gebhart/patrepeval huggingface dataset:
Reverse Phase Protein Microarrays: Fluorometric and Colorimetric Detection (2011)

The Reverse Phase Protein Microarray (RPMA) is an array platform used to quantitate proteins and their posttranslationally modified forms. RPMAs are applicable for profiling key cellular signaling pathways and protein networks, allowing direct comparison of the activation state of proteins from multiple samples within the same array. The RPMA format consists of proteins immobilized directly on a nitrocellulose substratum. The analyte is subsequently probed with a primary antibody and a series of reagents for signal amplification and detection. Due to the diversity, low concentration, and large dynamic range of protein analytes, RPMAs require stringent signal amplification methods, high quality image acquisition, and software capable of precisely analyzing spot intensities on an array. Microarray detection strategies can be either fluorescent or colorimetric. The choice of a detection system depends on (a) the expected analyte concentration, (b) type of microarray imaging system, and (c) type of sample. The focus of this chapter is to describe RPMA detection and imaging using fluorescent and colorimetric (diaminobenzidine (DAB)) methods.
Ad click prediction (2013)

Predicting ad click-through rates (CTR) is a massive-scale learning problem that is central to the multi-billion dollar online advertising industry. We present a selection of case studies and topics drawn from recent experiments in the setting of a deployed CTR prediction system. These include improvements in the context of traditional supervised learning based on an FTRL-Proximal online learning algorithm (which has excellent sparsity and convergence properties) and the use of per-coordinate learning rates.
Quantum Optics and Photonics (1984)

Contains reports on five research projects.
Omega-3 fatty acid supplementation in severe brain trauma: case for a large multicenter trial (2020)

ABBREVIATIONS BBB = blood-brain barrier; DHA = docosahexaenoic acid; EPA = eicosapentaenoic acid; GCS = Glasgow Coma Scale; ICP = intracranial pressure; O3FA = omega-3 polyunsaturated fatty acid; TBI = traumatic brain injury.
Control of sidewall roughness formation in through-silicon via etch at non-cryogenic temperatures (2022)

Through‐silicon via etch (TSV) is critical to current and future advanced packaging schemes. For heterogeneous integration approaches in particular, where modular components are tightly packed together, these processes play an integral role. While etch processes for silicon appear well understood and the frontiers of plasma etch have led us to advanced cyclic processes for device fabrication such as atomic layer etching, TSV applications are fundamentally different due to their relative size and aspect ratio targets. Unlike small-scale etching, TSV feature etching has not shown exponential change over time. To achieve TSV targets such as high etch rate, high aspect ratio, and clean profiles to support filling, known solutions are employed such as cryogenic wafer temperatures, alternative hard mask schemes, and extremely short gas cycle times; these solutions require specialized equipment and/or a more complex integration scheme. We explore the creation of high-aspect ratio, diffusion-limited TSV etches with high PR selectivity (&lt;50:1) and high aspect ratios while simultaneously aiming for a high etch rate all while using non-cryogenic temperatures and a standard photoresist mask. A focus on sidewall profile and sidewall damage is maintained.
Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry (2013)

Supplementary data are available at Bioinformatics online.
Role of shear stress on nitrite and NOS protein content in different size conduit arteries of swine (2009)

Regional difference in blood flow has no effect on iNOS and nNOS protein contents in these conduit arteries. Regional difference in eNOS expression and nitrite contents may be related to the WSS-induced NO by the endothelium under normal physiological conditions.
Virtualized Software-Defined Networks and Services (2016)

This comprehensive new resource presents the latest developments in key Software-Defined Network (SDN) technologies including SDN controllers, network control and management applications, southbound protocols, and northbound interfaces. NFV technologies are reviewed, including network function virtualization infrastructure, virtualized network functions, virtual network management and orchestration. Professionals find comprehensive discussions on the relationship between SDN and NFV and how they may integrate into unified future network architecture. Virtualization network services including, cloud, carrier Ethernet services, and IP VPN services are also covered.
Covalent versus non-covalent (biocatalytic) approaches for enantioselective sulfoxidation catalyzed by corrole metal complexes (2011)

Oxidation of thioanisoles, catalyzed by chiral manganese(III) and iron(III) corroles, provides the corresponding sulfoxides in moderate chemical yields and low enantioselectivities. Biocatalysis by non-chiral albumin-associated manganese(III) corroles proceeds much better and allows for the enantioselective synthesis of the pharmacologically important R-modafinil, in 88% yield and 73% ee.
A Versatile Approach to CF3‐Containing 2‐Pyrrolidones by Tandem Michael Addition–Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors (2015)

Abstract The groups of Santos Fustero at the University of Valencia (Spain) and Oscar Delgado at Janssen Research and Development (Spain) have been invited for the front cover of this issue. The image depicts the docking of one of the β‐secretase 1 (BACE1) inhibitors encapsulated in a sketch of the human brain. Read the full text of the article at 10.1002/chem.201501662 .
Error-correcting codes with bounded running digital sum (1993)

A new approach for encoding any string of information bits into a sequence having bounded running digital sum is presented. The results improve previously known values of the running digital sum for the same rate. Also discussed are ways of incorporating an error-correcting capability into these codes. Some general constructions are given and tables are constructed for specific cases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stress and Reliability Analysis of Electronic Packages With Ultra-Thin Chips (2003)

This research concerns itself with a stress and reliability analysis of electronic packages with ultra-thin chips based on the finite element method. The effect of chip and substrate thickness, substrate material, presence of underfill, dimensions, and shape of the bump on stress reduction is analyzed. Obtained results clearly show that chip thinning, when used with an appropriate design of the entire package, can significantly decrease stresses and stress intensity factors and improve the reliability of the package. The developed software provides an effective design tool to quantify the reliability, stresses, and deflections of a package with ultra-thin chips.
TNF-a, retinoid acid and STAT4 pathways are differentially regulated by the HDAC inhibitors, SAHA, TSA and Sirtinol in Waldenstrom's Macroglobulinemia (2009)

e14582 Background: HDAC inhibitors (HDAC-I) have emerged as a promising class of therapeutics for the treatment of lymphoplasmacytic malignancies, particularly in combination strategies. The basic mechanisms by which these agents modulate malignant cell growth remain to be clarified. In recent studies, we showed that SAHA, TSA, and Sirtinol have significant preclinical activity in Waldenstrom's macroglobulinemia (WM). As part of our effort to identify potential molecular targets for these agents, we performed gene expression profiling (GEP) using WM cells treated with these agents. Methods: We implemented the Bootstrap re-sampling technique on five BCWM1 GEP datasets to characterize the range of gene expression observed. Individual BCWM1 cells were treated with SAHA, TSA and Sirtinol at their established IC50 dosages for 6 and 24 hours prior to gene expression profiling. The genes which changed by two-fold, and fell outside of the 90% range of expression after drug treatment were identified. Results: SAHA upregulated TNF-α and downstream proteins including HSP70, TNFSF9, SERPINB2, as well as STAT4- dependent genes. Sirtinol upregulated metalloproteinase (MMP) and phosphodiesterase (PDE) family members through retinoic acid signaling. We also observed that SAHA, TSA and Sirtinol differentially upregulate elements of the MAP kinase pathways, including signaling through Erk, JNK, and p38 MAPK, indicating a global stress response to HDAC inhibition. Conclusions: The above studies suggest that HDAC inhibitors differentially effect growth of WM cells through both global as well as pathway specific alterations in signaling. Importantly, this data provides a platform for studying the mechanistic role of HDACs in WM, and provide a framework for the use of HDAC-I as single and combination. No significant financial relationships to disclose.
Muscle satellite cell heterogeneity and self-renewal (2014)

Adult skeletal muscle possesses extraordinary regeneration capacities. After muscle injury or exercise, large numbers of newly formed muscle fibers are generated within a week as a result of expansion and differentiation of a self-renewing pool of muscle stem cells termed muscle satellite cells. Normally, satellite cells are mitotically quiescent and reside beneath the basal lamina of muscle fibers. Upon regeneration, satellite cells are activated, and give rise to daughter myogenic precursor cells. After several rounds of proliferation, these myogenic precursor cells contribute to the formation of new muscle fibers. During cell division, a minor population of myogenic precursor cells returns to quiescent satellite cells as a self-renewal process. Currently, accumulating evidence has revealed the essential roles of satellite cells in muscle regeneration and the regulatory mechanisms, while it still remains to be elucidated how satellite cell self-renewal is molecularly regulated and how satellite cells are important in aging and diseased muscle. The number of satellite cells is decreased due to the changing niche during ageing, resulting in attenuation of muscle regeneration capacity. Additionally, in Duchenne muscular dystrophy (DMD) patients, the loss of satellite cell regenerative capacity and decreased satellite cell number due to continuous needs for satellite cells lead to progressive muscle weakness with chronic degeneration. Thus, it is necessary to replenish muscle satellite cells continuously. This review outlines recent findings regarding satellite cell heterogeneity, asymmetric division and molecular mechanisms in satellite cell self-renewal which is crucial for maintenance of satellite cells as a muscle stem cell pool throughout life. In addition, we discuss roles in the stem cell niche for satellite cell maintenance, as well as related cell therapies for approaching treatment of DMD.
Endoscopic Removal of a Bullet in Rosenmuller Fossa: Case Report (2016)

Fractures of the anterior skull base may occur in gunshot victims and can result in traumatic cerebrospinal fluid (CSF) leak. Less commonly, CSF leaks occur days or even weeks after the trauma occurred. Here, we present the case of a 21-year-old man with a delayed-onset, traumatic CSF leak secondary to a missile injury that left a bullet fragment in the Rosenmuller fossa. The patient was treated successfully with endoscopic, endonasal extraction of the bullet, and repair with a nasal septal flap. Foreign bodies lodged in Rosenmuller fossa can be successfully treated with endoscopic skull base surgery.
Early Human B Cell Response to Ebola Virus in Four U.S. Survivors of Infection (2019)

The human B cell response to natural filovirus infections early after recovery is poorly understood. Previous serologic studies suggest that some Ebola virus survivors exhibit delayed antibody responses with low magnitude and quality. Here, we sought to study the population of individual memory B cells induced early in convalescence. We isolated monoclonal antibodies (MAbs) from memory B cells from four survivors treated for Ebola virus disease (EVD) 1 or 3 months after discharge from the hospital. At the early time points postrecovery, the frequency of Ebola-specific B cells was low and dominated by clones that were cross-reactive with both Ebola glycoprotein (GP) and with the secreted GP (sGP) form. Of 25 MAbs isolated from four donors, only one exhibited neutralization activity. This neutralizing MAb, designated MAb EBOV237, recognizes an epitope in the glycan cap of the surface glycoprotein. <i>In vivo</i> murine lethal challenge studies showed that EBOV237 conferred protection when given prophylactically at a level similar to that of the ZMapp component MAb 13C6. The results suggest that the human B cell response to EVD 1 to 3 months postdischarge is characterized by a paucity of broad or potent neutralizing clones. However, the neutralizing epitope in the glycan cap recognized by EBOV237 may play a role in the early human antibody response to EVD and should be considered in rational design strategies for new Ebola virus vaccine candidates.<b>IMPORTANCE</b> The pathogenesis of Ebola virus disease (EVD) in humans is complex, and the mechanisms contributing to immunity are poorly understood. In particular, it appears that the quality and magnitude of the human B cell response early after recovery from EVD may be reduced compared to most viral infections. Here, we isolated human monoclonal antibodies from B cells of four survivors of EVD at 1 or 3 months after hospital discharge. Ebola-specific memory B cells early in convalescence were low in frequency, and the antibodies they encoded demonstrated poor neutralizing potencies. One neutralizing antibody that protected mice from lethal infection, EBOV237, was identified in the panel of 25 human antibodies isolated. Recognition of the glycan cap epitope recognized by EBOV237 suggests that this antigenic site should be considered in vaccine design and treatment strategies for EVD.
0124 PM2.5 and Heart Disease in a Cohort of Aluminium Workers: An Application of Longitudinal Targeted Maximum Likelihood-based Estimation (TMLE) (2014)

<h3>Objectives</h3> We estimated the effect of cumulative exposure to PM2.5 on the incidence of ischaemic heart disease (IHD) in aluminium workers followed for 15 years, adjusting for the healthy worker survivor effect. In previous analyses, higher cumulative exposure was found to be associated with lower mortality in this population. <h3>Method</h3> We used longitudinal TMLE to estimate the cumulative risk of ischaemic heart disease in the cohort if constantly exposed above an exposure cut-off and compared it to the risk if constantly exposed below. We stratified all analyses by work process because exposures were an order of magnitude higher in smelters than fabrication facilities. <h3>Results</h3> We selected cut-offs a priori at the median and 10th percentile exposure within each sub-cohort. Among the smelter workers, we estimated an increase in IHD risk of 2.1% (p = 0.22) after 15 years, comparing the always exposed to never exposed cohort using the median cut-off of 1.77 mg/m<sup>3</sup>. The difference was 2.9% (p = 0.01) using the 10th percentile cutoff of 0.10 mg/m<sup>3</sup>. For the fabrication workers, the differences were 0.1% (p = 0.47) using the median cut-off of 0.20 mg/m<sup>3</sup> and 2.5% (p &lt; 0.01) for the 10th percentile cut-off of 0.06 mg/m<sup>3</sup>. Results are presented as adjusted survival curves, describing the estimated cumulative risk for each cohort under each exposure regimen. <h3>Conclusions</h3> The TMLE estimator allows us to observe an association between cumulative PM2.5 exposure and heart disease that was not visible using standard analytical techniques. This work represents the first application of longitudinal TMLE to the field of occupational epidemiology.
In Vitro and In Vivo Evaluations of Soybean Residues Ensiled with Various Additives (1979)

Experiments were initiated to determine the efficacy of feeding chemically treated, ensiled soybean residues (SBR) to ruminants. SBR at 50, 60 and 70% moisture were treated with ammonium hydroxide (AH), propionic acid (P), sodium chlorite (SC) and wood molasses (WM) at the time of ensiling. All additives were added at the 2% level on a wet basis and ensiled in Mason jars for 30 days. In vitro cellulose digestibility (IVCD) and in vitro organic matter digestibility (IVOMD) were measured. IVCD and IVOMD were highest for samples ensiled at 60% moisture and lowest for samples ensiled at 70% moisture. AH improved IVCD of SBR ensiled at 50% moisture and IVOMD of SBR ensiled at 60% moisture. SC improved IVOMD of both 60 and 70% moisture residues and improved IVCD of the 70% moisture residue. WM and P had little effect on either parameter. For the in vivo evaluation, SBR (60% moisture) was ensiled in 220-liter plastic-lined drums. At the time of ensiling, SC or AH were added at the 5.1% level (dry matter basis). Thirty days after ensiling, a balance study was conducted using crossbred male lambs averaging 25 kg in weight. Ground, high quality fescue hay was added as 50% of the diet (dry matter basis) at time of feeding. No improvement in dry matter, neutral detergent fiber, or acid detergent fiber digestibilities were observed with additions of SC or AH. Lignin digestibility was improved by both additives. SC increased hemicellulose digestibility (HD) but depressed cellulose digestibility (CD). AH increased HD but had no effect on CD. Animals fed either AH or SC-treated ensiled SBR consumed equivalent quantities of feed but retained significantly less nitrogen than controls.
Examination of Platelet Function in Whole Blood Under Dynamic Flow Conditions With the Cone and Plate(let) Analyzer: Effect of Erythrocytosis and Thrombocytosis (2007)

We studied cone and plate(let) analysis (CPA) for evaluating global platelet function in whole blood under arterial flow conditions (~1,800 seconds–1). CPA allows direct visualization and quantitation of platelet adhesion (surface coverage [SC]) and determination of average aggregate size (AS) following brief shearing of a small blood sample (3.2% sodium citrate) in plastic wells. By using blood from healthy volunteers manipulated to alter platelet or RBC counts and blood from patients with myeloproliferative disorders (MPDs), quantitative and qualitative changes in SC and AS were observed. Thrombocytosis resulted in increased SC, whereas erythrocytosis increased AS. The RBC volume (mean corpuscular volume) had no effect. It is interesting that differences in CPA AS were discerned among subgroups of patients with MPD undergoing different treatment regimens. These studies suggest that CPA platelet deposition patterns may provide novel insight into global platelet function during hemodynamic flow.
Automated interpretation of MS/MS spectra of oligosaccharides (2005)

The program GLYCH is available upon request from the authors.
Ultrasonics (2013)

Using a stress wave at the outset, the ultrasonic technique offers versatility and convenience since the waves can be oriented in a manner most suitable for the measurement of stress and easily excited from a free surface. Methods are described for exciting the LCR wave parallel to the surface as well as shear waves deeper within a material. Practical examples of probes and systems as well as the necessary acoustoelastic constants are furnished. Additionally, the effect of material and instrumentation uncertainties are described as well as a recent bibliography. Typical applications discussed include measuring stresses in welds, pressure vessels, ductile iron and polymers as well as the effects of shock peening and reversible hydrogen attack.
Contextual Blocking Bandits (2020)

We study a novel variant of the multi-armed bandit problem, where at each time step, the player observes an independently sampled context that determines the arms' mean rewards. However, playing an arm blocks it (across all contexts) for a fixed and known number of future time steps. The above contextual setting, which captures important scenarios such as recommendation systems or ad placement with diverse users, invalidates greedy solution techniques that are effective for its non-contextual counterpart (Basu et al., NeurIPS19). Assuming knowledge of the context distribution and the mean reward of each arm-context pair, we cast the problem as an online bipartite matching problem, where the right-vertices (contexts) arrive stochastically and the left-vertices (arms) are blocked for a finite number of rounds each time they are matched. This problem has been recently studied in the full-information case, where competitive ratio bounds have been derived. We focus on the bandit setting, where the reward distributions are initially unknown; we propose a UCB-based variant of the full-information algorithm that guarantees a $\mathcal{O}(\log T)$-regret w.r.t. an $α$-optimal strategy in $T$ time steps, matching the $Ω(\log(T))$ regret lower bound in this setting. Due to the time correlations caused by blocking, existing techniques for upper bounding regret fail. For proving our regret bounds, we introduce the novel concepts of delayed exploitation and opportunistic subsampling and combine them with ideas from combinatorial bandits and non-stationary Markov chains coupling.
Invasive papillary carcinoma of the breast: mammographic appearance. (1990)

The mammographic findings in 18 patients with invasive papillary carcinoma were studied retrospectively. The mammograms of 10 patients showed a multinodular pattern, and seven patients had solitary nodules. One patient had an irregular, ill-defined mass in the retroareolar region. Two patients were found to have carcinoma in the contralateral breast, and two patients had intraductal carcinoma adjacent to the invasive papillary carcinoma. The varied mammographic features that may occur with this rare breast malignancy are discussed.
Bone Morphogenetic Proteins in Bone Stimulate Osteoclasts and Osteoblasts During Bone Development (2006)

Overexpression of noggin in bone revealed that BMP signals regulate bone development through stimulation of osteoblasts and osteoclasts.
IL-10 expression defines an immunosuppressive dendritic cell population induced by antitumor therapeutic vaccination (2016)

Vaccination induces immunostimulatory signals that are often accompanied by regulatory mechanisms such as IL-10, which control T-cell activation and inhibit vaccine-dependent antitumor therapeutic effect. Here we characterized IL-10-producing cells in different tumor models treated with therapeutic vaccines. Although several cell subsets produced IL-10 irrespective of treatment, an early vaccine-dependent induction of IL-10 was detected in dendritic cells (DC). IL-10 production defined a DC population characterized by a poorly mature phenotype, lower expression of T-cell stimulating molecules and upregulation of PD-L1. These IL-10+ DC showed impaired in vitro T-cell stimulatory capacity, which was rescued by incubation with IL-10R and PD-L1-inhibiting antibodies. In vivo IL-10 blockade during vaccination decreased the proportion of IL-10+ DC and improved their maturation, without modifying PD-L1 expression. Similarly, PD-L1 blockade did not affect IL- 10 expression. Interestingly, vaccination combined with simultaneous blockade of IL-10 and PD-L1 induced stronger immune responses, resulting in a higher therapeutic efficacy in tumor-bearing mice. These results show that vaccine-induced immunoregulatory IL- 10+ DC impair priming of antitumor immunity, suggesting that therapeutic vaccination protocols may benefit from combined targeting of inhibitory molecules expressed by this DC subset.