ap5-HTB2 are both intronless and highly homologous to each other, sharing 79.5% sequence identity at the amino acid level. Sequence comparison reveals that these receptors are 33.1 to 23.3% identical to the following 5-HT receptors: 5-HTdro1 > 5-HT6 > 5-HTlym > mouse 5-HT1B > 5-HTdro2A > mouse 5-HT7 > rat 5-HT2A. Both Ap5-HTB1 and Ap5-HTB2 encode functional 5-HT receptors. When expressed in cultured cells, these receptors stimulate phospholipase C in response to 5-HT in a dose-dependent manner. This stimulation can be blocked by specific 5-HT receptor antagonists. Using RT-PCR and Western blot analysis, we have detected these receptors in the CNS (Ap5-HTB2) and in the reproductive system (Ap5-HTB1). The nucleotide sequences of Ap5-HTB1 and Ap5-HTB2 were submitted to GenBank; the accession numbers are L43557 and L43558, respectively.
Detecting Wireless Spy Cameras Via Stimulating and Probing (2018)

The rapid proliferation of wireless video cameras has raised serious privacy concerns. In this paper, we propose a stimulating-and-probing approach to detecting wireless spy cameras. The core idea is to actively alter the light condition of a private space to manipulate the spy camera's video scene, and then investigates the responsive variations of a packet flow to determine if it is produced by a wireless camera. Following this approach, we develop Blink and Flicker -- two practical systems for detecting wireless spy cameras. Blink is a lightweight app that can be deployed on off-the-shelf mobile devices. It asks the user to turn on/off the light of her private space, and then uses the light sensor and the wireless radio of the mobile device to identify the response of wireless cameras. Flicker is a robust and automated system that augments Blink to detect wireless cameras in both live and offline streaming modes. Flicker employs a cheap and portable circuit, which harnesses daily used LEDs to stimulate wireless cameras using human-invisible flickering. The time series of stimuli is further encoded using FEC to combat ambient light and uncontrollable packet flow variations that may degrade detection performance. Extensive experiments show that Blink and Flicker can accurately detect wireless cameras under a wide range of network and environmental conditions.
Printed electrochemical based biosensors on flexible substrates (2010)

A flexible substrate electrochemical biosensor was successfully printed on a polyethylene terephthalate (PET) film with silver (Ag) electrodes using silver nanoparticle based ink. The electrochemical impedance spectroscopy (EIS) response of the printed sensor for detecting low concentrations of bio/chemical species revealed a very high sensitivity at pico molar (pM) concentration levels of D-Proline, Sarcosine, Cadmium sulphide (CdS) and Potassium chloride (KCl). The impedance response of the biosensor towards these species was analyzed and is reported in this paper.
Gene therapy for intraperitoneally disseminated pancreatic cancers by Escherichia coli uracil phosphoribosiltransferase (UPRT) gene mediated by restricted replication‐competent adenoviral vectors (2002)

Although patients with unresectable pancreatic tumors have been treated with 5-fluorouracil (5FU)-based combination chemotherapy, the drug resistance of cancer cells presents a crucial therapeutic problem. It was reported that UPRT overcomes 5FU resistance. UPRT catalyzes the synthesis of 5-fluorouridine monophosphate (FUMP) from Uracil and phosphoribosylpyrophosphate (PRPP). The antitumor effect of 5FU is enhanced by augmenting 5-fluorodeoxyuridine monophosphate (FdUMP) converted from FUMP, which inhibits thymidylate synthetase (TS). We first demonstrated that injecting an E1-deficient adenoviral vector (Adv) expressing UPRT (AxCAUPRT) followed by 5-FU treatment resulted in a volume reduction of xenotransplanted human tumors. In examining the therapeutic effect of AxCAUPRT/5-FU against peritoneal dissemination, we found that non-selective gene transduction of AxCAUPRT caused severe adverse effects arising from the increase of F-dUMP in normal intestine. Because the therapeutic gene delivered by a restricted replication-competent Adv lacking 55 kDa E1B protein (AxE1AdB) is speculated to be expressed selectively in tumors, mice with established tumors were injected with AxE1AdB and E1-deleted Adv expressing the lacZ reporter gene (AxCAlacZ). The expression of the reporter gene (lacZ) was selectively enhanced in disseminated tumors. The therapeutic advantage of restricted replication competent Adv that expresses UPRT (AxE1AdB-UPRT) was evaluated in an intraperitoneal disseminated tumor model. To study the anti-tumor effect of AxE1AdB-UPRT/5FU, mice with disseminated AsPC-1 tumors were administered the Adv, followed by the 5FU treatment. It was shown that the treatment with AxE1AdB-UPRT/5FU caused a dramatic reduction of the disseminated tumor burden without toxicity in normal tissues. Our results showed that the AxE1AdB-UPRT/5FU system is a promising tool for intraperitoneal disseminated pancreatic cancer.
Plasma midkine level is a prognostic factor for human neuroblastoma (2008)

Neuroblastoma is the third-most-common solid tumor of childhood. To date, no reliable blood marker for neuroblastoma has been established. The growth factor midkine is highly expressed in human carcinomas and its knockdown leads to tumor growth suppression in animal models. The present study evaluated the plasma midkine level in human neuroblastoma patients. Plasma samples were obtained from patients found through mass screening, as well as from sporadic neuroblastoma patients. The total number of cases examined was 756. Among them, prognostic information was available for 175 sporadic cases and 287 mass-screening cases. Midkine levels were significantly higher in neuroblastoma patients, including both mass-screening cases and sporadic cases, than in non-tumor controls (P < 0.0001). The midkine level was significantly correlated with the statuses of MYCN amplification, TRKA expression, ploidy, stage and age (P < 0.0001, < 0.0001, = 0.004, < 0.0001 and < 0.0001, respectively), which are known prognostic factors for neuroblastoma. There was a striking correlation between high plasma midkine level and poor prognosis (P < 0.0001). Within sporadic cases, the midkine level was also strikingly higher than in non-tumor controls (P < 0.0001), and correlated with the statuses of MYCN amplification and stage (P = 0.0005 and = 0.003, respectively). There was a significant correlation between high plasma midkine level and poor prognosis (P = 0.04). Taken together, the present data indicate that plasma midkine level is a prognostic factor for human neuroblastoma.
A Framework for Land Cover Classification Using Discrete Return LiDAR Data: Adopting Pseudo-Waveform and Hierarchical Segmentation (2014)

Acquiring current, accurate land-use information is critical for monitoring and understanding the impact of anthropogenic activities on natural environments. Remote sensing technologies are of increasing importance because of their capability to acquire information for large areas in a timely manner, enabling decision makers to be more effective in complex environments. Although optical imagery has demonstrated to be successful for land cover classification, active sensors, such as light detection and ranging (LiDAR), have distinct capabilities that can be exploited to improve classification results. However, utilization of LiDAR data for land cover classification has not been fully exploited. Moreover, spatial-spectral classification has recently gained significant attention since classification accuracy can be improved by extracting additional information from the neighboring pixels. Although spatial information has been widely used for spectral data, less attention has been given to LiDAR data. In this work, a new framework for land cover classification using discrete return LiDAR data is proposed. Pseudo-waveforms are generated from the LiDAR data and processed by hierarchical segmentation. Spatial features are extracted in a region-based way using a new unsupervised strategy for multiple pruning of the segmentation hierarchy. The proposed framework is validated experimentally on a real dataset acquired in an urban area. Better classification results are exhibited by the proposed framework compared to the cases in which basic LiDAR products such as digital surface model and intensity image are used. Moreover, the proposed region-based feature extraction strategy results in improved classification accuracies in comparison with a more traditional window-based approach.
A Multidatabase ExTRaction PipEline (METRE) for Facile Cross Validation in Critical Care Research (2023)

Transforming raw EHR data into machine learning model-ready inputs requires considerable effort. One widely used EHR database is Medical Information Mart for Intensive Care (MIMIC). Prior work on MIMIC-III cannot query the updated and improved MIMIC-IV version. Besides, the need to use multicenter datasets further highlights the challenge of EHR data extraction. Therefore, we developed an extraction pipeline that works on both MIMIC-IV and eICU Collaborative Research Database and allows for model cross validation using these 2 databases. Under the default choices, the pipeline extracted 38766 and 126448 ICU records for MIMIC-IV and eICU, respectively. Using the extracted time-dependent variables, we compared the Area Under the Curve (AUC) performance with prior works on clinically relevant tasks such as in-hospital mortality prediction. METRE achieved comparable performance with AUC 0.723- 0.888 across all tasks. Additionally, when we evaluated the model directly on MIMIC-IV data using a model trained on eICU, we observed that the AUC change can be as small as +0.019 or -0.015. Our open-source pipeline transforms MIMIC-IV and eICU into structured data frames and allows researchers to perform model training and testing using data collected from different institutions, which is of critical importance for model deployment under clinical contexts.
Zika virus evolution in the presence of dengue virus-elicited cross-reactive immunity (2020)

Abstract Zika virus (ZIKV), belongs to Flavivirus, causes neurological disorders including Guillain Barré syndrome and fetal microcephaly, and is responsible for widespread epidemics in countries where other flaviviruses, such as dengue (DENV), and yellow fever viruses, are endemic. However, how the cross-reactive, pre-existing immunity impacts the evolution of flaviviruses is poorly understood. To mimic the natural transmission cycle of ZIKV between vertebrate (human) hosts with pre-existing flavivirus immunity and invertebrate hosts (mosquito), ZIKV was subjected to 10 alternating cycles of passaging between DENV-immune mice and mosquito cells. We identified two mutations in the passaged ZIKV strains- one in the NS2B gene (I39V), both after passage in DENV-naïve and DENV-immune mice, and a mutation in the E gene (T470M), only after passage in DENV-immune mice. These mutations increase ZIKV virulence and pathogenesis in non-pregnant and pregnant Ifnar1−/− mice and abrogate cross-protection mediated by the pre-existing DENV immunity. In addition, ZIKV strain with the I39V mutation was more virulent than the parental ZIKV strain in human fetal neural progenitor cells (NPCs), and ZIKV variants in position 39 of the NS2B protein were observed in recent clinical isolates of ZIKV. Our data thus identify a mutational hotspot in the ZIKV NS2B protein and a mutation in the ZIKV E protein that arose as a consequence of the pre-existing immune pressure. Our results uncover the evolutionary strategies by which ZIKV can become pathogenic in both DENV-naïve and DENV-immune populations. Mechanistic studies of evolution in the presence and absence of cross-reactive immunity will benefit the development of safe and efficient flavivirus vaccines.
Photoactive Excited States in Explosive Fe(II) Tetrazine Complexes: A Time-Dependent Density Functional Theory Study (2016)

Time-dependent density functional theory was used to investigate optical absorption of novel Fe(II) coordination complexes with tetrazine ligands. These octahedral compounds absorb near-infrared (NIR) light and can be applied as secondary explosives with low laser-initiation thresholds compared to pentaerythritol tetranitrate. Herein, numerous ligand architectures are studied to determine relationships between molecular structure and optical absorption in order to tune the low-energy charge transfer (CT) band. Geometrical structures and vertical excitation energies calculated with the TPSSh density functional and 6-311G basis set are in excellent agreement with experiment, with a maximum deviation from UV–vis spectra of 0.10 eV. By altering molecular substituents of the ligand scaffold, the CT band can be tuned between 500 and 1100 nm. Additional conjugation in the ligand scaffold pushes the CT band into the NIR region of the spectrum. Triazolo-tetrazine ligands shift the CT band by approximately 0.70 eV relative to that of Fe(II) coordinated with bipyridine ligands. Oxygenated analogues of several compounds are also studied in order to predict optical response, while improving explosive performance. A natural population analysis suggests that the high nitrogen content of the ligand scaffolds in these energetic compounds lessens their metal-to-ligand charge transfer character compared to that of Fe(II) coordinated with bipyridine ligands. The proposed model quantum chemistry is used to establish structure–property relationships for optical properties in this class of materials in order to make optical initiation with conventional lasers a more feasible approach.
DENSITY IN HYDROSTATIC ATMOSPHERES (1963)

Abstract : A theoretical and numerical analysis was made of factors determining the height of the level of constant atmospheric density (isopycnic level) above any base. The physical relationship be tween this level and the level of maximum per cent departure from standard of density is given. While the atmospheres considered in the numerical analysis approximate the Earth's troposphere, the resulting figures, if used in conjunction with the developed theory, may be considered indica tive of the behavior of hydrostatic atmospheres in general. (Author)
Introduction of unnatural amino acids into proteins using expressed protein ligationStandard IUPAC single- and triple-letter codes for amino acids are used throughout the article (1999)

Here we describe the results of studies designed to explore the scope and limitations of expressed protein ligation (EPL), a protein semisynthesis approach that allows unnatural amino acids to be site specifically introduced into large proteins. Using Src homology 3 domains from the proteins c-Abl and c-Crk as model systems, we show here that EPL can be performed in the presence of moderate concentrations of the chemical denaturant, guanidine hydrochloride, and the organic solvent dimethylsulfoxide. Use of these solubilizing agents allowed the successful preparation of two semisynthetic proteins, 10 and 12, both of which could not be prepared using standard procedures due to the low solubility of the synthetic peptide reactants in aqueous buffers. We also report the results of thiolysis and kinetic studies which indicate that stable alkyl thioester derivatives of recombinant proteins can be generated for storage and purification purposes, and that 2-mercaptoethanesulfonic acid compares favorably with thiophenol as the thiol cofactor for EPL reactions, while having superior handling properties. Finally, we describe the semisynthesis of the fluorescein/rhodamine-containing construct (12) and the ketone-containing construct (14). The efficiency of these two syntheses indicates that EPL offers a facile way of incorporating these important types of biophysical and biochemical probes into proteins. © 2000 John Wiley & Sons, Inc. Biopoly 51: 343–354, 1999
Antimutagenic activity of methanolic extracts of four ayurvedic medicinal plants. (2008)

Methanolic extracts of Acorus calamus (Rhizome), Hemidesmus indicus (Stem), Holarrhena antidysenterica (Bark) and Plumbago zeylanica (Root), were tested for their antimutagenic potential. These extracts, at tested concentrations, showed no sign of mutagenicity to Salmonella typhimurium tester strains. The extracts of the plants exhibited varying level of antimutagenicity. At a dose of 100 microg/plate, the extracts exhibited the inhibition of His+ revertants from 18.51% to 82.66% against direct acting mutagens, methyl methanesulphonate (MMS) and sodium azide (NaN3) induced mutagenicity in Salmonella tester strains TA 97a, TA 100, TA 102 and TA 104. However, at lower concentrations (25 and 50 mcirog/plate) of the plant extracts, a decrease in antimutagenic activity was recorded. Dose dependent antimutagenic activity of the extracts is also evident from linear regression analysis of the data. The over all antimutagenic potential of above four extracts was found to be in order of A. calamus > H. indicus > H. antidysenterica > P. zeylanica. Further, total phenolic content of these extracts did not correlate with its antimutagenic activity in A. calamus and P. zeylanica.
Object as Hotspots: An Anchor-Free 3D Object Detection Approach via Firing of Hotspots (2019)

Accurate 3D object detection in LiDAR based point clouds suffers from the challenges of data sparsity and irregularities. Existing methods strive to organize the points regularly, e.g. voxelize, pass them through a designed 2D/3D neural network, and then define object-level anchors that predict offsets of 3D bounding boxes using collective evidences from all the points on the objects of interest. Contrary to the state-of-the-art anchor-based methods, based on the very nature of data sparsity, we observe that even points on an individual object part are informative about semantic information of the object. We thus argue in this paper for an approach opposite to existing methods using object-level anchors. Inspired by compositional models, which represent an object as parts and their spatial relations, we propose to represent an object as composition of its interior non-empty voxels, termed hotspots, and the spatial relations of hotspots. This gives rise to the representation of Object as Hotspots (OHS). Based on OHS, we further propose an anchor-free detection head with a novel ground truth assignment strategy that deals with inter-object point-sparsity imbalance to prevent the network from biasing towards objects with more points. Experimental results show that our proposed method works remarkably well on objects with a small number of points. Notably, our approach ranked 1st on KITTI 3D Detection Benchmark for cyclist and pedestrian detection, and achieved state-of-the-art performance on NuScenes 3D Detection Benchmark.
Dexmedetomidine attenuates the toxicity of β‑amyloid on neurons and astrocytes by increasing BDNF production under the regulation of HDAC2 and HDAC5 (2018)

Cytotoxicity of β-Amyloid (Aβ) is a major contributor to the pathogenesis of Alzheimer's disease. Dexmedetomidine (Dex) has been revealed to have multiple neuroprotective actions as a clinical anesthetic agent. The aim of the present study was to investigate the protection of Dex against Aβ in neurons and astrocytes, and the possible protective mechanisms. Primary neurons and astrocytes were isolated respectively from the hippocampus and cerebral cortex of neonatal Sprague Dawley rats. The neurons and astrocytes were incubated with Aβ in the presence or absence of Dex, which was followed by evaluation of the cell viability and apoptosis. Reverse transcription‑quantitative polymerase chain reaction, western blotting and ELISA assays were performed to assess the levels of specific genes or proteins. The results revealed that Aβ decreased the viabilities of neurons and astrocytes in a dose‑dependent manner, and elevated the rate of apoptosis. However, Dex attenuated the detrimental effects of Aβ. Aβ caused deacetylation of histone H3 by promoting the accumulation of histone deacetylase (HDAC)‑2 and HDAC5 in the cell nucleus, resulting in the reduced production of brain‑derived neurotrophic factor (BDNF). However, Dex reversed the Aβ‑induced deacetylation of histone H3 and thus, increased BDNF production. Using a HDAC inhibitor or recombinant BDNF protein also protected the neurons and astrocytes against Aβ cytotoxicity. These results suggested that the protective effect of Dex against Aβ is particularly relevant to BDNF. Thus, the present study provides a foundation for the further study of Dex protection against Aβ in animal models and pre‑clinical researches.
(Invited) Kinetics and Thermodynamics of Swcnts and Bnnts Encapsulation with α-Sexithiophene in Liquid Phase (2022)

Single-Walled Carbon Nanotubes (SWNTs) and Boron Nitride Nanotubes (BNNTs) come with hollow 1D centers, which can serve to define narrow spaces for encapsulating small organic dyes. The encapsulation process is of scientific interest because it can be used to tailor the optical properties of the resulting dyes@NTs nanohybrids. Past works have shown that the dyes@SWCNT exhibits a strongly enhanced Raman scattering cross section, while the dyes@BNNTs do emit robust, generally red-shifted, luminescence at wavelengths down to the near-IR. In both cases, the nanotube protects the encapsulated dyes from photobleaching, provides high confinement, and reinforces intermolecular interactions between dyes into specific aggregation states. Here, we compare the liquid phase encapsulation process of α-sexithiophene (6T), which is a conjugated rod-like dye, inside SWCNTs and BNNTs. Raman and luminescence imaging experiments are used to monitor the 6T encapsulation process of a large ensemble of individual nanotubes in liquid-phase. This method probes statistically the encapsulation kinetics using hundreds of individual nanotubes according to various parameters (dye concentration and temperature). The results highlight a kinetic model in which single and double aggregates is formed sequentially. This kinetics and the associated thermodynamic parameters for the 6T encapsulation will be presented and discussed so as to gain a better control over the emission properties of the nanohybrids.