gebhart/patrepeval huggingface dataset:
Temporal Machine Learning Analysis of Prior Mammograms for Breast Cancer Risk Prediction (2023)

The identification of women at risk for sporadic breast cancer remains a clinical challenge. We hypothesize that the temporal analysis of annual screening mammograms, using a long short-term memory (LSTM) network, could accurately identify women at risk of future breast cancer. Women with an imaging abnormality, which had been biopsy-confirmed to be cancer or benign, who also had antecedent imaging available were included in this case-control study. Sequences of antecedent mammograms were retrospectively collected under HIPAA-approved guidelines. Radiomic and deep-learning-based features were extracted on regions of interest placed posterior to the nipple in antecedent images. These features were input to LSTM recurrent networks to classify whether the future lesion would be malignant or benign. Classification performance was assessed using all available antecedent time-points and using a single antecedent time-point in the task of lesion classification. Classifiers incorporating multiple time-points with LSTM, based either on deep-learning-extracted features or on radiomic features, tended to perform statistically better than chance, whereas those using only a single time-point failed to show improved performance compared to chance, as judged by area under the receiver operating characteristic curves (AUC: 0.63 ± 0.05, 0.65 ± 0.05, 0.52 ± 0.06 and 0.54 ± 0.06, respectively). Lastly, similar classification performance was observed when using features extracted from the affected versus the contralateral breast in predicting future unilateral malignancy (AUC: 0.63 ± 0.05 vs. 0.59 ± 0.06 for deep-learning-extracted features; 0.65 ± 0.05 vs. 0.62 ± 0.06 for radiomic features). The results of this study suggest that the incorporation of temporal information into radiomic analyses may improve the overall classification performance through LSTM, as demonstrated by the improved discrimination of future lesions as malignant or benign. Further, our data suggest that a potential field effect, changes in the breast extending beyond the lesion itself, is present in both the affected and contralateral breasts in antecedent imaging, and, thus, the evaluation of either breast might inform on the future risk of breast cancer.
State Space Modeling of an Offshore Wind Power Plant With an MMC-HVDC Connection for an Eigenvalue-Based Stability Analysis (2022)

Large offshore wind power plants (OWPPs) installed far from the coastline are emerging to benefit from the strong and steady wind resources available at these locations. The high-voltage direct-current (HVDC) transmission system based on the modular multilevel converter (MMC) is the most appropriate solution to transmit the produced energy to the onshore grid, in a way that a complex power-electronic-based electrical system is formed at the OWPP. Undesired interactions can occur between the MMC-based HVDC station, the several wind-turbine (WT) converters, and the passive elements of the offshore grid. To guarantee a safe and reliable operation of the OWPP, a small-signal analysis must be performed in advance to predict possible unstable situations and their root causes, in a way as to take corrective measures to avoid them. In this paper, a state space model of an OWPP is developed in which a recently proposed model in multiple <i>dq</i> frames is adopted for the MMC. With the developed model, an eigenvalue-based stability assessment is carried out, where participation factors are calculated to identify the main contributors to the unstable modes that appear as a consequence of undesired low-frequency interactions at the offshore grid. As far as the authors know, an eigenvalue-based stability assessment of an OWPP with an MMC-HVDC connection is a topic rarely or never explored in the literature before and, thus, this is the main contribution of this paper. An adaptation to the MMC state space model is proposed so that the converter&#x2019;s dynamics in grid-forming mode can be represented, and this is another contribution of this paper. Finally, various studies are presented to prove that the adopted approximated MMC model is accurate enough for small-signal stability analyses.
Isolation and Structural Characterization of Siderophores, Madurastatins, Produced by a Pathogenic Actinomadura madurae. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Plasmon Induced Transparency with Asymmetric π-Shaped Metamaterials (2012)

We propose a planar metamaterial composed of asymmetrically positioned π-shaped structures that exhibits plasmon induced transparency (PIT). The system enables fine tuning of PIT spectral behavior and near field enhancement control and provides smaller mode volumes.
Telehealth: from the abstract to necessity to competency (2021)

The COVID-19 pandemic caused significant disruption in medical education. With disruption comes the opportunity for innovation. Telehealth had been growing rapidly in many fields of medicine prior to the pandemic; however, the necessities of social distancing, scarcity of personal protective equipment, and mandates to prevent unnecessary exposures for healthcare workers and patients alike, brought opportunities for the exponential expansion of telehealth. With the expansion of telehealth services came the need to expand the curriculum in telehealth to prepare medical students to return to vastly transformed clinical settings as well as prepare them for a future clinical landscape likely to incorporate telehealth to a much greater degree. The University of Colorado School of Medicine (CUSOM) rapidly developed a course in telehealth to prepare students for this changing clinical environment. Simultaneously, a faculty development curriculum was created to support clinical faculty new to telehealth in basic skills and teaching in a virtual environment. Lastly, adaptations were made to the summative Clinical Practice Exam administered to students at the completion of clerkships to incorporate telehealth. Recognizing the importance of achieving competence in telehealth, the CUSOM has taken steps to invest in the development of comprehensive and integrated telehealth curricula. Many creative and innovative solutions have been adopted in the wake of this pandemic to allow medical education to continue despite many hurdles and barriers; many of these will not persist past the pandemic. However, we expect telehealth clinical skills and the curricula developed to support them to remain relevant long past the time when the COVID-19 pandemic has faded into history.
<title>Reconfigurable free-space optical interconnection module for pipelined optoelectronic parallel processing</title> (2001)

Optical interconnections and integrated optoelectronic devices are expected to be promising candidates that expand interconnection bandwidth between large-scale integrated circuits (LSIs). We have constructed an optoelectronic parallel computing system that has a reconfigurable free- space parallel optical interconnection module called OCULAR- II. It has a multi-layer architecture that eliminates the data transfer bottleneck between optoelectronic processing modules by reconfigurable free-space optical interconnections. An optoelectronic processing module is composed of a two-dimensional processing element array where each pixel has its own optical output channel by a VCSEL and optical input channel. The optical interconnection is integrated into a compact module where an optically addressable phase only spatial light modulator and an imaging optical system are compactly fabricated. Each component of the OCULAR-II system has been designed to be modular and compact. Therefore, just cascading optoelectronic processing modules and optical interconnection modules makes a pipelined parallel processing system. In the optical interconnection module, a custom designed Fourier Transform lens has been used to reduce the working distance of the lens system. A computer generated hologram (CGH) is written on a liquid crystal display (LCD) that is coupled by a fiber optic plate (FOP) to the optically addressable SLM. The interconnection topology between optoelectronic chips is controlled by changing the CGH patterns, which is calculated in advance. A global interconnectivity among processor arrays is also achievable since the communication channels are constructed via optical path in free space. The data broadcasting between processors that are located spatially far away can be efficiently implemented by free-space optical links in OCULAR-II's optical interconnection module.
Guanidine alkaloid analogs as inhibitors of HIV-1 Nef interactions with p53, actin, and p56 lck (2004)

With current anti-HIV treatments targeting only 4 of the 15 HIV proteins, many potential viral vulnerabilities remain unexploited. We report small-molecule inhibitors of the HIV-1 protein Nef. In addition to expanding the anti-HIV arsenal, small-molecule inhibitors against untargeted HIV proteins could be used to dissect key events in the HIV lifecycle. Numerous incompletely characterized interactions between Nef and cellular ligands, for example, present a challenge to understanding molecular events during HIV progression to AIDS. Assays with phage-displayed Nef from HIV(NL4-3) were used to identify a series of guanidine alkaloid-based inhibitors of Nef interactions with p53, actin, and p56(lck). The guanidines, synthetic analogs of batzellidine and crambescidin natural products, inhibit the Nef-ligand interactions with IC(50) values in the low micromolar range. In addition, sensitive in vivo assays for Nef inhibition are reported. Although compounds that are effective in vitro proved to be too cytotoxic for cellular assays, the reported Nef inhibitors provide proof-of-concept for disrupting a new HIV target and offer useful leads for drug development.
Ba6P12N17O9Br3 – A Column‐Type Phosphate Structure Solved from Single‐Nanocrystal Data Obtained by Automated Electron Diffraction Tomography (2011)

Abstract Oxonitridophosphate Ba 6 P 12 N 17 O 9 Br 3 was synthesized by heating a multicomponent mixture of BaBr 2 , BaS, phosphoryl triamide and thiophosphoryl triamide in an evacuated and sealed silica‐glass ampoule to 750 °C. Ba 6 P 12 N 17 O 9 Br 3 was obtained as the main product as a nanocrystalline powder. The crystal structure was determined ab initio on the basis of electron diffraction data acquired from a single needle‐shaped nanocrystal by automated diffraction tomography. Ba 6 P 12 N 17 O 9 Br 3 crystallizes in the hexagonal space group P 6 3 / m (no. 176) with unit cell parameters a = 14.654(19), c = 8.255(9) Å and Z = 2. Its structure includes triangular, column‐shaped anions of ∞ 1 {(P 12 N 17 O 9 ) 9– }, which are built from vertex‐sharing P(O,N) 4 tetrahedra with 3‐rings and three‐coordinate nitrogen atoms. The 1D anions are separated by Ba 2+ and Br – ions, which are arranged in channels parallel to the phosphate anions along [001]. The Ba 2+ ions are eight‐ and nine‐coordinated by Br – and O/N atoms, respectively.
Quantitative Phosphoproteomics of the Human Neural Stem Cell Differentiation into Oligodendrocyte by Mass Spectrometry (2012)

Cellular processes such as proliferation, differentiation, and adaptation to environmental changes are regulated byprotein phosphorylation. In order to enhance the understanding of molecular dynamics for biological process in detail, it is necessaryto develop sensitive and comprehensive analytical methods for the determination of protein phosphorylation. Neural stemcells hold great promise for neural repair following an injury or disease. In this study, we made differentiated oligodendrocytesfrom human neural stem cells using over-expression of olig2 gene. We confirmed using quantitative phosphoproteome analysisapproach that combines stable isotope labeling by amino acids in cell culture (SILAC) and TiO2 micro-column for phosphopeptideenrichment with MS2 and MS3 mass spectrometry. We detected 275 phosphopeptides which were modulated at least 2-foldbetween human neural stem cells and oligodendrocytes. Among them, 23 phosphoproteins were up-regulated in oligodendrocytesand 79 phosphoproteins were up-regulated in F3 cells.
Design optimizations of InGaAsN(Sb) subcells for concentrator photovoltaic systems (2016)

The InGaAsN(Sb) material system is an attractive candidate for use in lattice-matched four-junction (4J) solar cells based on germanium substrates. Design optimizations for an InGaAsN(Sb) subcell are proposed for optimal power conversion efficiency within a 4J solar cell under a highly concentrated AM1.5D solar spectrum. The performance of the subcell is modeled using drift-diffusion simulations using Crosslight Apsys. An InGaAsN(Sb) test subcell was fabricated to obtain realistic materials parameters for the optimization of subcell performance. A thin InGaAsN(Sb) subcell is suggested for operation at 1000 Sun illumination intensities at low carrier lifetimes and mobilities.
1.2 kV trench insulated gate bipolar transistors (IGBT's) with ultralow on-resistance (1999)

In this letter, we report the full development of 1.2 kV Trench IGBT's with ultralow on-resistance, latch-up free operation and highly superior overall performance when compared to state of the art IGBT's. The minimum forward voltage drop at the standard current density of 100 A/cm/sup 2/ was 1.1 V for nonirradiated devices and 2.1 V for irradiated devices. The maximum controllable current density was in excess of 1000 A/cm/sup 2/.
Reduced serotonergic transmission alters sensitivity to cost and reward via 5-HT 1A and 5-HT 1B receptors in monkeys (2023)

Abstract Deficiency of the serotonin (5-HT) system is considered one of the core biological pathologies of depression and other psychiatric disorders whose key symptom is decreased motivation. Yet, the exact role of 5-HT in motivation remains controversial and elusive. Here, we pharmacologically manipulated the 5-HT system and quantified effects on motivation in terms of incentives and costs for goal-directed action in monkeys. Reversible inhibition of 5-HT synthesis increased refusal responses and reaction times in goal-directed task performance, indicating decreased motivation that could be separated into value-dependent and -independent components. To identify the receptor subtypes involved in these components, we systemically administered antagonists specific for four major 5-HT receptor subtypes: 5-HT 1A , 5-HT 1B , 5-HT 2A , and 5-HT 4 . Positron emission tomography visualized the unique distribution of each subtype in limbic brain regions and determined the systemic antagonist dose that achieved approximately 30% occupancy. We found that blockade of 5-HT 1A , but not other receptor subtypes, increased sensitivity to future workload and time-delay to reward, and decreased motivation in a value-independent manner. Moreover, blocking only 5-HT 1B receptors reduced the impact of incentive value on motivation. These results suggest that two distinct processes, mediated by 5-HT 1A and 5-HT 1B receptors, lead to reduced motivation in 5-HT system deficiency.
Single Channel Probe Utilizing the EGN Model to Estimate Link Parameters for Network Abstraction (2017)

We experimentally demonstrate multi-span link parameter abstraction using a single channel 11.5GBd probe. EGN based abstraction gave γ=1.14W <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> km <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1</sup> c.f. 0.72W <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> km <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> for a GN based abstraction. The GN model overestimates the abstracted SNR by 0.4dB c.f. the EGN model at 1000km.
Noninvasive imaging of lentiviral-mediated reporter gene expression in living mice (2003)

Lentiviral-mediated gene delivery holds significant promise for sustained gene expression within living systems. Vesicular stomatitis virus glycoprotein-pseudotyped human immunodeficiency virus type 1-based lentiviral vectors can be used to introduce transgenes in a broad spectrum of dividing as well as nondividing cells. In the current study, we construct a lentiviral vector carrying two reporter genes separated by an internal ribosomal entry site and utilize that virus in delivering both genes into neuroblastoma cells in cell culture and into cells implanted in living mice. We utilize two reporter genes, a mutant herpes simplex virus type 1 (HSV1) sr39tk as a reporter gene compatible with positron emission tomography (PET) and a bioluminescent optical reporter gene, firefly luciferase (Fluc), to image expression in living mice by an optical charge-coupled device (CCD) camera. By using this lentivirus, neuroblastoma (N2a) cells are stably transfected and a high correlation (R(2) = 0.91) between expressions of the two reporter genes in cell culture is established. Imaging of both reporter genes using microPET and optical CCD camera in living mice is feasible, with the optical approach being more sensitive, and a high correlation (R(2) = 0.86) between gene expressions is again observed in lentiviral-infected N2a tumor xenografts. Indirect imaging of HSV1-sr39tk suicide gene therapy utilizing Fluc is also feasible and can be detected with increased sensitivity by using the optical CCD. These preliminary results validate the use of lentiviral vectors carrying reporter genes for multimodality imaging of gene expression and should have many applications, including imaging of xenografts, metastasis, and cell trafficking as well as noninvasive monitoring of lentiviral-mediated gene delivery and expression.
MicroRNA-10A* and MicroRNA-21 Modulate Endothelial Progenitor Cell Senescence Via Suppressing High-Mobility Group A2 (2012)

miR-10A* and miR-21 regulate EPC senescence via suppressing Hmga2 expression and modulation of microRNAs may represent a potential therapeutic intervention in improving EPC-mediated angiogenesis and vascular repair.
Assemblies of Colloidal CdSe Tetrapod Nanocrystals with Lengthy Arms for Flexible Thin-Film Transistors (2017)

Herein, we report unique features of the assemblies of tetrapod-shaped colloidal nanocrystals (TpNCs) with lengthy arms applicable to flexible thin-film transistors. Due to the extended nature of tetrapod geometry, films made of the TpNC assemblies require reduced numbers of inter-NC hopping for the transport of charge carriers along a given channel length; thus, enhanced conductivity can be achieved compared to those made of typical spherical NCs without arms. Moreover, electrical conduction through the assemblies is tolerant against mechanical bending because interconnections between TpNCs can be well-preserved under bending. Interestingly, both the conductivity of the assemblies and their mechanical tolerance against bending are improved with an increase in the length of tetrapod arms. The arm length-dependency was demonstrated in a series of CdSe TpNC assemblies with different arm lengths (l = 0-90 nm), whose electrical conduction was modulated through electrolyte gating. From the TpNCs with the longest arm length included in the study (l = 90 nm), the film conductivity as high as 20 S/cm was attained at 3 V of gate voltage, corresponding to electron mobility of >10 cm<sup>2</sup>/(V s) even when evaluated conservatively. The high channel conductivity was retained (∼90% of the value obtained from the flat geometry) even under high bending (bending radius = 5 mm). The results of the present study provide new insights and guidelines for the use of colloidal nanocrystals in solution-processed flexible electronic device applications.
Optical Image Collection v1 (2020)

Mass spectrometry imaging is an exciting technology, which enables simultaneous analysis of multiple molecular components directly from single cells, tissues, and organs. In combination with histological methods, this technique provides information about the spatial distribution of molecules in various biological tissues. Particularly, MALDI-MS imaging increases the coverage of metabolites by using different matrices and ionization modes. In coordination with in situ analysis of proteins, transcripts and epigenetic marks, the complementary spatial information on metabolites will establish metabolic pathways that are dominant and characteristic of disease states. We have recently developed and optimized a spatial metabolomics approach to image small molecules in human kidneys and biopsy sized material. With our combined expertise at UTHSA, PNNL and EMBL and recent advances, we have established methods for identifying metabolites in human kidneys, employed ultra-high mass resolution MS imaging for tissue analysis, and developed a bioinformatics resource (METASPACE) to annotate metabolites for anatomical localization and 3-D reconstruction. Our integrated technology can easily connect with other TIS sites to provide biochemical readouts of genes/proteins in specific tissue and cellular compartments.
Dual targeting of therapeutics to endothelial cells: collaborative enhancement of delivery and effect (2015)

Anchoring pharmacologic agents to the vascular lumen has the potential to modulate critical processes at the blood-tissue interface, avoiding many of the off-target effects of systemically circulating agents. We report a novel strategy for endothelial dual targeting of therapeutics, which both enhances drug delivery and enables targeted agents to partner enzymatically to generate enhanced biologic effect. Based on the recent discovery that paired antibodies directed to adjacent epitopes of platelet endothelial cell adhesion molecule (PECAM)-1 stimulate each other's binding, we fused single-chain fragments (scFv) of paired anti-mouse PECAM-1 antibodies to recombinant murine thrombomodulin (TM) and endothelial protein C receptor (EPCR), endothelial membrane proteins that partner in activation of protein C (PC). scFv/TM and scFv/EPCR bound to mouse endothelial PECAM-1 with high affinity (EC50 1.5 and 3.8 nM, respectively), and codelivery induced a 5-fold increase in PC activation not seen when TM and EPCR are anchored to distinct cell adhesion molecules. In a mouse model of acute lung injury, dual targeting reduces both the expression of lung inflammatory markers and trans-endothelial protein leak by as much as 40%, as compared to either agent alone. These findings provide proof of principle for endothelial dual targeting, an approach with numerous potential biomedical applications.
Fast Solutions in Power System Simulation through Coupling with\n Data-Driven Power Flow Models for Voltage Estimation (2020)

Power systems solvers are vital tools in planning, operating, and optimizing\nelectrical distribution networks. The current generation of solvers employ\ncomputationally expensive iterative methods to compute sequential solutions. To\naccelerate these simulations, this paper proposes a novel method that replaces\nthe physics-based solvers with data-driven models for many steps of the\nsimulation. In this method, computationally inexpensive data-driven models\nlearn from training data generated by the power flow solver and are used to\npredict system solutions. Clustering is used to build a separate model for each\noperating mode of the system. Heuristic methods are developed to choose between\nthe model and solver at each step, managing the trade-off between error and\nspeed. For the IEEE 123 bus test system this methodology is shown to reduce\nsimulation time for a typical quasi-steady state time-series simulation by\navoiding the solver for 86.7% of test samples, achieving a median prediction\nerror of 0.049%.\n