gebhart/patrepeval huggingface dataset:
<title>Remotely operated MR-guided neurosurgical device in MR operating room</title> (2001)

A robust near real-time MRI based surgical guidance and navigation scheme has been developed, validated and used. The key concept of the method is to use intra-operative MRI to facilitate the trajectory alignment process of a biopsy needle in neurobiopsy. Since the trajectory corresponding to the biopsy needle pivoted at an entry point on patient skull has two degrees of freedom, the orientation of the needle can be tracked using a 2D imaging plane placed perpendicular to the desired trajectory. Using a near real- time visual feedback during the adjustment of an alignment guidance device, the required trajectory alignment was translated into a simple in-plane targeting task on computer monitor. The orientation adjustment was achieved remotely via a set of MR-compatible strings, which were connected to a joystick. The concept of MR-guided targeting was successfully validated on a phantom set-up. This MR based guidance technique has practically allowed neurosurgeons to accomplish the required needle alignment to an arbitrary trajectory remotely in a straight forward procedure on any conventional MR scanner. Before needle insertion, the trajectory can be validated. Two successful biopsy cases using the new methodology and device have shown that the remotely operated device under MR-guidance is both effective and accurate for neurosurgery.
<title>Fast evaluation of demagnetizing field in three-dimensional micromagentics using multipole approximation</title> (2000)

Computational micromagnetics in three dimensions is of increasing interest with the development of magnetostrictive sensors and actuators. In solving the Landau-Lifshitz-Gilbert (LLG) equation, the governing equation of magnetic dynamics for ferromagnetic materials, we need to evaluate the effective field. The effective field consists of several terms, among which the demagnetizing field is of long-range nature. Evaluating the demagnetizing field directly requires work of O(N<SUP>2</SUP>) for a grid of N cells and thus it is the bottleneck in computational micromagnetics. A fast hierarchical algorithm using multipole approximation is developed to evaluate the demagnetizing field. We first construct a mesh hierarchy and divide the grid into boxes of different levels. The lowest level box is the whole grid while the highest level boxes are just cells. The approximate field contribution from the cells contained in a box is characterized by the box attributes, which are obtained via multipole approximation. The algorithm computes field contributions from remote cells using attributes of appropriate boxes containing those cells, and it computes contributions from adjacent cells directly. Numerical results have shown that the algorithm requires work of O(NlogN) and at the same time it achieves high accuracy. It makes micromagnetic simulation in three dimensions feasible.
A naturally occurring point mutation confers broad range tolerance to herbicides that target acetolactate synthase. (1996)

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Imaging with random 3D reference structures (2003)

We describe a sensor system based on 3D 'reference structures' which implements a mapping from a 3D source volume on to a 2D sensor plane. The reference structure used here is a random three dimensional distribution of polystyrene beads. We show how this bead structure spatially segments the source volume and present some simple experimental results of 2D and 3D imaging.
Frequency agility investigations on compact omnidirectional antennas using variable inductors (2010)

This paper investigates the possibility to introduce a variable inductor on a compact antenna structure in order to obtain a frequency agility. The structure is a compact shorted microstrip antenna characterized by omnidirectional radiation properties over a narrow frequency band which has to be broadened for telecommunication systems. For that, a variable inductor is placed on the antenna structure and tuned so as to obtain frequency reconfigurability.
Genomic characterization of malignant progression in neoplastic pancreatic cysts (2020)

Intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs) are non-invasive neoplasms that are often observed in association with invasive pancreatic cancers, but their origins and evolutionary relationships are poorly understood. In this study, we analyze 148 samples from IPMNs, MCNs, and small associated invasive carcinomas from 18 patients using whole exome or targeted sequencing. Using evolutionary analyses, we establish that both IPMNs and MCNs are direct precursors to pancreatic cancer. Mutations in SMAD4 and TGFBR2 are frequently restricted to invasive carcinoma, while RNF43 alterations are largely in non-invasive lesions. Genomic analyses suggest an average window of over three years between the development of high-grade dysplasia and pancreatic cancer. Taken together, these data establish non-invasive IPMNs and MCNs as origins of invasive pancreatic cancer, identifying potential drivers of invasion, highlighting the complex clonal dynamics prior to malignant transformation, and providing opportunities for early detection and intervention.
Correlated structure-optical properties studies of plasmonic nanoparticles (2014)

Interest in nanotechnology is driven by unprecedented means to tailor the physical behaviour via structure and composition. Unlike bulk materials, minute changes in size and shape can affect the optical properties of nanoparticles. Characterization, understanding, and prediction of such structure-function relationships is crucial to the development of novel applications such as plasmonic sensors, devices, and drug delivery systems. Such knowledge has been recently vastly expanded through systematic, high throughput correlated measurements, where the localized surface plasmon resonance (LSPR) is probed optically and the particle shape investigated with electron microscopy. This paper will address some of the recent experimental advances in single particle studies that provide new insight not only on the effects of size, composition, and shape on plasmonic properties but also their interrelation. Plasmon resonance frequency and decay, substrate effects, size, shape, and composition will be explored for a variety of plasmonic systems.
Survivable Bluetooth location networks (2004)

In this paper, we analyze survivability issues of auxiliary Bluetooth location networks (BLN) for location-aware or context-driven mobile networks. We assume that there exist service servers that need to know user location in real-time, to send context-oriented information to user handhelds when necessary. The BLN transmits position information to service servers, without user participation. It is not subject to line-of-sight constraints and is supported by existing commercial handhelds. BLN users carry either a Bluetooth-enabled handheld or any mobile data terminal and a Bluetooth badge. The BLN is composed of wireless Bluetooth nodes, which establish a spontaneous network topology at system initialization. The BLN can coexist with other Bluetooth systems.
Augmented Reality for Teaching Endotracheal Intubation: MR Imaging to Create Anatomically Correct Models (2003)

Clinical procedures have traditionally been taught at the bedside, in the morgue and in the animal lab. Augmented Reality (AR) technology (the merging of virtual reality and real objects or patients) provides a new method for teaching clinical and surgical procedures. Improved patient safety is a major advantage. We describe a system which employs AR technology to teach endotracheal intubation, using the Visible Human datasets, as well as MR images from live patient volunteers.
Nationalism imagined? Hidden impacts of the uprising of 1857 (2018)

This article challenges the myth that Indian nationalism was a major cause of the Rebellion or Uprising of 1857, arguing rather that nationalism was its ultimate result. But it goes much further, demonstrating that this unsuccessful Uprising of 1857 generated a new consciousness, as it taught Indians about the need to learn to protect and represent themselves better. While the East India Company (EIC) swiftly regained control and transferred sovereignty to the British Crown on 1 November 1858, tightening the noose of colonial subjugation for almost another century, the article argues that significant loss of trust in the feudal lords in 1857 opened the door to a new form of consciousness about the need for more competence in self-rule. The analysis suggests, therefore, that a combination of declining medieval feudalism and growth of modern nationalism in India, guided in due course by better equipped elite members of the middle classes, began to germinate as a largely hidden, unintended consequence of the failure of the 1857 Revolt, a phenomenon noted, but underrated, by historical scholarship.
Cognitive improvement after 6 weeks of soy supplements in postmenopausal women is limited to frontal lobe function (2005)

The results suggest that the main improvement after 6 weeks of soy supplementation was in frontal lobe function. Significant improvements in the same three measures of frontal lobe function were previously found after 12 weeks of soy supplements in postmenopausal women. The effects of soy on memory seem less robust.
Peroxide Formation by Mycoplasmas which Infect Man (1968)

The hemolytic activity of 8 human and 3 animal species of mycoplasmas was studied. With the exception of T-strains of human origin, each of the mycoplasmas tested hemolyzed guinea pig red blood cells.
Electropulsing-induced phase transformations and their effects on the single point diamond turning of a tempered alloy AZ91 (2012)

Abstract The effects of electropulsing on microstructure changes and phase transformations of a tempered Mg-9Al-1Zn alloy sheet were investigated by using X-ray diffraction and transmission electron microscopy. The results indicate that with increasing frequency of electropulsing, precipitation and decomposition of β-phase were tremendously accelerated sequentially. The effects of electropulsing on single-point diamond turning processing were investigated by examining cutting force and surface roughness variations, and are discussed from the point of view of dislocation dynamics.
Estimating Multi-Dimensional Sparsity Level for Spectrum Sensing (2023)

Identifying spectrum opportunities is a crucial element of efficient spectrum utilization for future wireless networks. Spectrum sensing offers a convenient means for revealing such opportunities. Studies showed that usage of the spectrum has a high correlation over multi-dimensions, including time and frequency. However, multi-dimensional spectrum sensing requires high-cost processes. Applying compressive sensing allows for subNyquist sampling. This reduces associated training, feedback, and computation overheads of a spectrum sensing method. However, the accuracy of the signal sparsity assumption and knowledge of the precise sparsity level are necessary for the applicability of compressive sensing. It is common practice to assume a level of known sparsity. On the other hand, in reality, this presumption is incorrect. This paper proposes a method for estimating the multidimensional sparsity for spectrum sensing. By extrapolating it from its counterpart with respect to a compact discrete Fourier basis, the proposed method calculates the sparsity level over a dictionary. A machine learning estimation method achieves this inference. Extensive simulations validate a high-quality sparsity estimation. To validate this observation, real-world measurements are used, where one of the biggest Turkish telecom operators has private uplink bands in the frequency range between 852-856 MHz.
Modeling and risk analysis of bromate formation from ozonation of bromide-containing waters (1996)

Empirical bromate formation models were developed from batch ozonation data to simulate the effects of important water quality characteristics and treatment processes on bromate formation. Bromate formation was favored at high pH, bromide concentration, alkalinity, and ozone dose. On the other hand, increasing DOC and ammonia concentration decreased bromate formation. Validation of the bromate models demonstrated that the models accurately simulated bromate formation. Risk analysis of bromate formation was performed on 5 utilities in which ozone was used, and it was concluded that under typical ozonation conditions, the associated risk related to bromate formation could be as high as 10−3.
Detecting COVID-19 from Breath: A Game Changer for a Big Challenge (2021)

Coronavirus disease 2019 (COVID-19) is probably the most commonly heard word of the last 12 months. The outbreak of this virus (SARS-CoV-2) is strongly compromising worldwide healthcare systems, social behavior, and everyone's lives. The early diagnosis of COVID-19 and isolation of positive cases has proven to be fundamental in containing the spread of the infection. Even though the polymerase chain reaction (PCR) based methods remain the gold standard for SARS-CoV-2 detection, the urgent demand for rapid and wide-scale diagnosis precipitated the development of alternative diagnostic approaches. The millions of tests performed every day worldwide are still insufficient to achieve the desired goal, that of screening the population during daily life. Probably the most appealing approach to consistently monitor COVID-19 spread is the direct detection of SARS-CoV-2 from exhaled breath. For instance, the challenging incorporation of reliable, highly sensitive, and cost-efficient detection methods in masks could represent a breakthrough in the development of portable and noninvasive point-of-care diagnosis for COVID-19. In this perspective paper, we discuss the critical technical aspects related to the application of breath analysis in the diagnosis of viral infection. We believe that, if achieved, it could represent a game-changer in containing the pandemic spread.
Time Synchronization in 5G Wireless Edge: Requirements and Solutions for Critical-MTC (2019)

The wireless edge is about distributing intelligence to wireless devices wherein the distribution of accurate time reference is essential for time-critical machine-type communication (cMTC). In 5G-based cMTC, enabling time synchronization in the wireless edge means moving beyond the current synchronization needs and solutions in 5G radio access. In this article, we analyze the device-level synchronization needs of potential cMTC applications: industrial automation, power distribution, vehicular communication, and live audio/video production. We present an overthe- air synchronization scheme comprising 5G air interface parameters and discuss their associated timing errors. We evaluate the estimation error in device-to-base-station propagation delay from timing advance under random errors and show how to reduce the estimation error. In the end, we identify the random errors specific to dense multipath fading environments and discuss countermeasures.
Energy Efficiency of the IEEE 802.15.4 Standard in Dense Wireless Microsensor Networks: Modeling and Improvement Perspectives (2007)

Wireless microsensor networks, which have been the topic of intensive research in recent years, are now emerging in industrial applications. An important milestone in this transition has been the release of the IEEE 802.15.4 standard that specifies interoperable wireless physical and medium access control layers targeted to sensor node radios. In this paper, we evaluate the potential of an 802.15.4 radio for use in an ultra low power sensor node operating in a dense network. Starting from measurements carried out on the off-the-shelf radio, effective radio activation and link adaptation policies are derived. It is shown that, in a typical sensor network scenario, the average power per node can be reduced down to 211m mm mW. Next, the energy consumption breakdown between the different phases of a packet transmission is presented, indicating which part of the transceiver architecture can most effectively be optimized in order to further reduce the radio power, enabling self-powered wireless microsensor networks.
Data from Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;The spatial organization of different types of cells in tumor tissues reveals important information about the tumor microenvironment (TME). To facilitate the study of cellular spatial organization and interactions, we developed Histology-based Digital-Staining, a deep learning-based computation model, to segment the nuclei of tumor, stroma, lymphocyte, macrophage, karyorrhexis, and red blood cells from standard hematoxylin and eosin–stained pathology images in lung adenocarcinoma. Using this tool, we identified and classified cell nuclei and extracted 48 cell spatial organization-related features that characterize the TME. Using these features, we developed a prognostic model from the National Lung Screening Trial dataset, and independently validated the model in The Cancer Genome Atlas lung adenocarcinoma dataset, in which the predicted high-risk group showed significantly worse survival than the low-risk group (&lt;i&gt;P&lt;/i&gt; = 0.001), with a HR of 2.23 (1.37–3.65) after adjusting for clinical variables. Furthermore, the image-derived TME features significantly correlated with the gene expression of biological pathways. For example, transcriptional activation of both the T-cell receptor and programmed cell death protein 1 pathways positively correlated with the density of detected lymphocytes in tumor tissues, while expression of the extracellular matrix organization pathway positively correlated with the density of stromal cells. In summary, we demonstrate that the spatial organization of different cell types is predictive of patient survival and associated with the gene expression of biological pathways.&lt;/p&gt;Significance:&lt;p&gt;These findings present a deep learning-based analysis tool to study the TME in pathology images and demonstrate that the cell spatial organization is predictive of patient survival and is associated with gene expression.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Rodriguez-Antolin, p. 1912&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
EXCESS POTASSIUM INDUCES LARVAL METAMORPHOSIS IN FOUR MARINE INVERTEBRATE SPECIES (1986)

An increase in the concentration of K+ in defined seawater medium induces settlement and metamorphosis in larvae of the marine molluscs Phestilla sibogae, Haliotis rufescens, and Astraea undosa, and in larvae of the marine annelid Phragmatopoma californica. The effect is dose-dependent, optimal at approximately double the normal concentration of K+ in seawater, and specific for the K+ ion. The ability of K+ to directly influence cell membrane potential is proposed as an explanation for its broad effectiveness as a metamorphic inducer for larvae that recruit to different habitats. Depolarization of externally accessible, excitable cells thus is suggested to be a mechanism common to the induction of settlement and metamorphosis of a number of species. For Phestilla and Haliotis, the inductive effect of excess K+ is additive with that of the substratum-derived inducers or analogs. The sensitivity of induction by K+ to external tetraethylammonium (TEA, a K+-channel blocker) reported previously for Haliotis (Baloun and Morse, 1984) is not present in Phestilla or Phragmatopoma. Results presented here indicate that the addition of excess K+ may provide a widely useful technique for inducing metamorphosis, and for analyzing the mechanisms which govern this process, in other marine invertebrate larvae.
Nε-Acryloyllysine Piperazides as Irreversible Inhibitors of Transglutaminase 2: Synthesis, Structure–Activity Relationships, and Pharmacokinetic Profiling (2018)

Transglutaminase 2 (TGase 2)-catalyzed transamidation represents an important post-translational mechanism for protein modification with implications in physiological and pathophysiological conditions, including fibrotic and neoplastic processes. Consequently, this enzyme is considered a promising target for the diagnosis of and therapy for these diseases. In this study, we report on the synthesis and kinetic characterization of N<sup>ε</sup>-acryloyllysine piperazides as irreversible inhibitors of TGase 2. Systematic structural modifications on 54 new compounds were performed with a major focus on fluorine-bearing substituents due to the potential of such compounds to serve as radiotracer candidates for positron emission tomography. The determined inhibitory activities ranged from 100 to 10 000 M<sup>-1</sup> s<sup>-1</sup>, which resulted in comprehensive structure-activity relationships. Structure-activity correlations using various substituent parameters accompanied by covalent docking studies provide an advanced understanding of the molecular recognition for this inhibitor class within the active site of TGase 2. Selectivity profiling of selected compounds for other transglutaminases demonstrated an excellent selectivity toward transglutaminase 2. Furthermore, an initial pharmacokinetic profiling of selected inhibitors was performed, including the assessment of potential membrane permeability and liver microsomal stability.
Hydrostatic pressure effects on the optical transitions in the free-standing porous silicon film (1993)

Optical absorption and photoluminescence spectra in the range 1.2–2.2 eV have been measured in free-standing films of porous Si under hydrostatic pressures up to 6.4 GPa at room temperature. The absorption rises nearly exponentially in the low energy region. Under pressure, the whole spectrum shifts toward lower energies with a pressure coefficient of about −90 meV/GPa. The photoluminescence spectrum also exhibits a redshift of about −40 meV/GPa. These results are interpreted by analogy with the pressure-induced shrinkage of the optical energy gap seen in amorphous chalcogenide semiconductors.
Impact of Collection Volume and DNA Extraction Method on the Detection of Biomarkers and HPV DNA in First-Void Urine (2021)

The potential of first-void (FV) urine as a non-invasive liquid biopsy for detection of human papillomavirus (HPV) DNA and other biomarkers has been increasingly recognized over the past decade. In this study, we investigated whether the volume of this initial urine stream has an impact on the analytical performance of biomarkers. In parallel, we evaluated different DNA extraction protocols and introduced an internal control in the urine preservative. Twenty-five women, diagnosed with high-risk HPV, provided three home-collected FV urine samples using three FV urine collection devices (Colli-Pee) with collector tubes that differ in volume (4, 10, 20 mL). Each collector tube was prefilled with Urine Conservation Medium spiked with phocine herpesvirus 1 (PhHV-1) DNA as internal control. Five different DNA extraction protocols were compared, followed by PCR for GAPDH and PhHV-1 (qPCR), HPV DNA, and HBB (HPV-Risk Assay), and ACTB (methylation-specific qPCR). Results showed limited effects of collection volume on human and HPV DNA endpoints. In contrast, significant variations in yield for human endpoints were observed for different DNA extraction methods (<i>p</i> < 0.05). Additionally, the potential of PhHV-1 as internal control to monitor FV urine collection, storage, and processing was demonstrated.