gebhart/patrepeval huggingface dataset:
Altered Autonomic Function and Reduced Arousability in Apparent Life-Threatening Event Infants with Obstructive Sleep Apnea (2002)

The aim of this study was to examine cardiorespiratory control in infants presenting with an apparent life-threatening event (ALTE). We performed six to eight 45 degrees head-up tilts in 10 ALTE infants (age, 14 +/- 3 weeks) and 12 age-matched control subjects during slow wave sleep and rapid eye movement sleep (REM). All infants underwent full overnight polygraphic sleep recordings with noninvasive measurement of beat-to-beat blood pressure. All control infants had normal sleep breathing. In contrast, 5 of the 10 ALTE infants had more than two obstructive apneas per hour of sleep, with short hypoxic episodes (obstructive sleep apnea [OSA]). In slow wave sleep, in response to the tilt, the ALTE infants with OSA showed a reduced heart rate response, and three of the five showed a marked postural hypotension. The ALTE infants with OSA also had altered heart rate and blood pressure variability and an increased arousal threshold in REM (p = 0.0002). By contrast, those ALTE infants with normal sleep breathing had cardiovascular and arousal responses similar to those of the control infants. We conclude that a number of ALTE infants with OSA have abnormal cardiovascular autonomic control that, combined with their decreased arousability in REM, may provide an explanation for the ALTE episodes.
Bioinformatic analysis reveals an association of HOXB7 gene expression withoncogenic pathways and phenotypic properties in cancer (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

4799 

Expression monitoring using microarrays is a tool for characterizing gene function in cancer. We hypothesized that a mathematical approach that emphasized the underlying data structure would aid in mapping specific groups of genes to particular sample classes. Our objective was to evaluate our new tool designed to mine large scale multi dimensional data, termed, Sorting Points Into Neighborhoods (SPIN) ., We used the Affymetrix U133A GeneChip to study 144 microdissected samples from patients with colon cancer for whom clinical, pathological and outcome information is available. The samples included: 47 primary carcinomas; 24 adenomas; 22 normal colons; 16 liver metastasis; 19 lung metastasis; 11 normal liver; and 5 normal lung. SPIN utilizes traits of distance matrices to order data in a way that highlights their underlying structure. For gene array experiments SPIN provides two-way sorting, using the genes to order the samples and vice versa . Graphical output generated by SPIN includes a two-way sorted expression matrix, sorted distance matrices and PCA images colored according to the order suggested by the algorithm. SPIN’ s advantage over traditional methods (e.g., hierarchical clustering) is that the color-coded images allow the user to infer not only the partition into clusters, but also observe their shapes and relative relationships. After log-transformation and variance filtration, thousands of genes and the 144 samples were sorted by SPIN . The reordered expression matrix clearly separates the samples according to tissue types (colon, lung, liver), and also tumors from normal tissue, and adenomas from adenocarcinomas. Genes partition into several clusters; some are tissue-specific and others are associated with clinical and pathological disease state. Colon tissue that was isolated from liver metastases arrayed into an elongated, ellipsoid cluster extending from colon samples towards liver samples (a similar picture is seen for lung metastasis). The genes that induced the elongation were characteristic of liver (or lung), suggesting that this pattern reflects admixture of the metastasis samples with cells from the liver or lung. With appropriate calibration, the proportion and origin of contaminating cells can be specified. SPIN also revealed that normal colon samples arrayed in an elongated cluster. The genes responsible for this shape represented residual non-epithelial tissue. Primary colon tumor samples exhibit this pattern of elongation to a lesser extent (less admixture); however, their cluster is extended in an orthogonal direction, encompassing many cell-cycle genes. This variation apparently captures the relative quantities of proliferating cells in the samples, which are significantly higher in the tumors. Therefore, SPIN can also be utilized to estimate the proportion and type of abnormal cells in a complex mixture and to associate particular sample groups with specific changes in gene expression.
On-the-Fly Pipeline Parallelism (2015)

Pipeline parallelism organizes a parallel program as a linear sequence of stages. Each stage processes elements of a data stream, passing each processed data element to the next stage, and then taking on a new element before the subsequent stages have necessarily completed their processing. Pipeline parallelism is used especially in streaming applications that perform video, audio, and digital signal processing. Three out of 13 benchmarks in PARSEC, a popular software benchmark suite designed for shared-memory multiprocessors, can be expressed as pipeline parallelism. Whereas most concurrency platforms that support pipeline parallelism use a “construct-and-run” approach, this article investigates “on-the-fly” pipeline parallelism, where the structure of the pipeline emerges as the program executes rather than being specified a priori . On-the-fly pipeline parallelism allows the number of stages to vary from iteration to iteration and dependencies to be data dependent. We propose simple linguistics for specifying on-the-fly pipeline parallelism and describe a provably efficient scheduling algorithm, the P iper algorithm, which integrates pipeline parallelism into a work-stealing scheduler, allowing pipeline and fork-join parallelism to be arbitrarily nested. The P iper algorithm automatically throttles the parallelism, precluding “runaway” pipelines. Given a pipeline computation with T 1 work and T ∞ span (critical-path length), P iper executes the computation on P processors in T P ≤ T 1 / P + O ( T ∞+lg P ) expected time. P iper also limits stack space, ensuring that it does not grow unboundedly with running time. We have incorporated on-the-fly pipeline parallelism into a Cilk-based work-stealing runtime system. Our prototype Cilk-P implementation exploits optimizations such as “lazy enabling” and “dependency folding.” We have ported the three PARSEC benchmarks that exhibit pipeline parallelism to run on Cilk-P. One of these, x264 , cannot readily be executed by systems that support only construct-and-run pipeline parallelism. Benchmark results indicate that Cilk-P has low serial overhead and good scalability. On x264 , for example, Cilk-P exhibits a speedup of 13.87 over its respective serial counterpart when running on 16 processors.
WNOS: Enabling Principled Software-Defined Wireless Networking (2021)

This article investigates the basic design principles for a new Wireless Network Operating System (WNOS), a radically different approach to software-defined networking (SDN) for infrastructure-less wireless networks. Departing from well-understood approaches inspired by OpenFlow, WNOS provides the network designer with an abstraction hiding (i) the lower-level details of the wireless protocol stack and (ii) the distributed nature of the network operations. Based on this abstract representation, the WNOS takes network control programs written on a centralized, high-level view of the network and automatically generates distributed cross-layer control programs based on distributed optimization theory that are executed by each individual node on an abstract representation of the radio hardware. We first discuss the main architectural principles of WNOS. Then, we discuss a new approach to automatically generate solution algorithms for each of the resulting subproblems in an automated fashion. Finally, we illustrate a prototype implementation of WNOS on software-defined radio devices and test its effectiveness by considering specific cross-layer control problems. Experimental results indicate that, based on the automatically generated distributed control programs, WNOS achieves 18%, 56% and 80.4% utility gain in networks with low, medium and high levels of interference; maybe more importantly, we illustrate how the global network behavior can be controlled by modifying a few lines of code on a centralized abstraction.
Tuning Precursor Reactivity toward Nanometer-Size Control in Palladium Nanoparticles Studied by in Situ Small Angle X-ray Scattering (2018)

Synthesis of monodisperse nanoparticles (NPs) with precisely controlled size is critical for understanding their size-dependent properties. Although significant synthetic developments have been achieved, it is still challenging to synthesize well-defined NPs in a predictive way due to a lack of in-depth mechanistic understanding of reaction kinetics. Here we use synchrotron-based small-angle X-ray scattering (SAXS) to monitor in situ the formation of palladium (Pd) NPs through thermal decomposition of Pd–TOP (TOP: trioctylphosphine) complex via the “heat-up” method. We systematically study the effects of different ligands, including oleylamine, TOP, and oleic acid, on the formation kinetics of Pd NPs. Through quantitative analysis of the real-time SAXS data, we are able to obtain a detailed picture of the size, size distribution, and concentration of Pd NPs during the syntheses, and these results show that different ligands strongly affect the precursor reactivity. We find that oleylamine does not change the reactivity of the Pd–TOP complex but promote the formation of nuclei due to strong ligand–NP binding. On the other hand, TOP and oleic acid substantially change the precursor reactivity over more than an order of magnitude, which controls the nucleation kinetics and determines the final particle size. A theoretical model is used to demonstrate that the nucleation and growth kinetics are dependent on both precursor reactivity and ligand–NP binding affinity, thus providing a framework to explain the synthesis process and the effect of the reaction conditions. Quantitative understanding of the impacts of different ligands enables the successful synthesis of a series of monodisperse Pd NPs in the broad size range from 3 to 11 nm with nanometer-size control, which serve as a model system to study their size-dependent catalytic properties. The in situ SAXS probing can be readily extended to other functional NPs to greatly advance their synthetic design.
Power management on 14 nm Intel&#x00AE; Core&#x2212; M processor (2015)

The desire to deliver breakthrough performance in a tablet form factor required several innovations in the 14nm Intel® flagship Core™ processor (Broadwell). Better frequency control algorithms including duty cycling graphics cores were developed to improve energy efficiency. New power sharing algorithms were developed to maximize performance of multiple compute domains within tight thermal and power delivery constraints. Innovations resulted in upto 50% increase in performance and upto 25% improvement in battery life over a Haswell system thermally constrained to a 4.5W fanless form factor.
Nonlinear mechanisms of filamentation in broad-area semiconductor lasers (1996)

There are three nonlinear mechanisms that can lead to filamentation in broad-area semiconductor lasers: gain-saturation-induced changes in the refractive index through the linewidth-enhancement factor, self-focusing due to heat-induced index changes, and self-defocusing through intensity-dependent index changes in the cladding layer. We present a theoretical model to analyze these mechanisms and their relative roles in destabilizing the laser output. We find that there exists a critical value for the linewidth-enhancement factor below which broad area lasers are stable for wide stripe widths (as wide as 250 /spl mu/m) and high pumping levels (as high as 20 times threshold). We also find that broad-area lasers are less susceptible to filamentation through self-defocusing and show how an intensity-dependent index in the cladding layer may be used to suppress filamentation caused by the linewidth-enhancement factor.
An angle-sensitive CMOS imager for single-sensor 3D photography (2011)

Conventional cameras capture 2D photographs at a single plane of focus. Acquisition of a 3D photograph with multiple planes of focus typically requires scanning the focus of a single camera, or using arrays of cameras or lenses. This paper demonstrates a 150kpixel image sensor, which captures 3D scenes. The chip is manufactured in commodity 0.18μm CMOS and requires only a single convex lens at a fixed focal length in ambient light. As traditional image sensors only capture the intensity of the light at each location, they lose significant information about out-of-focus objects. Recovering the angular distribution of incident light permits recovery of the blurred, out-of-focus objects. This paper presents a CMOS imager that locally captures both the intensity and incident angle of the light striking it.
51.3: Design for Reducing Autostereoscopic Display Crosstalk using a Liquid Crystal Gradient‐index Lens (2014)

Abstract A 2D/3D switchable liquid crystal display with low crosstalk of 0.9% is developed using a liquid crystal gradient‐index lens. The low crosstalk is achieved with a design approach using low‐birefringence liquid crystal and chromium electrodes as a light shield.
Acoustic emission and machine learning for in situ monitoring of a gold–copper ore weakening by electric pulse (2020)

The excessive energy consumption from the mining industry are currently receiving international attention. A promising method able to enhance significantly the comminution process efficiency worldwide is by using electric pulse fragmentation treatment. However, to insure a minimum energy consumption in real scale operation, an online process monitoring is of utmost importance. This work presents an in situ and real-time monitoring method by combining acoustic emission sensor and advanced machine learning algorithms. The proposed method was developed on a gold-copper ore in well-controlled single stone experiments and in semi-continuous process, reproducing a real industrial environment. In single stone experiment, the pulse energies was varied from 200 to 750 J leading to three weakening behaviours; no discharge, surface discharge and fragmentation. Acoustic signals for these categories have been decomposed with wavelet packets, and sub-band energies have been chosen as features. Then, only the most informative features were selected via standard linear principal component analysis. Finally, the classification was performed via a traditional support vector machine. In the semi-continuous experiments, an unsupervised learning method was used for classification task based on Laplacian support vector machine. Results for single stone tests showed accuracy above 90% for the three categories. For semi-continuous tests, we demonstrated that the unsupervised classification can be applied efficiently to estimate the amount of weakening of the passed through ore. We are very confident that the proposed method can be easily industrialised to monitor in situ and in real-time the electric discharge process within a comminution operation.
Asymptotic Analysis of SU-MIMO Channels With Transmitter Noise and Mismatched Joint Decoding (2014)

Hardware impairments in radio-frequency components of a wireless system cause unavoidable distortions to transmission that are not captured by the conventional linear channel model. In this paper, a 'binoisy' single-user multiple-input multiple-output (SU-MIMO) relation is considered where the additional distortions are modeled via an additive noise term at the transmit side. Through this extended SU-MIMO channel model, the effects of transceiver hardware impairments on the achievable rate of multi-antenna point-to-point systems are studied. Channel input distributions encompassing practical discrete modulation schemes, such as, QAM and PSK, as well as Gaussian signaling are covered. In addition, the impact of mismatched detection and decoding when the receiver has insufficient information about the non-idealities is investigated. The numerical results show that for realistic system parameters, the effects of transmit-side noise and mismatched decoding become significant only at high modulation orders.
Computational Fluid Dynamics Prediction of Blood Damage in a Centrifugal Pump (2003)

This study explores a quantitative evaluation of blood damage that occurs in a continuous flow left ventricular assist device due to fluid stress. Computational fluid dynamics (CFD) analysis is used to track the shear stress history of 388 particle streaklines. The accumulation of shear and exposure time is integrated along the streaklines to evaluate the levels of blood trauma. This analysis, which includes viscous and turbulent stresses, provides a statistical estimate of possible damage to cells flowing through the pump. In vitro normalized index of hemolysis values for clinically available ventricular assist devices were compared to our damage indices. This allowed for an order of magnitude comparison between our estimations and experimentally measured hemolysis levels, which resulted in a reasonable correlation. This work ultimately demonstrates that CFD is a convenient and effective approach to analyze the Lagranian behavior of blood in a heart assist device.
Maximizing Output Power of a CFPG Micro Energy-Harvester for Wearable Medical Sensors (2014)

Energy Harvesting refers to the process of capturing and storing energy from the ambient environment. Kinetic energy harvested from the human body motion seems to be one of the most convenient and attractive solutions for wearable wireless sensors in healthcare applications. Due to their small siz
Prolonged recurrence-free survival following OK432-stimulated dendritic cell transfer into hepatocellular carcinoma during transarterial embolization (2010)

Despite curative locoregional treatments for hepatocellular carcinoma (HCC), tumour recurrence rates remain high. The current study was designed to assess the safety and bioactivity of infusion of dendritic cells (DCs) stimulated with OK432, a streptococcus-derived anti-cancer immunotherapeutic agent, into tumour tissues following transcatheter hepatic arterial embolization (TAE) treatment in patients with HCC. DCs were derived from peripheral blood monocytes of patients with hepatitis C virus-related cirrhosis and HCC in the presence of interleukin (IL)-4 and granulocyte-macrophage colony-stimulating factor and stimulated with 0·1 KE/ml OK432 for 2 days. Thirteen patients were administered with 5 × 10⁶ of DCs through arterial catheter during the procedures of TAE treatment on day 7. The immunomodulatory effects and clinical responses were evaluated in comparison with a group of 22 historical controls treated with TAE but without DC transfer. OK432 stimulation of immature DCs promoted their maturation towards cells with activated phenotypes, high expression of a homing receptor, fairly well-preserved phagocytic capacity, greatly enhanced cytokine production and effective tumoricidal activity. Administration of OK432-stimulated DCs to patients was found to be feasible and safe. Kaplan-Meier analysis revealed prolonged recurrence-free survival of patients treated in this manner compared with the historical controls (P = 0·046, log-rank test). The bioactivity of the transferred DCs was reflected in higher serum concentrations of the cytokines IL-9, IL-15 and tumour necrosis factor-α and the chemokines CCL4 and CCL11. Collectively, this study suggests that a DC-based, active immunotherapeutic strategy in combination with locoregional treatments exerts beneficial anti-tumour effects against liver cancer.
A Glycoprotein Hormone Expressed in Corticotrophs Exhibits Unique Binding Properties on Thyroid-Stimulating Hormone Receptor (2005)

Corticotroph-derived glycoprotein hormone (CGH), also referred to as thyrostimulin, is a noncovalent heterodimer of glycoprotein hormone alpha 2 (GPHA2) and glycoprotein hormone beta 5 (GPHB5). Here, we demonstrate that both subunits of CGH are expressed in the corticotroph cells of the human anterior pituitary, as well as in skin, retina, and testis. CGH activates the TSH receptor (TSHR); (125)I-CGH binding to cells expressing TSHR is saturable, specific, and of high affinity. In competition studies, unlabeled CGH is a potent competitor for (125)I-TSH binding, whereas unlabeled TSH does not compete for (125)I-CGH binding. Binding and competition analyses are consistent with the presence of two binding sites on the TSHR transfected baby hamster kidney cells, one that can interact with either TSH or CGH, and another that binds CGH alone. Transgenic overexpression of GPHB5 in mice produces elevations in serum T(4) levels, reductions in body weight, and proptosis. However, neither transgenic overexpression of GPHA2 nor deletion of GPHB5 produces an overt phenotype in mice. In vivo administration of CGH to mice produces a dose-dependent hyperthyroid phenotype including elevation of T(4) and hypertrophy of cells within the inner adrenal cortex. However, the distinctive expression patterns and binding characteristics of CGH suggest that it has endogenous biological roles that are discrete from those of TSH.
Automatic Detection and Measurement of Structures in Fetal Head Ultrasound Volumes Using Sequential Estimation and Integrated Detection Network (IDN) (2014)

Routine ultrasound exam in the second and third trimesters of pregnancy involves manually measuring fetal head and brain structures in 2-D scans. The procedure requires a sonographer to find the standardized visualization planes with a probe and manually place measurement calipers on the structures of interest. The process is tedious, time consuming, and introduces user variability into the measurements. This paper proposes an automatic fetal head and brain (AFHB) system for automatically measuring anatomical structures from 3-D ultrasound volumes. The system searches the 3-D volume in a hierarchy of resolutions and by focusing on regions that are likely to be the measured anatomy. The output is a standardized visualization of the plane with correct orientation and centering as well as the biometric measurement of the anatomy. The system is based on a novel framework for detecting multiple structures in 3-D volumes. Since a joint model is difficult to obtain in most practical situations, the structures are detected in a sequence, one-by-one. The detection relies on Sequential Estimation techniques, frequently applied to visual tracking. The interdependence of structure poses and strong prior information embedded in our domain yields faster and more accurate results than detecting the objects individually. The posterior distribution of the structure pose is approximated at each step by sequential Monte Carlo. The samples are propagated within the sequence across multiple structures and hierarchical levels. The probabilistic model helps solve many challenges present in the ultrasound images of the fetus such as speckle noise, signal drop-out, shadows caused by bones, and appearance variations caused by the differences in the fetus gestational age. This is possible by discriminative learning on an extensive database of scans comprising more than two thousand volumes and more than thirteen thousand annotations. The average difference between ground truth and automatic measurements is below 2 mm with a running time of 6.9 s (GPU) or 14.7 s (CPU). The accuracy of the AFHB system is within inter-user variability and the running time is fast, which meets the requirements for clinical use.