gebhart/patrepeval huggingface dataset:
Comparing Interpretation of High-Resolution Aerial Imagery by Humans and Artificial Intelligence to Detect an Invasive Tree Species (2021)

Timely, accurate maps of invasive plant species are critical for making appropriate management decisions to eliminate emerging target populations or contain infestations. High-resolution aerial imagery is routinely used to map, monitor, and detect invasive plant populations. While conventional image interpretation involving human analysts is straightforward, it can require high demands for time and resources to produce useful intelligence. We compared the performance of human analysts with a custom Retinanet-based deep convolutional neural network (DNN) for detecting individual miconia (Miconia calvescens DC) plants, using high-resolution unmanned aerial system (UAS) imagery collected over lowland tropical forests in Hawai’i. Human analysts (n = 38) examined imagery at three linear scrolling speeds (100, 200 and 300 px/s), achieving miconia detection recalls of 74 ± 3%, 60 ± 3%, and 50 ± 3%, respectively. The DNN achieved 83 ± 3% recall and completed the image analysis in 1% of the time of the fastest scrolling speed tested. Human analysts could discriminate large miconia leaf clusters better than isolated individual leaves, while the DNN detection efficacy was independent of leaf cluster size. Optically, the contrast in the red and green color channels and all three (i.e., red, green, and blue) signal to clutter ratios (SCR) were significant factors for human detection, while only the red channel contrast, and the red and green SCRs were significant factors for the DNN. A linear cost analysis estimated the operational use of a DNN to be more cost effective than human photo interpretation when the cumulative search area exceeds a minimum area. For invasive species like miconia, which can stochastically spread propagules across thousands of ha, the DNN provides a more efficient option for detecting incipient, immature miconia across large expanses of forested canopy. Increasing operational capacity for large-scale surveillance with a DNN-based image analysis workflow can provide more rapid comprehension of invasive plant abundance and distribution in forested watersheds and may become strategically vital to containing these invasions.
Advanced Line-Heating Process for Hull-Steel Assembly (2000)

Ishikawajima-Harima Heavy Industries Co., Ltd. (IHI) has successfully employed the logic of the Finite Element Method on the principle of Thermal Forming or Line Heating, which facilitates use of computer aided, fully automated line heating machines for forming any curvature precisely and efficiently on a hull steel plate in the shipbuilding process. It is undesirable for the future in line heating that only an experienced technician is able to be skilled in the use of existing line heating f1 or steel plate forming. Accuracy of shape formed by existing line heating is not necessarily well controlled and work at succeeding stages is adversely affected by inaccurate interim products, though it is a very useful method informing steel plates and all apparatus required for line heating is just light tools. The IHI-Advanced Line-heating Process for Hull-steel Assembly (IHI-ALPHA) has succeeded in solving these problems.
Assessment of Sponge-on-String Device Parameters for the Non-endoscopic Detection of Barrettʼs Esophagus: Results from a Randomized Trial: 2016 ACG Presidential Poster Award (2016)

Introduction: Minimally invasive devices such as a sponge-on-string device (SoS) combined with discriminant markers are essential to make screening for Barrett's esophagus (BE) a practical and effective strategy. Such approaches must be safe, well-tolerated, and provide sufficient analyte for accurate diagnosis. In a randomized blinded study, we assessed two configurations of a SoS device for the following metrics: success rates for swallowing and retrieval, tolerability, preference relative to endoscopy, DNA yield, and BE detection by assay of selected methylated DNA markers. Methods: A SoS device (EsophaCap, Capnostics) was swallowed by and withdrawn from BE cases and non-BE controls confirmed by endoscopy done within 24 hours. Participants were randomized to a 25 mm/10 pores per inch (ppi) or a 25 mm/20 ppi sponge. Following SoS retrieval, participants completed a tolerability assessment (rating pain, choking, gagging and anxiety separately plus overall tolerability, on a 1-10 visual analog scale); they also indicated if they would have the procedure again and if they preferred SoS or endoscopy. A mucosal injury score (ranging from 1 (no trauma) to 6 (perforation)) was assessed from video recordings of the subsequent endoscopy. Following retrieval, the sponge was placed in a cell-preservative solution and agitated; the cell suspension was centrifuged and the resulting pellet then treated with lysis buffer. DNA extracted from lysis buffer was quantified, and our previously described methylated DNA markers for BE were assayed by methylation-specific PCR.Table 1: Comparison of outcomes assessed in the two groupsResults: 41 subjects (20 BE cases, 21 controls) were randomized: 21 to 25/10 ppi SoS and 20 to 25/20 ppi SoS. The capsule was successfully swallowed and retrieved in 40 subjects (98%). One BE case was found to not meet entry criteria and was excluded. Median age of cases (66) and controls (61) was comparable; 79% of cases and 50% of controls were men. Median BE segment length was 5 cm (IQR 4-8). Results of outcomes assessed are shown (Table). There were no major adverse events. At 100% specificity, sensitivity for BE by a 2-marker panel (methylated VAV3&ZNF682) was 100% for both sponge configurations. Conclusion: Non-endoscopic detection of BE with a SoS device and assay of selected methylation markers appears to be safe, well-tolerated, and accurate. The 25/10 ppi sponge was better tolerated and yielded highest DNA amount. Further studies are warranted to corroborate and extend these encouraging findings.
A Single-Gene Cause in 29.5% of Cases of Steroid-Resistant Nephrotic Syndrome (2014)

Steroid-resistant nephrotic syndrome (SRNS) is the second most frequent cause of ESRD in the first two decades of life. Effective treatment is lacking. First insights into disease mechanisms came from identification of single-gene causes of SRNS. However, the frequency of single-gene causation and its age distribution in large cohorts are unknown. We performed exon sequencing of NPHS2 and WT1 for 1783 unrelated, international families with SRNS. We then examined all patients by microfluidic multiplex PCR and next-generation sequencing for all 27 genes known to cause SRNS if mutated. We detected a single-gene cause in 29.5% (526 of 1783) of families with SRNS that manifested before 25 years of age. The fraction of families in whom a single-gene cause was identified inversely correlated with age of onset. Within clinically relevant age groups, the fraction of families with detection of the single-gene cause was as follows: onset in the first 3 months of life (69.4%), between 4 and 12 months old (49.7%), between 1 and 6 years old (25.3%), between 7 and 12 years old (17.8%), and between 13 and 18 years old (10.8%). For PLCE1, specific mutations correlated with age of onset. Notably, 1% of individuals carried mutations in genes that function within the coenzyme Q10 biosynthesis pathway, suggesting that SRNS may be treatable in these individuals. Our study results should facilitate molecular genetic diagnostics of SRNS, etiologic classification for therapeutic studies, generation of genotype-phenotype correlations, and the identification of individuals in whom a targeted treatment for SRNS may be available.
Hepatocellular uptake of sulfobromophthalein and bilirubin is selectively inhibited by an antibody to the liver plasma membrane sulfobromophthalein/bilirubin binding protein. (1986)

To clarify sulfobromophthalein (BSP) and bilirubin uptake mechanisms, isolated rat hepatocytes were incubated with [35S]BSP. The initial uptake velocity (V0), determined from the first, linear portion of the cumulative uptake curve, was saturable (Michaelis constant [Km] = 6.2 +/- 0.5 microM; Vmax = 638 +/- 33 pmol X min-1 per 10(5) hepatocytes), maximal at 37 degrees C and pH 7.4, and competitively inhibited by bilirubin, but not by taurocholate, cholate, or oleate. Preloading with unlabeled BSP led to trans-stimulation of V0. Sodium substitution or pretreatment of hepatocytes with ouabain or metabolic inhibitors had no effect on V0; trypsin reduced V0 by 39% (P less than 0.001). A rabbit antiserum to the rat liver plasma membrane (LPM)-BSP/bilirubin binding protein selectively reduced V0 of 5 microM [35S]BSP and [14C]bilirubin by 41 and 42%, respectively (P less than 0.01); uptakes of [3H]oleate, [3H]cholate and [3H]taurocholate were not affected. Hence, the LPM-BSP/bilirubin binding protein plays a role in the carrier-mediated uptake of BSP and bilirubin by hepatocytes.
Improving Materials Accountancy for Reprocessing using hiRX (2014)

Abstract not provided.
Diatom frustules as light traps enhance DSSC efficiency (2012)

Diatoms are one of the most successful photosynthetic organisms and given the important role that their shells (frustules) play in light trapping we explored their use in multilayered materials for application as photoanodes in dye sensitised solar cells (DSSCs). We find a substantial improvement in energy conversion efficiency of 30%, increasing from 3.5% to 4.6% with diatom incorporation.
Structural characterization of new fluorinated mesogens obtained through halogen-bond driven self-assembly (2017)

We describe the synthesis and characterization of new trimeric complexes obtained upon halogen-bond driven self-assembly of 1,4-diiodotetrafluorobenzene or α,ω– diiodoperfluoroalkanes, acting as XB-donors, with an alkoxystilbazole derivative functionalized with a methacrylate terminal group, acting as XB-acceptor. Despite the fact that the starting materials are not mesomorphic in nature, the obtained halogen-bonded complexes exhibit monotropic LC behaviour with smectic A phases possibly resulting from segregation between fluorocarbon and hydrocarbon chains. The obtained supramolecular mesogens possess reactive groups suitable for incorporation into liquid crystalline elastomeric actuators.
54.2: Light Weight Glass Funnel Designs for CRTs (2001)

Abstract To strengthen and to prolong the market position of the cathode‐ray tube (CRT), one of the main requirements today is to reduce tube weight and thus to save glass material. A method to design weight reduced glass funnels under the restrictions of the glass and tube manufacturers processes will be presented.
A Far-Field-Viewing Sensor for Making Analytical Measurements in Remote Locations (1999)

We demonstrate a far-field-viewing GRINscope sensor for making analytical measurements in remote locations. The GRINscope was fabricated by permanently affixing a micro-Gradient index (GRIN) lens on the distal face of a 350-micron-diameter optical imaging fiber. The GRINscope can obtain both chemical and visual information. In one application, a thin, pH-sensitive polymer layer was immobilized on the distal end of the GRINscope. The ability of the GRINscope to visually image its far-field surroundings and concurrently detect pH changes in a flowing stream was demonstrated. In a different application, the GRINscope was used to image pH- and O2-sensitive particles on a remote substrate and simultaneously measure their fluorescence intensity in response to pH or pO2 changes.
Wireless channel from physical layer security perspective (2022)

One of the critical requirements of the future wireless networks is the provision of secure communication against wide range of attacks. Contrary to the conventional cryptography-based security, physical layer security (PLS), in the broadest sense, intends to exploit different features of the wireless channel to secure not only the information being communicated but the whole communication process from myriad types of attacks. Future generations of the wireless networks will be built on various new technologies such as massive multiple input multiple output (mMIMO), reconfigurable intelligent surfaces (RIS), and sensing, and are expected to accommodate some newly emerging use-cases that never existed in the legacy networks. Both, the new technologies and the use-cases are accompanied with some new and unique channel characteristics which can be leveraged by the channel-based PLS concept. This chapter explores these newly revealed channel features to highlight their potential advantages and challenges if exploited for PLS. Specifically, the chapter provides a ground work on the critical qualities that define the eligibility of a certain channel feature for the PLS application. Afterward, channel features unique to different scenarios (such as high mobility in vehicle-to-vehicle and high speed train communication) or technologies (such as mMIMO and communication at higher frequency bands) in 5G and beyond networks are discussed form the PLS perspective. The chapter also touches upon the evolving class of security attack that intend to disrupt the channel-based PLS concept by attacking the channel characteristics/features rather than the communication itself. The chapter is then concluded by summarizing some possible research directions for the channel-based PLS concept.
New Upper Bounds on A(n,d) (2005)

Upper bounds on the maximum number of codewords in a binary code of a given length and minimum Hamming distance are considered. New bounds are derived by a combination of linear programming and counting arguments. Some of these bounds improve on the best known analytic bounds. Several new record bounds are obtained for codes with small lengths.
Unambiguous Device Identification and Fast Connection Setup in Bluetooth (2001)

The paper addresses two problems of Bluetooth which arise in situations where a user device performs transactions with a specific server device out of a number of similar devices in the proximity, such as ticket machines or point-of-sales terminals. Firstly, the server that a connection should be set up with, needs to be uniquely identified and selected. Secondly, with the current Bluetooth protocol specifications the connection setup may take a prohibitively long time. The paper revisits the Bluetooth inquiry and page procedures and their duration. We discuss two ways of uniquely identifying the target device relying on manual user interaction, and compare the times needed for connection establishment. We further propose to use a second short-range communication medium, such as an integrated infrared interface or an RFID transponder, to facilitate the connection setup. This eliminates the need for manual selection of the target device and further speeds up the connection establishment.
Increased detection of structural templates using alignments of designed sequences (2003)

Protein structure prediction by comparative modeling benefits greatly from the use of multiple sequence alignment information to improve the accuracy of structural template identification and the alignment of target sequences to structural templates. Unfortunately, this benefit is limited to those protein sequences for which at least several natural sequence homologues exist. We show here that the use of large diverse alignments of computationally designed protein sequences confers many of the same benefits as natural sequences in identifying structural templates for comparative modeling targets. A large-scale massively parallelized application of an all-atom protein design algorithm, including a simple model of peptide backbone flexibility, has allowed us to generate 500 diverse, non-native, high-quality sequences for each of 264 protein structures in our test set. PSI-BLAST searches using the sequence profiles generated from the designed sequences ("reverse" BLAST searches) give near-perfect accuracy in identifying true structural homologues of the parent structure, with 54% coverage. In 41 of 49 genomes scanned using reverse BLAST searches, at least one novel structural template (not found by the standard method of PSI-BLAST against PDB) is identified. Further improvements in coverage, through optimizing the scoring function used to design sequences and continued application to new protein structures beyond the test set, will allow this method to mature into a useful strategy for identifying distantly related structural templates.
Comparison of Brain Masking Techniques in Functional Magnetic Resonance Imaging (2007)

Exclusion of non-brain matter in functional magnetic resonance imaging is required for performing functional localization in particular, as well as functional image analysis in general. This paper presents a comparison of the commonly used brain masking techniques in functional magnetic resonance imaging. In addition, a masking algorithm based on connected components analysis along with Gaussian smoothing is introduced. The contiguous binary brain mask obtained by the new algorithm is shown to be more effective than the ones obtained by the commonly deployed masking algorithms. The introduced algorithm can also be applied to different image modalities that need to be registered to the space of anatomy or to the native space of echo planar images.
Supplemental Table 5 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Supplemental Table 5&lt;/p&gt;
CMOS-integrated nanoscale memristive crossbars for CNN and optimization acceleration (2020)

While memristive crossbars have been reported to offer substantial performance efficiency benefits orders of magnitude above digital processors, there remain high risks in analog computing platforms using emerging non-volatile memory technologies, primarily due to device performance, variability, yield, and interactions with peripheral circuits. We directly integrated CMOS and nanoscale (down to 25 nm) memristors for fully on-chip reading/programming/computing demonstrations. We operate in a low power regime, program with fine control, showing high yield and low variability across our memristive arrays. With the integrated chip, we successfully demonstrated a multi-layer convolutional neural network with MNIST classification accuracy of above 95.3%, demonstrating several concepts in proposed architectures for hybrid analog-digital computing. The ability to tackle NP-hard optimization problems is also experimentally demonstrated with this platform. This work de-risks many of the chief concerns for an accelerator based on analog rather than purely digital computing circuits, as well as validating the core elements of a future in-memory computing architecture.
A Transceiver ASIC for a Single-Cable 64-Element Intra-Vascular Ultrasound Probe (2021)

This article presents an application-specific integrated circuit (ASIC) designed for intra-vascular ultrasound imaging that interfaces 64 piezoelectric transducer elements to an imaging system using a single micro-coaxial cable. Thus, it allows a single-element transducer to be replaced by a transducer array to enable 3-D imaging. The 1.5-mm-diameter ASIC is intended to be mounted at the tip of a catheter, directly integrated with a 2-D array of piezoelectric transducer elements. For each of these elements, the ASIC contains a high-voltage (HV) switch, allowing the elements to transmit an acoustic wave in response to an HV pulse generated by the imaging system. A low-noise amplifier then amplifies the resulting echo signals and relays them as a signal current to the imaging system, while the same cable provides a 3-V supply. Element selection and other settings can be programmed by modulating configuration data on the supply, thus enabling full synthetic aperture imaging. An integrated element test mode measures the element capacitance to detect bad connections to the transducer elements. The ASIC has been fabricated in a 0.18- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> HV CMOS technology and consumes only 6 mW in receive. Electrical measurements show correct switching of 30-V transmit pulses and a receive amplification with a 71-dB dynamic range, including 12 dB of programmable gain over a 3-dB bandwidth of 21 MHz. The functionality of the ASIC has been successfully demonstrated in a 3-D imaging experiment.
A comparative analysis of host responses to avian influenza infection in ducks and chickens highlights a role for the interferon-induced transmembrane proteins in viral resistance (2015)

Taken together these results support a model where the IFITM123 protein family and RIG-I all play a crucial role in the tolerance of ducks to highly pathogenic and low pathogenic strains of avian influenza viruses when compared to the chicken.
Plaque-forming cell responses to trinitrophenyl (TNP)-l-glutamic acid60-l-alanine30-l-tyrosine10 (GAT) in microcultures are not under conventional Ir gene control. (1981)

The IgM plaque-forming cell response to trinitrophenyl (TNP)-conjugated L-glutamic acid60-L-alanine30-L-tyrosine10 (GAT) was studied in an in vitro microculture system. Contrary to expectations, this response was not found to be under conventional H-2 linked Ir gene control. Thus, both classical responder BALB/c (H-2d) and non-responder DBA/1 (H-2q) spleen cells gave equivalent anti-TNP PFC responses to TNP-GAT in these cultures. Experiments were performed to determined if haptenation had changed the GAT carrier so as to remove it from GAT-specific Ir gene control. It could be demonstrated that TNP-GAT elicited in vivo anti-GAT PFC responses showing typical Ir control in the BALB/c and DBA/1 strains; that anti-hapten and anti-carrier PFC responses to DNP-GAT in vivo were similarly controlled; and that the TNP-GAT compound remained a T cell- and Ia+ accessory cell-dependent antigen in vitro. Furthermore, the microculture system allowed GAT-specific T helper cells to be detected in the spleens of DBA/1 mice treated with GAT in vivo under conditions eliciting a predominant suppressor T cell response under usual conditions of assay. These findings contrast with the Ir gene regulation of TNP-(T,G)-A--L responses seen under identical culture conditions. The implications of these results for our understanding of the site of Ir gene action and the target of suppression in the GAT model are discussed.
Induction of Egr-1 Is Associated with Anti-Metastatic and Anti-Invasive Ability of β-Lapachone in Human Hepatocarcinoma Cells (2007)

beta-lapachone, a quinone compound obtained from the bark of the lapacho tree (Tabebuia avellanedae), was reported to have anti-inflammatory and anti-cancer activities. In this study, we investigated novel functions of beta-lapachone in terms of anti-metastasis and anti-invasion abilities using human hepatocarcinoma cell lines, HepG2 and Hep3B. beta-lapachone dose-dependently inhibited cell viability and migration of both HepG2 and Hep3B cells, as determined by methylthiazoletetrazolium (MTT) assay and wound healing assay. RT-PCR and Western blot data revealed that beta-lapachone dramatically increased the levels of protein, as well as mRNA expression of early growth response gene-1 (Egr-1) and throbospondin-1 (TSP-1) at an early point in time, and then decreased in a time-dependent manner. In addition, down-regulation of Snail and up-regulation of E-cadherin expression were observed in beta-lapachone-treated HepG2 and Hep3B cells, and this the associated with decreased invasive ability as measured by matrigel invasion assay. Taken together, our results strongly suggest that beta-lapachone may be expected to inhibit the progression and metastasis of hepatoma cells, at least in part by inhibiting the invasive ability of the cells via up-regulation of the expression of the Egr-1, TSP-1, and E-cadherin.