gebhart/patrepeval huggingface dataset:
Cytotoxicity of Receptor-Mediated 16 [125I]Iodo-estradiol in Cultured MCF-7 Human Breast Cancer Cells (1989)

Therapeutic strategies using 125I-labeled steroid hormones are attractive in light of the estrogen dependence of many human breast cancers and the favorable microdosimetry resulting from 125I decay. We determined the uptake, specific estrogen receptor (ER) binding, and cytotoxicity of 16 alpha-[125I]iodoestradiol in cultured MCF-7 human breast cancer cells. The cytotoxicity of receptor-mediated 125I appears to be sufficient in MCF-7 cells to warrant in vivo experimentation. Furthermore, cytotoxicity not specific to ERs is minimal within the dose range necessary for ER saturation and specific cell killing. Competitive toxicity studies using nonradioactive 17 beta-estradiol demonstrate an unequivocal relationship between ER binding and clonogenic viability.
Conversion of a Group II Intron into a New Multiple-Turnover Ribozyme that Selectively Cleaves Oligonucleotides: Elucidation of Reaction Mechanism and Structure/Function Relationships (1995)

The self-splicing ai5g group II intron was transformed into a three-part ribozyme that site-specifically cleaves small oligonucleotide substrates with multiple turnover. The ribozyme is composed of intron domain 1 (D1, 425 nucleotides), with catalytically essential domain 5 (D5, 58 nucleotides) provided separately as a reaction cofactor. Together, the D1/D5 complex cleaves small substrates analogous in sequence to the 5'-splice site of the intron. Activity of the ribozyme was studied using a combination of single- and multiple-turnover experiments in which the concentrations of the RNA components were varied in order to probe their individual role in the overall mechanism. Values for kcat, Km, and kcat/Km were the same within experimental error for the two enzymological approaches. These kinetic analyses reveal that the ribozyme utilizes a classic Michaelis-Menten reaction mechanism in which the chemical step of catalysis (kcat = kchem = approximately 0.03 min-1 at full saturation) is rate limiting for the overall reaction. The D1/D5 complex binds tightly to the substrate (Km = 6.3 nM) and specifically recognizes sequences both 5' and 3' to the ribozyme cleavage site. These studies represent the first quantitative analysis of group II recognition and affinity for the 5'-splice site. As observed in previous studies on the role of D5 RNA, D5 binds tightly to the ternary complex (Km = 870 nM). The second-order rate constant for RNA cleavage (kcat/Km = 3.3 x 10(6)) is an order of magnitude slower than that observed for other ribozymes in this mechanistic class, all of which are rate-limited by steps other than chemistry. That kcat equals kchem in this ribozyme is supported by the overall kinetic analysis and by the observation that an Rp phosphorothioate is cleaved approximately 3-fold more slowly than a phosphate at the cleavage site. These studies represent a preliminary examination of stereochemical preference by a group II intron active site in the transition state. The substrate specificity, reaction conditions, and mutational sensitivity of this ribozyme are consistent with a reaction analogous to the first step of group II intron self-splicing, although its stereochemical preference is analogous to a second-step reversal.
Mitochondria-targeted vitamin E analogs inhibit breast cancer cell energy metabolism and promote cell death (2013)

We conclude that mitochondria-targeted small molecular weight chromanols exhibit selective anti-proliferative effects and cytotoxicity in multiple breast cancer cells, and that esterification of the hydroxyl group in mito-chromanols is not a critical requirement for its anti-proliferative and cytotoxic effect.
Neuregulin 1 hypomorphic mutant mice: enhanced baseline locomotor activity but normal psychotropic drug-induced hyperlocomotion and prepulse inhibition regulation (2009)

Neuregulin 1 (Nrg1) has been widely recognized as a candidate gene for schizophrenia. This study therefore investigated mice heterozygous for a mutation in the transmembrane domain of this trophic factor (Nrg1+/- mice) in a number of behavioural test systems with relevance to schizophrenia, including psychotropic drug-induced locomotor hyperactivity and prepulse inhibition (PPI) of startle. Baseline locomotor activity in the open field or in photocell cages was slightly, but significantly enhanced in Nrg1+/- mice compared to wild-type littermate controls at age 12-16 wk, but not at age 6 months. The ability of amphetamine, phencyclidine (PCP) or MK-801 to induce locomotor hyperactivity was not significantly different between the genotypes. There was no difference in baseline PPI, startle or startle habituation and there was no difference in the effect of apomorphine, amphetamine or MK-801 on any of these parameters. Only treatment with the 5-HT1A receptor agonist 8-hydroxy-dipropylaminotetralin (8-OH-DPAT) showed a differential effect between genotypes, with a disruption of PPI occurring in Nrg1+/- mice compared to no effect in wild-type controls. This treatment also induced a significant reduction of startle which could have influenced the result. The density of dopamine D2 receptors in the forebrain and of 5-HT1A receptors in the hippocampus and raphe nuclei was not different between Nrg1+/- mice and controls. These studies add to the knowledge about behavioural effects in this mouse model of impaired Nrg1 function and suggest that a number of the behavioural tests with relevance to schizophrenia are normal in these mice.
GFD-SSD: Gated Fusion Double SSD for Multispectral Pedestrian Detection (2019)

Pedestrian detection is an essential task in autonomous driving research. In addition to typical color images, thermal images benefit the detection in dark environments. Hence, it is worthwhile to explore an integrated approach to take advantage of both color and thermal images simultaneously. In this paper, we propose a novel approach to fuse color and thermal sensors using deep neural networks (DNN). Current state-of-the-art DNN object detectors vary from two-stage to one-stage mechanisms. Two-stage detectors, like Faster-RCNN, achieve higher accuracy, while one-stage detectors such as Single Shot Detector (SSD) demonstrate faster performance. To balance the trade-off, especially in the consideration of autonomous driving applications, we investigate a fusion strategy to combine two SSDs on color and thermal inputs. Traditional fusion methods stack selected features from each channel and adjust their weights. In this paper, we propose two variations of novel Gated Fusion Units (GFU), that learn the combination of feature maps generated by the two SSD middle layers. Leveraging GFUs for the entire feature pyramid structure, we propose several mixed versions of both stack fusion and gated fusion. Experiments are conducted on the KAIST multispectral pedestrian detection dataset. Our Gated Fusion Double SSD (GFD-SSD) outperforms the stacked fusion and achieves the lowest miss rate in the benchmark, at an inference speed that is two times faster than Faster-RCNN based fusion networks.
Proteoglycans of developing bone. (1983)

We purified and characterized the bone proteoglycans from fetal calves, growing rats, and human fetuses. The major proteoglycan is part of the mineralized tissue matrix and only 10-20% can be extracted prior to demineralization. This bone proteoglycan is a small glycoconjugate (Mr = 80,000-120,000) containing approximately 20-30% protein and either one or two chondroitin sulfate chains (Mr = 40,000) attached to a relatively monodisperse protein core (Mr = 38,000). "O"-linked and "N"-linked oligosaccharide units are also present. Antibodies directed against the protein core of calf bone proteoglycan do not cross-react with cartilage, skin, corneal, or basement membrane proteoglycans in immunoassays and have minimal cross-reactivity with scleral proteoglycans. Quantitative immunoassays and indirect immunofluorescence were used to show that the molecule is localized to forming bone trabeculae and dentin, but not to any other tissue. Osteoblasts and osteoprogenitor cells adjacent to areas undergoing rapid osteogenesis also contain this small proteoglycan. A second proteoglycan (Mr approximately equal to 1,000,000) was extracted from newly forming bone prior to demineralization. This large proteoglycan, which was isolated from the cartilage-free areas of developing intramembranous bone, has a protein core similar to that of the cartilage aggregating proteoglycan and cross-reacts with antisera raised against these cartilage proteoglycans but not with the small mineral-entrapped proteoglycan. It contains larger (Mr = 40,000) and fewer chondroitin sulfate chains than its cartilage-derived analogue, and is localized to the soft connective tissue mesenchyme lying between growing bone trabeculae. More fully formed compact bone did not contain detectable quantities of this proteoglycan.
Laboratory Manual for GENETIC ENGINEERING (2009)

Laboratory Manual for Genetic Engineering , Laboratory Manual for Genetic Engineering , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Human immunodeficiency virus type 1 capsid formation in reticulocyte lysates (1996)

The Gag polyprotein of human immunodeficiency virus (HIV) (Pr55Gag) contains sufficient information to direct particle assembly events when expressed within tissue culture cells. HIV Gag proteins normally form particles at a plasma membrane assembly site, in a manner analogous to that of the type C avian and mammalian leukemia/sarcoma viruses. It has not previously been demonstrated that immature HIV capsids can form without budding through an intact cellular membrane. In this study, a rabbit reticulocyte lysate translation reaction was used to recreate HIV capsid formation in vitro. Production of HIV-1 Pr55Gag and of a matrix-deleted Gag construct resulted in the formation of a subset of Gag protein structures with an equilibrium density of 1.15 g/ml. Gel filtration chromatography revealed these Gag protein structures to be larger than 2 x 10(6) Da, consistent with the formation of large multimers or capsids. These Gag protein structures were protease sensitive in the absence of detergent, indicating that they did not contain a complete lipid envelope. Spherical structures were detected by electron microscopy within the reticulocyte lysate reaction mixtures and appeared essentially identical to immature HIV capsids or retrovirus-like particles. These results demonstrate that the HIV Gag protein is capable of producing immature capsids in a cell-free reaction and that such capsids lack a complete lipid envelope.
High levels of amyloid-β protein from S182 (Glu246) familial Alzheimerʼs cells (1995)

Most early-onset familial Alzheimer disease is associated with missense mutations in S182, a membrane protein on chromosome 14. We investigated amyloid-beta protein (A beta) precursor (A beta PP) metabolism in skin fibroblasts from S182 (Glu246)-affected individuals and unaffected family members. Steady-state A beta PP levels were similar among all lines as was the degree of increase in soluble A beta PP released upon stimulation of cells with either phorbol ester or serum. Among all lines studied, A beta levels were consistently detectable only in the medium of a single line of S182 (Glu246) cells, consistent with the conclusion that some S182 mutant lines may accumulate A beta in their conditioned media. Studies of cells from additional individuals and under other conditions will be required to establish this association of elevated A beta levels with S182 mutations.
Electrospray ionization mass spectrometry of AZT H‐phosphonates conjugated with steroids (2003)

AZT H-phosphonates conjugated with steroids were synthesized and determined by positive and negative ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). The fragmentation pathways were investigated in detail. There are very different characteristic fragment ions in the positive and negative ion MS/MS spectra. The azide group of compounds 6a and 6b underwent either elimination of HN(3) or rearrangement to an amine in both positive and negative ion mass spectrometry.
Analyzing Song Structure With Spectral Clustering. (2014)

[TODO] Add abstract here.
Development of energy aware TDMA-based MAC protocol for wireless sensor network system (2009)

The development of wireless sensor networks (WSN) can be motivated by several types of applications such as habitat monitoring, smart healthcare system, building automation, and etc. These applications however, demand an energy-efficient WSN that can prolong the network lifetime and can provide high throughput, low latency and delay, and high packet received rate data communication. The ability of wireless network structure to minimize network lifetime is among the hot topic due to limitation resources such as energy, processing and memory, in sensor network architecture itself. This paper proposes a novel approach that tries to reduce idle energy consumption by implementing active-sleep algorithm named energy aware A-MAC protocol. The result from the computational model shows that the algorithm can prolong network lifetime due to efficiency in energy consumption from time slot management.
Developing genetically engineered mouse models using engineered nucleases: Current status, challenges, and the way forward (2016)

The rapid development of engineered nucleases such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regulated interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonuclease 9 (Cas9) system has ushered in the era of ‘renaissance in precision genome engineering’ with profound potential to generate mouse models of human diseases. However, with accumulating experience, some drawbacks that we must seriously consider have appeared along with the recent advances in molecular genetics. Here, we highlight recent technical advances of engineered nucleases, discuss the challenges we have faced while using these ‘state of the art’ genome-editing technologies to generate genetically engineered mouse models (GEMs) and, and look toward the potential future uses of these technologies.
ChemInform Abstract: CHEMOSELECTIVE N‐ETHYLATION OF BOC AMINO ACIDS WITHOUT RACEMIZATION (1985)

Abstract Die N‐Ethylierung der geschützten Aminosäuren (I) verläuft in Gegenwart einer Lithium‐base selektiv und ohne Racemisierung zu den Verbindungen (II).
A Scalable and Energy-Efficient Context Monitoring Framework for Mobile Personal Sensor Networks (2009)

The key feature of many emerging pervasive computing applications is to proactively provide services to mobile individuals. One major challenge in providing users with proactive services lies in continuously monitoring users' context based on numerous sensors in their PAN/BAN environments. The context monitoring in such environments imposes heavy workloads on mobile devices and sensor nodes with limited computing and battery power. We present SeeMon, a scalable and energy-efficient context monitoring framework for sensor-rich, resource-limited mobile environments. Running on a personal mobile device, SeeMon effectively performs context monitoring involving numerous sensors and applications. On top of SeeMon, multiple applications on the mobile device can proactively understand users' contexts and react appropriately. This paper proposes a novel context monitoring approach that provides efficient processing and sensor control mechanisms. We implement and test a prototype system on two mobile devices: a UMPC and a wearable device with a diverse set of sensors. Example applications are also developed based on the implemented system. Experimental results show that SeeMon achieves a high level of scalability and energy efficiency.
Focal Cooling Suppresses Spontaneous Epileptiform Activity without Changing the Cortical Motor Threshold (2002)

In this patient with tumor-related epilepsy, focal cooling of the cortex reproducibly abolished interictal epileptiform discharges without changing the motor threshold to electrical stimulation.
Control of NKT Cell Differentiation by Tissue-Specific Microenvironments (2003)

CD1d-restricted Valpha14 NKT cells play an important role in both Th1- and Th2-type immune responses. To determine whether NKT cells develop two functionally distinct subsets that provoke different types of responses, we examined the phenotypes and cellular functions of NK1.1(+) and DX5(+) T cells. We found that both NK1.1(+) and DX5(+) T cells are CD1d-restricted Valpha14 T cells with identical Ag specificities, phenotypes, tissue locations, and functions. Similar to the NK1.1 marker, the DX5 marker (CD49b) is expressed on mature NKT cells in both NK1.1 allele-positive and allele-negative strains. However, when NK1.1(+) and DX5(+) NKT cells isolated from different tissues were compared, we found that thymic and splenic NKT cells differed not only in their cytokine profiles, but also in their phenotype and requirements for costimulatory signals. Thymic NKT cells displayed the phenotype of activated T cells and could be fully activated by TCR ligation. In contrast, splenic NKT cells displayed the phenotype of memory T cells and required a costimulatory signal for activation. Furthermore, the function and phenotype of thymic and splenic NKT cells were modulated by APCs from various tissues that expressed different levels of costimulatory molecules. Modulation of NKT cell function and differentiation may be mediated by synergic effects of costimulatory molecules on the surface of APCs. The results of the present study suggest that the costimulatory signals of tissue-specific APCs are key factors for NKT cell differentiation, and these signals cannot be replaced by anti-CD28 or anti-CD40 ligand Abs.
<title>Scene-adaptive motion interpolation structures based on temporal masking in human visual perception</title> (1993)

In this paper we present a novel technique to dynamically adapt motion interpolation structures by temporal segmentation. The interval between two reference frames is adjusted according to the temporal variation of the input video. The difficulty of bit rate control for this dynamic group of pictures (GOP) structure is resolved by taking advantage of temporal masking in human vision. Six different frame types are used for efficient bit rate control, and telescopic search is used for fast motion estimation because frame distances between reference frames are dynamically varying. Constant picture quality can be obtained by variable bit rate coding using this approach and the statistical bit rate behavior of the coder is discussed. Advantages for low bit rate coding and storage media applications and implications for HDTV coding are discussed. Simulations on test video including HDTV sequences are presented for various GOP structures and different bit rates, and the results compare favorably with those for conventional fixed GOP structures.
Novel Peptidomimetics of the Antifungal Cyclic Peptide Rhodopeptin:  Synthesis of Mimetics and Their Antifungal Activity (2001)

[reaction: see text]. Novel peptidomimetics of the antifungal cyclic peptide Rhodopeptin were synthesized. As with the cyclic peptides, the presence of all three Rhodopeptin side chains was found to be indispensable for peptidomimetic activity. We discovered new compounds exhibiting greater antifungal activity and improved physiochemical properties in comparison to the parent compounds.
Prostate-Specific Membrane Antigen Targeted Imaging and Therapy of Prostate Cancer Using a PSMA Inhibitor as a Homing Ligand (2009)

Prostate cancer (PCa) is a major cause of mortality and morbidity in Western society today. Current methods for detecting PCa are limited, leaving most early malignancies undiagnosed and sites of metastasis in advanced disease undetected. Major deficiencies also exist in the treatment of PCa, especially metastatic disease. In an effort to improve both detection and therapy of PCa, we have developed a PSMA-targeted ligand that delivers attached imaging and therapeutic agents selectively to PCa cells without targeting normal cells. The PSMA-targeted radioimaging agent (DUPA−99mTc) was found to bind PSMA-positive human PCa cells (LNCaP cell line) with nanomolar affinity (KD = 14 nM). Imaging and biodistribution studies revealed that DUPA−99mTc localizes primarily to LNCaP cell tumor xenografts in nu/nu mice (% injected dose/gram = 11.3 at 4 h postinjection; tumor-to-muscle ratio = 75:1). Two PSMA-targeted optical imaging agents (DUPA−FITC and DUPA−rhodamine B) were also shown to efficiently label PCa cells and to internalize and traffic to intracellular endosomes. A PSMA-targeted chemotherapeutic agent (DUPA−TubH) was demonstrated to kill PSMA-positive LNCaP cells in culture (IC50 = 3 nM) and to eliminate established tumor xenografts in nu/nu mice with no detectable weight loss. Blockade of tumor targeting upon administration of excess PSMA inhibitor (PMPA) and the absence of targeting to PSMA-negative tumors confirmed the specificity of each of the above targeted reagents for PSMA. Tandem use of the imaging and therapeutic agents targeted to the same receptor could allow detection, staging, monitoring, and treatment of PCa with improved accuracy and efficacy.
Host Species Barriers to Influenza Virus Infections (2006)

Most emerging infectious diseases in humans originate from animal reservoirs; to contain and eradicate these diseases we need to understand how and why some pathogens become capable of crossing host species barriers. Influenza virus illustrates the interaction of factors that limit the transmission and subsequent establishment of an infection in a novel host species. Influenza species barriers can be categorized into virus-host interactions occurring within individuals and host-host interactions, either within or between species, that affect transmission between individuals. Viral evolution can help surmount species barriers, principally by affecting virus-host interactions; however, evolving the capability for sustained transmission in a new host species represents a major adaptive challenge because the number of mutations required is often large.
Recognition and activation by ureas and thioureas: stereoselective reactions using ureas and thioureas as hydrogen-bonding donors (2005)

Hydrogen-bonding interaction plays a crucial role in the molecular recognition and activation processes of various biologically important reactions that are mediated by enzymes and antibodies in living organisms. Recently, it has been shown that a hydrogen-bonding donor can be used as a general acid catalyst for various types of reactions in organic chemistry. In this article, we describe enantioselective reactions catalyzed by urea and thiourea derivatives as general acid catalysts as well as diastereoselective reactions. This perspective provides an overview of this rapidly growing field.