gebhart/patrepeval huggingface dataset:
Targeting p90 Ribosomal S6 Kinase Eliminates Tumor-Initiating Cells by Inactivating Y-Box Binding Protein-1 in Triple-Negative Breast Cancers (2012)

Y-box binding protein-1 (YB-1) is the first reported oncogenic transcription factor to induce the tumor-initiating cell (TIC) surface marker CD44 in triple-negative breast cancer (TNBC) cells. In order for CD44 to be induced, YB-1 must be phosphorylated at S102 by p90 ribosomal S6 kinase (RSK). We therefore questioned whether RSK might be a tractable molecular target to eliminate TICs. In support of this idea, injection of MDA-MB-231 cells expressing Flag-YB-1 into mice increased tumor growth as well as enhanced CD44 expression. Despite enrichment for TICs, these cells were sensitive to RSK inhibition when treated ex vivo with BI-D1870. Targeting RSK2 with small interfering RNA (siRNA) or small molecule RSK kinase inhibitors (SL0101 and BI-D1870) blocked TNBC monolayer cell growth by ∼100%. In a diverse panel of breast tumor cell line models RSK2 siRNA predominantly targeted models of TNBC. RSK2 inhibition decreased CD44 promoter activity, CD44 mRNA, protein expression, and mammosphere formation. CD44(+) cells had higher P-RSK(S221/227) , P-YB-1(S102) , and mitotic activity relative to CD44(-) cells. Importantly, RSK2 inhibition specifically suppressed the growth of TICs and triggered cell death. Moreover, silencing RSK2 delayed tumor initiation in mice. In patients, RSK2 mRNA was associated with poor disease-free survival in a cohort of 244 women with breast cancer that had not received adjuvant treatment, and its expression was highest in the basal-like breast cancer subtype. Taking this further, we report that P-RSK(S221/227) is present in primary TNBCs and correlates with P-YB-1(S102) as well as CD44. In conclusion, RSK2 inhibition provides a novel therapeutic avenue for TNBC and holds the promise of eliminating TICs.
Evaluation of PEG-Based Hydrogel Influence on Estrogen-Receptor-Driven Responses in MCF7 Breast Cancer Cells (2019)

Extracellular matrix (ECM) mimicking hydrogel scaffolds have greatly improved the physiological relevance of <i>in vitro</i> assays, but introduce another dimension that creates variability in cell related readouts when compared to traditional 2D cells-on-plastic assays. We have developed a synthetic poly(ethylene glycol) (PEG) based ECM mimicking hydrogel and tested it against two gold standard animal-based naturally derived hydrogel scaffolds in MCF7 cell response. We have used the percent coefficient of variation (CV) as a metric to evaluate the reproducibility of said responses. Results indicated that PEG hydrogels performed similarly to naturally derived gold standards, and variance was similar in basic characterization assays, such as viability and cell adherence. PEG based hydrogels had lower CV values in estrogen receptor driven responses to several doses of estrogen in both estrogen receptor transactivation and estrogen induced proliferation.
A stoichiometrically derived algal growth model and its global analysis (2010)

Organisms are composed of multiple chemical elements such as carbon, nitrogen, and phosphorus. The scarcity of any of these elements can severely restrict organismal and population growth. However, many trophic interaction models only consider carbon limitation via energy flow. In this paper, we construct an algal growth model with the explicit incorporation of light and nutrient availability to characterize both carbon and phosphorus limitations. We provide a global analysis of this model to illustrate how light and nutrient availability regulate algal dynamics.
Texture analysis of optical coherence tomography speckle for characterizing biological tissues in vivo (2013)

We demonstrate a method for differentiating tissue disease states using the intrinsic texture properties of speckle in optical coherence tomography (OCT) images of normal and tumor tissues obtained in vivo. This approach fits a gamma distribution function to the nonlog-compressed OCT image intensities, thus allowing differentiation of normal and tumor tissues in an ME-180 human cervical cancer mouse xenograft model. Quantitative speckle intensity distribution analysis thus shows promise for identifying tissue pathologies, with potential for early cancer detection in vivo.
Deep Learning for Spatio-Temporal Data Mining: A Survey (2019)

With the fast development of various positioning techniques such as Global Position System (GPS), mobile devices and remote sensing, spatio-temporal data has become increasingly available nowadays. Mining valuable knowledge from spatio-temporal data is critically important to many real world applications including human mobility understanding, smart transportation, urban planning, public safety, health care and environmental management. As the number, volume and resolution of spatio-temporal datasets increase rapidly, traditional data mining methods, especially statistics based methods for dealing with such data are becoming overwhelmed. Recently, with the advances of deep learning techniques, deep leaning models such as convolutional neural network (CNN) and recurrent neural network (RNN) have enjoyed considerable success in various machine learning tasks due to their powerful hierarchical feature learning ability in both spatial and temporal domains, and have been widely applied in various spatio-temporal data mining (STDM) tasks such as predictive learning, representation learning, anomaly detection and classification. In this paper, we provide a comprehensive survey on recent progress in applying deep learning techniques for STDM. We first categorize the types of spatio-temporal data and briefly introduce the popular deep learning models that are used in STDM. Then a framework is introduced to show a general pipeline of the utilization of deep learning models for STDM. Next we classify existing literatures based on the types of ST data, the data mining tasks, and the deep learning models, followed by the applications of deep learning for STDM in different domains including transportation, climate science, human mobility, location based social network, crime analysis, and neuroscience. Finally, we conclude the limitations of current research and point out future research directions.
Myeloma cells block RUNX2/CBFA1 activity in human bone marrow osteoblast progenitors and inhibit osteoblast formation and differentiation (2005)

Decreased bone formation contributes to the development of bone lesions in multiple myeloma (MM) patients. In this study, we have investigated the effects of myeloma cells on osteoblast formation and differentiation and the potential role of the critical osteoblast transcription factor RUNX2/CBFA1 (Runt-related transcription factor 2/core-binding factor Runt domain alpha subunit 1) in the inhibition of osteoblastogenesis in MM. We found that human myeloma cells suppress the formation of human osteoblast progenitors in bone marrow (BM) cultures. Moreover, an inhibitory effect on osteocalcin, alkaline phosphatase, collagen I mRNA, protein expression, and RUNX2/CBFA1 activity by human preosteoblastic cells was observed in cocultures with myeloma cells. The inhibitory effect was more pronounced in the cell-to-cell contact conditions compared with those without the contact and involved the very late antigen 4 (VLA-4) integrin system. Among the soluble osteoblast inhibitors screened, we show the potential contribution of interleukin-7 (IL-7) in the inhibitory effect on osteoblast formation and RUNX2/CBFA1 activity by human myeloma cells in coculture. Finally, our in vitro results were supported in vivo by the finding of a significant reduction in the number of Runx2/Cbfa1-positive cells in the BM biopsies of patients with MM who had osteolytic lesions compared with those who did not have bone lesions, suggesting the critical involvement of RUNX2/CBFA1 in the decreased bone formation in MM.
The Highly Selective Sulfonylation of Cycloheptaamylose and Syntheses of Its Pure Amino Derivatives (1977)

Abstract Mesitylenesulfonyl chloride reacted selectively with primary hydroxyl groups of cycloheptaamylose to give hexakis (6-O-mesitylsulfonyl)cycloheptaamylose (II) and heptakis(mesitylsulfonyl)cycloheptaamylose (I). The selectivity of mesitylenesulfonyl chloride in the preferential sulfonylation is 24 times larger than that of tosyl chloride. Pure hexakis(6-azido-6-deoxy)cycloheptaamylose (III) and hexakis(6-amino-6-deoxy)cycloheptaamylose (IV) were synthesized from II. Pure heptakis(6-amino-6-deoxy)cycloheptaamylose (VII) and mixture of positional isomers of hexakis(6-amino-6-deoxy)mesitylsulfonylcycloheptaamylose (VIII)* were obtained by the catalytic hydrogenation of the corresponding azido compounds V and VI,* which were themselves given by the reaction of I with sodium azide. These amino derivatives, IV, VII, and VIII,* showed significant antimicrobial activities against such gram-negative bacteria as Escherichia, Shigella, and Pseudomonas. These compounds also exhibited hypocholesterolemic effects in the chick when added in the diet for two weeks, probably through sequestration of intestinal bile acids.
Effective and regioselective iodination of arenes using iron(III) nitrate in the presence of tungstophosphoric acid (2005)

An easy, cheap, and effective method for iodination of various aromatic compounds takes place with molecular iodine and iron nitrate nonahydrate as the oxidant in the presence of a catalytic amount of tungstophosphoric acid in dichloromethane, with good yield and high regioselectivity under very mild conditions.Key words: iodination, arenes, iodine, iron(III) nitrate, tungstophosphoric acid.
Optical nanomechanical sensor using a silicon photonic crystal cantilever embedded with a nanocavity resonator (2009)

We present in-depth discussion of the design and optimization of a nanomechanical sensor using a silicon cantilever comprising a two-dimensional photonic crystal (PC) nanocavity resonator arranged in a U-shaped silicon PC waveguide. For example, the minimum detectable strain, vertical deflection at the cantilever end, and force load are observed as 0.0133%, 0.37 mum, and 0.0625 muN, respectively, for a 30 mum long and 15 mum wide cantilever. In the graph of strain versus resonant wavelength shift, a rather linear relationship is observed for various data derived from different cantilevers. Both the resonant wavelength and the resonant wavelength shift of cantilevers under deformation or force loads are mainly a function of defect length change. Results point out that all these mechanical parameters are mainly dependent on the defect length of the PC nanocavity resonator. This new PC cantilever sensor shows promising linear characteristics as an optical nanomechanical sensor.
Electrolytes and Interphases in Sodium‐Based Rechargeable Batteries: Recent Advances and Perspectives (2020)

Abstract For sodium (Na)‐rechargeable batteries to compete, and go beyond the currently prevailing Li‐ion technologies, mastering the chemistry and accompanying phenomena is of supreme importance. Among the crucial components of the battery system, the electrolyte, which bridges the highly polarized positive and negative electrode materials, is arguably the most critical and indispensable of all. The electrolyte dictates the interfacial chemistry of the battery and the overall performance, having an influence over the practical capacity, rate capability (power), chemical/thermal stress (safety), and lifetime. In‐depth knowledge of electrolyte properties provides invaluable information to improve the design, assembly, and operation of the battery. Thus, the full‐scale appraisal of both tailored electrolytes and the concomitant interphases generated at the electrodes need to be prioritized. The deployment of large‐format Na‐based rechargeable batteries also necessitates systematic evaluation and detailed appraisal of the safety‐related hazards of Na‐based batteries. Hence, this review presents a comprehensive account of the progress, status, and prospect of various Na + ‐ion electrolytes, including solvents, salts and additives, their interphases and potential hazards.
A framework for non-realistic projections (1998)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1998.
Spiders, Satan, and Uncertainty: Turning Idle Tutoring Sessions into Teaching Opportunities (2018)

Though brand new writing tutors are given an army of tools and resources to aid students in the writing process, it is inevitable that they will come across a session that they just do not know how to handle. Whether it be vague and confusing assignment descriptions, unenthusiastic students, or a discipline outside of the tutor’s knowledge-base, seemingly fruitless sessions will land in the room of almost every tutor. This essay aims to help tutors recognize when sessions may not be going anywhere, and offer them advice and specific ideas for handling these sessions in a way that has students leaving with an understanding of the writing process and a greater confidence in that process.
Analysis and visualization of the output mode-matching requirements for squeezing in Advanced LIGO and future gravitational wave detectors (2020)

The sensitivity of ground-based gravitational-wave (GW) detectors will be improved in the future via the injection of frequency-dependent squeezed vacuum. The achievable improvement is ultimately limited by losses of the interferometer electromagnetic field that carries the GW signal. The analysis and reduction of optical loss in the GW signal chain will be critical for optimal squeezed light-enhanced interferometry. In this work, we analyze a strategy for reducing output-side losses due to spatial mode mismatch between optical cavities with the use of adaptive optics. Our goal is not to design a detector from the top down, but rather to minimize losses within the current design. Accordingly, we consider actuation on optics already present and one transmissive optic to be added between the signal recycling mirror and the output mode cleaner. The results of our calculation show that adaptive mode-matching with the current Advanced LIGO design is a suitable strategy for loss reduction that provides less than 2% mean output mode-matching loss. The range of actuation required is $+47\text{ }\text{ }\ensuremath{\mu}\mathrm{D}$ on SR3, $+140\text{ }\text{ }\mathrm{mD}$ on OM1 and OM2, $+50\text{ }\text{ }\mathrm{mD}$ on the SRM substrate, and $\ensuremath{-}50\text{ }\text{ }\mathrm{mD}$ on the added new transmissive optic. These requirements are within the demonstrated ranges of real actuators in similar or identical configurations to the proposed implementation. We also present a novel technique that graphically illustrates the matching of interferometer modes and allows for a quantitative comparison of different combinations of actuators.
Morphological and biochemical properties of a new human breast cancer cell line. (1979)

DU4475 is a new human breast cell line derived from a cutaneous metastatic nodule from a patient with advanced breast cancer. It has been in continuous culture for more than 1 year and has survived 140 subcultivations. The cells grow in suspension, displaying clusters and free-floating aggregates with serpentine-like outgrowths. The cell line is hypotetraploid with modal chromosome numbers between 86 and 93 and possesses five to six distinctive marker chromosomes. The cells grow readily in athymic nude mice and produce tumors from which cells can be reintroduced to culture in vitro.
Probing the effect of surface chemistry on the electrical properties of ultrathin gold nanowire sensors (2014)

Ultrathin metal nanowires are ultimately analytical tools that can be used to survey the interfacial properties of the functional groups of organic molecules immobilized on nanoelectrodes. The high ratio of surface to bulk atoms makes such ultrathin nanowires extremely electrically sensitive to adsorbates and their charge and/or polarity, although little is known about the nature of surface chemistry interactions on metallic ultrathin nanowires. Here we report the first studies about the effect of functional groups of short-chain alkanethiol molecules on the electrical resistance of ultrathin gold nanowires. We fabricated ultrathin nanowire electrical sensors based on chemiresistors using conventional microfabrication techniques, so that the contact areas were passivated to leave only the surface of the nanowires exposed to the environment. By immobilizing alkanethiol molecules with head groups such as -CH3, -NH2 and -COOH on gold nanowires, we examined how the charge proximity due to protonation/deprotonation of the functional groups affects the resistance of the sensors. Electrical measurements in air and in water only indicate that beyond the gold-sulfur moiety interactions, the interfacial charge due to the acid-base chemistry of the functional groups of the molecules has a significant impact on the electrical resistance of the wires. Our data demonstrate that the degree of dissociation of the corresponding functional groups plays a major role in enhancing the surface-sensitive resistivity of the nanowires. These results stress the importance of recognizing the effect of protonation/deprotonation of the surface chemistry on the resulting electrical sensitivity of ultrathin metal nanowires and the applicability of such sensors for studying interfacial properties using electrodes of comparable size to the electrochemical double layer.
Ultra-wideband source and antenna research (2000)

Ultra-wideband (UWB) microwave sources and antennas are of interest for a variety of applications, such as transient radar, mine detection, and unexploded ordnance (UXO) location and identification. Much of the current research is being performed at the Air Force Research Laboratory (AFRL) at Kirtland AFB, NM. The approach to high power source development has included high pressure gas switching, oil switching, and solid-state-switched arrays. Recent advances in triggered gas switch technology and solid-state-switched shockline technology have opened up new possibilities for the development of much higher power systems and have thus opened the door to many new applications. The research into UWB transient antennas has also made significant contributions to the development and improvement of wideband continuous wave (CW) antenna designs and has brought new knowledge about the complex behavior of ferrites, dielectrics, and resistive materials in short pulse, very high voltage environments. This has in turn led to advances in the technology of transformers, transmission lines, insulators, and UWB optics. This paper reviews the progress to date along these lines and discusses new areas of research into UWB technology development.
Joint Estimation of Frequency Offset and Doppler Shift in High Mobility Environments Based on Orthogonal Angle Domain Subspace Projection (2017)

Conventional frequency preshift technology cannot distinguish between the large Doppler shift and the frequency offset aroused by crystal oscillator, which significantly hinders the system performance improvement in high mobility environments when the frequency offset is present. In this paper, a joint frequency offset and Doppler shift estimation algorithm in high mobility environment based on orthogonal angle domain subspace projection is proposed, which can track the fast time-varying Doppler shift and separate the Doppler shift from the frequency offset. First, an orthogonal angle domain subspace projection algorithm is proposed to project the Doppler spread caused by high mobility into equivalent Doppler shifts in each orthogonal subspace. Second, it utilizes equivalent Doppler shift of all orthogonal subspaces to jointly estimate the maximal Doppler shift and frequency offset. Finally, the estimates are used to compensate the frequency error in the received signal. Moreover, the maximum Doppler shift estimation, together with the projection vectors and the received power on each orthogonal subspace, is fed back and exploited in the subsequent transmitted signal. Simulation results show that the proposed method can estimate the two parameters accurately and eliminate almost all the errors on the Doppler rapidly changing area when SNR is up to 15 dB. Compared with the conventional receiver with automatic frequency control, the receiver with our proposed method achieves better system performance even on the Doppler rapidly changing area.
A DSM architecture for a parallel computer Cenju-4 (2002)

A parallel computer Cenju-4 is a cache-coherent non-uniform memory access (ccNUMA) multiprocessor and designed to be scalable up to 1024 nodes. For scalability, Cenju-4 adopts a bit-pattern directory. This scheme enables more precise representation than other imprecise schemes, such as a coarse vector scheme. Cenju-4 utilizes multicast and gathering functions of the network for delivering invalidation request messages and for collecting replies. This enables store access latency to be scalable, even when the block is shared among all nodes. Cenju-4 also prevents starvation and deadlock by queuing certain types of messages in the main memory. This enables a full solution to the starvation problem with centralized directory scheme, and to the deadlock problem with one physical or virtual network. The buffer sizes required for queuing messages at each node are only 32K bytes and two 64K bytes on a 2024-node system. In this paper, we present the design of the DSM architecture and some performance results.
An advocacy intervention program for women with abusive partners: Initial evaluation (1992)

Experimentally tested the hypotheses that (1) battered women are in need of numerous community resources upon exit from a domestic violence shelter, (2) working with advocates increases women's effectiveness in obtaining needed resources and social support, and (3) success in obtaining resources and social support increases women's levels of life satisfaction and decreases their risk of further abuse. The initial findings of a short-term intervention project designed to provide postshelter advocacy services to women with abusive partners are presented. One-hundred forty-one battered women were interviewed immediately upon their exit from a domestic violence shelter as well as 10 weeks thereafter. Half the sample was randomly assigned to receive the services of trained advocates who assisted them in accessing needed community resources. Women who worked with advocates reported being more effective in accessing resources and had higher levels of social support and overall quality of life postintervention. Although all women reported some decrease in postshelter abuse, there were no differences between those with and those without advocates, and abuse continued to be a problem for many women.
From Microjoining to Nanojoining (2010)

A review is provided of the recent advances and challenges in nanojoining, as compared to microjoining and even regular joining processes. Nanojoining examples are given and analyzed in various joining categories such as solid- state bonding, soldering/brazing and fusion welding. Proposed strategies for nanoassembly and nanojoining, e.g., self- organization and inkjet printing, are also highlighted. Joining (welding, brazing, soldering, bonding, etc.), whether at macro-, micro- or nano-scale, is an essential step of man-made product manufacturing and assembly, providing mechanical support and integration, electrical connection, optical coupling, environmental protection, etc. (1) This review focuses only on joining processes that aim to produce permanent unions between macro-, micro- and nano-sized building blocks to be assembled, through the formation of primary (and occasionally secondary) chemical bonds between the faying surfaces. The exception to this metallurgical definition is mechanical joining (fastening, riveting, crimping, etc.), in which the original free surfaces of the parts are retained mostly unaltered in mechanical joints. The continuing miniaturization of engineered devices and systems, coupled with ever-growing demands for cost reduction, enhanced performance and reliability, etc. brings