gebhart/patrepeval huggingface dataset:
Constrained Clustering using Gaussian Processes (2020)

Constrained clustering is an important machine learning, signal processing and data mining tool, for discovering clusters in data, in the presence of additional domain information. The present work introduces a probabilistic scheme for constrained clustering based on the popular Gaussian Process framework. The proposed scheme accommodates pairwise, must-and cannot-link constraints between data, does not require hyperparameter tuning, and enables assessment of the reliability of obtained results. Preliminary results on real data showcase the potential of the proposed approach.
Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation (2008)

The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse an online repository of SOPs.
High-sensitivity spin-based electrometry with an ensemble of nitrogen-vacancy centers in diamond (2017)

We demonstrate a spin-based, all-dielectric electrometer based on an ensemble of nitrogen-vacancy (NV[superscript −]) defects in diamond. An applied electric field causes energy-level shifts symmetrically away from the NV[superscript −]'s degenerate triplet states via the Stark effect; this symmetry provides immunity to temperature fluctuations allowing for shot-noise-limited detection. Using an ensemble of NV[superscript −]s, we demonstrate shot-noise-limited sensitivities approaching 1 (V/cm)/√Hz under ambient conditions, at low frequencies (<10 Hz), and over a large dynamic range (20 dB). A theoretical model for the ensemble of NV[superscript −]s fits well with measurements of the ground-state electric susceptibility parameter 〈k[subscript ⊥]〉. Implications of spin-based, dielectric sensors for micron-scale electric-field sensing are discussed.
Defective localization of the Wilson disease protein (ATP7B) in the mammary gland of the toxic milk mouse and the effects of copper supplementation (2000)

Toxic milk (tx) is a copper disorder of mice that causes a hepatic accumulation of copper similar to that seen in patients with Wilson disease. Both disorders are caused by a defect in the ATP7B copper-transporting ATPase. A feature of the tx phenotype is the production of copper-deficient milk by lactating dams homozygous for the tx mutation; the milk is lethal to the pups. It has not been determined whether the production of copper-deficient milk is a direct consequence of impaired expression of ATP7B protein in the mammary gland. With the use of immunohistochemistry, our study demonstrated that the ATP7B protein was mislocalized in the lactating tx mouse mammary gland, which would explain the inability of the tx mouse to secrete normal amounts of copper in milk. Confocal microscopy analysis showed that, in the lactating tx mammary gland, ATP7B was predominantly perinuclear in comparison with the diffuse, cytoplasmic localization of ATP7B in the lactating normal mammary gland. Lactating tx mice showed impaired delivery of copper from the mammary gland to the milk and this was not ameliorated by dietary copper supplementation. In contrast, the normal mouse mammary gland responded to increased dietary copper by increasing the amount of copper in milk. A change in the distribution of the ATP7B protein from perinuclear in the non-lactating gland to a diffuse, cytoplasmic localization in the lactating gland of the normal (DL) mouse suggests that the relocalization of APT7B is a physiological process that accompanies lactation. We conclude that the impaired copper transport from the mammary gland into milk in lactating tx mice is related to the mislocalization of ATP7B.
Identification of Human Endogenous Retrovirus-Specific T Cell Responses in Vertically HIV-1-Infected Subjects (2011)

Human endogenous retrovirus (HERV)-specific T cell responses in HIV-1-infected adults have been reported. Whether HERV-specific immunity exists in vertically HIV-1-infected children is unknown. We performed a cross-sectional analysis of HERV-specific T cell responses in 42 vertically HIV-1-infected children. HERV (-H, -K, and -L family)-specific T cell responses were identified in 26 of 42 subjects, with the greatest magnitude observed for the responses to HERV-L. These HERV-specific T cell responses were inversely correlated with the HIV-1 plasma viral load and positively correlated with CD4(+) T cell counts. These data indicate that HERV-specific T cells may participate in controlling HIV-1 replication and that certain highly conserved HERV-derived proteins may serve as promising therapeutic vaccine targets in HIV-1-infected children.
Robust Operation of Integrated Electric-Gas Systems Considering Frequency Regulation (2021)

This paper addresses the secure and economic operation problem of integrated electricity and natural gas system (IEGS), considering its participation in the power system’s frequency regulation (FR). IEGS can make profits by participating in the Frequency Regulation Auxiliary Service Market (FRASM) through the power reserve (PR) of the gas turbine (GT). However, the time required for FR is uncertain, which poses a challenge for its safe operation. We establish a robust model to balance security and the economy. Since the gas network is described by highly nonlinear partial differential equations that hinder the solution, we linearized the gas network by the difference method. Then the solution is obtained through a two-stage robust optimization algorithm. Our proposed model introduces the dynamic security concept into the IEGS operation optimization when participating in FRASM for the first time. The simulation results verify the effectiveness and necessity of the proposed model and algorithm.
Four wave mixing of finite amplitude Alfven waves (1995)

Summary form only given. Past treatments of coherent wave mixing of Alfven waves have generally been restricted to three wave interactions. This paper presents the first results that show that finite amplitude Alfven waves can also undergo four wave mixing. This observation opens the possibility of a variety of new low frequency nonlinear phenomena in plasmas. The wave mixing process is also unique in the sense that all the interacting waves are exact solutions of the nonlinear equation. We use the resistive derivative nonlinear Schrodinger (DNLS) equation to study the four wave interaction of Alfven waves. This equation describes the finite amplitude Alfven waves and solitons. It is shown that the frequencies and wave numbers of time harmonic solution of the DNLS equation satisfy the criterion for four wave mixing. Four such waves can, therefore, interact coherently with each other in the plasma. Assuming that the complex wave amplitudes evolve slowly in time and space, the evolution equations governing the wave amplitudes are derived. These equations are then used to identify quantities that remain invariant in time in a dissipationless plasma. One such quantity is the total wave magnetic energy. We also use the evolution equations and conservation relations to explore two applications. First, we investigate the evolution of two small amplitude Alfven waves in the presense of two large amplitude pump waves. The second application considers the interaction of four waves in a dissipative plasma. We also describe extensions of the basic plasma model and geometry that can be useful in studying other applications of four wave mixing.
Correction: Elucidating a dissolution–deposition reaction mechanism by multimodal synchrotron X-ray characterization in aqueous Zn/MnO2 batteries (2023)

Correction for ‘Elucidating a dissolution–deposition reaction mechanism by multimodal synchrotron X-ray characterization in aqueous Zn/MnO 2 batteries’ by Varun R. Kankanallu et al. , Energy Environ. Sci. , 2023, https://doi.org/10.1039/D2EE03731A.
<title>Modal analysis of an aircraft fuselage panel using experimental and finite-element techniques</title> (1998)

The application of electro-optic holography (EOH) for measuring the center bay vibration modes of an aircraft fuselage panel under forced excitation is presented. The requirement of free-free panel boundary conditions made the acquisition of quantitative EOH data challenging since large scale rigid body motions corrupted measurements of the high frequency vibrations of interest. Image processing routines designed to minimize effects of large scale motions were applied to successfully resurrect quantitative EOH vibrational amplitude measurements from extremely noisy data. EOH and scanning laser doppler vibrometer results have been used to validate and update finite element models of the fuselage panel. Various modeling techniques were evaluated for characterization of the panel normal modes at frequencies up to 1000 Hz. These models are briefly described, and comparisons between computational predictions and experimental measurements are presented.
Abstract 2219: Development of an assay to detect transcription misincorporation errors in Escherichia coli (2015)

Abstract In contrast to errors in DNA replication which can product heritable mutations, errors in transcription cause only transient alterations. The temporary nature of these transcription mistakes has made them difficult to detect and genetic screens to identify mutations that lower the fidelity of transcription have been problematic. We addressed this problem by developing methods to turn transient transcription errors into permanent genetic changes. The principle is based on suppression of a mutation in the active site of the cre recombinase. This assay is based on two parts: a source of Cre, which is actually the transcription misincorporation substrate, and a genetic reporter with a phenotypic change created by Cre-mediated recombination between lox sites. To develop a substrate for E. coli we chose the galactokinase gene (galK) as our reporter. From an alignment of the galK protein from E.coli, H. sapiens and L. lactis we identified sites that might be able to accept a 12aa insertion encoded by the LoxP sequence without disrupting its function. We selected four different sites that were away from the GalK active site and on the surface of the protein. We started our project using the strain MG1655, which is galK (+), able to grow in galactose as a carbon source and red on a MacConkey galactose plate (MAcGal). Using oligo recombineering, we first inserted a 7 base sequence, which caused a frame-shift mutation, the cells became galK (-) and, therefore white on MacGal. To put it back in frame, we next replaced the 7 bases with a 36 base loxP site, which, if it does not disrupt the function of galK will make the cells galK (+) again. To our surprise, the insertion of this LoxP site was completely successful, putting the gene back in frame and making the cells galK (+) and, therefore, red at each of the four sites we chose. A derivative of this reporter was made with the a portion of the galK gene inverted at one of the loxP sites. Active Cre recombinase can be detected by flipping the inversion to restore galK function. The active site mutant cre-Y324C exhibits a very low inversion rate. Mutations that reduce the accuracy of transcription, such as cells defective in greA, exhibit an elevated frequency of galK (+) inversions. This system will be used to identify additional mutations that reduce the fidelity of transcription in E. coli. Citation Format: Jorge A. Irizarry-Caro, Mary Ernst, Carolyn Court, Alison Rattray, Mikhail Bubunenko, Ding Jin, Donald Court, Jeffrey Strathern. Development of an assay to detect transcription misincorporation errors in Escherichia coli. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2219. doi:10.1158/1538-7445.AM2015-2219
Abstract 4132: Rapid microfluidic-based isolation of tumor cells from pleural effusions for cytodiagnostics. (2013)

Abstract Pleural effusions accumulate in patients with cancer or other illnesses and are often drained to provide symptomatic relief. Cells within this fluid are concentrated and analyzed to determine the cause of effusion. In patients with cancer, tumor cells may be present in the effusions and provide a source of cells for further diagnostics and mutational analysis. However, blood cell components and other non-cellular materials can create a significant background and can obscure the search for tumor cells. Furthermore, blood cell impurities can adversely impact the search for genomic or proteomic changes in the tumor cells by creating a large wild type background. A purity of at least 20% of target cells is necessary to ensure that background signal is suppressed. We have developed a microfluidic based “Centrifuge Chip” for the rapid isolation and purification of cancer cells. The Centrifuge Chip utilizes microvortices to trap cells based on size without the need for affinity-based capture. Isolated cells can subsequently be released on-demand and are viable to grow or can be analyzed for molecular changes. We utilized this chip for the isolation of tumor cells and mesothelial cells at high purity from pleural effusions and similar complex fluids such as blood. We then stained the cells with CK/DAPI for tumor cells and CD45 for white blood cells. Samples with high numbers of CK positive cells were deemed suspicious for malignancy; all our results were cross-checked to the standard Cytospin results. We routinely achieved improved purities in all samples, with greater than 70-fold increase in purity for samples positive for malignancy, and are developing a quantitative PCR (QPCR) based system to confirm the presence of activating EGFR or KRAS mutations in lung cancer cells isolated from patients with malignant pleural effusions secondary to lung cancer. The Centrifuge Chip can achieve rapid isolation of tumor cells from complex biofluids and allows for easier access to such cells for molecular analysis that will provide clinicians with critical information required for targeted cancer therapies. Citation Format: James Che, Albert Mach, Derek Go, Ish Talati, Yong Ying, Jianyu Rao, Dino Di Carlo, Rajan Kulkarni. Rapid microfluidic-based isolation of tumor cells from pleural effusions for cytodiagnostics. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4132. doi:10.1158/1538-7445.AM2013-4132
Enhanced Graphene Oxide Electrical Properties for Thin-Film Electronics Using an Active/Shrinkable Substrate (2022)

The advances in material science along with the development of fabrication techniques have enabled the realization of thin-film-based electronics on active substrates. This has substantially enhanced and supported the deployment of electronic devices in several emerging applications with flexible functionality. In this work, we report a novel fabrication of graphene oxide (GO)-based memristor devices on an active/shrinkable substrate. The standard lithography process is used to fabricate planar Au-rGO-Au devices on a polymer substrate that has the ability to shrink at a certain temperature (i.e., 170 °C). Upon heating, the devices are shrunk to 50% of their original size. A detailed electrical characterization has been carried out to study the switching behavior of the fabricated devices before and after shrinking. The results prove that upon shrinking, the device preserves its switching ability with enhanced electrical parameters (i.e., switching voltage). Also, material characterization performed for the deposited GO on the active substrate shows improved properties of the GO film due to the enhanced arrangement of GO flakes after shrinking. The novel approach proposed in this work provides new insights into and offers the ability to scale thin-film electronics postfabrication and thus overcome some of the device scaling challenges due to manufacturing limitations. It also unfolds a new path for the realization of GO-based electronic devices with improved electrical properties, which is a crucial aspect of the development of highly flexible and lightweight green electronics.
Low-cost locally manufacturable unilateral imperial external fixator for low- and middle-income countries (2022)

Treating open fractures in long bones can be challenging and if not performed properly can lead to poor outcomes such as mal/non-union, deformity, and amputation. One of the most common methods of treating these fracture types is temporary external fixation followed by definitive fixation. The shortage of high-quality affordable external fixators is a long-recognised need, particularly in Low- and Middle-Income Countries (LMICs). This research aimed to develop a low-cost device that can be manufactured locally to international standards. This can provide surge capacity for conflict zones or in response to unpredictable incidents and situations. The fixator presented here and developed by us, the Imperial external fixator, was tested on femur and tibia specimens under 100 cycles of 100 N compression-tension and the results were compared with those of the Stryker Hoffmann 3 frame. The Imperial device was stiffer than the Stryker Hoffmann 3 with a lower median interfragmentary motion (of 0.94 vs. 1.48 mm). The low-cost, easy to use, relatively lightweight, and easy to manufacture (since minimum skillset and basic workshop equipment and materials are needed) device can address a critical shortage and need in LMICs particularly in conflict-affected regions with unpredictable demand and supply. The device is currently being piloted in three countries for road traffic accidents, gunshot wounds and other conflict trauma-including blast cohorts.
On the Temperature Dependence of Monolithically Integrated Ga(NAsP)/(BGa)P/Si QW Lasers (2010)

Lasing operation up to 120K is reported in novel direct band-gap Ga(NAsP)/(BGa)P lasers grown monolithically on a silicon substrate. A carrier leakage process is found to dominate the temperature dependence of the laser threshold current.
Effects of taxol on microtubule arrays in cultured higher plant cells (1986)

Abstract Treatment with 10 μm taxol disrupted mitotic and cytoplasmic arrays of microtubules (MT) in cultured cells of two higher plants, Vicia hajastana (vetch) and Zinnia elegans. When treated for 1, 24, and 48 h, cells in both cultures showed similar effects. After 1 h, multipolar arrays of MT were noted in prophase, large aster‐like arrays of MT appeared in metaphase, and extra MT shared poles with otherwise normal‐appearing metaphase and anaphase configurations. After 24 and 48 h, some phragmoplasts were multipartite or misplaced. In interphase cells, micronuclei and multinucleate cells were evidence of irregular mitosis and cytokinesis. Cytoplasmic MT in elongated cells were oriented parallel to, instead of at right angles to the long axis of the cell. Some interphase cells lost asymmetry while maintaining organized arrays of MT. Taxol appears to disrupt mitotic and cytoplasmic arrays of MT, seemingly overriding the mechanism(s) regulating MT polymerization and orientation.
Unslotted DS/CDMA packet radio network using CLSP and packet-length adaptation in Rayleigh fading channel (2003)

We to high uncertainty of radio channel and imperfect power control, throughput-delay performance of packet radio networks (PRN) may suffer from disgraceful degradations. This paper shows that, while error-correcting channel coding has not yet been effective in heavily-correlated flat fading environments, adapting the length of radio packets to time-varying channel conditions is a simple adaptive technique for maintaining and improving the system performance and the energy-efficiency of mobile terminals. Based on a comprehensive study of correlation between fade duration statistics and packet length over a flat Rayleigh fading channel, robust adaptation mechanisms and performance characteristics are derived for an unslotted CLSP/DS-CDMA PRN system.
Quantifying the oxygen sensitivity of seed germination using a population-based threshold model (2007)

Abstract Seeds vary widely in the sensitivity of germination to oxygen (O 2 ) partial pressure, depending upon the species, temperature, dormancy state and physiological status of the seeds. Most analyses of the O 2 sensitivity of germination have focused on final germination percentages and estimated the O 2 percentage in air that is required to reduce germination to a given percentage (usually 50%). In contrast, we have applied a population-based threshold model utilizing time courses of germination to quantify three parameters related to seed germination sensitivity to O 2 availability: the median base (or threshold) O 2 percentage, the standard deviation of O 2 thresholds among seeds in the population, and an oxygen–time constant that relates O 2 percentage to germination timing. The model fits germination responses accurately across a wide range of O 2 concentrations. The response to O 2 was logarithmic in all cases, with the O 2 percentage required for 50% germination ranging from 21% to as low as 0.005%, depending upon the species, the temperature and the seed dormancy level. Modelling indicated that some seeds can adapt to low O 2 percentages and shift their thresholds to lower values over time. Lower temperatures decreased the minimum O 2 threshold, as did after-ripening. Seed priming generally reduced the oxygen–time constant and increased the standard deviation of germination responses, but had relatively little effect on the O 2 sensitivity per se . The population-based threshold model can be used to quantify the O 2 sensitivity of seed germination and to predict germination rates and percentages when O 2 availability is limiting.
Rural cadastral surveying with the global positioning system (1991)

Abstract Cadastral surveys have traditionally been performed using the well established techniques of traversing and radiation. The equipment used to accomplish these surveys has evolved from optical theodolites and steel bands, to total station and data recorder technology. With the recent advances in satellite technology, space based positioning systems are now capable of replacing conventional survey methods for many survey applications. This paper presents the results of a rural cadastral survey performed using the Global Positioning System (GPS). The survey was also performed using conventional total station techniques. A comparison of the results obtained reveals positional differences of one to four centimetres between the two data collection techniques.