gebhart/patrepeval huggingface dataset:
DASH: a Recipe for a Flash-based Data Intensive Supercomputer (2010)

Data intensive computing can be defined as computation involving large datasets and complicated I/O patterns. Data intensive computing is challenging because there is a five-orders-of-magnitude latency gap between main memory DRAM and spinning hard disks; the result is that an inordinate amount of time in data intensive computing is spent accessing data on disk. To address this problem we designed and built a prototype data intensive supercomputer named DASH that exploits flash-based Solid State Drive (SSD) technology and also virtually aggregated DRAM to fill the latency gap . DASH uses commodity parts including Intel® X25-E flash drives and distributed shared memory (DSM) software from ScaleMP®. The system is highly competitive with several commercial offerings by several metrics including achieved IOPS (input output operations per second), IOPS per dollar of system acquisition cost, IOPS per watt during operation, and IOPS per gigabyte (GB) of available storage. We present here an overview of the design of DASH, an analysis of its cost efficiency, then a detailed recipe for how we designed and tuned it for high data-performance, lastly show that running data-intensive scientific applications from graph theory, biology, and astronomy, we achieved as much as two orders-of- magnitude speedup compared to the same applications run on traditional architectures.
Growth stimulation of endothelial cells by simultaneous culture with Sarcoma 180 cells in diffusion chambers. (1977)

Endothelial cells derived from pig aorta were cultured in Petri dishes containing Sarcoma 180 cells growing in Millipore diffusion chambers. The presence of tumor cells consistently increased the colony-forming ability of the endothelial cells, an effect not produced by control-killed cells or 3T3 fibroblasts. This observation suggests that the cultured tumor cell retains the ability to produce diffusible substances that stimulate endothelial cell growth. These products may be similar to the angiogenic factors elaborated by malignant cells in vivo. The use of such a method may allow a closer study of the effect of tumor cells on the growth of a variety of tissues.
Inhibitors of complement and neutrophils: a critical evaluation of their role in the treatment of sepsis. (1992)

Pentoxifylline has been shown to decrease neutrophil adhesion and provides increased survival rate in various animal models of sepsis. Early studies regarding monoclonal antibodies to adhesion molecules are exciting. However, the possible effects of these agents in sepsis has yet to be studied. Drugs have been discovered that show potential to block the numerous destructive agents released by degranulating neutrophils.
On Policy Feedback: Insights From Survey Experiments (2011)

In comparative social science, policy feedback has become a widely popular device with which to\nunderstand policy persistence and the impacts of state-making and political entrepreneurship on\nmass opinion. Although the existence of such effects is frequently taken for granted, recent work has\nchallenged prevailing assumptions about the unproblematic nature of feedback from policy change to\nmass opinion. This is an opportune time to put policy feedback to further test. We do so by bringing to\nbear the two main theoretical perspectives that underlie established and recent scholarship, and applying\nfor the first time survey experiments to evaluate key expectations. Focusing on the relatively novel\ndomain of counter-terrorism policy, we analyze data drawn from a national survey conducted in 2009.\nResults from embedded experiments suggest new evidence for policy feedback effects. Analysis of\nmechanisms suggests limits in interest-centered explanations, and the relevance of some under-studied,\ncognitive factors. We discuss implications and limits of our study for policy feedback scholarship, and\nwith further reference to the case of U.S. attitudes toward the war on terror.
Repetition suppression of faces is modulated by emotion (2004)

Single-unit recordings and functional brain imaging studies have shown reduced neural responses to repeated stimuli in the visual cortex. By using event-related functional MRI, we compared the activation evoked by repetitions of neutral and fearful faces, which were either task relevant (targets) or irrelevant (distracters). We found that within the inferior occipital gyri, lateral fusiform gyri, superior temporal sulci, amygdala, and the inferior frontal gyri/insula, targets evoked stronger responses than distracters and their repetition was associated with significantly reduced responses. Repetition suppression, as manifested by the difference in response amplitude between the first and third repetitions of a target, was stronger for fearful than neutral faces. Distracter faces, regardless of their repetition or valence, evoked negligible activation, indicating top-down attenuation of behaviorally irrelevant stimuli. Our findings demonstrate a three-way interaction between emotional valence, repetition, and task relevance and suggest that repetition suppression is influenced by high-level cognitive processes in the human brain.
Sensorless Speed and Position Control of Induction Motors Tutorial (2001)

Controlled induction motor drives without me- chanical sensors for speed or motor shaft position have the attraction of low cost and high reliability. The identification of rotor speed is generally based on measured terminal volt- ages and currents. Dynamic models are used to estimate the magnitude and spatial orientation of the fundamental mag- netic flux waves in the stator or in the rotor. Open loop esti- mators and closed loop observers differ with respect to accu- racy, robustness, and sensitivity against model parameter variations. Dynamic performance and steady-state speed ac- curacy in the low speed range is achieved by exploiting para- sitic effects of the machine. The overview in this paper uses signal flow graphs of complex space vector quantities to pro- vide an insightful description of the systems used in sensor- less control of induction motors.
Design techniques and performance of an LSI-based 2B1Q transceiver (2003)

Examines a 2B1Q transceiver system which was selected as the standard for an ISDN (integrated services digital network) loop transmission systems in the US. An LSI-based 2B1Q transceiver consisting of three LSI chips has been developed. Echo tail suppression, receiver design to configure stable decision feedback equalizer (DFE) operation and to improve NEXT performance, and the accurate analog front end circuit are discussed. Experimental results show that satisfactory performance is obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Deep Learning Approach for Brain Tumor Classification and Segmentation Using a Multiscale Convolutional Neural Network (2021)

In this paper, we present a fully automatic brain tumor segmentation and classification model using a Deep Convolutional Neural Network that includes a multiscale approach. One of the differences of our proposal with respect to previous works is that input images are processed in three spatial scales along different processing pathways. This mechanism is inspired in the inherent operation of the Human Visual System. The proposed neural model can analyze MRI images containing three types of tumors: meningioma, glioma, and pituitary tumor, over sagittal, coronal, and axial views and does not need preprocessing of input images to remove skull or vertebral column parts in advance. The performance of our method on a publicly available MRI image dataset of 3064 slices from 233 patients is compared with previously classical machine learning and deep learning published methods. In the comparison, our method remarkably obtained a tumor classification accuracy of 0.973, higher than the other approaches using the same database.
Heterogeneous and small cell networks: Part 2 [Guest Editorial] (2013)

e are back this month with a sequel to our May 2013 Feature Topic on heterogeneous and small cell networks (Het- SNets). In this follow-up, we have six more articles that address cognitive radio, moving cells, WiFi offloading, and energy efficiency aspects of HetSNets. The first article, by Song et al., provides a holistic view of hyper-dense HetSNet deployments by comparing massive antenna and dense deployment, and providing some enabling technologies that can handle the technical challenges in HetSNets.
A 32 tap digitally controlled programmable transversal filter (2003)

A digitally controlled programmable transversal filter (DCPTF) has been developed that uses a 32-tap LiNbO/sub 3/ delay line and two LSI GaAs ICs to digitally control tap weight magnitude and sign. Compared to previously reported PTR devices, this third-generation device is significantly reduced in size and power, yet retains state-of-the-art performance. The device is completely programmable, constrained only by the bandwidth (100 MHz centered at 100 MHz) and the number of taps. The DCPTF is designed in 16-tap blocks to easily expand the number of taps. A calibration method is presented which removes nonideal GaAs FET (field-effect transistor) array gain states due to process variations. The on/off ratio of each individual tap is greater than 35 dB. The DCPTF is demonstrated as a bandpass filter with programmable center frequency and bandwidth.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison (2007)

Through this work: 1) substantial sequence information has been provided for U. maydis genome annotation; 2) new genes were identified through the discovery of 619 contigs that had previously escaped annotation; 3) evidence is provided that suggests the regulation of nitrogen metabolism in U. maydis differs from that of other model fungi, and 4) Alternative splicing and anti-sense transcription were identified in U. maydis and, amid similar observations in other basidiomycetes, this suggests these phenomena may be widespread in this group of fungi. These advances emphasize the importance of EST analysis in genome annotation.
Signal processing by the HOG MAP kinase pathway (2008)

Signaling pathways relay information about changes in the external environment so that cells can respond appropriately. How much information a pathway can carry depends on its bandwidth. We designed a microfluidic device to reliably change the environment of single cells over a range of frequencies. Using this device, we measured the bandwidth of the Saccharomyces cerevisiae signaling pathway that responds to high osmolarity. This prototypical pathway, the HOG pathway, is shown to act as a low-pass filter, integrating the signal when it changes rapidly and following it faithfully when it changes more slowly. We study the dependence of the pathway's bandwidth on its architecture. We measure previously unknown bounds on all of the in vivo reaction rates acting in this pathway. We find that the two-component Ssk1 branch of this pathway is capable of fast signal integration, whereas the kinase Ste11 branch is not. Our experimental techniques can be applied to other signaling pathways, allowing the measurement of their in vivo kinetics and the quantification of their information capacity.
Aaa Proteins (2000)

AAA ATPases (those associated with various cellular activities) play important roles in numerous cellular activities including proteolysis, protein folding, membrane trafficking, cytoskeletal regulation, organelle biogenesis, DNA replication, and intracellular motility. Recent structural and
Realizing Network on Chip Design of H.264 Decoder Based on Throughput Aware Mapping (2006)

A new chip design era in the coming nano-scale, so called network on chip (NoC), has been introduced based on the demand of the intensive use and seamless integration of many heterogeneous semiconductor intellectual property (IP) blocks in the form of embedded and distributed processors, memories, DSPs, and interfaces. The NoC design, with its own characteristics, very strictly requires the satisfaction of several physical constraints such as the network latency, the used area as well as the power consumption of design. In this paper, we introduce the queuing theory based and power model based of the router in order to analyzes the throughput, size and energy consumption of heterogeneous network on chip architectures. This article also presents the method to automatically map IPs onto the given architectures to obtain the maximum throughput while keep the minimum energy consumption. Some realizations of H.264 decoder on regular NoC architectures such as 2D mesh and fat-tree are simulated. The results show that the network throughput is maximized with the optimized mapping scheme. The energy dissipation consequently calculated and shown that it is very much saved compared to that of random mapping.
Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives (2014)

Infectious diseases are responsible for over 25% of deaths globally, but many more individuals are exposed to deadly pathogens. The outcome of infection results from a set of diverse factors including pathogen virulence factors, the environment, and the genetic make-up of the host. The completion of the human reference genome sequence in 2004 along with technological advances have tremendously accelerated and renovated the tools to study the genetic etiology of infectious diseases in humans and its best characterized mammalian model, the mouse. Advancements in mouse genomic resources have accelerated genome-wide functional approaches, such as gene-driven and phenotype-driven mutagenesis, bringing to the fore the use of mouse models that reproduce accurately many aspects of the pathogenesis of human infectious diseases. Treatment with the mutagen N-ethyl-N-nitrosourea (ENU) has become the most popular phenotype-driven approach. Our team and others have employed mouse ENU mutagenesis to identify host genes that directly impact susceptibility to pathogens of global significance. In this review, we first describe the strategies and tools used in mouse genetics to understand immunity to infection with special emphasis on chemical mutagenesis of the mouse germ-line together with current strategies to efficiently identify functional mutations using next generation sequencing. Then, we highlight illustrative examples of genes, proteins, and cellular signatures that have been revealed by ENU screens and have been shown to be involved in susceptibility or resistance to infectious diseases caused by parasites, bacteria, and viruses.
Dosage Forms: Non-Parenteral (2013)

Dosage form is a drug delivery system designed to deliver the active ingredient to the body and, upon administration should deliver the drug at a rate and amount that assures the desired pharmacological effect. This entry examines the various dosage forms for pharmaceutical drugs and discusses their respective functions and applications as well as their strengths and weaknesses in terms of drug delivery.
Prediction and biochemical characterization of intrinsic disorder in the structure of proteolysis-inducing factor/dermcidin. (2007)

Proteolysis-inducing factor/dermcidin (PIF/DCD) is a novel human gene, located on chromosome 12, locus 12q13.1, that encodes a secreted 110-amino acid protein. Two transcripts for the protein have been identified in normal skin, breast, placenta and brain, and in various primary and metastatic tumor cells. The putative native-state structure of PIF/DCD has not been resolved. Here, we describe some biochemical features of the soluble recombinant 11-kDa protein produced in Escherichia coli. The native 11-kDa polypeptide displayed an anomalous mobility on 1% SDS-PAGE under reduced conditions and appeared as a single approximately 16-kDa band. Under nonreduced conditions, we detected by mass spectrometry, the presence of multiple peaks corresponding to m/z values of 21 kDa, which we confirmed as a dimeric form with a disulfide bridge between cysteine 34 of each 11-kDa monomer. The native protein exhibited an unusually high susceptibility to proteolytic attack by trypsin, and up to 13 peptides derived from its C-terminus were produced after 5 min of incubation. The secondary structure analysis of PIF/DCD native protein in aqueous solution, by circular dichroism spectroscopy, revealed regions with non-well-defined secondary structure but that acquired alpha-helix and beta-sheet secondary structures in the presence of TFE/water mixtures and micellar and non-micellar SDS molecules. By using PONDR, DisEMBL, DisProt, and GlobPlot computational predictors, we identified a long disorder region at the N-terminus of PIF/DCD amino acid sequence. This segment (from 19-50 residues) is critical for some of its biological activities, including neuron survival. This result is coherent with successive failure of crystallization of the protein. Taken together, these data suggest that the disorder and order transition may be relevant for some biological functions of PIF/DCD.
Leptin and Reproduction (2002)

Leptin, a hormone secreted from adipose tissue, plays an important role in reproductive physiology. It has been shown to stimulate the reproductive system by rescuing the sterility of leptin-deficient mice and advancing the onset of puberty in normal mice. Although leptin is not critical for the biology of pregnancy in mice, its ability to reduce food intake is blunted in mid-gestation suggesting that late pregnancy may be a leptin-resistant state. Modifier genes originating from the Balb/cJ genetic background profoundly alter the sterile-obese phenotype of ob/ob mice by reducing their obesity and stimulating their reproductive system despite the absence of leptin. The mechanism of leptin's action on the reproductive system remains to be determined but is likely to be mediated by multiple factors.
A Post-processing for Binary Mask Estimation Toward Improving Speech Intelligibility in Noise (2013)

시간-주파수 영역에서의 이진 마스킹을 이용하여 잡음환경에서 잡음을 제거하여 음질을 향상하는 방법에 대해 논하고자 한다. 잡음이 섞여 있는 음성신호를 시간-주파수 영역으로 분해하여, 상대적으로 잡음이 많이 섞여 있는 시간-주파수 영역 (시간-주파수 유닛의 신호 대 잡음 비 (Signal-to-Noise Ratio: SNR)가 낮은 영역)의 신호에 마스크 "0"을 할당하여 제거함으로써 음성명료도를 향상시킬 수 있다. 이전의 연구에서는 가우시안 혼합 모델을 이용하여 마스크 "0"과 마스크 "1"을 분류하는 방법을 사용하였다. 각 주파수 밴드별로 수집된 데이터를 이용하여 가우시안 혼합 모델을 학습하고 테스트 데이터가 들어오면 현재의 시간-주파수 마스크가 "0"인지 "1"인지 판별하게 된다. 본 논문에서는 이러한 알고리즘에 주파수 영역에서의 종속성을 고려하여 추정된 마스크에 대해 후처리를 수행하는 알고리즘을 제안한다. 주파수 영역에서의 종속성에 관한 후처리는 비터비 (Viterbi) 알고리즘을 이용하며, 제안된 후처리 알고리즘을 적용하여 이진 마스크 추정 오차를 줄여 음성 명료도 향상을 기대할 수 있다. This paper deals with a noise reduction algorithm which uses the binary masking in the time-frequency domain. To improve speech intelligibility in noise, noise-masked speech is decomposed into time-frequency units and mask "0" is assigned to masker-dominant region removing time-frequency units where noise is dominant compared to speech. In the previous research, Gaussian mixture models were used to classify the speech-dominant region and noise-dominant region which correspond to mask "1" and mask "0", respectively. In each frequency band, data were collected and trained to build the Gaussian mixture models and detection procedure is performed to the test data where each time-frequency unit belongs to speech-dominant region or noise-dominant region. In this paper, we consider the correlation of masks in the frequency domain and propose a post-processing method which exploits the Viterbi algorithm.
Clinical and Pharmacokinetic Study of Clofarabine in Chronic Lymphocytic Leukemia: Strategy for Treatment (2006)

Levels of clofarabine triphosphate at higher doses and prolonged maintenance of clofarabine triphosphate in leukemic lymphocytes provide a rationale to treat CLL in a weekly clofarabine schedule.
Prosodic modeling for improved speech recognition and understanding (2001)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.
Transforming growth factor-β1 induces EMT by the transactivation of epidermal growth factor signaling through HA/CD44 in lung and breast cancer cells (2015)

Epithelial-mesenchymal transition (EMT), a process closely related to tumor development, is regulated by a variety of signaling pathways and growth factors, such as transforming growth factor-β1 (TGF-β1) and epidermal growth factor (EGF). Hyaluronan (HA) has been shown to induce EMT through either TGF-β1 or EGF signaling and to be a regulator of the crosstalk between these two pathways in fibroblasts. In this study, in order to clarify whether HA has the same effect in tumor cells, we utilized the lung cancer cell line, A549, and the breast cancer cell line, MCF-7, and found that the effects of stimulation with TGF-β1 were more potent than those of EGF in regulating the expression of EMT-associated proteins and in enhancing cell migration and invasion. In addition, we observed that TGF-β1 activated EGF receptor (EGFR) and its downstream AKT and extracellular signal-regulated kinase (ERK) pathways. Furthermore, we found that TGF-β1 upregulated the expression of hyaluronan synthases (HAS1, HAS2 and HAS3) and promoted the expression of CD44, a cell surface receptor for HA, which interacts with EGFR, resulting in the activation of the downstream AKT and ERK pathways. Conversely, treatment with 4-methylumbelliferone (4-MU; an inhibitor of HAS) prior to stimulation with TGF-β1, inhibited the expression of CD44 and EGFR, abolished the interaction between CD44 and EGFR. Furthermore, the use of shRNA targeting CD44 impaired the expression of EGFR, deactivated the AKT and ERK pathways, reversed EMT and decreased the migration and invasion ability of cells. In conclusion, our data demonstrate that TGF-β1 induces EMT by the transactivation of EGF signaling through HA/CD44 in lung and breast cancer cells.
Testing interconnects: a pin adjacency approach (2002)

This paper looks at a new fault model used for shorts between nets on a PCB, the pin-adjacency fault model, and the implementation of two algorithms. The pin-adjacency detection and diagnosis algorithms for detecting and diagnosing these bridging faults. The authors represent the nets and their likelihood to short as a graph, and in conjunction with the new algorithms are able to generate reduced test sets. This represents a huge saving over existing algorithms which assume that any two nets are likely to short, as opposed to the new more realistic pin-adjacency fault model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Hereditary Angioedema Consensus 2010 (2010)

and was cosponsored by CHAEN
A Rapid Method for Determining the Proportion of Viable Bacteria in a Culture (1956)

Summary: A method of making graticules on the surface of Cellophane is described. The proportion of viable bacteria in a culture can be estimated by inoculating a sample on to such a graticule, and counting the organisms before and after a short period of growth.