gebhart/patrepeval huggingface dataset:
Optimization Based Tumor Classification from Microarray Gene Expression Data (2011)

The performance of our algorithm overall was better than the other algorithms reported in the literature and classifiers found in WEKA data-mining package. Since it does not require a parameter optimization and it performs consistently very high prediction rate on different type of data sets, HBE method is an effective and consistent tool for cancer type prediction with a small number of gene markers.
An empirical study of greedy local search for satisfiability testing (1993)

Administration of 3 microg dexamethasone at day 8 of incubation into the allantoic cavity resulted in various embryopathies in embryos by the 15th day of incubation. Chicken alpha-foetoprotein (chAFP) and serum albumin concentrations, when examined at the 12th day of incubation, were below the corresponding controls (P<0.01), whereas total serum protein was only slightly lower, On day 15 chAFP concentrations were similar to those of the controls, serum albumin values were markedly reduced and total serum protein was significantly decreased. The results suggested a selective reduction of serum albumin synthesis in the 15-day-old chick embryo. Following administration of 2 IU insulin on the first day of incubation, into the yolk sac, one third of the embryos developed embryopathies. ChAFP, serum albumin and whole serum protein values were unchanged on either the 12th day or 15th day of incubation. Inoculation of 100 microg adrenaline into the allantoic cavity on the sixth day of incubation resulted in embryopathies in only a few instances. ChAFP total serum protein values were not affected. However, serum albumin concentrations were significantly lower on the 12th day, but not on the 15th. The responses to L-thyroxine were both time- and dose-dependent. Inoculation of 2 microg thyroxine on the second day of incubation resulted in few embryopathies. ChAFP levels were significantly lower on the 12th and 15th day of incubation. In contrast, serum albumin and total serum protein concentrations were normal at both times. Similar results were obtained when 2 microg of thyroxine were administered at the third day of incubation. Thus in order to inhibit selectively chAFP synthesis, administration of 2 microg thyroxine on day 2 or 3 of incubation is suggested. When 10 microg thyroxine were injected on day 8 of incubation, 80% of the embryos showed embryopathies on day 12 of incubation. ChAFP and serum albumin levels were markedly depressed. The concentration of total serum protein was significantly decreased on day 12 but less so, though still significantly, on day 15. These results demonstrate the possibility to influence selectively chAFP and serum albumin synthesis, thereby facilitating studies on chemically induced teratological, including pathophysiological, processes in the avian embryo.
Widespread occurrence of "87 kDa," a major specific substrate for protein kinase C. (1986)

An 87-kDa phosphoprotein, identified previously as a major, specific substrate for Ca2+/phospholipid/diacylglycerol-dependent protein kinase (protein kinase C) in broken cell preparations from rat brain, has been characterized with respect to its species, tissue, and subcellular distribution. A similar protein was present in monkey, human, mouse, and bovine brain and in Torpedo californica electric organ. The protein was also identified in a variety of nonneuronal rat and bovine tissues. The rat protein had an apparent molecular mass 4-7 kDa lower, and was slightly more acidic, than the protein in bovine tissues. The 87-kDa proteins from various bovine tissues were identical by the following criteria: each was phosphorylated by exogenous protein kinase C, was of comparable molecular mass, generated multiple spots within the pH range of 4.4-4.9 upon isoelectric focusing, yielded identical patterns upon digestion with Staphylococcus aureus V8 protease, and was recognized by a specific 87-kDa antiserum. The relative concentrations of the 87-kDa protein in bovine tissues were highest in brain, spleen, and lung, moderate in testis, pancreas, adrenal, kidney, and liver, and lowest in heart and skeletal muscle. In the brain, the 87-kDa protein was concentrated in the synaptosomal membrane and in the cytosol. The membrane-bound protein was extractable with nonionic detergents but not with NaCl. This species, tissue, and subcellular distribution of the 87-kDa protein is similar to that of protein kinase C.
The Rb2/p130 gene product is a nuclear protein whose phosphorylation is cycle regulated (1995)

The Rb2/p130 protein has been shown to have a high sequence homology with the retinoblastoma gene product (pRb), one of the most well-characterized tumor suppressor genes, and with pRB-related p107, especially in their conserved pocket domains, which display a primary role in the function of these proteins. In this study, we report on the biochemical and immunocytochemical characterization of the Rb2/p130 protein, using a polyclonal antibody developed against its "spacer" region included in the pocket domain of the whole protein. We show that pRb2/p130 is a phosphoprotein located at the nuclear level and that its phosphorylation pathway can be dramatically reduced by phosphatase treatment. Moreover pRb2/p130 with p107, is one of the major targets of the E1A viral oncoprotein-associated kinase activity, showing a phosphorylation pattern which is modulated during the cell cycle, reaching a peak of activation at the onset of S-phase.
A polynomial algorithm to find an independent set of maximum weight in a fork-free graph (2006)

The class of fork-free graphs is an extension of claw-free graphs and their subclass of line graphs. The first polynomial-time solution to the maximum weight independent set problem in the class of line graphs, which is equivalent to the maximum matching problem in general graphs, has been proposed by Edmonds in 1965 and then extended to the entire class of claw-free graphs by Minty in 1980. Recently, Alekseev proposed a solution for the larger class of fork-free graphs, but only for the unweighted version of the problem, i.e. finding an independent set of maximum cardinality. In the present paper, we describe the first polynomial-time algorithm to solve the problem for weighted fork-free graphs.
Deep-Learning-Incorporated Augmented Reality Application for Engineering Lab Training (2022)

Deep learning (DL) algorithms have achieved significantly high performance in object detection tasks. At the same time, augmented reality (AR) techniques are transforming the ways that we work and connect with people. With the increasing popularity of online and hybrid learning, we propose a new framework for improving students’ learning experiences with electrical engineering lab equipment by incorporating the abovementioned technologies. The DL powered automatic object detection component integrated into the AR application is designed to recognize equipment such as multimeter, oscilloscope, wave generator, and power supply. A deep neural network model, namely MobileNet-SSD v2, is implemented for equipment detection using TensorFlow’s object detection API. When a piece of equipment is detected, the corresponding AR-based tutorial will be displayed on the screen. The mean average precision (mAP) of the developed equipment detection model is 81.4%, while the average recall of the model is 85.3%. Furthermore, to demonstrate practical application of the proposed framework, we develop a multimeter tutorial where virtual models are superimposed on real multimeters. The tutorial includes images and web links as well to help users learn more effectively. The Unity3D game engine is used as the primary development tool for this tutorial to integrate DL and AR frameworks and create immersive scenarios. The proposed framework can be a useful foundation for AR and machine-learning-based frameworks for industrial and educational training.
Enhancing Perovskite Solar Cell Performance through Femtosecond Laser Polishing (2020)

Nonradiative recombination loss is a key process that determines the performance of perovskite solar cells, and how to control it is significant for the research and development of perovskites. Generally, traditional chemical modification/passivation methods are complicated and prone to secondary contamination. Herein, femtosecond (fs) laser polishing as a promising technique is demonstrated to ameliorate the surface of perovskite films, reduce nonradiative recombination loss, and improve solar cell performance. The high‐intensity fs laser pulses can remove around 20 nm‐thick perovskite top layer through an ionization process, help to decrease the grain boundary density, and enlarge the grain size of perovskite films after recrystallization. It is believed that fs laser polishing is a time‐effective and highly precise technique that is suitable for large‐scale device production, thus will trigger more applications in optoelectronics.
A human IgG-like bispecific antibody co-targeting epidermal growth factor receptor and the vascular endothelial growth factor receptor 2 for enhanced antitumor activity (2015)

Both Epidermal Growth Factor Receptor (EGFR) and the Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) play critical roles in tumorigenesis. We hypothesized co-targeting EGFR and VEGFR2 using a bispecific antibody might have significant therapeutic potential. Here,we designed and produced a human IgG-like bispecific antibody (Bi-Ab) based on the variable regions of cetuximab (an anti-EGFR antibody) and mAb-04 (an anti-VEGFR2 antibody developed in our lab) . The Bi-Ab was found to inhibit the proliferation, survival and invasion of cancer cells via ablating phosphorylation of receptor and downstream signaling. In vivo efficacy was demonstrated against established HT-29 and SKOV-3 xenografts grown in nude mice. Studies revealed our Bi-Ab was able to restrain xenografted tumor growth and prolong survival of mice through inhibiting cell proliferation,promoting apoptosis and anti-angiogenesis. In contrast to cetuximab or mAb-04 alone, our Bi-Ab exhibits enhanced antitumor activity and has equal or slightly superior activity to their combination (Combi). It shows promise as a therapeutic agent, especially for use against tumors EGFR and/or VEGFR2 over-expressing malignancies.
Detection of amplified int-2/FGF-3 gene in primary breast carcinomas using differential polymerase chain reaction (2001)

Amplification of int-2/FGF-3 gene was investigated by differential polymerase chain reaction (dPCR) in 440 archival primary breast carcinoma tissues. Of these, 23 were comedo ductal carcinoma in situ (DCIS), 18 were non-comedo DCIS, 41 were comedo DCIS with adjacent invasive ductal carcinomas, 19 were non-comedo DCIS with adjacent invasive ductal carcinomas, 270 were invasive ductal carcinomas, 33 were invasive lobular carcinomas, 21 were colloid carcinomas and 15 were medullary carcinomas. Int-2 was amplified in 22% (96/440) of the primary breast carcinomas. It was shown that int-2 was amplified in 13% (3/23) of the comedo DCIS, 17% (7/41) of the comedo DCIS and 29% (12/41) of the adjacent invasive ductal carcinomas, 26% (71/270) of the invasive ductal carcinomas, 18% (6/33) of the invasive lobular carcinomas, 10% (2/21) of the colloid carcinomas and 13% (2/15) of the medullary carcinomas. In contrast, int-2 was not amplified in non-comedo DCIS and invasive ductal carcinomas with adjacent non-comedo DCIS lesions. A significant association was observed between int-2 amplification in the in situ components and adjacent invasive lesion (P<0.05). All tumors with int-2 amplification in the in situ lesions (7/7) also demonstrated same degree of amplification in the adjacent invasive components. However, 9% (5/53) of the tumors with no amplified int-2 gene in the in situ components showed int-2 amplification in the adjacent invasive lesions. A significant relationship was noted between amplification of int-2 and lymph node metastases (P<0.05) and poorly differentiated tumors (P<0.05) but not with estrogen receptor status (P>0.05) and proliferation index (Ki-67 and PCNA) (P>0.05). In Malaysia, majority of the patients belong to younger age group (<50 years old) but a comparison of the age groups showed that the amplification of int-2 was not statistically associated with patient age (P>0.05). These observations indicate that amplification of int-2 tends to strengthen the view that int-2 may have the potential to be an indicator of poor prognosis regardless of the age of the patient. Moreover, the presence of int-2 amplification in preinvasive, preinvasive and adjacent invasive lesions, and invasive carcinomas suggest that int-2 could be a marker of genetic instability occurring in early and late stages of tumor development.
Preliminary 6 month results from the argus<sup>tm</sup> ii epiretinal prosthesis feasibility study (2009)

The Argus II 60 channel epiretinal prosthesis has been developed in order to provide partial restoration of vision to subjects blinded from outer retinal degenerative disease. To date the device has been implanted in 21 subjects as part of a feasibility study. In 6 month post-implantation door finding and line tracking orientation and mobility testing, subjects have shown improvements of 86% and 73%, respectively, for system on vs. system off. In high-contrast Square Localization tests using a touch screen monitor 87% of tested subjects performed significantly better with the system on compared with off. These preliminary results show that the Argus II system provides some functional vision to blind subjects.
Muscarinic receptor binding in the parotid gland. Different affinities of some anticholinergic drugs between the parotid gland and ileum. (1982)

Some properties of the muscarinic receptors in guinea pig parotid gland were studied by receptor binding, using 1-Quinuclidinyl [phenyl 4-3H] benzilate ((-)3H-QNB) as radio-ligand. In equilibrium experiments, (-)3H-QNB was specifically bound with high affinity (KD 1.1 X 10(-10)M) to a limited number of sites (0.37 pmoles/mg protein) in homogenates of parotid gland. The binding could be described by a simple bimolecular association model. Muscarinic antagonists and agonists effectively inhibited the binding, whereas a variety of other drugs had little or no effect. In competition experiments the affinities of five muscarinic antagonists were compared in the guinea pig parotid gland and ileum. Two of these drugs--namely, oxybutynine and dicyclomine--had a very much higher affinity for the binding-sites in the parotid gland than the ileum (24 vs. 34 times). Whether this observation might be caused by heterogeneous binding-sites for oxybutynine and dicyclomine or some other phenomenon is under further investigation.
Torque Ripple Minimization of BLDC Motor by Using Vector Control (2015)

This paper provides an alternative approach to reduce torque ripple in Square-wave PM Motors (BLDC motor). Instead of conventional square-wave form, the method uses the principle of vector control to optimally design the wave-form of reference current in such a way that the torque ripple is minimal. The proposed Vector Control has advantage of the torque ripple is greatly reduced, and the flux weakening for constant-power high-speed mode can be achieved by injecting a negative d-axis current into the control system, just like for the case of PM Synchronous Motors (sine type machines).
Short Bowel Syndrome and Malabsorption - Causes and Prevention (2014)

Several operative strategies to prevent SBS are useful. Timing and extent of reoperation need careful consideration. Minimizing intestinal resection, bowel-conserving techniques for complications such as fistula or strictures, and remodeling procedures are important.
HLA-G and Other Immune Checkpoint Molecules as Targets for Novel Combined Immunotherapies (2022)

HLA-G is an HLA-class Ib molecule that is involved in the establishment of tolerance at the maternal/fetal interface during pregnancy. The expression of HLA-G is highly restricted in adults, but the de novo expression of this molecule may be observed in different hematological and solid tumors and is related to cancer progression. Indeed, tumor cells expressing high levels of HLA-G are able to suppress anti-tumor responses, thus escaping from the control of the immune system. HLA-G has been proposed as an immune checkpoint (IC) molecule due to its crucial role in tumor progression, immune escape, and metastatic spread. We here review data available in the literature in which the interaction between HLA-G and other IC molecules is reported, in particular PD-1, CTLA-4, and TIM-3, but also IDO and TIGIT. Clinical trials using monoclonal antibodies against HLA-G and other IC are currently ongoing with cancer patients where antibodies and inhibitors of PD-1 and CTLA-4 showed encouraging results. With this background, we may envisage that combined therapies using antibodies targeting HLA-G and another IC may be successful for clinical purposes. Indeed, such immunotherapeutic protocols may achieve a better rescue of effective anti-tumor immune response, thus improving the clinical outcome of patients.
Methotrexate Induces Apoptosis of Postpartum Placental Cytotrophoblasts (2017)

<b><i>Background:</i></b> Though methotrexate (MTX) is known to inhibit proliferation of trophoblasts derived from ectopic and intrauterine pregnancies, its action on trophoblasts derived from postpartum placenta remains questionable. This study was designed to ascertain the efficacy of MTX in inducing cell death of postpartum placental cytotrophoblasts (PPTC). <b><i>Methodology:</i></b> Primary human cytotrophoblasts were isolated from placentae of 1st and 2nd trimester intrauterine pregnancies and from postpartum placentae. The isolated trophoblasts were identified based on the expression of cytokeratin 7. MTX-induced inhibition of proliferation of cytotrophoblasts was detected by flow cytometry combined with the WST-1 assay. Secretion of HCG-β and invasiveness were evaluated to assess the effect of MTX on blocking the differentiated cellular function of cytotrophoblasts in relation to the gestational age. The efficacy of MTX in inducing apoptosis of cytotrophoblasts was estimated by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling. <b><i>Results:</i></b> MTX significantly inhibited the proliferation and differentiation of cytotrophoblasts. MTX-induced cell apoptosis of PPTC was confirmed by increased expression of Fas, FasL, Bax, cleaved caspases 3, 7, 8, and 9, and decreased expression of Bcl-2. <b><i>Conclusion:</i></b> MTX inhibits replication and differentiation of cytotrophoblasts and appears to be an efficient inducer of PPTC apoptosis.
NOCTURIA (2000)

Purpose: We review the current state of knowledge of nocturia and present algorithms for diagnosis, classification and treatment. \nMaterials and Methods: We reviewed the recent literature on nocturia, and state-of-the-art methods of diagnosis, classification and treatment. \nResults: Nocturia, which is among the most bothersome of all urological symptoms, has heretofore been poorly classified and understood. Multiple factors may result in nocturia, including pathological conditions, such as cardiovascular disease, diabetes mellitus, lower urinary tract obstruction, anxiety or primary sleep disorders, and behavioral and environmental factors. Nocturia may be attributed to nocturnal polyuria (nocturnal urine overproduction) and/or diminished nocturnal bladder capacity. Distinction between these conditions is made by a simple arithmetic analysis of a 24-hour voiding diary. \nConclusions: Nocturia has been poorly studied, and its etiology and pathogenesis have been classified only recently. We present a scheme for diagnosis and care of patients suffering from loss of sleep due to nocturnal voiding.
Functional Cardiotoxicity Profiling and Screening Using the xCELLigence RTCA Cardio System (2011)

Cardiac safety testing of lead drug candidates is an important part of the drug discovery and development process. All new chemical entities need to be subjected to extensive preclinical assessment for cardiac liability, especially for a potentially fatal form of ventricular arrhythmia referred to as Torsades de Pointes. We have developed an innovative label-free, real-time system, the xCELLigence RTCA Cardio System, which is designed to monitor contractility of cardiomyocytes based on impedance measurement. The assay is performed using specially designed microtiter plates that are integrated with gold microelectrodes. The system was validated using mouse embryonic stem cell-derived cardiomyocytes, human-induced pluripotent stem cell-derived cardiomyocytes, and rat neonatal primary cardiomyocytes by applying a variety of tool compounds and drugs with known mechanisms of action. Our data show that the time resolution in the assay can provide important information about compound action. Furthermore, the impedance-based beating profile in response to compound treatment can provide mechanistic toxicity information regarding the target being modulated and may be able to flag pro-arrhythmic compounds. We believe the real-time and kinetic aspect of this technology combined with beat-to-beat measurement of cardiomyocyte contraction would make this instrument an important part of preclinical cardiac safety assessment.
TGFβ-mediated suppression of CD248 in non-cancer cells via canonical Smad-dependent signaling pathways is uncoupled in cancer cells (2014)

The findings indicate that decoupling of CD248 regulation by TGFβ may contribute to its tumor-promoting properties, and underline the importance of exploring the TGFβ-CD248 signaling pathway as a potential therapeutic target for early prevention of cancer and proliferative disorders.
Constitutive activation of CREB in mice enhances temporal association learning and increases hippocampal CA1 neuronal spine density and complexity (2017)

Transcription factor CREB is believed to play essential roles in the formation of long-term memory (LTM), but not in learning and short-term memory (STM). Surprisingly, we previously showed that transgenic mice expressing a dominant active mutant of CREB (DIEDML) in the forebrain (DIEDML mice) demonstrated enhanced STM and LTM in hippocampal-dependent, rapid, one-trial learning tasks. Here we show that constitutive activation of CREB enhances hippocampal-dependent learning of temporal association in trace fear conditioning and delayed matching-to-place tasks. We then show that in DIEDML mice the apical tuft dendrites of hippocampal CA1 pyramidal neurons, required for temporal association learning, display increased spine density, especially of thin spines and of Homer1-negative spines. In contrast, the basal and apical oblique dendrites of CA1 neurons, required for rapid one-trial learning, show increased density of thin, stubby, and mushroom spines and of Homer1-positive spines. Furthermore, DIEDML mice showed increased dendritic complexity in the proximal portion of apical CA1 dendrites to the soma. In contrast, forebrain overexpression of CaMKIV, leading to enhanced LTM but not STM, show normal learning and CA1 neuron morphology. These findings suggest that dendritic region-specific morphological changes in CA1 neurons by constitutive activation of CREB may contribute to improved learning and STM.
Frequency-division technique for simultaneous wireless power transfer to two receivers (2016)

In this paper, we propose a frequency division technique for transferring wireless powers simultaneously to two receivers. The network is composed of one transmitter and two receivers, with three matching networks to match the two loading coils to the source at two different frequencies. The application scenario and the corresponding circuit model are presented. An illustrative example is finally analyzed to validate the proposed technique. The proposed frequency division approach can be potentially extended to multiple receivers.