gebhart/patrepeval huggingface dataset:
Deep-UV excitation fluorescence microscopy for detection of lymph node metastasis using deep neural network (2019)

Deep-UV (DUV) excitation fluorescence microscopy has potential to provide rapid diagnosis with simple technique comparing to conventional histopathology based on hematoxylin and eosin (H&E) staining. We established a fluorescent staining protocol for DUV excitation fluorescence imaging that has enabled clear discrimination of nucleoplasm, nucleolus, and cytoplasm. Fluorescence images of metastasis-positive/-negative lymph nodes of gastric cancer patients were used for patch-based training with a deep neural network (DNN) based on Inception-v3 architecture. The performance on small patches of the fluorescence images was comparable with that of H&E images. Gradient-weighted class activation mapping analysis revealed the areas where the trained model identified metastatic lesions in the images containing cancer cells. We extended the method to large-size image analysis enabling accurate detection of metastatic lesions. We discuss usefulness of DUV excitation fluorescence imaging with the aid of DNN analysis, which is promising for assisting pathologists in assessment of lymph node metastasis.
Max-Margin Deep Generative Models for (Semi-)Supervised Learning (2016)

Deep generative models (DGMs) are effective on learning multilayered representations of complex data and performing inference of input data by exploring the generative ability. However, it is relatively insufficient to empower the discriminative ability of DGMs on making accurate predictions. This paper presents max-margin deep generative models (mmDGMs) and a class-conditional variant (mmDCGMs), which explore the strongly discriminative principle of max-margin learning to improve the predictive performance of DGMs in both supervised and semi-supervised learning, while retaining the generative capability. In semi-supervised learning, we use the predictions of a max-margin classifier as the missing labels instead of performing full posterior inference for efficiency; we also introduce additional max-margin and label-balance regularization terms of unlabeled data for effectiveness. We develop an efficient doubly stochastic subgradient algorithm for the piecewise linear objectives in different settings. Empirical results on various datasets demonstrate that: (1) max-margin learning can significantly improve the prediction performance of DGMs and meanwhile retain the generative ability; (2) in supervised learning, mmDGMs are competitive to the best fully discriminative networks when employing convolutional neural networks as the generative and recognition models; and (3) in semi-supervised learning, mmDCGMs can perform efficient inference and achieve state-of-the-art classification results on several benchmarks.
A novel minimally invasive percutaneous facet augmentation device for the treatment of lumbar radiculopathy and axial back pain: technical description, surgical technique and case presentations (2009)

OBJECTIVE: to describe a new posterior minimally invasive method of facet stabilization for treatment of the degenerating lumbar motion segment. The biomechanics of this Percudyn (Interventional Spine; Irvine, CA) system are distinct from that of other interspinous dynamic stabilization systems as it acts bilaterally directly within the middle column of the spine. Based on biomechanical evalution, the paired prosthesis supports, cushions, and reinforces the facet complexes by limiting both extension and lateral bending thereby maintaining central and foraminal volumes. METHODS: the Percudyn device consists of a pedicle anchor upon which sits a cushioning polycarbonate-urethane stabilizer that serves as a mechanically reinforcing stop between the inferior and superior articular facets. A 1.5 cm skin incision is made bilaterally over the lower pedicle of the treated segment through which a Jamshidi needle is percutaneously targeted under biplanar fluoroscopic guidance into the caudal aspect of the superior articular process directly underneath the lip of the inferior facet from the level above. Progressive onestep tubular dilation is then performed to secure a small disposable working portal. Through this access, the Percudyn stabilizers are then placed over the wire and anchored bilaterally into the inferior pedicles of the degenerated motion segment. RESULTS: three patients (ages 26-41, male) with significant low back pain as well as radiculopathy with lateral recess stenosis from a large disc herniation/ ligamentum and facet hypertrophy (L4-5 and/or L5-S1) underwent a minimally invasive decompression/ discectomy and bilateral Percudyn placement at each disease level. Each patient had significant relief of both his radiculopathy and axial back pain post-operatively and was discharged home within 18 hours without sequelae. CONCLUSION: this novel technique of percutaneous posterior facet augmentation allows for safe placement of bilateral middle column prostheses that act as mechanical cushions between the articulating facets thereby limiting extension and lateral bending and also preventing compression of the neural elements. As the Percudyn device serves to reinforce the middle column directly at the level of the facet, it represents a new class of posterior motionpreserving stabilization which may serve to mitigate segmental axial back pain as has been described for other posterior dynamic stabilization systems.
Expression and Characterization of Recombinant, Tetrameric and Enzymatically Active Influenza Neuraminidase for the Setup of an Enzyme-Linked Lectin-Based Assay (2015)

Developing a universal influenza vaccine that induces broad spectrum and longer-term immunity has become an important potentially achievable target in influenza vaccine research and development. Hemagglutinin (HA) and neuraminidase (NA) are the two major influenza virus antigens. Although antibody responses against influenza virus are mainly directed toward HA, NA is reported to be more genetically stable; hence NA-based vaccines have the potential to be effective for longer time periods. NA-specific immunity has been shown to limit the spread of influenza virus, thus reducing disease symptoms and providing cross-protection against heterosubtypic viruses in mouse challenge experiments. The production of large quantities of highly pure and stable NA could be beneficial for the development of new antivirals, subunit-based vaccines, and novel diagnostic tools. In this study, recombinant NA (rNA) was produced in mammalian cells at high levels from both swine A/California/07/2009 (H1N1) and avian A/turkey/Turkey/01/2005 (H5N1) influenza viruses. Biochemical, structural, and immunological characterizations revealed that the soluble rNAs produced are tetrameric, enzymatically active and immunogenic, and finally they represent good alternatives to conventionally used sources of NA in the Enzyme-Linked Lectin Assay (ELLA).
Tight moments-based bounds for queueing systems (2011)

We present a new tool to analyze three queueing systems which have defied exact analysis so far: (i) the classical M/G/k multi-server system, (ii) queueing systems with fluctuating arrival and service rates, and (iii) the M/G/1 round-robin queue. We argue that rather than looking for exact expressions for the mean response time as a function of the job size distribution, a more fruitful approach is to find distributions which minimize or maximize the mean response time given the first n moments of the job size distribution.
Model selection for nested model classes with cost constraints (2002)

For model selection with nested classes, we propose to minimize Rissanen's stochastic complexity with a constraint on expected computational cost. The proposed solution uses the Wald statistic and dynamic programming for order selection, such that maximum likelihood estimates of only a small subset of hypothesized models need to be computed. Simulation results are presented to compare computational savings and detection performance for superimposed undamped exponentials in additive noise.
Columnarly Assembled Liquid-Crystalline Peptidic Macrocycles Unidirectionally Orientable over a Large Area by an Electric Field (2011)

Being inspired by naturally occurring peptidic macrocycles, we developed liquid-crystalline (LC) compounds 1 and 2 that are capable of self-assembling into hexagonal columnar mesophases over a wide temperature range that includes room temperature. Their bowl-shaped macrocyclic cores are conformationally robust because of the presence of internal H-bonds, while the columnar assembly is ensured by intermolecular H-bonding interactions involving the exocyclic amide units. When an electric field was applied to their LC films from a direction orthogonal to the film plane, the columns were oriented homeotropically over a large area.
Oxidative coupling of methane by absorbed oxygen species on SrTi1-xMgxO3-δ catalysts (1996)

In this study we investigated the comparison of the reactivity of methane on SrTi 0.5 Mg 0. 5O 3-δ , SrTiO 3 and Sr 2 TiO 4 and the property of the oxygen species adsorbed on SrTi 1-x Mg x O 3-δ catalysts
Alternative splicing coupled with transcript degradation modulates OAS1g antiviral activity (2019)

At the heart of an innate immune response lies a tightly regulated gene expression program. This precise regulation is crucial because small changes can shift the balance from protective to destructive immunity. Here we identify a frequently used alternative splice site in the gene oligoadenylate synthetase 1g (<i>Oas1g</i>), a key component of the 2-5A antiviral system. Usage of this splice site leads to the generation of a transcript subject to decay, and removal of the site leads to increased expression of <i>Oas1g</i> and an improved antiviral response. However, removal of the splice site also leads to an increase in apoptotic cell death, suggesting this splicing event exists as a compromise between the pathogen protective benefits and collateral damage associated with OAS1g activity. Across the innate immune response, we show that a multitude of alternative splicing events predicted to lead to decay exist, and thus have the potential to play a significant role in the regulation of gene expression in innate immunity.
Fast Component Interaction for Real-Time Systems (2006)

Open real-time systems provide for co-hosting hard-, soft- and non-real-time applications. Microkernel-based designs in addition allow for these applications to be mutually protected. Thus, trusted servers can coexist next to untrusted applications. These systems place a heavy burden on the performance of the message-passing mechanism, especially when based on microkernel-like inter-process communication. In this paper we introduce capacity-reserve donation (in short Credo), a mechanism for the fast interaction of interdependent components, which is applicable to common real-time resource-access models. We implemented Credo by extending L4's message-passing mechanism to provide proper resource accounting and time-donation control, thereby preserving desired real-time properties. We were able to achieve priority inheritance and stack-based priority-ceiling resource sharing with virtually no overhead added to L4's message-passing implementation. By providing a. mechanism that does not impose performance penalties, while still guaranteeing correct real-time behaviour, Credo allows for the usage of microkernels in general-purpose but also in specialized systems.
Demonstration of Real-time Cognitive Radar using Spectrally-Notched Random FM Waveforms (2020)

With the reality of increasing radio frequency (RF) spectral congestion, radar systems capable of dynamic spectrum sharing are needed. Recent work has demonstrated a real-time cognitive capability on a software defined radio (SDR) by generating pulse-agile LFM chirps that vary their center frequency and bandwidth to avoid dynamic interference on a per-pulse basis. Separately, spectral notching of random FM waveforms was developed and experimentally evaluated as another means with which to mitigate emulated interference, though real-time operation had not yet been demonstrated. Here the operational framework of the former is combined with the waveform agility of the latter to facilitate real-time generation of notched, random FM waveforms as part of an integrated cognitive SDR architecture. This implementation supports pulse repetition frequencies up to 2.2 kHz for on-the-fly waveform synthesis, can incorporate multiple spectral notches per waveform, and can achieve notch depths of 25 dB relative to peak power (with greater depth possible given greater computational resources). Performance examples are illustrated along with implementation decisions and design trade-offs.
Application of a Multiple Testing Procedure Controlling the Proportion of False Positives to Protein and Bacterial Data (2005)

Simultaneously testing multiple hypotheses is important in high-dimensional biological studies. In these situations, one is often interested in controlling the Type-I error rate, such as the proportion of false positives to total rejections (TPPFP) at a specific level, alpha. This article will present an application of the E-Bayes/Bootstrap TPPFP procedure, presented in van der Laan et al. (2005), which controls the tail probability of the proportion of false positives (TPPFP), on two biological datasets. The two data applications include firstly, the application to a mass-spectrometry dataset of two leukemia subtypes, AML and ALL. The protein data measurements include intensity and mass-to-charge (m/z) ratios of bone marrow samples, with two replicates per sample. We apply techniques to preprocess the data; i.e. correct for baseline shift of the data as well as appropriately smooth the intensity profiles over the m/z values. After preprocessing the data we show an application of a TPPFP multiple testing techniques (van der Laan et al. (2005)) to test the difference between two groups of patients (AML/ALL) with respect to their intensity values over various m/z ratios, thus indicative of testing proteins of different sizes. Secondly, we will show an illustration of the E-Bayes/Bootstrap TPPFP procedure on a bacterial data set. In this application we are interested in finding bacteria whose mean difference over time points is differentially expressed between two U.S. cities. With both of these data applications, we also show comparisons to the van der Laan et al. (2004b) tppfp augmentation method, and discover the E-Bayes/Bootstrap TPPFP method is less conservative, therefore rejecting more tests at a specific alpha level
A 500-W Direct Peroxide Fuel Cell for Space Power Systems (2007)

The research on a 500-Watt direct sodium-borohydride/hydrogen-peroxide (NaBH4/H2O2) fuel cell is presented here. Aqueous solutions of NaBH4 and hydrogen peroxide are directly used at the fuel cell anode and cathode, respectively, in place of gaseous reactants. Initial results indicate: 1) conversion efficiency over 60% at a practical current density of 250 mA/cm; 2) power density over 0.5 W/cm, at 60 degree Celsius. The kiloWatt-stack consists of 24 cells, generating an OCV (open circuit voltage) of ~ 42V. The design of the reactant manifold overcomes some issues unique to an all-liquid-reactant fuel cell. One such issue is possible short-circuiting of neighboring cells from the conductivity of fuel/oxidant. Another issue is possible excessive corrosion if the manifold is not designed properly. This NaBH4/H2O2 fuel cell technology is ideal for propulsion/power for aerospace systems such as spacecraft and unmanned aerial vehicles.
A Four-Chemokine Signature Is Associated with a T-cell–Inflamed Phenotype in Primary and Metastatic Pancreatic Cancer (2020)

A conserved 4-chemokine signature marks resectable and metastatic PDAC tumors with an active antitumor phenotype. This could have implications for the appropriate selection of PDAC patients in immunotherapy trials.
Multi-input and binary reproducible, high bandwidth floating point adder in a collective network (2023)

To add floating point numbers in a parallel computing system, a collective logic device receives the floating point numbers from computing nodes. The collective logic devices converts the floating point numbers to integer numbers. The collective logic device adds the integer numbers and generating a summation of the integer numbers. The collective logic device converts the summation to a floating point number. The collective logic device performs the receiving, the converting the floating point numbers, the adding, the generating and the converting the summation in one pass. One pass indicates that the computing nodes send inputs only once to the collective logic device and receive outputs only once from the collective logic device.
BLOOD-BASED BIOMARKER CHANGES IN A PHASE 2B TRIAL ASSESSING LOMECEL-B IN OLDER ADULTS WITH FRAILTY (2022)

Abstract Aging frailty (AF) is a multidimensional geriatric syndrome that is characterized by physical and cognitive symptoms, increasing the vulnerability of affected older adults to adverse health outcomes. Mechanistically, a low-grade chronic inflammatory state (inflammaging), endothelial dysfunction, and decreased regenerative capacity are thought to be major contributors to AF pathophysiology. Lomecel-B is an allogenic medicinal signaling cell(MSC) formulation that can potentially ameliorate AF through pleiotropic mechanisms, including anti-inflammatory, pro-vascular, and pro-regenerative activities. We completed a Phase 2b randomized, double-blinded, placebo-controlled trial designed to assess Lomecel-B benefits for AF via change versus placebo in the six-minute walk test(6MWT), to assess the dose-response relationship, and to evaluate bioactivity via changes in blood-based biomarkers. Enrolled subjects were aged 70–85 years with mild-to-moderate AF, a reduced 6MWT of 200-400m, and Tumor Necrosis Factor-α of ≥ 2.5pg/mL indicative of inflammaging. In total, 143 subjects received a single intravenous infusion of Lomecel-B at doses of 2.5 x 107 cells (25M, N=35), 5.0 x 107 cells (50M, N=30), 1.0 x 108 cells (100M, N=33), or 2.0 x 108 cells (200M, N=16), or placebo (N=29). Safety and efficacy assessments were performed at 1, 3, 6, and 9 months post-infusion. Increases in 6MWT and decreases in serum levels of the blood-based biomarker Soluble-Tie-2 were observed at 9 months in the Lomecel-B groups versus placebo. Notably, both observations were seen in a dose dependent fashion with 200M showing the highest effect. Based on the findings, a next-phase trial is being developed to advance this clinical program and will be presented.
Enzymatic regeneration of ATP (1974)

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1974.
Tissue factor expression during human and mouse development. (1996)

In the adult organism the cellular distribution of tissue factor (TF) expression corresponds to biological boundary layers forming a hemostatic barrier ready to activate blood coagulation after tissue injury. Whether TF expression might also play a role in development is unknown. To determine the significance of TF in ontogenesis, we examined the pattern of TF expression in mouse development and compared it with the distribution of TF in human post-implantation embryos and fetuses of corresponding gestational age. At early embryonic periods of murine (6.5 and 7.5 pc) and human (stage 5) development, there was strong expression of TF in both ectodermal and entodermal cells. In situ hybridization and immunohistochemistry demonstrated that TF mRNA and protein were expressed widely in epithelial areas with high levels of morphogenic activity during organogenesis. Staining for TF was seen during ontogenetic development in tissues such as epidermis, myocardium, bronchial epithelium, and hepatocytes, which express TF in the adult organism. Surprisingly, during renal development and in adults, expression of TF differed between humans and mice. In humans, maturing stage glomeruli were stained for TF whereas in mice, TF was absent from glomeruli but was present in the epithelia of tubular segments. In neuroepithelial cells, there was a substantial expression of TF. Moreover, there was robust TF expression in tissues such as skeletal muscle and pancreas, which do not express it in the adult. In contrast, expression of the physiological ligand for TF, factor VII, was not detectable during early stages of human embryogenesis using immunohistochemistry. The temporal and spatial pattern of TF expression during murine and human development supports the contention that TF serves as an important morphogenic factor during embryogenesis.
Quantum dots reveal endothelial NOX2 induces VCAM expression in LPS‐challenged inflamed whole lung (855.2) (2014)

Quantum Dot (QD) technology coupled with fluorescence imaging is a powerful tool to detect cellular proteins in vivo. Here we employ QDs as an imaging tool to detect vascular cell adhesion molecule‐1 (VCAM) expression in a model of lung inflammation. A key event in inflammation is the expression of VCAM. VCAM induction is reportedly responsible for the accumulation of neutrophils in lungs and for subsequent production of reactive oxygen species (ROS). NADPH oxidase 2 (NOX2), expressed by both endothelial cells and neutrophils, is a major contributor to ROS production post inflammation in the lungs. To date, the cellular sources of NOX2 (neutrophils or endothelium) that regulate VCAM expression in inflamed lungs is unknown. Using QD probes specific for VCAM, we found increased VCAM expression post LPS‐challenge in vitro, which was abrogated by the NOX2 inhibitor, apocynin. Ex vivo and in vivo lungs exhibited an 8‐10 fold higher incidence of VCAM expression in LPS‐challenged lungs over NOX2 null lungs. We next employed an endothelial specific NOX2 expressing transgenic mouse in a NOX2 null background (endoNOX2Tg) to reveal that endothelial NOX2 induces VCAM expression at levels that are intermediate between those expressed in wild‐type (WT) and NOX2 null mice. This result indicates that endothelial NOX2 is sufficient to induce VCAM expression due to an inflammatory stimulus. Grant Funding Source : Supported by T32‐HL07748.
Why do we need 6G? (2021)

The study and design of 5G seems to have reached its end and 5G communication systems are currently under deployment. In parallel, 5G standardization is as Release 16, which is going to complete the definition and the design guidelines of the 5G radio access network. Because of that, the interest of the scientific and industrial communities has already started focusing on the future 6G communication networks. The preliminary definition of future technology trends towards 2030, given by major standardization bodies, and the flagship 6G projects worldwide have started proposing various visions about what 6G will be. Side by side, various scientific articles, addressing the initial characterisation of 6G, have also been published. However, considering the promises of 5G, can 6G represent a significant technological advancement to justify a so-called new generation? In fact, now, 5G softwarized networks may just imply continuous network software upgrades (as it happens for the Internet) instead of new generations every ten years. This article starts describing the main characteristics that made 5G a breakthrough in telecommunications, also briefly introducing the network virtualisation and computing paradigms that have reformed telecommunications. Next, by providing rigorous definition of the terminology and a survey of the principal 6G visions proposed, the paper tries to establish important motivations and characteristics that can really justify the need for and the novelty of future 6G communication networks.