gebhart/patrepeval huggingface dataset:
4D ultrafast ultrasound flow imaging:in vivoquantification of arterial volumetric flow rate in a single heartbeat (2016)

We present herein 4D ultrafast ultrasound flow imaging, a novel ultrasound-based volumetric imaging technique for the quantitative mapping of blood flow. Complete volumetric blood flow distribution imaging was achieved through 2D tilted plane-wave insonification, 2D multi-angle cross-beam beamforming, and 3D vector Doppler velocity components estimation by least-squares fitting. 4D ultrafast ultrasound flow imaging was performed in large volumetric fields of view at very high volume rate (>4000 volumes s<sup>-1</sup>) using a 1024-channel 4D ultrafast ultrasound scanner and a 2D matrix-array transducer. The precision of the technique was evaluated in vitro by using 3D velocity vector maps to estimate volumetric flow rates in a vessel phantom. Volumetric Flow rate errors of less than 5% were found when volumetric flow rates and peak velocities were respectively less than 360 ml min<sup>-1</sup> and 100 cm s<sup>-1</sup>. The average volumetric flow rate error increased to 18.3% when volumetric flow rates and peak velocities were up to 490 ml min<sup>-1</sup> and 1.3 m s<sup>-1</sup>, respectively. The in vivo feasibility of the technique was shown in the carotid arteries of two healthy volunteers. The 3D blood flow velocity distribution was assessed during one cardiac cycle in a full volume and it was used to quantify volumetric flow rates (375 ± 57 ml min<sup>-1</sup> and 275 ± 43 ml min<sup>-1</sup>). Finally, the formation of 3D vortices at the carotid artery bifurcation was imaged at high volume rates.
Molecular markers for renal cell carcinoma. (2000)

For renal cell carcinoma (RCC), the TNM (tumor, node, metastasis) staging system and histopathologic grade provide the most time-tested and useful prognostic information. Other factors that may confer independent prognostic information are under active investigation, however, and are generating great interest. These investigational prognostic features range from evaluation of patient-related factors, such as performance status, to measures of overall DNA content, such as flow cytometry, to the evaluation of molecular markers (such as P53 and bcl–2) using immunohistochemistry. Although several of these candidate modalities have been shown to provide prognostic information, multivariate analysis (controlling for stage and grade) reveals that most do not supply independent information. Recently, as the genetics of RCC have become better understood, microsatellite analysis has become an exciting new technique under investigation. This technology permits detection of cancer-specific DNA alterations, including additions, deletions, and loss of heterozygosity.
High-Throughput Gene Mapping in Caenorhabditis elegans (2002)

Positional cloning of mutations in model genetic systems is a powerful method for the identification of targets of medical and agricultural importance. To facilitate the high-throughput mapping of mutations in Caenorhabditis elegans, we have identified a further 9602 putative new single nucleotide polymorphisms (SNPs) between two C. elegans strains, Bristol N2 and the Hawaiian mapping strain CB4856, by sequencing inserts from a CB4856 genomic DNA library and using an informatics pipeline to compare sequences with the canonical N2 genomic sequence. When combined with data from other laboratories, our marker set of 17,189 SNPs provides even coverage of the complete worm genome. To date, we have confirmed >1099 evenly spaced SNPs (one every 91 +/- 56 kb) across the six chromosomes and validated the utility of our SNP marker set and new fluorescence polarization-based genotyping methods for systematic and high-throughput identification of genes in C. elegans by cloning several proprietary genes. We illustrate our approach by recombination mapping and confirmation of the mutation in the cloned gene, dpy-18.
CHK2-decreased protein expression and infrequent genetic alterations mainly occur in aggressive types of non-Hodgkin lymphomas (2002)

The CHK2 gene codifies for a serine/threonine kinase that plays a central role in DNA damage response pathways. To determine the potential role of CHK2 alterations in the pathogenesis of lymphoid neoplasms we have examined the gene status, protein, and mRNA expression in a series of tumors and nonneoplastic lymphoid samples. A heterozygous Ile157Thr substitution, also present in the germ line of the patient, was detected in a blastoid mantle cell lymphoma (MCL). CHK2 protein and mRNA expression levels were similar in all types of lymphomas and reactive samples, and these levels were independent of the proliferative activity of the tumors. However, 5 tumors, one typical MCL, 2 blastoid MCLs, and 2 large cell lymphomas, showed marked loss of protein expression, including 2 samples with complete absence of CHK2 protein. These 2 lymphomas showed the highest number of chromosomal imbalances detected by comparative genomic hybridization in the whole series of cases. However, no mutations, deletions, or hypermethylation of the promoter region were identified in any of these tumors. mRNA levels were similar in cases with low and normal protein expression, suggesting a posttranscriptional regulation of the protein in these tumors. CHK2 gene and protein alterations were not related to p53 and ATM gene status. In conclusion, CHK2 alterations are uncommon in malignant lymphomas but occur in a subset of aggressive tumors independently of p53 or ATM alterations. The high number of chromosomal imbalances in tumors with complete absence of CHK2 protein suggests a role of this gene in chromosomal instability in human lymphomas.
Increasing Symbol Rate: Quasi‐Orthogonal Layers (2003)

This chapter contains sections titled: Orthogonal Designs Complexity Issues: Choosing Symbol Rate and Target Tx Diversity Multimodulation Schemes Matrix Modulation with Quasi-orthogonal Layers Summary
Smart houses in the smart grid and the search for value-added services in the cloud of things era (2013)

The smart grid is an emerging paradigm based on the introduction of sophisticated information and communication technologies coupled with the energy grid. Most of the ongoing research worldwide is focused too much on the smart metering, energy visualization as well as potential residential device management which is usually turning ON/OFF appliances. Less attention has been given to the next step, i.e. challenging area of realizing new sophisticated applications that utilize the latest management capabilities brought to the table by advanced networked embedded devices, the huge amount of fine-grained data they offer and services that operate on such big data. We take a closer look here to some aspects beyond the smart metering, towards innovative value-added applications and services that take into consideration the “Cloud of Things” ecosystem and its capabilities. We investigate how the latter impacts the development of applications and the benefits as well as challenges it brings. We also look at the role of the smart meter and the current “war zones” among stakeholders in the residential environment, and try to shed some more light on their motivation and impact. Finally in order to make more tangible the benefits in the “Cloud of Things” era, we demonstrate an application that taps into the service ecosystem and offers decision support to electric appliance buyers.
Manufacture and

In-Vitro

Assessment of Bromsulphthalein and Phenolphthalein Loaded Polyester Microspheres (1994)

Poly(lactic acid) and Poly(glycolic acid) microspheres were manufactured by a solvent evaporation and precipitation technique respectively. Particle size and image analysis of the microspheres were performed to establish their morphology. Phenolphthalein and bromsulphthalein, were incorporated in the polymeric microspheres. The release of phenolphthalein in glycine buffer pH 10.8 and bromsulphthalein in phosphate buffer pH 7.4 at 25°C was delayed compared with dye alone. This data has been correlated with the in-vivo performance of the polymeric matrix dye delivery systems.
Experiment Turbulence Compensation of 50-Gbaud/s Orbital-Angular-Momentum QPSK Signals Using Intensity-only based SPGD Algorithm (2014)

An intensity-based algorithm is employed to derive the correction phase pattern for a distorted probe orbital-angular-momentum (OAM) beam. This correction pattern is used to compensate the distortions of three multiplexed OAM beams, each carrying a 50-Gbaud QPSK signal. The crosstalk between channels is reduced by &gt;5 dB with this approach.
Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations (2021)

Prevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.
Coupling, competition, and stability of modes in random lasers (2004)

We studied analytically and numerically the complex properties of random lasing modes. Mode repulsion in frequency domain for inhomogeneously broadened gain media was confirmed by our numerical results. We constructed a coupled-mode model to explain the synchronized lasing behavior for modes whose frequency difference is less than the homogeneous gain width. The stability of coupled modes was investigated. The effective competition coefficient ${C}_{e}$ for two modes with both gain competition and field coupling is obtained analytically. In our numerical experiments, we also found the coupled oscillations of two lasing modes. From the analytical derivation, we demonstrated that such oscillations could reveal the field-coupling strength between the random modes.
Efficient Approximations for the Marginal Likelihood of Incomplete Data\n Given a Bayesian Network (2013)

We discuss Bayesian methods for learning Bayesian networks when data sets are\nincomplete. In particular, we examine asymptotic approximations for the\nmarginal likelihood of incomplete data given a Bayesian network. We consider\nthe Laplace approximation and the less accurate but more efficient BIC/MDL\napproximation. We also consider approximations proposed by Draper (1993) and\nCheeseman and Stutz (1995). These approximations are as efficient as BIC/MDL,\nbut their accuracy has not been studied in any depth. We compare the accuracy\nof these approximations under the assumption that the Laplace approximation is\nthe most accurate. In experiments using synthetic data generated from discrete\nnaive-Bayes models having a hidden root node, we find that the CS measure is\nthe most accurate.\n
Peptidomimetic BACE1 Inhibitors for Treatment of Alzheimer's Disease: Design and Evolution (2010)

This chapter contains sections titled: Introduction Substrate-Based (Peptidic) Inhibitors Peptidomimetic Statine and Homostatine Inhibitors Hydroxyethylamine-Based Inhibitors Other Peptidomimetics Conclusions References
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA (2014)

Originally published in PROTEINS: Structure, Function, and Bioinformatics 2013;81(7):1232–1244 (DOI:10.1002/prot.24273). The authors found a mistake in the dataset log. The wavelength of the native dataset collection was 0.97627 Å, while 1.0000 Å was incorrectly stated in the printed paper.
Supplementary Figure 1 from MicroRNA Signatures in Human Ovarian Cancer (2023)

Supplementary Figure 1 from MicroRNA Signatures in Human Ovarian Cancer
A highly potent antibody effective against SARS-CoV-2 variants of concern (2021)

Control of the ongoing SARS-CoV-2 pandemic is endangered by the emergence of viral variants with increased transmission efficiency, resistance to marketed therapeutic antibodies, and reduced sensitivity to vaccine-induced immunity. Here, we screen B cells from COVID-19 donors and identify P5C3, a highly potent and broadly neutralizing monoclonal antibody with picomolar neutralizing activity against all SARS-CoV-2 variants of concern (VOCs) identified to date. Structural characterization of P5C3 Fab in complex with the spike demonstrates a neutralizing activity defined by a large buried surface area, highly overlapping with the receptor-binding domain (RBD) surface necessary for ACE2 interaction. We further demonstrate that P5C3 shows complete prophylactic protection in the SARS-CoV-2-infected hamster challenge model. These results indicate that P5C3 opens exciting perspectives either as a prophylactic agent in immunocompromised individuals with poor response to vaccination or as combination therapy in SARS-CoV-2-infected individuals.
Wafer-scale colloidal lithography based on self-assembly of polystyrene nanospheres and atomic layer deposition (2010)

This paper reports a facile and robust wafer-scale colloidal lithography using polystyrene nanospheres. This technique is based on a combination of two simple and scalable processes: the self-assembly of polystyrene nanospheres by spin coating and the atomic layer deposition. Patterns, such as two dimensional hole-arrays, can be routinely fabricated over 4 inch diameter wafers owing to high reproducibility of this novel method. The hole size and pitch can be controlled by heat treatment and the use of polystyrene nanospheres with different diameters, respectively. We demonstrate five- to ten-fold enhancement in the photoluminescence of phosphor films by constructing two dimensional SiNx photonic crystals on the films using this technique. It is expected that atomic layer deposition assisted polystyrene colloidal lithography would be incorporated easily in the mass fabrication of optoelectronic devices, such as light emitting diodes.
Mining Interesting Temporal Patterns: An Information Theoretic Approach (2005)

Tata Research Development & Design Centre, 54 B Hadapsar Industrial Estate,Pune 411 013, India.gk.palshikar@tcs.comAbstract. Interesting patterns in temporal databases have equivalently beentreated in literature as novelties or surprises. In this paper we propose a Infor-mation Theoretic framework for detecting interestingness that can handle mostsubjective notions of what might be interesting in temporal data . Based on thisframework, a mutual information measure is derived using kernel based nonpara-metric probability density estimation techniques to assess interestingness of atemporal sub-sequence given another. This measure is then utilized in a slidingwindows algorithm to detect all possible interesting sub-sequences with respectto a reference sequence. The algorithm’s effectiveness is shown to be indepen-dent of the parameter choice for the density estimates and its advantages overother prominent techniques are discussed.
Does Instrumented Anterior Scoliosis Surgery Lead to Kyphosis, Pseudarthrosis, or Inadequate Correction in Adults? (2002)

The results of anterior spinal fusion using a single solid rod in adults with idiopathic scoliosis in this series are excellent, with 100% fusion rate, no development of kyphosis, and no incidence of hardware failure.
Scalable Spectrum Access System for Massive Machine Type Communication (2018)

Future 5G networks aspire to enable new services with vastly different data rate, latency and scalability requirements. The consensus is that these new services will fall into three categories: eMBB, URLLC, and mMTC. Due to unique characteristics of these services and the limited availability of finite spectrum resources, 5G will need to carefully map appropriate bands and spectrum usage models for each service. The SAS is an emerging spectrum sharing model that is gaining momentum in the U.S. SAS presents an opportunity for operators to access the 3.5 GHz military radar band for commercial use. This article discusses the feasibility of the current SAS model in the context of mMTC. We propose a scalable SAS framework that can manage the mMTC uplink interference to the incumbent with less overhead. The simulation setup models the interference levels in New York City and its surrounding counties. The results show that mMTC uplink transmission can be enabled using our framework even on the coast of New York, where mMTC density is high, without causing a harmful level of interference to the incumbent.
P‐21: Deflected Beam Analysis System for Electron Gun (2001)

Abstract A deflected beam analysis system for the design of electron gun has been developed. Magnetic field measurement machine is established to get the magnetic field distribution of a deflection yoke. The 3‐D Gaussian beamlet theory taking the magnetic field into account is used to obtain space charge density distribution. The comparison results between simulation and measurement show that deflection sensitivity and focus characteristic differences are within 1 % and 10 %, respectively.
MINING POSETS FROM LINEAR ORDERS (2013)

There has been much research on the combinatorial problem of generating the linear extensions of a given poset. This paper focuses on the reverse of that problem, where the input is a set of linear orders, and the goal is to construct a poset or set of posets that generates the input. Such a problem finds applications in computational neuroscience, systems biology, paleontology, and physical plant engineering. In this paper, two algorithms are presented for efficiently finding a single poset, if, such a poset exists whose linear extensions are exactly the same as the input set of linear orders. The variation of the problem where a minimum set of posets that cover the input is also explored. This variation is shown to be polynomially solvable for one class of simple posets (kite(2) posets) but NP-complete for a related class (hammock(2,2,2) posets).
A Case of Recessive Dystrophic Epidermolysis Bullosa Associated with Dwarfism with Special Reference to Pathophysiological Role of Growth Hormone (1990)

Epidermolysis bullosa is a group of disorders whose common primary feature is the formation of blisters following trivial trauma. Recessive dystrophic epidermolysis bullosa (RDEB), a subtype of epidermolysis bullosa, is frequently associated with growth retardation. This growth retardation has been reported to be caused by trophopathy following protein loss through skin lesions. Endocrine disorders as the cause of growth retardation in RDEB have not been clearly described. An 11-year-old female had a typical RDEB with dwarfism. Her height was 125cm and weight was 21kg, both of which were 2.5 SD below the average. The skin lesions were generalized and probably caused by undernourishment, infection, and blood loss through the skin. However, her serum albumin was at the lower normal limit, and the rapid turnover proteins were slightly decreased. Endocrinological examinations revealed that all the basal levels of pituitary, thyroid, and adrenal hormones were normal. Results of the exercise test, the insulin tolerance test, and the growth hormone-releasing factor test indicated the presence of hypothalamic disorder in secretion of growth hormone. This is the first report of RDEB in which hypothalamic disorder in growth hormone secretion was investigated. On the other hand, growth hormone is known to be involved in collagen metabolism, and a decrease in collagen fibrils and an increase in collagenase activities are found in the skin of RDEB. This implies that this hypothalamic disorder in growth hormone secretion may be involved in the pathophysiology of both dwarfism and the skin lesions in RDEB.
Logistic Regression (2018)

In Chapter 2, we looked at ways in which a variable can be estimated based on an independent variable. The dependent variables we were estimating were continuous (sales of ice cream, weight of baby). However, in most cases, we need to be forecasting or predicting for discrete variables—for example, whether a customer will churn or not, or whether a match will be won or not. These are the events that do not have a lot of distinct values. They have only a 1 or a 0—whether an event has happened or not.
Development of interim patient-reported outcome measures for the assessment of ulcerative colitis disease activity in clinical trials (2015)

Patient-reported outcomes items derived from the Mayo Clinic Score combined with endoscopy as a co-primary endpoint may be an appropriate interim outcome measure for ulcerative colitis trials.
HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples (2006)

This chapter contains sections titled: Introduction Materials and methods HUPO reference sample collection protocol Differential peptide display Stability studies and SELDI analysis SDS-PAGE analysis for stability studies 2-DE for stability studies SELDI-TOF analysis for protease inhibitor studies 2-DE for plasma protease inhibition studies Tryptic digestion and protein identification for protease inhibition studies Antibody microarray analysis using two-color rolling circle amplification Results Comparisons of specimen types Analysis of serum Analysis of plasma Evaluation of storage and handling conditions Evaluations of the use of protease inhibitors Analysis with SELDI-TOF MS of “time zero” effects of protease inhibitors in plasma Analysis by 2-DE Analysis with antibody arrays Discussion Other pre-analytical variables and control considerations Reference materials Concluding remarks References
FLASH vs. (simulated) FLASH (2000)

Simulation is the primary method for evaluating computer systems during all phases of the design process. One significant problem with simulation is that it rarely models the system exactly, and quantifying the resulting simulator error can be difficult. More importantly, architects often assume without proof that although their simulator may make inaccurate absolute performance predictions, it will still accurately predict architectural trends.This paper studies the source and magnitude of error in a range of architectural simulators by comparing the simulated execution time of several applications and microbenchmarks to their execution time on the actual hardware being modeled. The existence of a hardware gold standard allows us to find, quantify, and fix simulator inaccuracies. We then use the simulators to predict architectural trends and analyze the sensitivity of the results to the simulator configuration. We find that most of our simulators predict trends accurately, as long as they model all of the important performance effects for the application in question. Unfortunately, it is difficult to know what these effects are without having a hardware reference, as they can be quite subtle. This calls into question the value, for architectural studies, of highly detailed simulators whose characteristics are not carefully validated against a real hardware design.