gebhart/patrepeval huggingface dataset:
Computer vision for high content screening (2016)

High Content Screening (HCS) technologies that combine automated fluorescence microscopy with high throughput biotechnology have become powerful systems for studying cell biology and drug screening. These systems can produce more than 100 000 images per day, making their success dependent on automated image analysis. In this review, we describe the steps involved in quantifying microscopy images and different approaches for each step. Typically, individual cells are segmented from the background using a segmentation algorithm. Each cell is then quantified by extracting numerical features, such as area and intensity measurements. As these feature representations are typically high dimensional (>500), modern machine learning algorithms are used to classify, cluster and visualize cells in HCS experiments. Machine learning algorithms that learn feature representations, in addition to the classification or clustering task, have recently advanced the state of the art on several benchmarking tasks in the computer vision community. These techniques have also recently been applied to HCS image analysis.
Spectrum Breathing: Protecting Over-the-Air Federated Learning Against Interference (2023)

Federated Learning (FL) is a widely embraced paradigm for distilling artificial intelligence from distributed mobile data. However, the deployment of FL in mobile networks can be compromised by exposure to interference from neighboring cells or jammers. Existing interference mitigation techniques require multi-cell cooperation or at least interference channel state information, which is expensive in practice. On the other hand, power control that treats interference as noise may not be effective due to limited power budgets, and also that this mechanism can trigger countermeasures by interference sources. As a practical approach for protecting FL against interference, we propose Spectrum Breathing, which cascades stochastic-gradient pruning and spread spectrum to suppress interference without bandwidth expansion. The cost is higher learning latency by exploiting the graceful degradation of learning speed due to pruning. We synchronize the two operations such that their levels are controlled by the same parameter, Breathing Depth. To optimally control the parameter, we develop a martingale-based approach to convergence analysis of Over-the-Air FL with spectrum breathing, termed AirBreathing FL. We show a performance tradeoff between gradient-pruning and interference-induced error as regulated by the breathing depth. Given receive SIR and model size, the optimization of the tradeoff yields two schemes for controlling the breathing depth that can be either fixed or adaptive to channels and the learning process. As shown by experiments, in scenarios where traditional Over-the-Air FL fails to converge in the presence of strong interference, AirBreahing FL with either fixed or adaptive breathing depth can ensure convergence where the adaptive scheme achieves close-to-ideal performance.
Nonparametrical Statistical Techniques for Location Discovery-Friendly Deployment (2007)

We propose a new error modeling approach for location discovery in sensor networks, in the presence of range measurement noise. Our pair-wise consistency based approach, uses non-parametric statistical techniques to generate a probability density function of the measured distances as an error model, which serves as an objective function in solving the localization problem. The pair-wise consistency approach enables the development of an error model despite a lack of a-priori parametric knowledge of the network. Further, we propose an optimization-based localization algorithm based on this technique in centralized and localized modes of operation. Our algorithm considers the properties of the particular sensor network as well as the properties of the best achievable solution in the network. Moreover, our approach canvasses problems of node deployment to statistically guarantee targeted error measures. Our error models have been evaluated based on CENS datasets using the learn-and-test method. The experimental evaluation of our algorithm indicates that localization of only a few centimeters is consistently achieved when the average and median distance measurement errors are more than a meter, even when the nodes have low connectivity.
Vascular Response to Zotarolimus-Coated Balloons in Injured Superficial Femoral Arteries of the Familial Hypercholesterolemic Swine (2011)

The single delivery of zotarolimus via coated balloon is feasible, and therapeutic levels are maintained up to 28 days. The ZCB technology appears to be effective in the reduction of neointimal proliferation in the superficial femoral artery of the familial hypercholesterolemic swine.
Advancing CMOS with carbon electronics (2014)

A fresh look on carbon-based transistor channel materials like single-walled carbon nanotubes (CNT) and graphene nanoribbons (GNR) in future electronic applications is given. Although theoretical predictions initially promised that GNR (which do have a bandgap) would perform equally well as transistors based on CNTs, experimental evidence for the well-behaved transistor action is missing up to now. Possible reasons for the shortcomings as well as possible solutions to overcome the performance gap will be addressed. In contrast to GNR, short channel CNT field effect transistors (FET) demonstrate in the experimental realization almost ideal transistor characteristics down to very low bias voltages. Therefore, CNT-FETs are clear frontrunners in the search of a future CMOS switch, that will enable further voltage and gate length scaling. Essential features which distinguish CNT-FETs from alternative solution will be discussed and benchmarked. Finally, the gap to industrial wafer-level scale SWCNT integration will be addressed and strategies for achieving highly aligned carbon nanotube fabrics will be discussed. Without such a high yield wafer-scale integration, SWCNT circuits will be an illusional dream.
Symmetry breaking and geometric confinement in VO2: Results from a three-dimensional infrared nano-imaging (2014)

Epitaxial strain can play an important role in controlling the local phase dynamics of transition metal oxides. With scattering-type scanning near-field optical microscopy, we visualize the three dimensional landscape of phase inhomogeneity in strained VO2 films grown on [100]R TiO2 substrates. We demonstrate that three different symmetries are spontaneously broken in the vicinity of the VO2 phase transition: (1) Monoclinic-tetragonal (rutile) crystal symmetry breaking due to the structural phase transition, (2) in-plane (x-y plane) rotational symmetry breaking due to the formation of periodic strain domains, and (3) out-of-plane (z-axis) mirror symmetry breaking at the film cross-section due to substrate-induced epitaxial strain.
Characterization of a Slow‐Migrating Component of the Rabies Virus Matrix Protein Strongly Associated with the Viral Glycoprotein (2003)

We investigated multiple forms of rabies virus matrix (M) protein. Under non-reducing electrophoretic conditions, we detected, in addition to major bands of monomer forms (23- and 24-kDa) of M protein, an M antigen-positive slow-migrating minor band (about 54 kDa) in both the virion and infected cells. Relative contents of the 54-kDa and monomer components in the virion were about 20-30% and 70-80% of the whole M protein, respectively, while the content of the 54-kDa component was smaller (about 10-20% of the total M protein) in the cell than in the virion. The 54-kDa components could be extracted from the infected cells with sodium deoxycholate, but they were quite resistant to extraction with 1% nonionic detergents by which most monomer components were solubilized. The 54-kDa component was precipitated more efficiently than the monomer by a monoclonal antibody (mAb; #3-9-16), which recognized a linear epitope located at the N-terminal of the M protein. The mAb #3-9-16 coprecipitated the viral glycoprotein (G), which was demonstrated to be due to strong association between the G and 54-kDa component of the M protein. Monomers and the 54-kDa polypeptide migrated to the same isoelectric point (pI) in twodimensional (2-D) gel electrophoresis, implicating that the 54-kDa component was composed of component(s) of the same pI as that of the M protein monomers. From these results, we conclude that the M antigen-positive 54-kDa polypeptide is a homodimer of M protein, taking an N-terminal-exposed conformation, and is strongly associated with the viral glycoprotein. Possible association with a membrane microdomain of the cell will be discussed.
Magnetic Anisotropy of Ni-Doped ZnO Nanocrystalline Thin Films (2010)

We report structural and magnetization properties of nickel-doped zinc oxide thin films prepared on Si substrates by spray pyrolysis technique. Grazing angle X-ray diffraction measurements confirm the wurtzite structure of Zn 1- x Ni x O films and no secondary phase was found for ZnO thin films doped with 5% Ni or less. Hysteresis measurements demonstrate that the Ni-doped ZnO films are magnetically anisotropic and they exhibit intrinsic ferromagnetic behavior at room temperature. Higher magnetization in 3 kOe is observed for a field applied perpendicular to the sample surface compared with the in-plane direction.
Amorphous-crystalline nanostructured Nd-Fe-B permanent magnets using laser powder bed fusion: Metallurgy and magnetic properties (2023)

Laser powder-bed fusion (PBF-LB), a class of additive manufacturing (AM), has attracted wide interest in the production of Nd-Fe-B permanent magnets, benefiting from the minimisation of waste of rare-earth elements and the post-processing requirements. Most research on PBF-LB Nd-Fe-B has focused on reducing defects in printed parts alongside the improvement of the resultant magnetic properties. Detailed analysis of the microstructure that results in permanent magnetic properties is yet to be published. In this research, a combination of high-resolution microstructural investigations was conducted for this purpose. For the first time, an in-depth analysis of the grain structure in terms of morphology, size distribution, and texture is presented and correlated to the permanent magnetic performance. Melt pools showed a hierarchical grain size distribution of primary Nd2Fe14B phase grains with a polygonal morphology and random crystalline alignment, in addition to a small amount of Nd-rich and Nd-lean precipitates in the matrix of the Ti-rich amorphous grain boundaries. The permanent magnetic properties of this material are mainly determined by the nanostructured Nd2Fe14B grains and the amorphous Ti-rich iron-based intergranular phase but could be weakened by precipitates that act as magnetic pores. Remelting during PBF-LB led to the transformation of the coarse grains of the previously solidified layer to fine ones, favourable for the permanent magnetic properties. The mechanisms of these complex phase formations and transformations during processing and the development of the nanocrystalline microstructure are elucidated in this paper as a basis for informing the optimisation process for microstructural development.
Erratum: “Removal of bone in CT angiography of the cervical arteries by piecewise matched mask bone elimination” [Med. Phys. 31, 2924–2933 (2004)] (2005)

The authors would like to report an error in the layout of Table III. A number of rows in this table were misaligned. The correct table is given below.
Oxidative Reactions with Nonaqueous Enzymes (2001)

The objective of this work is to demonstrate a proof-of-concept of enzymatic oxidative processing in nonaqueous media using alkene epoxidation and phenolic polymerization as relevant targets. This project will provide both the fundamental and applied investigations necessary to initiate the implementation of oxidative biocatalysts as commercially relevant alternatives to chemical processing in general, and to phenolic polymerizations and alkene epoxidation specifically. Thus, this work will address the Bioprocessing Solicitation Area to: (1) makes major improvements to phenolic polymerization and alkene epoxidation technologies; (2) is expected to be cost competitive with competing conventional processes; and (3) produces higher yields with less waste.
Physical Assets by SHS in the Framework of ISRU and ISFR Paradigms for Human Space Missions on the Moon (2013)

In this work a brief overview of the most important technologies for space exploration, with particular emphasis on the Moon missions, is presented. It is shown that the focus has been on the technologies to extract consumables (O2, H2O, N2) for human life-support replenishment. The fact that the exploitation of extraterrestrial resources to obtain the desired materials during each ongoing mission, which has been the subject of several investigations since the sixties of the last century, is discussed. The paradigms ISRU (In Situ Resources Utilization) and ISFR (In Situ Fabrication and Repair) are then introduced. In particular, one of the most important process for the production of oxygen, i.e. the reduction of ilmenite by hydrogen is analyzed. In addition, the current iteration of the roadmap which identifies two feasible pathways for human missions after ISS (International Space Station) is addressed. Next, the fabrication of Lunar physical assets is taken into account, while focusing particularly on those processes where combustion-like reactions are exploited. The main results recently obtained in the literature in this regards are also summarized. In particular, the choice of the reducing agent and the influence of the most important processing parameters (composition of the starting mixture, gas pressure level, and gravity conditions) are examined in a systematic manner.
Using Metafeatures to Increase the Effectiveness of Latent Semantic Models in Web Search (2016)

In web search, latent semantic models have been proposed to bridge the lexical gap between queries and documents that is due to the fact that searchers and content creators often use different vocabularies and language styles to express the same concept. Modern search engines simply use the outputs of latent semantic models as features for a so-called global ranker. We argue that this is not optimal, because a single value output by a latent semantic model may be insufficient to describe all aspects of the model's prediction, and thus some information captured by the model is not used effectively by the search engine. To increase the effectiveness of latent semantic models in web search, we propose to create metafeatures-feature vectors that describe the structure of the model's prediction for a given query-document pair and pass them to the global ranker along with the models? scores. We provide simple guidelines to represent the latent semantic model's prediction with more than a single number, and illustrate these guidelines using several latent semantic models. We test the impact of the proposed metafeatures on a web document ranking task using four latent semantic models. Our experiments show that (1) through the use of metafeatures, the performance of each individual latent semantic model can be improved by 10.2% and 4.2% in NDCG scores at truncation levels 1 and 10; and (2) through the use of metafeatures, the performance of a combination of latent semantic models can be improved by 7.6% and 3.8% in NDCG scores at truncation levels 1 and 10, respectively.
Testing G-CSF responsiveness predicts the individual susceptibility to infection and consecutive treatment in recipients of high-dose chemotherapy (2010)

The individual risk of infection and requirements for medical treatment after high-dose chemotherapy have been unpredictable. In this prospective, multicenter, open-label study we investigated the potential of granulocyte colony-stimulating factor (G-CSF) responsiveness as a predictor. A total of 168 patients with multiple myeloma or lymphoma received a single dose of subcutaneous G-CSF (lenograstim, 263 μg) after high-dose chemotherapy. Highly variable leukocyte peaks were measured and grouped as low (quartile 1; leukocytes 100-10 100/μL), medium (quartile 2; leukocytes > 10 100-18 300/μL), and high (quartiles 3/4; leukocytes > 18 300-44 800/μL). G-CSF responsiveness (low vs medium vs high) was inversely correlated with febrile neutropenia (77% vs 60% vs 48%; P = .0037); the rate of infection, including fever of unknown origin (91% vs 67% vs 54%; P < .0001); days with intravenous antibiotics (9 vs 6 vs 5; P < .0001); and antifungal therapy (P = .042). In multivariate analysis, G-CSF responsiveness remained the only factor significantly associated with infection (P = .016). In addition, G-CSF responsiveness was inversely correlated with grade 3/4 oral mucositis (67% vs 33% vs 23%; P < .0001). G-CSF responsiveness appears as a signature of the myeloid marrow reserve predicting defense against neutropenic infection after intensive chemotherapy. This study is registered at http://www.clinicaltrials.gov as NCT01085058.
Physical layer algorithm and hardware verification of MIMO relays using cooperative partial detection (2010)

Cooperative communication with multi-antenna relays can significantly increase the reliability and speed. However, cooperative MIMO detection would impose considerable complexity overhead onto the relay if a full detect-and-forward (FDF) strategy is employed. In order to address this challenge, we propose a novel cooperative partial detection (CPD) strategy to partition the detection task between the relay and the destination. CPD utilizes the inherent structure of the tree-based sphere detectors, and modifies the tree traversal so that instead of visiting all the levels of the tree, only a subset of the levels, thus a subset of the transmitted streams, are visited. Based on this methodology, the destination combines the source signal and the partial relay signal to perform the detection step. We show, in both simulation and hardware verification on the WARP platform, that using the CPD approach, the relay can avoid the considerable overhead of MIMO detection while helping the source-destination link to improve its performance.
Supplementary Data S1-S16 from Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component (2023)

&lt;p&gt;vcf files for 16 WES samples analyzed in this study&lt;/p&gt;
Specific suppression of insulin sensitivity in growth hormone receptor gene‐disrupted (GHR‐KO) mice attenuates phenotypic features of slow aging (2014)

In addition to their extended lifespans, slow-aging growth hormone receptor/binding protein gene-disrupted (knockout) (GHR-KO) mice are hypoinsulinemic and highly sensitive to the action of insulin. It has been proposed that this insulin sensitivity is important for their longevity and increased healthspan. We tested whether this insulin sensitivity of the GHR-KO mouse is necessary for its retarded aging by abrogating that sensitivity with a transgenic alteration that improves development and secretory function of pancreatic β-cells by expressing Igf-1 under the rat insulin promoter 1 (RIP::IGF-1). The RIP::IGF-1 transgene increased circulating insulin content in GHR-KO mice, and thusly fully normalized their insulin sensitivity, without affecting the proliferation of any non-β-cell cell types. Multiple (nonsurvivorship) longevity-associated physiological and endocrinological characteristics of these mice (namely beneficial blood glucose regulatory control, altered metabolism, and preservation of memory capabilities) were partially or completely normalized, thus supporting the causal role of insulin sensitivity for the decelerated senescence of GHR-KO mice. We conclude that a delayed onset and/or decreased pace of aging can be hormonally regulated.
Search for black holes and other new phenomena in high-multiplicity final states in proton–proton collisions at s=13TeV (2017)

A search for new physics in energetic, high-multiplicity final states has been performed using protonproton collision data collected with the CMS detector at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 2.3 fb -1 . The standard model background, dominated by multijet production, is determined exclusively from control regions in data. No statistically significant excess of events is observed. Model-independent limits on the product of the cross section and the acceptance of a new physics signal in these final states are set and further interpreted in terms of limits on the production of black holes. Semiclassical black holes and string balls with masses as high as 9.5 TeV, and quantum black holes with masses as high as 9.0 TeV are excluded by this search in the context of models with extra dimensions, thus significantly extending limits set at a center-of-mass energy of 8 TeV with the LHC Run 1 data.
Integrative Genomic Analysis Implicates Gain of PIK3CA at 3q26 and MYC at 8q24 in Chronic Lymphocytic Leukemia (2012)

Purpose: The disease course of chronic lymphocytic leukemia (CLL) varies significantly within cytogenetic groups. We hypothesized that high-resolution genomic analysis of CLL would identify additional recurrent abnormalities associated with short time-to-first therapy (TTFT). Experimental Design: We undertook high-resolution genomic analysis of 161 prospectively enrolled CLLs using Affymetrix 6.0 SNP arrays, and integrated analysis of this data set with gene expression profiles. Results: Copy number analysis (CNA) of nonprogressive CLL reveals a stable genotype, with a median of only 1 somatic CNA per sample. Progressive CLL with 13q deletion was associated with additional somatic CNAs, and a greater number of CNAs was predictive of TTFT. We identified other recurrent CNAs associated with short TTFT: 8q24 amplification focused on the cancer susceptibility locus near MYC in 3.7%; 3q26 amplifications focused on PIK3CA in 5.6%; and 8p deletions in 5% of patients. Sequencing of MYC further identified somatic mutations in two CLLs. We determined which catalytic subunits of phosphoinositide 3-kinase (PI3K) were in active complex with the p85 regulatory subunit and showed enrichment for the α subunit in three CLLs carrying PIK3CA amplification. Conclusions: Our findings implicate amplifications of 3q26 focused on PIK3CA and 8q24 focused on MYC in CLL.
Design of an Underwater Acoustic MIMO OFDM System Using NI LabView and CompactDAQ (2020)

Recently, the orthogonal frequency-division multiplexing (OFDM) technology is receiving increasing attention in underwater acoustic (UA) communications. This paper presents the design of a real-time UA OFDM communication system with multiple transducers and hydrophones using the National Instruments CompactDAQ device and LabView software. The purpose of this system is to provide academic researchers a flexible and reconfigurable multiple-input multiple-output (MIMO) UA communication transceiver with an open-architecture to conveniently test and validate the performance of their MIMO transceiver algorithms, which is missing in the literature. The system design, including both the transmitter and receiver, is discussed. The performance of this MIMO UA communication system is verified through a UA communication experiment conducted in the Canning River, Western Australia. Compared with existing modems, the proposed implementation simplifies the prototype design and supports MTMO functions.